triples = ontology.getTriples(null, node.getTerm(), null);
diff --git a/app/src/main/java/de/uni_halle/informatik/biodata/mp/ModelPolisherCLILauncher.java b/app/src/main/java/de/uni_halle/informatik/biodata/mp/ModelPolisherCLILauncher.java
new file mode 100644
index 00000000..776449cd
--- /dev/null
+++ b/app/src/main/java/de/uni_halle/informatik/biodata/mp/ModelPolisherCLILauncher.java
@@ -0,0 +1,533 @@
+package de.uni_halle.informatik.biodata.mp;
+
+import static java.text.MessageFormat.format;
+
+import java.awt.*;
+import java.io.*;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.sql.SQLException;
+import java.text.MessageFormat;
+import java.util.*;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import de.zbit.util.prefs.SBProperties;
+import de.uni_halle.informatik.biodata.mp.annotation.AnnotationException;
+import de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions;
+import de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSBMLAnnotator;
+import de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator;
+import de.uni_halle.informatik.biodata.mp.fixing.FixingOptions;
+import de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer;
+import de.uni_halle.informatik.biodata.mp.io.*;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions;
+import de.uni_halle.informatik.biodata.mp.parameters.ParametersException;
+import de.uni_halle.informatik.biodata.mp.polishing.PolishingOptions;
+import de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher;
+import de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg;
+import de.uni_halle.informatik.biodata.mp.validation.ModelValidator;
+import de.uni_halle.informatik.biodata.mp.validation.ModelValidatorException;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.tuple.Pair;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+
+import de.zbit.AppConf;
+import de.zbit.Launcher;
+import de.zbit.util.ResourceManager;
+import de.zbit.util.prefs.KeyProvider;
+import de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions;
+import org.sbml.jsbml.ext.fbc.FBCConstants;
+import org.sbml.jsbml.ext.fbc.FBCModelPlugin;
+import org.sbml.jsbml.xml.parsers.ParserManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * The ModelPolisher class is the entry point of this application.
+ * It extends the Launcher class and provides functionality to polish SBML models.
+ * It handles command-line arguments to configure the polishing process, manages file input and output,
+ * and integrates various utilities for processing SBML, JSON, and MatLab files. The class supports
+ * operations such as reading, validating, and writing SBML documents, converting JSON and MatLab files
+ * to SBML, and annotating models with data from BiGG.
+ *
+ * The main functionalities include:
+ * - Command-line argument parsing and processing.
+ * - Batch processing of files and directories for model polishing.
+ * - File type detection and appropriate handling of SBML, JSON, and MatLab files.
+ * - HTML tag correction in SBML files.
+ * - SBML document validation and conversion.
+ * - Annotation of models using external databases.
+ * - Output management including file writing, COMBINE archive creation, and outputType.
+ *
+ * This class also handles error logging and provides detailed logging of the processing steps.
+ *
+ * @author Andreas Dräger
+ */
+public class ModelPolisherCLILauncher extends Launcher {
+
+ private static final ResourceBundle baseBundle = ResourceManager.getBundle(BundleNames.BASE_MESSAGES);
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.CLI_MESSAGES);
+ private static final Logger logger = LoggerFactory.getLogger(ModelPolisherCLILauncher.class);
+
+ private CommandLineParameters parameters;
+ private Registry registry;
+
+ /**
+ * Entry point
+ *
+ * @param args
+ * Commandline arguments passed, use help flag to obtain usage information
+ */
+ public static void main(String[] args) {
+ // Workaround for docker container
+ String home = System.getenv("HOME");
+ // / should only be home if system user has no corresponding home folder
+ if ("/".equals(home)) {
+ System.setProperty("java.util.prefs.systemRoot", ".java");
+ System.setProperty("java.util.prefs.userRoot", ".java/.userPrefs");
+ System.setProperty("slf4j.internal.verbosity", "WARN");
+
+ }
+ new ModelPolisherCLILauncher(args);
+ }
+
+
+ /**
+ * Initializes super class with Commandline arguments, which are converted into {@link AppConf} and passed to
+ * {@link ModelPolisherCLILauncher#commandLineMode(AppConf)}, which runs the rest of the program
+ *
+ * @param args
+ * Commandline arguments
+ */
+ public ModelPolisherCLILauncher(String... args) {
+ super(args);
+ }
+
+
+ /**
+ * @param appConf
+ * from super class initialization, holds commandline arguments
+ * @see de.zbit.Launcher#commandLineMode(de.zbit.AppConf)
+ */
+ @Override
+ public void commandLineMode(AppConf appConf) {
+ SBProperties args = appConf.getCmdArgs();
+
+ if (args.containsKey(ConfigOptions.CONFIG)) {
+ try {
+ parameters = new CommandLineParametersParser().parseCLIParameters(new File(args.getProperty(ConfigOptions.CONFIG)));
+ } catch (IOException e) {
+ logger.error("Could not read config file: {}", e.getMessage());
+ System.exit(1);
+ }
+ } else {
+ parameters = new CommandLineParameters(args);
+ }
+
+ registry = new IdentifiersOrg();
+
+ try {
+ validateIOParameters();
+
+ if (parameters.annotation().biggAnnotationParameters().annotateWithBiGG()) {
+ BiGGDB.init(parameters.annotation().biggAnnotationParameters().dbParameters());
+ }
+
+ if (parameters.annotation().adbAnnotationParameters().annotateWithAdb()) {
+ AnnotateDB.init(parameters.annotation().adbAnnotationParameters().dbParameters());
+ }
+
+ // Multi-file mode
+ if (parameters.input().isDirectory()) {
+ logger.info("Multi-file mode for directory {}.", parameters.input());
+
+ // DO NOT REMOVE - this is initializing the class, because it turned out to be not threadsafe,
+ // and it is used by the SBMLReader
+ ParserManager.getManager();
+
+ var inputFiles = FileUtils.listFiles(parameters.input(),
+ new String[]{"xml", "sbml", "json", "mat"}, true);
+ logger.info("Processing input files: {}", inputFiles.toString());
+
+ List> inputOutputPairs = new ArrayList<>();
+
+ for (var input : inputFiles) {
+ inputOutputPairs.add(Pair.of(input, SBMLFileUtils.getOutputFileName(input, parameters.output())));
+ }
+
+ logger.debug(inputOutputPairs.toString());
+
+ inputOutputPairs.parallelStream().forEach(pair -> {
+ try {
+ processFile(pair.getLeft(), pair.getRight());
+ } catch (ModelReaderException e) {
+ logger.info(MessageFormat.format("Skipping unreadable file \"{0}\".", pair.getLeft()));
+ } catch (SQLException | ModelWriterException | ModelValidatorException | AnnotationException e) {
+ throw new RuntimeException(e);
+ }
+ });
+
+ // Single-file mode
+ } else {
+ logger.info("Single-file mode.");
+ long startTime = System.currentTimeMillis();
+
+ processFile(parameters.input(), parameters.output());
+
+ // Log the time taken to process the file
+ long timeTaken = TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - startTime);
+ logger.info(String.format(MESSAGES.getString("FINISHED_TIME"), (timeTaken / 60), (timeTaken % 60)));
+ }
+
+ } catch (ModelValidatorException | ModelWriterException |
+ AnnotationException e) {
+ // TODO: produce some user-friendly output and log to a file that can be provided for trouble-shooting
+ throw new RuntimeException(e);
+ } catch (SQLException e) {
+ logger.error("There was an error while connecting to the database: {}", e.getMessage());
+ System.exit(1);
+ } catch (ModelReaderException e) {
+ logger.error("There was an error while reading the model: {}", e.getMessage());
+ System.exit(1);
+ } catch (ParametersException e) {
+ logger.error("The parameters you have entered are invalid: {}", e.getMessage());
+ System.exit(1);
+ }
+ }
+
+ private void validateIOParameters() throws ParametersException {
+ var input = parameters.input();
+ var output = parameters.output();
+
+ // Check if the input exists, throw an exception if it does not
+ if (!input.exists()) {
+ throw new ParametersException(format(MESSAGES.getString("READ_FILE_ERROR"), input), parameters);
+ }
+
+ // Ensure the output directory or file's parent directory exists
+ SBMLFileUtils.checkCreateOutDir(output);
+
+ // If the input is a directory but the output is not, exit with error
+ if (input.isDirectory() && !output.isDirectory()) {
+ throw new ParametersException(format(MESSAGES.getString("WRITE_DIR_TO_FILE_ERROR"),
+ input.getAbsolutePath(),
+ output.getAbsolutePath()),
+ parameters);
+ }
+
+ // If the output is a directory but the input is not, exit with error
+ if (output.isDirectory() && !input.isDirectory()) {
+ throw new ParametersException(format("Output \"{0}\" is a directory, but Input \"{1}\" is not",
+ output.getAbsolutePath(),
+ input.getAbsolutePath()),
+ parameters);
+ }
+
+ }
+
+
+ private void processFile(File input, File output) throws ModelReaderException, ModelWriterException, ModelValidatorException, AnnotationException, SQLException {
+ SBMLDocument doc = new ModelReader(parameters.sboParameters(), registry).read(input);
+
+ Model model = doc.getModel();
+ int count = getPolishingTaskCount(model);
+
+
+
+ if (!parameters.fixing().dontFix()) {
+ // TODO: das sollte sich durch JSBML UpdateListener ersetzen lassen
+ List fixingObservers = List.of(new PolisherProgressBar());
+ for (var o : fixingObservers) {
+ o.initialize(new ProgressInitialization(count));
+ }
+
+ new SBMLFixer(parameters.fixing(), fixingObservers).fix(doc, 0);
+
+ for (var o : fixingObservers) {
+ o.finish(new ProgressFinalization("Fixing Done."));
+ }
+ }
+
+ // TODO: das sollte sich durch JSBML UpdateListener ersetzen lassen
+ List polishingObservers = List.of(new PolisherProgressBar());
+ for (var o : polishingObservers) {
+ o.initialize(new ProgressInitialization(count));
+ }
+
+ // TODO: dispatch abhängig von level und version
+ new SBMLPolisher(
+ parameters.polishing(),
+ parameters.sboParameters(),
+ registry, polishingObservers).polish(doc);
+
+ for (var o : polishingObservers) {
+ o.finish(new ProgressFinalization("Polishing Done."));
+ }
+
+ if (parameters.annotation().biggAnnotationParameters().annotateWithBiGG()
+ || parameters.annotation().adbAnnotationParameters().annotateWithAdb()) {
+
+ // TODO: das sollte sich durch JSBML UpdateListener ersetzen lassen
+ List annotationObservers = List.of(new PolisherProgressBar());
+ int annotationTaskCount = getAnnotationTaskCount(model);
+ for (var o : annotationObservers) {
+ o.initialize(new ProgressInitialization(annotationTaskCount));
+ }
+
+ // TODO: dispatch abhängig von level und version
+ if (parameters.annotation().biggAnnotationParameters().annotateWithBiGG()) {
+ new BiGGSBMLAnnotator(new BiGGDB(), parameters.annotation().biggAnnotationParameters(), parameters.sboParameters(),
+ registry, annotationObservers).annotate(doc);
+ }
+
+ // TODO: dispatch abhängig von level und version
+ if (parameters.annotation().adbAnnotationParameters().annotateWithAdb()) {
+ new ADBSBMLAnnotator(new AnnotateDB(), parameters.annotation().adbAnnotationParameters()).annotate(doc);
+ }
+
+ for (var o : annotationObservers) {
+ o.finish(new ProgressFinalization("Annotation Done."));
+ }
+ }
+
+
+ output = new ModelWriter(parameters.outputType()).write(doc, output);
+
+ // TODO: das ist keine anständige Validierung!
+ if (parameters.sbmlValidation()) {
+ var mv = new ModelValidator();
+ // use offline validation
+ mv.validate(output);
+ }
+ }
+
+ private int getPolishingTaskCount(Model model) {
+ // Calculate the total number of tasks to initialize the progress bar.
+ int count = 1 // Account for model properties
+ // + model.getUnitDefinitionCount()
+ // TODO: see UnitPolisher TODO for why UnitDefinitionCount is replaced by 1
+ + 1
+ + model.getCompartmentCount()
+ + model.getParameterCount()
+ + model.getReactionCount()
+ + model.getSpeciesCount()
+ + model.getInitialAssignmentCount();
+
+ // Include tasks from FBC plugin if present.
+ if (model.isSetPlugin(FBCConstants.shortLabel)) {
+ FBCModelPlugin fbcModelPlug = (FBCModelPlugin) model.getPlugin(FBCConstants.shortLabel);
+ count += fbcModelPlug.getObjectiveCount() + fbcModelPlug.getGeneProductCount();
+ }
+ return count;
+ }
+
+ private int getAnnotationTaskCount(Model model) {
+ int annotationTaskCount = model.getCompartmentCount() + model.getSpeciesCount() + model.getReactionCount() + 50;
+ if (model.isSetPlugin(FBCConstants.shortLabel)) {
+ FBCModelPlugin fbcModelPlugin = (FBCModelPlugin) model.getPlugin(FBCConstants.shortLabel);
+ annotationTaskCount += fbcModelPlugin.getGeneProductCount();
+ }
+ return annotationTaskCount;
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getCitation(boolean)
+ */
+ @Override
+ public String getCitation(boolean HTMLstyle) {
+ if (HTMLstyle) {
+ return MESSAGES.getString("CITATION_HTML");
+ }
+ return MESSAGES.getString("CITATION");
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getCmdLineOptions()
+ */
+ @Override
+ public List> getCmdLineOptions() {
+ List> options = new LinkedList<>();
+ options.add(AnnotateDBOptions.class);
+ options.add(BiGGDBOptions.class);
+ options.add(GeneralOptions.class);
+ options.add(AnnotationOptions.class);
+ options.add(PolishingOptions.class);
+ options.add(FixingOptions.class);
+ options.add(CommandLineIOOptions.class);
+ options.add(ConfigOptions.class);
+ return options;
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getInstitute()
+ */
+ @Override
+ public String getInstitute() {
+ return baseBundle.getString("INSTITUTE");
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getInteractiveOptions()
+ */
+ @Override
+ public List> getInteractiveOptions() {
+ List> options = new LinkedList<>();
+ options.add(BiGGDBOptions.class);
+ options.add(AnnotateDBOptions.class);
+ options.add(GeneralOptions.class);
+ return options;
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getLogPackages()
+ */
+ @Override
+ public String[] getLogPackages() {
+ return new String[] {"edu.ucsd", "de.zbit"};
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getOrganization()
+ */
+ @Override
+ public String getOrganization() {
+ return baseBundle.getString("ORGANIZATION");
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getProvider()
+ */
+ @Override
+ public String getProvider() {
+ return baseBundle.getString("PROVIDER");
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getURLlicenseFile()
+ */
+ @Override
+ public URL getURLlicenseFile() {
+ try {
+ return new URI(baseBundle.getString("LICENSE")).toURL();
+ } catch (MalformedURLException | URISyntaxException exc) {
+ return null;
+ }
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getURLOnlineUpdate()
+ */
+ @Override
+ public URL getURLOnlineUpdate() {
+ return null;
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getVersionNumber()
+ */
+ @Override
+ public String getVersionNumber() {
+ String version = getClass().getPackage().getImplementationVersion();
+ return version == null ? "?" : version;
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getYearOfProgramRelease()
+ */
+ @Override
+ public short getYearOfProgramRelease() {
+ try {
+ return Short.parseShort(baseBundle.getString("YEAR"));
+ } catch (NumberFormatException exc) {
+ return (short) Calendar.getInstance().get(Calendar.YEAR);
+ }
+ }
+
+
+ /*
+ * (non-Javadoc)
+ * @see de.zbit.Launcher#getYearWhenProjectWasStarted()
+ */
+ @Override
+ public short getYearWhenProjectWasStarted() {
+ try {
+ return Short.parseShort(baseBundle.getString("INCEPTION_YEAR"));
+ } catch (Throwable t) {
+ return (short) 2014;
+ }
+ }
+
+
+ /*
+ * This method is inherited from the base class and is not utilized in this CLI application.
+ * The ModelPolisher application does not implement a graphical user interface.
+ *
+ * @return Always returns false as no GUI is created.
+ * @see de.zbit.Launcher#addCopyrightToSplashScreen()
+ */
+ @Override
+ protected boolean addCopyrightToSplashScreen() {
+ return false;
+ }
+
+
+ /*
+ * This method is inherited from the base class and is not utilized in this CLI application.
+ * The ModelPolisher application does not implement a graphical user interface.
+ *
+ * @return Always returns false as no GUI is created.
+ * @see de.zbit.Launcher#addVersionNumberToSplashScreen()
+ */
+ @Override
+ protected boolean addVersionNumberToSplashScreen() {
+ return false;
+ }
+
+
+ /**
+ * This method is inherited from the base class and is not utilized in this CLI application.
+ * The ModelPolisher application does not implement a graphical user interface.
+ *
+ * @param appConf The application configuration settings, not used in this context.
+ * @return Always returns null as no GUI is created.
+ * @see de.zbit.Launcher#initGUI(de.zbit.AppConf)
+ */
+ @Override
+ public Window initGUI(AppConf appConf) {
+ return null;
+ }
+}
diff --git a/app/src/main/resources/logback.xml b/app/src/main/resources/logback.xml
new file mode 100644
index 00000000..d22daf8f
--- /dev/null
+++ b/app/src/main/resources/logback.xml
@@ -0,0 +1,20 @@
+
+
+
+ %d [%thread] %X{run.id} %-5level %logger{36} - %msg%n
+
+
+
+
+
diff --git a/app/validator-server-config.py b/app/validator-server-config.py
new file mode 100644
index 00000000..779826d8
--- /dev/null
+++ b/app/validator-server-config.py
@@ -0,0 +1,5 @@
+import multiprocessing
+
+loglevel = 'info'
+bind = "0.0.0.0:8000"
+workers = multiprocessing.cpu_count() * 2 + 1
diff --git a/build.gradle b/build.gradle
deleted file mode 100644
index 4aa131d6..00000000
--- a/build.gradle
+++ /dev/null
@@ -1,181 +0,0 @@
-plugins {
- id "java"
- id "application"
- id 'com.github.jk1.dependency-license-report' version '2.0'
-}
-
-// Java versions for compilation and output
-java {
- sourceCompatibility = JavaVersion.VERSION_11
- targetCompatibility = JavaVersion.VERSION_11
-}
-
-defaultTasks "clean", "fatJar"
-archivesBaseName = "ModelPolisher"
-mainClassName = "ModelPolisher"
-version = "2.1-beta"
-
-sourceSets {
- main {
- java {
- srcDirs = ["src/main/java"]
- }
- resources {
- srcDirs = ["src/main/resources"]
- }
- }
- test {
- java {
- srcDirs = ["src/test/java"]
- }
- }
-}
-
-test {
- useJUnitPlatform()
- testLogging {
- events "passed", "skipped", "failed"
- }
-}
-
-repositories {
- mavenCentral()
- maven { url "https://oss.sonatype.org/content/repositories/snapshots" }
- // local dependencies
- flatDir {
- dirs "lib/de/zbit/SysBio/1390"
- }
-}
-
-dependencies {
- implementation "org.sbml.jsbml:jsbml:1.4"
- implementation "de.zbit:SysBio:1390"
- implementation "org.postgresql:postgresql:42.2.13"
- implementation "org.biojava:biojava-ontology:5.0.0"
- implementation 'us.hebi.matlab.mat:mfl-core:0.5.3'
- implementation "com.fasterxml.jackson.core:jackson-core:2.14.1"
- implementation "com.fasterxml.jackson.core:jackson-databind:2.14.1"
- implementation "net.sf.jtidy:jtidy:r938"
- implementation "de.uni-rostock.sbi:CombineArchive:1.4.0"
- implementation "com.zaxxer:HikariCP:3.4.2"
- testImplementation "org.junit.jupiter:junit-jupiter-api:5.5.2"
- testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:5.5.2"
-}
-
-test {
- testLogging {
- showStandardStreams = true
- }
-}
-
-// get latest version of MIRIAM registry
-task downloadMIRIAM() {
- doFirst {
- String registry = new URL("https://registry.api.identifiers.org/resolutionApi/getResolverDataset").getText()
- File parentDir = new File("src/main/resources/edu/ucsd/sbrg/miriam/");
- if (!parentDir.exists()) {
- mkdir(parentDir)
- }
- File registryFile = new File(parentDir.toString() + "/IdentifiersOrg-Registry.json")
- BufferedWriter writer = new BufferedWriter(new FileWriter(registryFile))
- writer.write(registry)
- writer.close()
- }
- processResources.dependsOn downloadMIRIAM
-}
-
-// config for all jar tasks
-tasks.withType(Jar) {
- dependsOn test
- destinationDirectory = file("$rootDir/target")
- manifest {
- attributes(
- "Version": project.version,
- "Implementation-Title": "ModelPolisher",
- "Implementation-Version": project.version,
- "Specification-Vendor": "University of California, San Diego",
- "Specification-Title": "ModelPolisher",
- "Implementation-Vendor-Id": "edu.ucsd.sbrg",
- "Implementation-Vendor": "University of California, San Diego",
- "Main-Class": "edu.ucsd.sbrg.bigg.ModelPolisher"
- )
- }
-}
-
-//with dependencies
-task fatJar(type: Jar) {
- duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-
- from sourceSets.main.output
- dependsOn configurations.runtimeClasspath
- from {
- configurations.runtimeClasspath.findAll { it.name.endsWith('jar') }.collect { zipTree(it) }
- }
-}
-
-//build docker container
-task devel(type: Exec) {
- commandLine "sh", "-c", "cp target/ModelPolisher-" + project.version + ".jar docker/java_docker && " +
- "export COMPOSE_FILE=docker-compose.devel.yml && " +
- "docker-compose pull && " +
- "docker-compose build && " +
- "rm docker/java_docker/ModelPolisher-" + project.version + ".jar"
- dependsOn fatJar
-}
-
-// zip lib folder for release
-task zipLibs(type: Zip) {
- from "lib"
- into "lib"
- include "**/**"
- archiveFileName = "lib.zip"
- destinationDirectory = file("target/")
-}
-
-// zip script files for release
-task zipScripts(type: Zip) {
- from "src/scripts"
- into "scripts"
- include "**/**"
- archiveFileName = "scripts.zip"
- destinationDirectory = file("target/")
-}
-
-// create lightJar for release
-task release() {
- dependsOn fatJar
- dependsOn tasks["zipLibs"]
- dependsOn tasks["zipScripts"]
-}
-
-// clean up target directory
-clean.doFirst {
- file(".gradle").deleteDir()
- file("target").deleteDir()
-}
-
-// bump jar version in ModelPolisher.sh
-if (project.file( "src/scripts/ModelPolisher.sh").exists()) {
- task bumpVersionMP() {
- replaceVersion(rootProject.projectDir.toString() + "/docker/java_docker/Dockerfile")
- replaceVersion(rootProject.projectDir.toString() + "/.travis.yml")
- replaceVersion(rootProject.projectDir.toString() + "/README.md")
- replaceVersion(rootProject.projectDir.toString() + "/src/scripts/ModelPolisher.sh")
- }
- processResources.dependsOn bumpVersionMP
-}
-
-def replaceVersion(path) {
- ArrayList content = new ArrayList<>()
- File travisFile = new File(path)
- String MPVersion = /ModelPolisher-(.*?)\d{1,2}(.\d{1,2}){1,2}.jar/
- travisFile.eachLine {
- line ->
- content.add(line.replaceAll(MPVersion, "ModelPolisher-" + "${version}.jar"))
- }
- BufferedWriter writer = new BufferedWriter(new FileWriter(travisFile))
- content.each {
- line -> writer.writeLine(line)
- }
- writer.close()
-}
diff --git a/dev/SBML_Project_Java_style.xml b/dev/SBML_Project_Java_style.xml
deleted file mode 100644
index aa81e20f..00000000
--- a/dev/SBML_Project_Java_style.xml
+++ /dev/null
@@ -1,315 +0,0 @@
-
-
-
-
-
diff --git a/dev/usage.txt b/dev/usage.txt
deleted file mode 100644
index 4d2193a9..00000000
--- a/dev/usage.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-The supplied style file is a modified version of the one found in the JSBML dev folder.
-This version is adjusted to work with the "Eclipse Code Formatter" plugin for IntelliJ IDEA.
diff --git a/doc/img/FlowDiagram.graphml b/doc/img/FlowDiagram.graphml
deleted file mode 100644
index 1e666751..00000000
--- a/doc/img/FlowDiagram.graphml
+++ /dev/null
@@ -1,567 +0,0 @@
-
-
-
-
-
-
-
- MAT
-
-
-
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-
-
-
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-
-
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-
- JSON
-
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-
-
-
-
-
-
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- SBML
-
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-
-
-
-
-
- Start
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- COBRA
-Parser
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- JSON
-Parser
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- SBML
-Reader
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- SBML
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- BiGG
-
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-
- Annotate?
-
-
-
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- Stop
-
-
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- XHTML
-template
-
-
-
-
-
-
-
-
-
-
- Auto
-Complete
-
-
-
-
-
-
-
-
-
-
-
-
- Annotate
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
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-
-
- no
-
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- yes
-
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-
-
diff --git a/doc/img/FlowDiagram.pdf b/doc/img/FlowDiagram.pdf
deleted file mode 100644
index 8d729c37..00000000
Binary files a/doc/img/FlowDiagram.pdf and /dev/null differ
diff --git a/docker-compose.devel.yml b/docker-compose.devel.yml
deleted file mode 100644
index 24876758..00000000
--- a/docker-compose.devel.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-# ------------------------------------------------
-# docker-compose for ModelPolisher development
-# run gradle devel first and then docker-compose -f docker-compose.devel.yml run ... or export COMPOSE_FILE and run normally
-# ------------------------------------------------
-version: '3'
-services:
- biggdb:
- image: mephenor/bigg_docker:1.6
- container_name: modelpolisher_biggdb
- ports:
- - 1310:5432
- adb:
- image: mephenor/adb_docker:0.1.1
- container_name: modelpolisher_adb
- ports:
- - 1013:5432
- polisher:
- build: ./docker/java_docker
- container_name: modelpolisher_java
- depends_on:
- - biggdb
- - adb
- stdin_open: true
- tty: true
diff --git a/docker-compose.yml b/docker-compose.yml
deleted file mode 100644
index 0131f539..00000000
--- a/docker-compose.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-# ------------------------------------------------
-# docker-compose for ModelPolisher release version
-# update docker hub images for new releases and change image accordingly
-# ------------------------------------------------
-version: '3'
-services:
- biggdb:
- image: mephenor/bigg_docker:1.6
- container_name: modelpolisher_biggdb
- ports:
- - 1310:5432
- adb:
- image: mephenor/adb_docker:0.1.1
- container_name: modelpolisher_adb
- ports:
- - 1013:5432
- polisher:
- image: mephenor/modelpolisher:2.1-beta
- depends_on:
- - biggdb
- - adb
- container_name: modelpolisher_java
- stdin_open: true
- tty: true
diff --git a/docker/adb_docker/Dockerfile b/docker/adb_docker/Dockerfile
deleted file mode 100644
index e93c19ce..00000000
--- a/docker/adb_docker/Dockerfile
+++ /dev/null
@@ -1,15 +0,0 @@
-FROM postgres:11.4
-MAINTAINER ktrivedi@cs.iitr.ac.in
-
-RUN adduser --disabled-password --gecos '' adb
-
-RUN apt-get update && \
- apt-get install curl -y && \
- # Create directory '/adb_dump/' and download adb-v0.1.1 dump as 'adb-v0.1.1.dump'
- mkdir /adb_dump && \
- curl -Lo /adb_dump/adb-v0.1.1.dump https://www.dropbox.com/s/qjiey8y88gt4h0l/adb-v0.1.1.dump?dl=0 && \
- rm -rf /var/lib/apt/lists/*
-
-COPY ./scripts/restore_adb.sh /docker-entrypoint-initdb.d/restore_adb.sh
-
-EXPOSE 5432
diff --git a/docker/adb_docker/scripts/restore_adb.sh b/docker/adb_docker/scripts/restore_adb.sh
deleted file mode 100644
index 1adc70f6..00000000
--- a/docker/adb_docker/scripts/restore_adb.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-psql -c "DROP DATABASE IF EXISTS adb";
-psql -c "CREATE DATABASE adb";
-psql -c "CREATE USER adb with ENCRYPTED PASSWORD 'adb'";
-psql -c "GRANT ALL PRIVILEGES ON DATABASE adb TO adb";
-bash -c "pg_restore -d adb -U adb --verbose /adb_dump/adb-v0.1.1.dump";
-
diff --git a/docker/bigg_docker/Dockerfile b/docker/bigg_docker/Dockerfile
deleted file mode 100644
index ba6e02b0..00000000
--- a/docker/bigg_docker/Dockerfile
+++ /dev/null
@@ -1,13 +0,0 @@
-FROM postgres:9.6.2
-MAINTAINER zajac.thomas1992@gmail.com
-
-RUN apt-get update && \
- apt-get install curl -y && \
- # Create directory '/bigg_database_dump/' and download bigg_database dump as 'database.dump'
- mkdir /bigg_database_dump && \
- curl -Lo /bigg_database_dump/database.dump https://www.dropbox.com/sh/ye05djxrpxy37da/AAB-rhgcEv9p8gcMpkYuowu8a/v1.6/database.dump?dl=0 && \
- rm -rf /var/lib/apt/lists/*
-
-COPY ./scripts/restore_biggdb.sh /docker-entrypoint-initdb.d/restore_biggdb.sh
-
-EXPOSE 5432
diff --git a/docker/bigg_docker/scripts/restore_biggdb.sh b/docker/bigg_docker/scripts/restore_biggdb.sh
deleted file mode 100644
index 46f40aa6..00000000
--- a/docker/bigg_docker/scripts/restore_biggdb.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-psql -c 'DROP DATABASE IF EXISTS bigg'
-psql -c 'CREATE DATABASE bigg'
-bash -c 'pg_restore -O -d bigg --verbose /bigg_database_dump/bigg_database.dump'
\ No newline at end of file
diff --git a/docker/java_docker/Dockerfile b/docker/java_docker/Dockerfile
deleted file mode 100644
index 7b0c87ad..00000000
--- a/docker/java_docker/Dockerfile
+++ /dev/null
@@ -1,6 +0,0 @@
-FROM openjdk:11-slim
-MAINTAINER zajac.thomas1992@gmail.com
-
-RUN mkdir -p /.java/.systemPrefs && mkdir /.java/.userPrefs && chmod -R 755 /.java
-COPY ModelPolisher-2.1-beta.jar /
-CMD "/bin/sh"
diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html
new file mode 100644
index 00000000..d15fbf08
--- /dev/null
+++ b/docs/allclasses-index.html
@@ -0,0 +1,410 @@
+
+
+
+
+All Classes and Interfaces (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
All Classes and Interfaces Interfaces Classes Enum Classes Record Classes Exceptions
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
This interface provides options for connecting to the ADB database.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
+
+
+
+
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
+
+
+
+
This class provides a connection to the BiGG database.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
+
+
+
+
+
+
Represents a BiGG identifier used to uniquely identify various biological entities
+ such as reactions, metabolites, and genes within the BiGG database.
+
+
+
+
This class is responsible for annotating an SBML Model with relevant metadata and references.
+
+
+
+
+
+
+
+
This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
+
+
+
+
This class is responsible for annotating SBML models using data from the BiGG database.
+
+
+
+
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
+
+
+
+
+
+
+
+
The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
+
+
+
+
+
+
This class is responsible for polishing the properties of a compartment in an SBML model to ensure
+ compliance with standards and completeness.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
A collection of helpful functions for dealing with SBML data structures.
+
+
+
+
+
+
The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
+
+
+
+
The IdentifiersOrgRegistryParser class is a singleton that provides functionality to parse the MIRIAM registry
+ from a JSON file and convert it into a Miriam object.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
+
+
+
+
+
+
This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Possible FileTypes of input file
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly
+ defined and present in the SBML model.
+
+
+
+
The UpdateListener class implements the TreeNodeChangeListener to monitor and respond to changes
+ within an SBML model's structure.
+
+
+
+
+
+
All Packages (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+Package Summary
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Constant Field Values (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/annotation/AbstractAnnotator.html b/docs/de/uni_halle/informatik/biodata/mp/annotation/AbstractAnnotator.html
new file mode 100644
index 00000000..edefb208
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/annotation/AbstractAnnotator.html
@@ -0,0 +1,206 @@
+
+
+
+
+AbstractAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+AbstractAnnotator
+public AbstractAnnotator ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
AnnotationException (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Throwable
+
addSuppressed , fillInStackTrace , getCause , getLocalizedMessage , getMessage , getStackTrace , getSuppressed , initCause , printStackTrace , printStackTrace , printStackTrace , setStackTrace , toString
+
+
+
+
+
+
+
+
AnnotationOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface AnnotationOptions
+extends de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+Nested Class Summary
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
If set to true, annotations will be added to species and reactions from AnnotateDB also.
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
If set to true, the model will be annotated with data from BiGG Models
+ database.
+
+
static final de.zbit.util.prefs.Option<File >
+
+
+
This XHTML file defines alternative document notes and makes them
+ exchangeable.
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
This option allows you to define the title of the SBML document's
+ description and hence the headline when the file is displayed in a web
+ browser.
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
This switch allows users to specify if also those database cross-links
+ should be extracted from BiGG Models database for which currently no entry
+ in the MIRIAM exists.
+
+
+
+
+
static final de.zbit.util.prefs.Option<File >
+
+
+
This XHTML file defines alternative model notes and makes them
+ exchangeable.
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
If set to true, no web content will be inserted in the SBML container nor
+ into the model within the SBML file.
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+ADD_ADB_ANNOTATIONS
+static final de.zbit.util.prefs.Option<Boolean > ADD_ADB_ANNOTATIONS If set to true, annotations will be added to species and reactions from AnnotateDB also.
+
+
+
+
+ANNOTATE_WITH_BIGG
+static final de.zbit.util.prefs.Option<Boolean > ANNOTATE_WITH_BIGG If set to true, the model will be annotated with data from BiGG Models
+ database. If set to false, the resulting model will not receive annotation
+ or correction from BiGG Models database
+
+
+
+
+MODEL_NOTES_FILE
+static final de.zbit.util.prefs.Option<File > MODEL_NOTES_FILE This XHTML file defines alternative model notes and makes them
+ exchangeable.
+
+
+
+
+NO_MODEL_NOTES
+static final de.zbit.util.prefs.Option<Boolean > NO_MODEL_NOTES If set to true, no web content will be inserted in the SBML container nor
+ into the model within the SBML file.
+
+
+
+
+INCLUDE_ANY_URI
+static final de.zbit.util.prefs.Option<Boolean > INCLUDE_ANY_URI This switch allows users to specify if also those database cross-links
+ should be extracted from BiGG Models database for which currently no entry
+ in the MIRIAM exists. If set to true, ModelPolisher also includes URIs that
+ do not contain the pattern identifiers.org.
+
+
+
+
+DOCUMENT_NOTES_FILE
+static final de.zbit.util.prefs.Option<File > DOCUMENT_NOTES_FILE This XHTML file defines alternative document notes and makes them
+ exchangeable.
+
+
+
+
+DOCUMENT_TITLE_PATTERN
+static final de.zbit.util.prefs.Option<String > DOCUMENT_TITLE_PATTERN This option allows you to define the title of the SBML document's
+ description and hence the headline when the file is displayed in a web
+ browser.
+
+
+
+
+
+
+
+
+
+
+
AnnotationsSorter (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.annotation.AnnotationsSorter
+
+public class AnnotationsSorter
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
Recursively goes through all annotations in the given SBase and
+ alphabetically sort annotations after grouping them by CVTerm.Qualifier.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+AnnotationsSorter
+public AnnotationsSorter ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+groupAndSortAnnotations
+public void groupAndSortAnnotations (org.sbml.jsbml.SBase sbase)
+Recursively goes through all annotations in the given SBase and
+ alphabetically sort annotations after grouping them by CVTerm.Qualifier.
+
+Parameters:
+sbase - :
+ SBase to start the merging process at, corresponding to an instance of SBMLDocument here,
+ though also used to pass current SBase during recursion
+
+
+
+
+
+
+
+
+
+
+
IAnnotateSBases (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+ADBReactionsAnnotator ADBSBMLAnnotator ADBSpeciesAnnotator BiGGCompartmentsAnnotator BiGGFBCAnnotator BiGGFBCSpeciesAnnotator BiGGGeneProductAnnotator BiGGModelAnnotator BiGGPublicationsAnnotator BiGGReactionsAnnotator BiGGSBMLAnnotator BiGGSpeciesAnnotator
+public interface IAnnotateSBases<SBMLElement extends org.sbml.jsbml.SBase>
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods Default Methods
+
+
+
+
+
+
default void
+
+
+
void
+
+
+
+
+
+
+
+
+
+
+
+
+
IProcessNotes (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+public interface IProcessNotes
+
+
+
+
+
ADBReactionsAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
annotate (org.sbml.jsbml.Reaction reaction)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
ADBSBMLAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.SBMLDocument>
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
annotate (org.sbml.jsbml.SBMLDocument doc)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
ADBSpeciesAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.Species>
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
annotate (org.sbml.jsbml.Species species)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
AbstractADBAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
protected void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.annotation.adb (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.annotation.adb
+
+
+
+
de.uni_halle.informatik.biodata.mp.annotation.adb Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/annotation/bigg/AbstractBiGGAnnotator.html b/docs/de/uni_halle/informatik/biodata/mp/annotation/bigg/AbstractBiGGAnnotator.html
new file mode 100644
index 00000000..a395c04c
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/annotation/bigg/AbstractBiGGAnnotator.html
@@ -0,0 +1,254 @@
+
+
+
+
+AbstractBiGGAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+
+
+
+biGGAnnotationParameters
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getBiGGIdFromResources
+
+Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase. This method
+ processes annotations for biological entities such as Species, Reaction, or GeneProduct.
+ Each entity's annotations are provided as a list of URIs, which are then parsed to retrieve the BiGG ID.
+
+Parameters:
+resources - A list of URIs containing annotations for the biological entity.type - The type of the biological entity, which can be one of the following:
+ BiGGDBContract.Constants.TYPE_SPECIESBiGGDBContract.Constants.TYPE_REACTIONBiGGDBContract.Constants.TYPE_GENE_PRODUCTReturns:
+An Optional.empty()
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
BiGGAnnotationException (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+Serializable
+
+See Also:
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Throwable
+
addSuppressed , fillInStackTrace , getCause , getLocalizedMessage , getMessage , getStackTrace , getSuppressed , initCause , printStackTrace , printStackTrace , printStackTrace , setStackTrace , toString
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BiGGAnnotationException
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
BiGGCVTermAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IReportDiffs IReportStatus
+
+Direct Known Subclasses:
+BiGGGeneProductAnnotator BiGGReactionsAnnotator BiGGSpeciesAnnotator
+Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
+ This class defines the basic structure and operations for adding annotations to SBML elements based on BiGG IDs.
+ It includes methods to check the validity of BiGG IDs, add annotations to SBML elements, and specifically handle
+ annotations for Species and Reactions using data from BiGG and other databases.
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
+
+
Abstract method to check the validity of a BiGG ID.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+findBiGGId
+
+Abstract method to check the validity of a BiGG ID. Implementations should return an Optional containing
+ the BiGG ID if it is valid, or an empty Optional if not.
+
+Returns:
+Optional containing the valid BiGG ID or empty if the ID is invalid.
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
BiGGCompartmentsAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.Compartment>IReportDiffs IReportStatus
+This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
+ It allows for the addition of both BiGG and SBO annotations to a compartment, and can also set the compartment's name
+ based on information retrieved from the BiGG database.
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
annotate (org.sbml.jsbml.Compartment compartment)
+
+
Annotates the compartment with BiGG and SBO terms.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+annotate
+public void annotate (org.sbml.jsbml.Compartment compartment)
+ throws SQLException Annotates the compartment with BiGG and SBO terms. If the compartment's name is not set or is set to "default",
+ it updates the name based on the BiGG database. This method only processes compartments that are recognized
+ within the BiGG Knowledgebase.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.Compartment>Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
BiGGDocumentNotesProcessor (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGDocumentNotesProcessor
+
+public class BiGGDocumentNotesProcessor
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
BiGGModelAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.Model>IReportDiffs IReportStatus
+This class is responsible for annotating an SBML Model with relevant metadata and references.
+ It handles the annotation of the model itself and delegates the annotation of contained elements such as
+ Compartment, Species, Reaction, and GeneProduct.
+ The annotations can include taxonomy information, database references, and meta identifiers.
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
Annotates the Model with relevant metadata and delegates the annotation of contained elements such as
+ Compartment, Species, Reaction, and GeneProduct.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+REF_SEQ_ACCESSION_NUMBER_PATTERN
+public static final String REF_SEQ_ACCESSION_NUMBER_PATTERN
+See Also:
+
+
+
+
+
+
+
+
+GENOME_ASSEMBLY_ID_PATTERN
+public static final String GENOME_ASSEMBLY_ID_PATTERN
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+annotate
+public void annotate (org.sbml.jsbml.Model model)
+ throws SQLException Annotates the
Model with relevant metadata and delegates the annotation of contained elements such as
+
Compartment,
Species,
Reaction, and
GeneProduct.
+
+ Steps:
+ 1. Retrieves the model's ID and uses it to fetch and add a taxonomy annotation if available.
+ 2. Checks if the model exists in the database and adds specific BiGG database annotations.
+ 3. Sets the model's MetaId to its ID if MetaId is not already set and the model has at least one CVTerm.
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.Model>Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
BiGGPublicationsAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
BiGGReactionsAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.Reaction>IReportDiffs IReportStatus
+This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
+ It extends the
BiGGCVTermAnnotator class, allowing it to manage controlled vocabulary (CV) terms
+ associated with the reaction. The class handles various aspects of reaction annotation including setting
+ the reaction's name, SBO term, and additional annotations. It also processes gene reaction rules and
+ subsystem information associated with the reaction.
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
Delegates the annotation process for each reaction in the given SBML model.
+
+
void
+
annotate (org.sbml.jsbml.Reaction reaction)
+
+
Annotates a reaction by setting its name, SBO term, and additional annotations.
+
+
+
+
+
This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding
+ BiGG ID based on existing annotations.
+
+
void
+
+
+
Parses gene reaction rules for a given reaction based on the BiGG database identifier.
+
+
void
+
+
+
Sets the name of the reaction based on the provided BiGGId.
+
+
void
+
+
+
Sets the SBO term for a reaction based on the given BiGGId.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+annotate
+public void annotate (List <org.sbml.jsbml.Reaction> reactions)
+ throws SQLException Delegates the annotation process for each reaction in the given SBML model.
+ This method iterates over all reactions in the model, updates the progress display,
+ and invokes the annotation for each reaction.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.Reaction>Throws:
+SQLException
+
+
+
+
+annotate
+public void annotate (org.sbml.jsbml.Reaction reaction)
+ throws SQLException Annotates a reaction by setting its name, SBO term, and additional annotations. It also processes gene reaction rules
+ and subsystem information associated with the reaction. This method retrieves a BiGG ID for the reaction, either from
+ the reaction's ID directly or through associated annotations. If a valid BiGG ID is found, it proceeds with the
+ annotation and parsing processes.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.Reaction>Throws:
+SQLException
+
+
+
+
+findBiGGId
+
+This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding
+ BiGG ID based on existing annotations. It first checks if the reaction ID matches the expected BiGG ID format
+ and verifies its existence in the database. If the ID does not match or is not found, it then attempts to
+ extract a BiGG ID from the reaction's annotations. This involves parsing the CVTerms associated with the reaction,
+ extracting URLs, validating them, and then querying the BiGG database for corresponding reaction IDs that match
+ the reaction's compartment.
+
+Specified by:
+findBiGGId BiGGCVTermAnnotator <org.sbml.jsbml.Reaction>Returns:
+An OptionalOptional.empty()
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
BiGGSBMLAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.SBMLDocument>IReportDiffs IReportStatus
+This class is responsible for annotating SBML models using data from the BiGG database.
+ It handles the addition of annotations related to compartments, species, reactions, and gene products.
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
annotate (org.sbml.jsbml.SBMLDocument doc)
+
+
Annotates an SBMLDocument using data from the BiGG Knowledgebase.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+annotate
+
+Annotates an SBMLDocument using data from the BiGG Knowledgebase. This method processes various components of the
+ SBML model such as compartments, species, reactions, and gene products by adding relevant annotations from BiGG.
+ It also handles the addition of publications and notes related to the model.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.SBMLDocument>Parameters:
+doc - The SBMLDocument that contains the model to be annotated.Throws:
+SQLException AnnotationException
+
+
+
+
+
+
+
+
+
+
+
BiGGSpeciesAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.Species>IReportDiffs IReportStatus
+This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
+ It extends the
BiGGCVTermAnnotator class, allowing it to manage controlled vocabulary (CV) terms
+ associated with the species. The class handles various aspects of species annotation including setting
+ the species' name, SBO term, and additional annotations. It also sets the chemical formula and charge
+ for the species using FBC (Flux Balance Constraints) extensions.
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
protected
+
+
+
protected
+
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
Delegates annotation processing for all chemical species contained in the Model.
+
+
void
+
annotate (org.sbml.jsbml.Species species)
+
+
This method annotates a species with various details fetched from the BiGG Knowledgebase.
+
+
+
+
+
Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
+
+
void
+
+
+
Updates the name of the species based on data retrieved from the BiGG Knowledgebase.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+annotate
+public void annotate (List <org.sbml.jsbml.Species> species)
+ throws SQLException Delegates annotation processing for all chemical species contained in the Model.
+ This method iterates over each species in the model and applies specific annotations.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.Species>Throws:
+SQLException
+
+
+
+
+annotate
+public void annotate (org.sbml.jsbml.Species species)
+ throws SQLException This method annotates a species with various details fetched from the BiGG Knowledgebase. It performs the following:
+ 1. Sets the species name based on the BiGGId. If the species does not have a name, it uses the BiGGId as the name.
+ 2. Assigns an SBO (Systems Biology Ontology) term to the species based on the BiGGId.
+ 3. Adds additional annotations to the species, such as database cross-references.
+
+ The BiGGId used for these operations is either derived from the species' URI list or directly from its ID if available.
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.Species>Throws:
+SQLException
+
+
+
+
+findBiGGId
+
+Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
+ This method first tries to create a BiGGId from the species ID. If the species ID does not correspond to a known
+ BiGGId in the database, it then searches through the species' annotations to find a valid BiGGId.
+
+Specified by:
+findBiGGId BiGGCVTermAnnotator <org.sbml.jsbml.Species>Returns:
+An OptionalOptional.empty()
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
+
+
+
BiGGFBCAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
BiGGFBCSpeciesAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
annotate (org.sbml.jsbml.Species species)
+
+
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
BiGGGeneProductAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IAnnotateSBases <org.sbml.jsbml.ext.fbc.GeneProduct>IReportDiffs IReportStatus
+Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
+ This class extends
BiGGCVTermAnnotator and specifically handles the annotation of
GeneProduct instances.
+ It includes methods to validate gene product IDs, retrieve and set labels, and add annotations based on BiGG IDs.
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
Adds annotations to a gene product based on a given
BiGGId.
+
+
void
+
annotate (List <org.sbml.jsbml.ext.fbc.GeneProduct> geneProducts)
+
+
This method handles the annotation of gene products in a given SBML model.
+
+
void
+
annotate (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
+
+
Annotates a gene product by adding relevant metadata and references.
+
+
+
findBiGGId (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
+
+
Validates the ID of a
GeneProduct against the expected BiGG ID format and attempts to retrieve a
+ corresponding
BiGGId from existing annotations if the initial ID does not conform to the BiGG format.
+
+
+
getLabel (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct,
+ BiGGId biggId)
+
+
Retrieves the label for a gene product based on the provided BiGGId.
+
+
void
+
+
+
Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+BIGG_GENE_ID_PATTERN
+public static final String BIGG_GENE_ID_PATTERN
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+annotate
+public void annotate (List <org.sbml.jsbml.ext.fbc.GeneProduct> geneProducts)
+ throws SQLException This method handles the annotation of gene products in a given SBML model. It checks if the model has the FBC plugin
+ set and then proceeds to annotate each gene product found within the model. The progress bar is updated to reflect
+ the number of gene products being annotated.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.ext.fbc.GeneProduct>Throws:
+SQLException
+
+
+
+
+annotate
+public void annotate (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
+ throws SQLException Annotates a gene product by adding relevant metadata and references.
+ This method first checks the gene product's ID for validity and retrieves a corresponding BiGGId if available.
+ It then attempts to get a label for the gene product. If no label is found, the method returns early.
+ If a label is present, it updates the gene product reference in the association, adds annotations using the BiGGId,
+ and sets the gene product's metaId if it has any CV terms. Finally, it sets the gene product's label name.
+
+Specified by:
+annotate IAnnotateSBases <org.sbml.jsbml.ext.fbc.GeneProduct>Throws:
+SQLException
+
+
+
+
+findBiGGId
+public BiGGId findBiGGId (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
+ throws SQLException Validates the ID of a
GeneProduct against the expected BiGG ID format and attempts to retrieve a
+ corresponding
BiGGId from existing annotations if the initial ID does not conform to the BiGG format.
+ The method first checks if the gene product's ID matches the BiGG ID pattern. If it does not match, it then
+ tries to find a valid BiGG ID from the gene product's annotations. If a valid BiGG ID is found among the annotations,
+ it updates the ID; otherwise, it retains the original ID.
+Specified by:
+findBiGGId BiGGCVTermAnnotator <org.sbml.jsbml.ext.fbc.GeneProduct>Returns:
+An Optional <BiGGId >
+Throws:
+SQLException
+
+
+
+
+
+
+
+setGPLabelName
+public void setGPLabelName (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct,
+ String label)
+ throws SQLException Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database.
+ If the current label is set to "None", it updates the label to the provided one. It then attempts to fetch
+ the gene name corresponding to this label from the BiGG database. If a gene name is found, it checks if the
+ current gene product name is different from the fetched name. If they differ, it logs a warning and updates
+ the gene product name. If no gene name is found, it logs this as a fine-level message.
+
+Parameters:
+label - The label to set or use for fetching the gene name. This label should correspond to a BiGGIdAbstractSBase.getId().Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
+
+
+
BiGGGeneProductReferencesAnnotator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductReferencesAnnotator
+
+public class BiGGGeneProductReferencesAnnotator
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
update (org.sbml.jsbml.ext.fbc.GeneProduct gp)
+
+
Updates the reference of a gene product in the geneProductReferences map using the gene product's ID.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BiGGGeneProductReferencesAnnotator
+public BiGGGeneProductReferencesAnnotator ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+update
+public void update (org.sbml.jsbml.ext.fbc.GeneProduct gp)
+Updates the reference of a gene product in the geneProductReferences map using the gene product's ID.
+ If the gene product ID starts with "G_", it strips this prefix before updating.
+ If the map is initially empty, it initializes the map with the current model's reactions.
+
+Parameters:
+gp - The GeneProduct whose reference needs to be updated.
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+
+
+
+
+
Classes
+
+
+
+
+
+
+
+
+
+
Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/annotation/bigg/package-summary.html b/docs/de/uni_halle/informatik/biodata/mp/annotation/bigg/package-summary.html
new file mode 100644
index 00000000..7537834c
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/annotation/bigg/package-summary.html
@@ -0,0 +1,130 @@
+
+
+
+
+de.uni_halle.informatik.biodata.mp.annotation.bigg (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.annotation.bigg
+
+
+
+
+
+
+
+
All Classes and Interfaces Classes Exceptions
+
+
+
+
+
+
+
+
+
+
+
This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
+
+
+
+
Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
+
+
+
+
+
+
This class is responsible for annotating an SBML Model with relevant metadata and references.
+
+
+
+
+
+
This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
+
+
+
+
This class is responsible for annotating SBML models using data from the BiGG database.
+
+
+
+
This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.annotation.bigg Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/annotation/package-summary.html b/docs/de/uni_halle/informatik/biodata/mp/annotation/package-summary.html
new file mode 100644
index 00000000..c9e665e3
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/annotation/package-summary.html
@@ -0,0 +1,110 @@
+
+
+
+
+de.uni_halle.informatik.biodata.mp.annotation (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.annotation
+
+
+
+
+
+
+
+
All Classes and Interfaces Interfaces Classes Exceptions
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.annotation Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Interface Hierarchy
+
+de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases <SBMLElement>
+de.uni_halle.informatik.biodata.mp.annotation.IProcessNotes
+de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+
PostgresConnectionPool (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
+
+public class PostgresConnectionPool
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+PostgresConnectionPool
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+close
+public void close ()
+
+
+
+
+
+
+
+
+
+
+
AnnotateDB (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class AnnotateDB
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Retrieves a set of annotated URLs based on the type and BiGG ID provided.
+
+
static void
+
+
+
static void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+AnnotateDB
+public AnnotateDB ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+getAnnotations
+
+Retrieves a set of annotated URLs based on the type and BiGG ID provided.
+ This method queries the database to find matching annotations and constructs URLs using the retrieved data.
+
+Parameters:
+type - The type of the BiGG ID, which can be either a metabolite or a reaction.biggId - The BiGG ID for which annotations are to be retrieved. The ID may be modified if it starts
+ with specific prefixes or ends with an underscore.Returns:
+A sorted set of URLs that are annotations for the given BiGG ID. If the type is neither metabolite
+ nor reaction, or if an SQL exception occurs, an empty set is returned.
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
AnnotateDBContract.Constants.Column (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Column
+public Column ()
+
+
+
+
+
+
+
+
+
+
+
AnnotateDBContract.Constants.Table (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Table
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
AnnotateDBContract.Constants (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
+
+
+Enclosing class:
+AnnotateDBContract
+public abstract static class AnnotateDBContract.Constants
+
extends Object
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
+
+
static class
+
+
+
static class
+
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+BIGG_REACTION
+public static final String BIGG_REACTION
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Constants
+public Constants ()
+
+
+
+
+
+
+
+
+
+
+
AnnotateDBContract (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract
+
+public final class AnnotateDBContract
+
extends Object
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
+
+
static class
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+AnnotateDBContract
+public AnnotateDBContract ()
+
+
+
+
+
+
+
+
+
+
+
AnnotateDBOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface AnnotateDBOptions
+extends de.zbit.util.prefs.KeyProvider
+This interface provides options for connecting to the ADB database.
+
+
+
+
+
+
+Nested Class Summary
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
static final de.zbit.util.prefs.Option<Integer >
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+HOST
+static final de.zbit.util.prefs.Option<String > HOST
+
+
+
+PORT
+static final de.zbit.util.prefs.Option<Integer > PORT
+
+
+
+USER
+static final de.zbit.util.prefs.Option<String > USER
+
+
+
+PASSWD
+static final de.zbit.util.prefs.Option<String > PASSWD
+
+
+
+DBNAME
+static final de.zbit.util.prefs.Option<String > DBNAME
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.db.adb (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.db.adb
+
+
+
+
+
+
+
+
All Classes and Interfaces Interfaces Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
This interface provides options for connecting to the ADB database.
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.db.adb Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Interface Hierarchy
+
+de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+
BiGGDB.ForeignReaction (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
+
+
+Enclosing class:
+BiGGDB
+public class BiGGDB.ForeignReaction
+
extends Object Represents a reaction from an external data source mapped to the BiGG database, including its compartment details.
+ "Foreign" in this context refers to the origin of the reaction data from a source outside of the primary BiGG database schema,
+ typically involving cross-referencing with external databases or data sources.
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
Constructs a new ForeignReaction instance.
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+reactionId
+public final String reactionId
+
+
+
+compartmentId
+public final String compartmentId
+
+
+
+compartmentName
+public final String compartmentName
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ForeignReaction
+public ForeignReaction (String reactionId,
+ String compartmentId,
+ String compartmentName) Constructs a new ForeignReaction instance.
+
+Parameters:
+reactionId - The BiGG ID of the reaction.compartmentId - The BiGG ID of the compartment.compartmentName - The name of the compartment.
+
+
+
+
+
+
+
+
+
+
+
BiGGDB (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class BiGGDB
+
extends Object This class provides a connection to the BiGG database.
+
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
+
+
class
+
+
+
Represents a reaction from an external data source mapped to the BiGG database, including its compartment details.
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Retrieves a set of unique BiGG IDs from a specified table in the database.
+
+
+
+
+
Retrieves the BiGG ID associated with a given synonym and type from the specified data source.
+
+
+
+
+
Retrieves a collection of ForeignReaction objects for a given synonym and data source ID.
+
+
+
+
+
Retrieves the version date of the BiGG database.
+
+
+
+
+
Retrieves the charge for a given component and model from the database.
+
+
+
+
+
Retrieves the charge associated with a specific component in a given compartment when the model ID is unknown.
+
+
+
+
+
Retrieves the chemical formula for a given component within a specific model in the BiGG database.
+
+
+
+
+
Retrieves the unique chemical formula for a given component within a specific compartment.
+
+
+
+
+
Retrieves the name of the compartment associated with the given BiGG ID from the database.
+
+
+
+
+
Retrieves the name of the component associated with the given BiGG ID from the database.
+
+
+
+
+
Retrieves the type of the component associated with the given BiGG ID from the database.
+
+
+
+
+
Retrieves all possible MIRIAM-compliant gene identifiers from the database based on a given label.
+
+
+
+
+
Retrieves the gene name from the database based on a given label.
+
+
+
+
+
Retrieves formatted gene reaction rules for a specific reaction and model from the database.
+
+
+
+
+
Retrieves the genome accession for a given model ID from the BiGG database.
+
+
+
+
+
Retrieves the organism associated with a given BiGG model abbreviation from the database.
+
+
+
+
+
Retrieves a list of publications associated with a given BiGG model abbreviation from the database.
+
+
+
+
+
Retrieves the name of a reaction based on its BiGG ID abbreviation, ensuring the name is not empty.
+
+
+
+
+
Executes a provided SQL query to retrieve gene reaction rules from the database.
+
+
+
+
+
Retrieves a set of resource URLs for a given BiGG ID, optionally filtering to include only those containing 'identifiers.org'.
+
+
+
+
+
Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs.
+
+
+
+
+
Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID.
+
+
+
+
+
Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation.
+
+
static void
+
+
+
static void
+
+
+
boolean
+
+
+
boolean
+
+
+
boolean
+
+
+
boolean
+
+
+
boolean
+
+
+
Determines if a given reaction ID corresponds to a pseudoreaction in the database.
+
+
boolean
+
+
+
+
+
+
Executes a SQL query with a single parameter and returns the result as an Optional.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BiGGDB
+public BiGGDB ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+getBiGGVersion
+
+Retrieves the version date of the BiGG database.
+
+ This method queries the database to fetch the date and time of the last update
+ from the DATABASE_VERSION table. It returns an
Optional containing the
+ date if the query is successful and the date exists, otherwise it returns an empty
Optional.
+Returns:
+Optional <Date >OptionalThrows:
+SQLException
+
+
+
+
+getSubsystems
+
+Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs.
+ This method executes a SQL query to fetch subsystems from the database where both the model and reaction
+ match the provided BiGG IDs. Only subsystems with a non-zero length are considered.
+
+Parameters:
+modelBiGGid - The BiGG ID of the model.reactionBiGGid - The BiGG ID of the reaction.Returns:
+A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
+Throws:
+SQLException
+
+
+
+
+getSubsystemsForReaction
+
+Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID.
+ This method executes a SQL query to fetch subsystems from the database where the reaction
+ matches the provided BiGG ID. Only subsystems with a non-zero length are considered.
+
+Parameters:
+reactionBiGGid - The BiGG ID of the reaction for which subsystems are to be retrieved.Returns:
+A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+
+
+
+singleParamStatement
+
+Executes a SQL query with a single parameter and returns the result as an Optional.
+ This method is designed to handle queries that are expected to return a single result.
+ If multiple results are found, a severe log is recorded indicating the issue.
+
+Parameters:
+query - The SQL query to be executed. It should contain exactly one placeholder for the parameter.param - The parameter value to be used in the SQL query.Returns:
+An Optional <String >
+Throws:
+SQLException
+
+
+
+
+
+
+
+
+
+
+getGeneIds
+
+Retrieves all possible MIRIAM-compliant gene identifiers from the database based on a given label.
+ This method queries the database for gene identifiers that match the provided label and are compliant
+ with MIRIAM standards. Non-compliant entries are ignored.
+
+Parameters:
+label - The label used to query gene identifiers.Returns:
+A TreeSet containing unique, sorted MIRIAM-compliant gene identifiers.
+Throws:
+SQLException
+
+
+
+
+getGeneName
+
+Retrieves the gene name from the database based on a given label.
+ This method constructs a SQL query to fetch the synonym of a gene that matches the given label,
+ ensuring that the gene is associated with a valid data source and genome region, and that the
+ synonym is not empty. The query specifically looks for entries where the data source's BIGG ID
+ matches the REFSEQ naming convention.
+
+Parameters:
+label - The label used to query the gene name, typically a BIGG ID.Returns:
+An OptionalOptional
+Throws:
+SQLException
+
+
+
+
+getGeneReactionRule
+
+Retrieves formatted gene reaction rules for a specific reaction and model from the database.
+ This method constructs a SQL query to fetch and format the gene reaction rules associated with
+ the given reaction ID and model ID. The formatting includes replacing logical operators 'or' and 'and'
+ with || and &&, respectively, and substituting certain characters to comply with SBML standards.
+
+Parameters:
+reactionId - The ID of the reaction for which gene reaction rules are to be retrieved.modelId - The ID of the model associated with the reaction.Returns:
+A list of formatted gene reaction rules as strings.
+Throws:
+SQLException
+
+
+
+
+getReactionRules
+
+Executes a provided SQL query to retrieve gene reaction rules from the database.
+ This method prepares a statement with the given query, setting the specified reactionId and modelId as parameters.
+ It then executes the query and collects the results into a list of strings.
+
+Parameters:
+query - The SQL query string that retrieves gene reaction rules, expecting two placeholders for parameters.reactionId - The ID of the reaction to be used as the first parameter in the SQL query.modelId - The ID of the model to be used as the second parameter in the SQL query.Returns:
+A list of strings where each string is a gene reaction rule retrieved based on the given IDs.
+Throws:
+SQLException
+
+
+
+
+getOrganism
+
+Retrieves the organism associated with a given BiGG model abbreviation from the database.
+ This method constructs and executes a SQL query that joins the GENOME and MODEL tables to find the organism
+ corresponding to the specified model abbreviation.
+
+Parameters:
+abbreviation - The abbreviation of the model for which the organism is to be retrieved.Returns:
+An Optional containing the organism name if found, otherwise an empty Optional.
+Throws:
+SQLException
+
+
+
+
+getPublications
+
+Retrieves a list of publications associated with a given BiGG model abbreviation from the database.
+ This method constructs and executes a SQL query that joins the PUBLICATION, PUBLICATION_MODEL, and MODEL tables
+ to find the publications related to the specified model abbreviation.
+
+Parameters:
+abbreviation - The abbreviation of the model for which the publications are to be retrieved.Returns:
+A list of pairs where each pair consists of a publication type and its corresponding ID.
+Throws:
+SQLException
+
+
+
+
+getReactionName
+
+Retrieves the name of a reaction based on its BiGG ID abbreviation, ensuring the name is not empty.
+ This method constructs and executes a SQL query that selects the reaction name from the REACTION table
+ where the BIGG_ID matches the specified abbreviation and the name is not an empty string.
+
+Parameters:
+abbreviation - The abbreviation of the reaction for which the name is to be retrieved.Returns:
+An Optional containing the reaction name if found and not empty, otherwise an empty Optional.
+Throws:
+SQLException
+
+
+
+
+
+
+
+getTaxonId
+
+Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation.
+ This method queries the database to find the taxon ID associated with the model's abbreviation.
+ If multiple taxon IDs are found for the same abbreviation, a severe log message is generated.
+
+Parameters:
+abbreviation - The abbreviation of the model for which the taxon ID is being queried.Returns:
+An OptionalOptional
+Throws:
+SQLException
+
+
+
+
+getGenomeAccesion
+
+Retrieves the genome accession for a given model ID from the BiGG database.
+ The accession can be used to construct URLs for accessing genomic data from various sources.
+ The URLs can be formed using the accession ID with the following patterns:
+ - https://identifiers.org/refseq:{$id}
+ - https://www.ncbi.nlm.nih.gov/nuccore/{$id}
+ - https://www.ncbi.nlm.nih.gov/assembly/{$id}
+
+Parameters:
+id - The model ID present in BiGG.Returns:
+The accession string which can be appended to the base URLs mentioned above.
+ If the query fails or no accession is found, an empty string is returned.
+Throws:
+SQLException
+
+
+
+
+getAllBiggIds
+
+Retrieves a set of unique BiGG IDs from a specified table in the database.
+ This method queries the database for all unique BiGG IDs in the specified table and returns them as a set.
+ The IDs are ordered by their natural ordering in the database.
+
+Parameters:
+table - The name of the database table from which to retrieve BiGG IDs.Returns:
+A Set of strings containing unique BiGG IDs from the specified table. If an SQL error occurs,
+ the returned set will be empty.
+Throws:
+SQLException
+
+
+
+
+getChargeByCompartment
+
+Retrieves the charge associated with a specific component in a given compartment when the model ID is unknown.
+ This method executes a SQL query to find a distinct charge value for a component based on its BiGG ID and
+ the compartment's BiGG ID. The method ensures that the charge value is not empty and returns it if it is unique.
+
+Parameters:
+componentId - The BiGG ID of the component.compartmentId - The BiGG ID of the compartment.Returns:
+An OptionalOptional
+Throws:
+SQLException
+
+
+
+
+getCharge
+
+Retrieves the charge for a given component and model from the database.
+ This method executes a SQL query to select distinct charge values associated with the specified component ID
+ and model ID. It ensures that the charge value is not null.
+
+Parameters:
+componentId - The BiGG ID of the component.modelId - The BiGG ID of the model.Returns:
+An Optional containing the charge if exactly one distinct charge is found, otherwise an empty Optional.
+ If multiple distinct charges are found, a warning is logged.
+Throws:
+SQLException
+
+
+
+
+isPseudoreaction
+
+Determines if a given reaction ID corresponds to a pseudoreaction in the database.
+ A pseudoreaction is typically used to represent non-biochemical data flows such as biomass accumulation,
+ demand reactions, or exchange reactions.
+
+Parameters:
+reactionId - The BiGG ID of the reaction to be checked.Returns:
+true if the reaction is a pseudoreaction, false otherwise.
+Throws:
+SQLException
+
+
+
+
+getBiggIdFromSynonym
+
+Retrieves the BiGG ID associated with a given synonym and type from the specified data source.
+ This method constructs a SQL query based on the type of biological entity (species, reaction, or gene product)
+ and executes it to fetch the corresponding BiGG ID from the database.
+
+Parameters:
+dataSourceId - The ID of the data source where the synonym is registered.synonym - The synonym used to identify the entity in the data source.type - The type of the entity, which can be species, reaction, or gene product.Returns:
+An Optional containing the BiGG ID if exactly one unique ID is found, otherwise an empty Optional.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
BiGGDBContract.Constants.Column (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Column
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Column
+public Column ()
+
+
+
+
+
+
+
+
+
+
+
BiGGDBContract.Constants.Table (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Table
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
BiGGDBContract.Constants (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
+
+
+Enclosing class:
+BiGGDBContract
+public abstract static class BiGGDBContract.Constants
+
extends Object
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
+
+
static class
+
+
+
static class
+
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+TYPE_SPECIES
+public static final String TYPE_SPECIES
+See Also:
+
+
+
+
+
+
+
+
+TYPE_REACTION
+public static final String TYPE_REACTION
+See Also:
+
+
+
+
+
+
+
+
+TYPE_GENE_PRODUCT
+public static final String TYPE_GENE_PRODUCT
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Constants
+public Constants ()
+
+
+
+
+
+
+
+
+
+
+
BiGGDBContract (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public final class BiGGDBContract
+
extends Object
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
+
+
static class
+
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
BiGGDBOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface BiGGDBOptions
+extends de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+Nested Class Summary
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
static final de.zbit.util.prefs.Option<Integer >
+
+
+
static final de.zbit.util.prefs.Option<String >
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+HOST
+static final de.zbit.util.prefs.Option<String > HOST
+
+
+
+PORT
+static final de.zbit.util.prefs.Option<Integer > PORT
+
+
+
+USER
+static final de.zbit.util.prefs.Option<String > USER
+
+
+
+PASSWD
+static final de.zbit.util.prefs.Option<String > PASSWD
+
+
+
+DBNAME
+static final de.zbit.util.prefs.Option<String > DBNAME
+
+
+
+
+
+
+
+
+
+
BiGGId (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class BiGGId
+
extends Object Represents a BiGG identifier used to uniquely identify various biological entities
+ such as reactions, metabolites, and genes within the BiGG database. This class provides methods to parse, validate,
+ and manipulate BiGG IDs according to the standards specified in the BiGG database.
+
+ The BiGG ID typically consists of several parts:
+ - A prefix indicating the type of entity (e.g., 'R' for reaction, 'M' for metabolite, 'G' for gene).
+ - An abbreviation which is the main identifier part.
+ - A compartment code that specifies the cellular location of the metabolite.
+ - A tissue code that indicates the tissue specificity of the identifier, applicable in multicellular organisms.
+
+ This class also includes methods to create BiGG IDs from strings, validate them against known patterns, and
+ extract specific parts like the compartment code. It supports handling special cases and correcting common
+ formatting issues in BiGG IDs.
+
+ For a formal description of the structure of BiGG ids see the proposed
+
+ BiGG ID specification .
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Creates a BiGG ID for a reaction based on the provided string identifier.
+
+
boolean
+
+
+
+
+
+
Extracts the compartment code from a given identifier if it matches the expected pattern.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
int
+
+
+
boolean
+
+
+
boolean
+
+
+
boolean
+
+
+
boolean
+
+
+
static boolean
+
+
+
void
+
+
+
+ Only contain upper and lower case letters, numbers, and underscores
+ /[0-9a-zA-Z][a-zA-Z0-9_]+/, only ASCII and don't start with numbers
+ When converting old BIGG IDs to BIGG2 IDs, replace a dash with two
+ underscores.
+
+
void
+
+
+
One or two characters in length, and contain only lower case letters and
+ numbers, and must begin with a lower case letter.
+
+
void
+
+
+
+ R: reaction
+ M: metabolite /[RM]/
+ NOTE: Do we want to have the id entity use R and M, and just remove
+ them when constructing the model, or have them just as
+ [abbreviation]_[compartment code] and add the prefix when they are put
+ into SBML models? Also SBML id's use capital letters (/[RM]/).
+
+
void
+
+
+
One or two characters in length, and contain only upper case letters and
+ numbers, and must begin with an upper case letter.
+
+
+
+
+
Generates a BiGG ID for this object based on its properties.
+
+
+
+
+
Constructs a BiGG ID using the provided components.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BiGGId
+public BiGGId ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+createReactionId
+public static BiGGId createReactionId (String id,
+ boolean isPseudo) Creates a BiGG ID for a reaction based on the provided string identifier.
+ The method can correct the ID to conform to BiGG standards and adjust the prefix based on whether it is a pseudo-reaction.
+
+Parameters:
+id - The raw reaction ID string.isPseudo - If true, the ID is treated as a pseudo-reaction, affecting the prefix handling.Returns:
+An Optional containing the BiGGId if the ID is non-empty, or an empty Optional if the ID is empty.
+
+
+
+
+
+isValid
+public static boolean isValid (String queryId)
+
+
+
+
+
+
+
+
+
+getAbbreviation
+public String getAbbreviation ()
+
+
+
+setAbbreviation
+public void setAbbreviation (String abbreviation)
+ Only contain upper and lower case letters, numbers, and underscores
+ /[0-9a-zA-Z][a-zA-Z0-9_]+/, only ASCII and don't start with numbers
+ When converting old BIGG IDs to BIGG2 IDs, replace a dash with two
+ underscores. For example, ala-L becomes ala__L.
+ Reactions should be all upper case. Metabolites should be primarily
+ lower case, but upper case letters are allowed (ala__L is preferred to
+ ALA__L).
+
+Parameters:
+abbreviation - the abbreviation to set
+
+
+
+
+getCompartmentCode
+public String getCompartmentCode ()
+
+
+
+setCompartmentCode
+public void setCompartmentCode (String compartmentCode) One or two characters in length, and contain only lower case letters and
+ numbers, and must begin with a lower case letter. /[a-z][a-z0-9]?/
+
+Parameters:
+compartmentCode - the compartmentCode to set
+
+
+
+
+
+
+
+setPrefix
+public void setPrefix (String prefix)
+ R: reaction
+ M: metabolite /[RM]/
+ NOTE: Do we want to have the id entity use R and M, and just remove
+ them when constructing the model, or have them just as
+ [abbreviation]_[compartment code] and add the prefix when they are put
+ into SBML models? Also SBML id's use capital letters (/[RM]/).
+
+Parameters:
+prefix - the prefix to set
+
+
+
+
+
+
+
+setTissueCode
+public void setTissueCode (String tissueCode) One or two characters in length, and contain only upper case letters and
+ numbers, and must begin with an upper case letter. /[A-Z][A-Z0-9]?/
+
+Parameters:
+tissueCode - the tissueCode to set
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+isSetAbbreviation
+public boolean isSetAbbreviation ()
+
+
+
+
+isSetCompartmentCode
+public boolean isSetCompartmentCode ()
+
+
+
+
+isSetPrefix
+public boolean isSetPrefix ()
+
+
+
+
+isSetTissueCode
+public boolean isSetTissueCode ()
+
+
+
+
+toBiGGId
+
+Generates a BiGG ID for this object based on its properties. The BiGG ID is constructed by concatenating
+ the available properties (prefix, abbreviation, compartment code, and tissue code) in that order, each separated
+ by an underscore. Each property is included only if it is set (i.e., not null).
+
+Returns:
+A string representing the BiGG ID, constructed by concatenating the set properties with underscores.
+ If none of the properties are set, returns an empty string.
+
+
+
+
+
+toBiGGId
+
+Constructs a BiGG ID using the provided components. Each component is separated by an underscore.
+ If a component is null or empty, it is omitted from the final ID.
+
+Parameters:
+prefix - The first part of the BiGG ID, typically representing the type of entity (e.g., 'R', 'M', 'G').abbreviation - The main identifier, usually an alphanumeric string that uniquely describes the entity.compartmentCode - A code indicating the compartmentalization, relevant for compartmentalized entities.tissueCode - A code representing the tissue specificity, applicable to certain biological models.Returns:
+A string representing the constructed BiGG ID, formed by concatenating the provided components with underscores.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Publication (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
Creates an instance of a Publication record class.
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
final boolean
+
+
+
Indicates whether some other object is "equal to" this one.
+
+
final int
+
+
+
Returns a hash code value for this object.
+
+
+
+
+
Returns the value of the referenceId record component.
+
+
+
+
+
Returns the value of the referenceType record component.
+
+
+
+
+
Returns a string representation of this record class.
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Publication
+public Publication (String referenceType,
+ String referenceId) Creates an instance of a Publication record class.
+
+Parameters:
+referenceType - the value for the referenceType record componentreferenceId - the value for the referenceId record component
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+toString
+public final String toString ()
Returns a string representation of this record class. The representation contains the name of the class, followed by the name and value of each of the record components.
+
+Specified by:
+toString Record Returns:
+a string representation of this object
+
+
+
+
+
+hashCode
+public final int hashCode ()
+Returns a hash code value for this object. The value is derived from the hash code of each of the record components.
+
+Specified by:
+hashCode Record Returns:
+a hash code value for this object
+
+
+
+
+
+equals
+public final boolean equals (Object o) Indicates whether some other object is "equal to" this one. The objects are equal if the other object is of the same class and if all the record components are equal. All components in this record class are compared with
Objects::equals(Object,Object).
+Specified by:
+equals Record Parameters:
+o - the object with which to compareReturns:
+true if this object is the same as the o argument; false otherwise.
+
+
+
+
+referenceType
+
+Returns the value of the referenceType record component.
+
+Returns:
+the value of the referenceType record component
+
+
+
+
+
+referenceId
+
+Returns the value of the referenceId record component.
+
+Returns:
+the value of the referenceId record component
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.db.bigg (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.db.bigg
+
+
+
+
+
+
+
+
All Classes and Interfaces Interfaces Classes Record Classes
+
+
+
+
+
+
+
This class provides a connection to the BiGG database.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Represents a BiGG identifier used to uniquely identify various biological entities
+ such as reactions, metabolites, and genes within the BiGG database.
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.db.bigg Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Interface Hierarchy
+
+de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.db (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.db
+
+
+
+
de.uni_halle.informatik.biodata.mp.db Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/eco/DAG.html b/docs/de/uni_halle/informatik/biodata/mp/eco/DAG.html
new file mode 100644
index 00000000..18ada444
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/eco/DAG.html
@@ -0,0 +1,183 @@
+
+
+
+
+DAG (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class DAG
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
DAG (org.biojava.nbio.ontology.Term term)
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
void
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+DAG
+public DAG (org.biojava.nbio.ontology.Term term)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Node (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class Node
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
Node (org.biojava.nbio.ontology.Term term)
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
addChild (org.biojava.nbio.ontology.Term child)
+
+
void
+
+
+
void
+
addParent (org.biojava.nbio.ontology.Term parent)
+
+
boolean
+
+
+
+
+
+
+
+
+
+
findTerm (org.biojava.nbio.ontology.Term term)
+
+
Returns the Node containing the specified Term or null, if not present
+
+
+
+
+
+
+
+
org.biojava.nbio.ontology.Term
+
+
+
int
+
+
+
static void
+
+
+
void
+
+
+
void
+
+
+
void
+
setTerm (org.biojava.nbio.ontology.Term term)
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Node
+public Node (org.biojava.nbio.ontology.Term term)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+addChild
+public void addChild (org.biojava.nbio.ontology.Term child)
+
+
+
+
+
+
+
+addParent
+public void addParent (org.biojava.nbio.ontology.Term parent)
+
+
+
+
+
+
+
+setChildren
+public void setChildren (List <Node > children)
+
+
+
+setParents
+public void setParents (List <Node > parents)
+
+
+
+setTerm
+public void setTerm (org.biojava.nbio.ontology.Term term)
+
+
+
+
+
+
+
+
+
+
+findTerm
+public Node findTerm (org.biojava.nbio.ontology.Term term) Returns the Node containing the specified Term or null, if not present
+
+
+
+
+
+
+
+
+
+
+getTerm
+public org.biojava.nbio.ontology.Term getTerm ()
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.eco (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.eco
+
+
+
+
de.uni_halle.informatik.biodata.mp.eco Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.eco.DAG
+de.uni_halle.informatik.biodata.mp.eco.Node
+
+
+
+
+
+
+
AbstractFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+
+
protected
+
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+
+
+
+AbstractFixer
+public AbstractFixer ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
CompartmentFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (List <org.sbml.jsbml.Compartment> rs)
+
+
void
+
fix (org.sbml.jsbml.Compartment compartment,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (List <org.sbml.jsbml.Compartment> rs)
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Compartment>
+
+
+
+
+fix
+public void fix (org.sbml.jsbml.Compartment compartment,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Compartment>
+
+
+
+
+
+
+
+
+
+
+
FixingOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface FixingOptions
+extends de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+Nested Class Summary
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
static final de.zbit.util.prefs.Option<Double []>
+
+
+
static final de.zbit.util.prefs.Option<String []>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+DONT_FIX
+static final de.zbit.util.prefs.Option<Boolean > DONT_FIX
+
+
+
+FLUX_COEFFICIENTS
+static final de.zbit.util.prefs.Option<Double []> FLUX_COEFFICIENTS
+
+
+
+FLUX_OBJECTIVES
+static final de.zbit.util.prefs.Option<String []> FLUX_OBJECTIVES
+
+
+
+
+
+
+
+
+
+
IFixSBases (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods Default Methods
+
+
+
+
+
+
default void
+
+
+
void
+
+
+
+
+
+
+
+
+
+
+
+
+
IFixSpeciesReferences (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods Default Methods
+
+
+
+
+
+
default void
+
fix (List <org.sbml.jsbml.SpeciesReference> elements)
+
+
void
+
fix (org.sbml.jsbml.SpeciesReference element)
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+default void fix (List <org.sbml.jsbml.SpeciesReference> elements)
+
+
+
+fix
+void fix (org.sbml.jsbml.SpeciesReference element)
+
+
+
+
+
+
+
+
+
+
+
ModelFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (org.sbml.jsbml.Model model,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (org.sbml.jsbml.Model model,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Model>
+
+
+
+
+
+
+
+
+
+
+
ReactionFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (List <org.sbml.jsbml.Reaction> rs)
+
+
void
+
fix (org.sbml.jsbml.Reaction reaction,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (List <org.sbml.jsbml.Reaction> rs)
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+fix
+public void fix (org.sbml.jsbml.Reaction reaction,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+
+
+
+
+
+
+
SBMLFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (org.sbml.jsbml.SBMLDocument sbmlDocument,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (org.sbml.jsbml.SBMLDocument sbmlDocument,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.SBMLDocument>
+
+
+
+
+
+
+
+
+
+
+
SpeciesFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (List <org.sbml.jsbml.Species> rs)
+
+
void
+
fix (org.sbml.jsbml.Species species,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (List <org.sbml.jsbml.Species> rs)
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Species>
+
+
+
+
+fix
+public void fix (org.sbml.jsbml.Species species,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Species>
+
+
+
+
+
+
+
+
+
+
+
SpeciesReferenceFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.fixing.SpeciesReferenceFixer
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (org.sbml.jsbml.SpeciesReference sr)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+SpeciesReferenceFixer
+public SpeciesReferenceFixer ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
FBCSpeciesFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (org.sbml.jsbml.Species species,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+FBCSpeciesFixer
+public FBCSpeciesFixer ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (org.sbml.jsbml.Species species,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.Species>
+
+
+
+
+
+
+
+
+
+
+
ListOfObjectivesFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (org.sbml.jsbml.ext.fbc.ListOfObjectives objectives,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (org.sbml.jsbml.ext.fbc.ListOfObjectives objectives,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.ext.fbc.ListOfObjectives>
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.fixing.ext.fbc (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
+
+
+
+
de.uni_halle.informatik.biodata.mp.fixing.ext.fbc Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer (implements de.uni_halle.informatik.biodata.mp.reporting.IReportStatus )
+
+de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.FBCSpeciesFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.ListOfObjectivesFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+
+
+
+
+
+
+
+
+
GroupsFixer (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
fix (List <org.sbml.jsbml.ext.groups.Group> rs)
+
+
void
+
fix (org.sbml.jsbml.ext.groups.Group group,
+ int index)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+fix
+public void fix (List <org.sbml.jsbml.ext.groups.Group> rs)
+Specified by:
+fix IFixSBases <org.sbml.jsbml.ext.groups.Group>
+
+
+
+
+fix
+public void fix (org.sbml.jsbml.ext.groups.Group group,
+ int index)
+
+Specified by:
+fix IFixSBases <org.sbml.jsbml.ext.groups.Group>
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.fixing.ext.groups (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.fixing.ext.groups
+
+
+
+
de.uni_halle.informatik.biodata.mp.fixing.ext.groups Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer (implements de.uni_halle.informatik.biodata.mp.reporting.IReportStatus )
+
+de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.fixing (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.fixing
+
+
+
+
+
All Classes and Interfaces Interfaces Classes
+
+
+
+
+
+
+
+
+
+
+
IFixSBases <SBMLElement extends org.sbml.jsbml.SBase>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.fixing Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer (implements de.uni_halle.informatik.biodata.mp.reporting.IReportStatus )
+
+de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+de.uni_halle.informatik.biodata.mp.fixing.ModelFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>)
+
+
+de.uni_halle.informatik.biodata.mp.fixing.SpeciesReferenceFixer (implements de.uni_halle.informatik.biodata.mp.fixing.IFixSpeciesReferences )
+
+
+
+
+
+Interface Hierarchy
+
+de.uni_halle.informatik.biodata.mp.fixing.IFixSBases <SBMLElement>
+de.uni_halle.informatik.biodata.mp.fixing.IFixSpeciesReferences
+de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+
CombineArchive (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class CombineArchive
+
extends Object The
CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
+ It supports writing an RDF glossary derived from the SBML document and packaging both the SBML file and its
+ RDF glossary into a single COMBINE archive file. This class handles the creation, formatting, and management
+ of files necessary for the archive, ensuring they adhere to the COMBINE specification.
+
+
Key functionalities include:
+
+ Generating RDF glossary from the SBML document annotations.
+ Writing the RDF glossary to a file with proper formatting using JTidy.
+ Creating a COMBINE archive that includes the SBML file and the RDF glossary.
+ Handling file operations such as checking for existing files, deleting, and writing new files.
+
+
+
This class is essential for users looking to export SBML models and their annotations in a standardized
+ archive format that can be easily shared and processed by various bioinformatics tools.
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+COMBINE_SPECIFICATION
+public static final String COMBINE_SPECIFICATION
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+CombineArchive
+public CombineArchive (org.sbml.jsbml.SBMLDocument doc,
+ File output)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
DeleteOnCloseFileInputStream (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
IOOptions.OutputType (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Nested Class Summary
+
+
+
+
+
+
+Enum Constant Summary
+Enum Constants
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
Returns the enum constant of this class with the specified name.
+
+
+
+
+
Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+
+
+
+
Methods inherited from class java.lang.Enum
+
clone , compareTo , describeConstable , equals , finalize , getDeclaringClass , hashCode , name , ordinal , toString , valueOf
+
+
+
+
+
+
+
+
+Enum Constant Details
+
+
+
+
+
+
+Method Details
+
+
+
+values
+
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+Returns:
+an array containing the constants of this enum class, in the order they are declared
+
+
+
+
+
+valueOf
+
+Returns the enum constant of this class with the specified name.
+The string must match exactly an identifier used to declare an
+enum constant in this class. (Extraneous whitespace characters are
+not permitted.)
+
+Parameters:
+name - the name of the enum constant to be returned.Returns:
+the enum constant with the specified name
+Throws:
+IllegalArgumentException NullPointerException
+
+
+
+
+getFileExtension
+public String getFileExtension ()
+
+
+
+
+
+
+
+
+
+
IOOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface IOOptions
+extends de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
+
+
+
Decides whether the output file should directly be compressed and if
+ so, which archive type should be used.
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+OUTPUT_TYPE
+
+Decides whether the output file should directly be compressed and if
+ so, which archive type should be used.
+
+
+
+
+
+
+
+
+
+
+
IReadModelsFromFile (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+ModelReader
+public interface IReadModelsFromFile
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
org.sbml.jsbml.SBMLDocument
+
+
+
+
+
+
+
+
+
+
+
+
+
IWriteModels (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+ModelWriter
+public interface IWriteModels
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
write (org.sbml.jsbml.SBMLDocument doc)
+
+
+
+
+
+
+
+
+
+
+
+
IWriteModelsToFile (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+ModelWriter
+public interface IWriteModelsToFile
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
write (org.sbml.jsbml.SBMLDocument doc,
+ File output)
+
+
+
+
+
+
+
+
+
+
+
+
ModelReader (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
org.sbml.jsbml.SBMLDocument
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
ModelReaderException (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+Serializable
+public class ModelReaderException
+
extends Throwable
+See Also:
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Throwable
+
addSuppressed , fillInStackTrace , getCause , getLocalizedMessage , getMessage , getStackTrace , getSuppressed , initCause , printStackTrace , printStackTrace , printStackTrace , setStackTrace , toString
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ModelReaderException
+public ModelReaderException (String s,
+ File input)
+
+
+
+ModelReaderException
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
ModelWriter (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
write (org.sbml.jsbml.SBMLDocument doc)
+
+
+
write (org.sbml.jsbml.SBMLDocument doc,
+ File output)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
ModelWriterException (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+Serializable
+public class ModelWriterException
+
extends Exception
+See Also:
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
org.sbml.jsbml.SBMLDocument
+
+
+
+
+
+
+
+
+
Methods inherited from class java.lang.Throwable
+
addSuppressed , fillInStackTrace , getCause , getLocalizedMessage , getMessage , getStackTrace , getSuppressed , initCause , printStackTrace , printStackTrace , printStackTrace , setStackTrace , toString
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ModelWriterException
+public ModelWriterException (String s,
+ Exception e,
+ org.sbml.jsbml.SBMLDocument doc,
+ File output)
+
+
+
+ModelWriterException
+public ModelWriterException (String s,
+ org.sbml.jsbml.SBMLDocument doc,
+ File output,
+ File archiveFile)
+
+
+
+
+
+
+
+Method Details
+
+
+
+doc
+public org.sbml.jsbml.SBMLDocument doc ()
+
+
+
+
+
+
+
+archiveFile
+public File archiveFile ()
+
+
+
+
+
+
+
+
+
+
SBMLFileUtils.FileType (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Nested Class Summary
+
+
+
+
+
+
+Enum Constant Summary
+Enum Constants
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Returns the enum constant of this class with the specified name.
+
+
+
+
+
Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+
+
+
+
Methods inherited from class java.lang.Enum
+
clone , compareTo , describeConstable , equals , finalize , getDeclaringClass , hashCode , name , ordinal , toString , valueOf
+
+
+
+
+
+
+
+
+Enum Constant Details
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+values
+
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+Returns:
+an array containing the constants of this enum class, in the order they are declared
+
+
+
+
+
+valueOf
+
+Returns the enum constant of this class with the specified name.
+The string must match exactly an identifier used to declare an
+enum constant in this class. (Extraneous whitespace characters are
+not permitted.)
+
+Parameters:
+name - the name of the enum constant to be returned.Returns:
+the enum constant with the specified name
+Throws:
+IllegalArgumentException NullPointerException
+
+
+
+
+
+
+
+
+
+
+
SBMLFileUtils (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class SBMLFileUtils
+
extends Object
+
+
+
+
+
+Nested Class Summary
+Nested Classes
+
+
+
+
+
static enum
+
+
+
Possible FileTypes of input file
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
static void
+
+
+
Creates output directory or output parent directory, if necessary
+
+
+
+
+
Determines the type of the input file based on its extension or content.
+
+
+
+
+
Fix output file name to contain xml extension
+
+
static boolean
+
+
+
Check if file is directory by calling
File.isDirectory() on an existing file or check presence of '.' in
+ output.getName(), if this is not the case
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+SBMLFileUtils
+public SBMLFileUtils ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getFileType
+
+Determines the type of the input file based on its extension or content.
+ This method checks if the file is an SBML, MatLab, or JSON file by utilizing the SBFileFilter class.
+
+Parameters:
+input - The file whose type needs to be determined.Returns:
+FileType The type of the file, which can be SBML_FILE, MAT_FILE, JSON_FILE, or UNKNOWN if the type cannot be determined.
+
+
+
+
+
+getOutputFileName
+public static File getOutputFileName (File file,
+ File output) Fix output file name to contain xml extension
+
+Parameters:
+file - :
+ File to get name for in input directoryoutput - :
+ Path to output directoryReturns:
+File in output directory with correct file ending for SBML
+
+
+
+
+
+isDirectory
+public static boolean isDirectory (File file) Check if file is directory by calling
File.isDirectory() on an existing file or check presence of '.' in
+ output.getName(), if this is not the case
+
+
+
+checkCreateOutDir
+public static void checkCreateOutDir (File output) Creates output directory or output parent directory, if necessary
+
+Parameters:
+output - :
+ File denoting output location
+
+
+
+
+
+
+
+
+
+
+
UpdateListener (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+PropertyChangeListener EventListener org.sbml.jsbml.util.TreeNodeChangeListener
+public class UpdateListener
+
extends Object
+implements org.sbml.jsbml.util.TreeNodeChangeListener The
UpdateListener class implements the
TreeNodeChangeListener to monitor and respond to changes
+ within an SBML model's structure. This class specifically handles updates to
+ identifiers (IDs) of model elements like reactions and gene products, ensuring that all references remain consistent
+ across the model. It also manages the addition of new nodes to the model, particularly focusing on gene product
+ references, and maintains a mapping from gene identifiers to their associated gene product references.
+
+ The TreeNodeChangeListener base class provides the interface for receiving notifications when changes occur
+ to any node within a tree structure, which in the context of SBML, corresponds to elements within the model's
+ hierarchical structure.
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
Constructs an UpdateListener instance and initializes the geneIdToAssociation map.
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
Handles the event when a new node is added to the TreeNode structure.
+
+
void
+
nodeRemoved (org.sbml.jsbml.util.TreeNodeRemovedEvent event)
+
+
void
+
+
+
Responds to property change events, specifically focusing on changes to the ID property of tree nodes.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+UpdateListener
+public UpdateListener ()
+Constructs an UpdateListener instance and initializes the geneIdToAssociation map.
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+propertyChange
+
+Responds to property change events, specifically focusing on changes to the ID property of tree nodes.
+ This method handles the update of IDs within the model, ensuring that all references to the old ID
+ are updated to the new ID across various components such as reactions and gene products.
+
+Specified by:
+propertyChange PropertyChangeListener Parameters:
+evt - The property change event that contains information about the old and new values of the property.
+
+
+
+
+nodeAdded
+
+Handles the event when a new node is added to the TreeNode structure.
+ Specifically, when a GeneProductRef node is added, this method updates the
+ geneIdToAssociation map to include this new association. It ensures that each
+ gene product ID is mapped to a set of its associated GeneProductRefs.
+
+Specified by:
+nodeAdded in interface org.sbml.jsbml.util.TreeNodeChangeListenerParameters:
+node - The TreeNode that has been added. Expected to be an instance of GeneProductRef.
+
+
+
+
+nodeRemoved
+public void nodeRemoved (org.sbml.jsbml.util.TreeNodeRemovedEvent event)
+
+Specified by:
+nodeRemoved in interface org.sbml.jsbml.util.TreeNodeChangeListener
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.io
+
+
+
+
+
All Classes and Interfaces Interfaces Classes Enum Classes Exceptions
+
+
+
+
+
+
+
The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Possible FileTypes of input file
+
+
+
+
The UpdateListener class implements the TreeNodeChangeListener to monitor and respond to changes
+ within an SBML model's structure.
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+Enum Class Hierarchy
+
+
+
+
+
COBRAUtils (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+
+public class COBRAUtils
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
+
asString (us.hebi.matlab.mat.types.Array array)
+
+
+
asString (us.hebi.matlab.mat.types.Array array,
+ String parentName,
+ int parentIndex)
+
+
+
+
+
Necessary to check for a special whitespace (code 160) at beginning of id
+ (iCHOv1.mat, possibly other models) and to remove trailing ';'
+
+
static boolean
+
exists (us.hebi.matlab.mat.types.Array cell,
+ int i)
+
+
static boolean
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+COBRAUtils
+public COBRAUtils ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+isEmptyString
+public static boolean isEmptyString (String string)
+Parameters:
+string - the StringReturns:
+true if the given Stringnull or
+ empty or equals empty square brackets.
+
+
+
+
+checkId
+
+Necessary to check for a special whitespace (code 160) at beginning of id
+ (iCHOv1.mat, possibly other models) and to remove trailing ';'
+
+Returns:
+trimmed id without ';' at the end
+
+
+
+
+
+exists
+public static boolean exists (us.hebi.matlab.mat.types.Array cell,
+ int i)
+
+
+
+
+asString
+public static String asString (us.hebi.matlab.mat.types.Array array)
+
+
+
+asString
+public static String asString (us.hebi.matlab.mat.types.Array array,
+ String parentName,
+ int parentIndex)
+
+
+
+
+
+
+
+
+
+
GeneParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra.GeneParser
+
+public class GeneParser
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
GeneParser (org.sbml.jsbml.ext.fbc.FBCModelPlugin plugin,
+ int index)
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+GeneParser
+public GeneParser (org.sbml.jsbml.ext.fbc.FBCModelPlugin plugin,
+ int index)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+parse
+public void parse ()
+
+
+
+
+
+
+
+
+
+
+
MatlabParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra.MatlabParser
+
+public class MatlabParser
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
org.sbml.jsbml.SBMLDocument
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
ModelField (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Nested Class Summary
+
+
+
+
+
+
+Enum Constant Summary
+Enum Constants
+
+
+
+
+
+
Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v =
+ 0 or g(μ ) ⋅ A ⋅ v + B ⋅ v = 0 with
+ g(μ ) being some continuous nonlinear function of μ ;
+
+
+
+
+
+
The bound vector of metabolite concentration change rates (usually but not
+ always all zero, i.e., steady-state): S ⋅ v = b .
+
+
+
+
Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v =
+ 0 or g(μ ) ⋅ A ⋅ v + B ⋅ v = 0 with
+ g(μ ) being some continuous nonlinear function of μ ;
+
+
+
+
The objective function vector for max(c' ⋅ v ) for corresponding
+ reactions.
+
+
+
+
Literature references for the reactions.
+
+
+
+
+
+
These are human-readable notes for reactions.
+
+
+
+
Confidence score for each reaction.
+
+
+
+
The csense field expresses equality constraints in the model.
+
+
+
+
Human-redable information about the model, e.g., the model name.
+
+
+
+
The "disabled" field comes from the reconstruction tool rBioNet.
+
+
+
+
The Enzyme Commission codes for the reactions.
+
+
+
+
+
+
+
+
The list of all genes in the model, where each contained gene corresponds
+ to a AbstractSBase.getId().
+
+
+
+
+
+
Boolean gene-protein-reaction (GPR) rules in a readable format (AND/OR).
+
+
+
+
Lower reaction flux bounds for corresponding reactions
+
+
+
+
Value of charge for corresponding metabolite.
+
+
+
+
Optional: if present, it must have same dimension as
mets.
+
+
+
+
Elemental formula for each metabolite.
+
+
+
+
Optional: if present, it must have same dimension as
mets.
+
+
+
+
Inichi String for each corresponding metabolite.
+
+
+
+
KEGG ID for each corresponding metabolite.
+
+
+
+
Descriptive metabolite names, must have same dimension as
mets.
+
+
+
+
Pub Chem ID for each corresponding metabolite.
+
+
+
+
Metabolite name abbreviation; metabolite ID; order corresponds to S matrix.
+
+
+
+
Optional: if present, it must have same dimension as
mets.
+
+
+
+
+
+
+
+
+
+
Objective sense, i.e., to minimize or maximize the objective.
+
+
+
+
Proteins associated with each reaction.
+
+
+
+
A vector consisting of zeros and ones that translate to binary and determine
+ if the corresponding reaction of that index is reversible (1) or not (0).
+
+
+
+
Boolean rule for the corresponding reaction which defines gene-reaction
+ relationship.
+
+
+
+
+
+
Cell array of strings, can any value in a range of 0 to 4.
+
+
+
+
+
+
+
+
A matrix with rows corresponding to reaction list and columns corresponding
+ to gene list.
+
+
+
+
Reaction identifiers in KEGG, but sometimes also contains
ecNumbers.
+
+
+
+
TODO: description KEGG Orthology
+
+
+
+
Descriptive reaction names, length of this array must be identical to the
+ number of reactions.
+
+
+
+
Cell array of strings.
+
+
+
+
Cell array of strings which can contain optional information on references
+ for each specific reaction.
+
+
+
+
+
+
The Systems Biology Ontology Term to describe the role of a reaction.
+
+
+
+
Stoichiometric matrix in sparse format.
+
+
+
+
This defines groups of reactions that belong to a common reaction subsystem.
+
+
+
+
Upper reaction flux bounds for corresponding reactions
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies, if case can't be
+ matched
+
+
+
+
+
Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies using struct
+ field as prefix of knwon model field
+
+
+
+
+
Returns the enum constant of this class with the specified name.
+
+
+
+
+
Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+
+
+
+
Methods inherited from class java.lang.Enum
+
clone , compareTo , describeConstable , equals , finalize , getDeclaringClass , hashCode , name , ordinal , toString , valueOf
+
+
+
+
+
+
+
+
+Enum Constant Details
+
+
+
+A
+
+Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v =
+ 0 or g(μ ) ⋅ A ⋅ v + B ⋅ v = 0 with
+ g(μ ) being some continuous nonlinear function of μ ;
+
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+b
+
+The bound vector of metabolite concentration change rates (usually but not
+ always all zero, i.e., steady-state):
S ⋅ v = b . Must have same
+ dimension as
mets.
+
+ The mat files where the b vector isn't zero include constraints that couple
+ the flux through the model's reactions to the BOF. These are mat files
+ joining reconstructions of two or more species. These constraints are
+ represented in the b and A fields.
+
+ If this cannot be expressed in SBML, then an error message would be
+ appropriate. The SBML file would probably not result in a functional joined
+ model though.
+
+ Data type: double array. Length must be identical to the number of reactions.
+
+
+
+B
+
+Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v =
+ 0 or g(μ ) ⋅ A ⋅ v + B ⋅ v = 0 with
+ g(μ ) being some continuous nonlinear function of μ ;
+
+See Also:
+
+
+
+
+
+
+
+
+c
+
+The objective function vector for max(
c' ⋅ v ) for corresponding
+ reactions. The dimension of this element must be identical to the number of
+ reactions. Dimensions that have a zero value in this field, do not
+ contribute to the objective function.
+
+ Data type: double array.
+ Corresponds to FluxObjective.getCoefficient().
+
+
+
+citations
+
+Literature references for the reactions.
+
+
+
+
+
+
+
+
+
+
+confidenceScores
+
+Confidence score for each reaction.
+ Confidence scores must have the same dimension as the reactions. These are
+ an optional input, but it provides additional information on the reaction
+ content. Adding them as notes would be a good idea.
+
+
+
+
+csense
+
+The csense field expresses equality constraints in the model. If this field
+ is not defin object.getType();ed in the reconstruction, equality constraints are assumed when
+ performing the optimization. Its value is a
String whose length
+ must equal the number of metabolites. An 'E' at index
i means that
+ in this dimension
S ⋅ v = b (equality), 'G' means ≥ greater
+ than or equal to and an 'L' denotes ≤.
+See Also:
+
+
+
+
+
+
+
+
+description
+
+Human-redable information about the model, e.g., the model name. This field
+ can optionally have sub-entries.
+
+
+
+
+disabled
+
+The "disabled" field comes from the reconstruction tool rBioNet.
+ The tool offers the option to disable certain reactions.
+ If no reactions are disabled, then the "disabled" field in empty.
+
+
+
+
+ecNumbers
+
+The Enzyme Commission codes for the reactions. Length must be identical to
+ the number of reactions.
+
+
+
+
+
+
+
+
+
+
+genes
+
+The list of all genes in the model, where each contained gene corresponds
+ to a AbstractSBase.getId(). Data type: cell array of string.
+
+
+
+
+
+
+
+grRules
+
+Boolean gene-protein-reaction (GPR) rules in a readable format (AND/OR).
+ Data type: cell array of strings.
+ Example: (8639.1) or (26.1) or (314.2) or (314.1). Dimensions must
+ be identical to the number of reactions. Corresponds to
+ GeneProductAssociation
+
+
+
+
+lb
+
+Lower reaction flux bounds for corresponding reactions
+
+
+
+
+metCharge
+
+Value of charge for corresponding metabolite.
+ Must have same dimension as
mets. Data type: double array.
+ For SBML Level < 3, it corresponds to
Species.getCharge(). Since
+ Level 3, it corresponds to
FBCSpeciesPlugin.getCharge().
+
+
+
+metCHEBIID
+
+Optional: if present, it must have same dimension as
mets.
+ Data type: cell array of strings. Corresponds to the annotation of
+
Species
+
+
+
+
+
+
+metHMDB
+
+Optional: if present, it must have same dimension as
mets.
+ Data type: cell array of strings.
+
+
+
+metInchiString
+
+Inichi String for each corresponding metabolite.
+ Optional: if present, it must have same dimension as
mets.
+ Data type: cell array of strings.
+
+
+
+metKeggID
+
+KEGG ID for each corresponding metabolite.
+ Optional: if present, it must have same dimension as
mets.
+ Data type: cell array of strings.
+
+
+
+metNames
+
+Descriptive metabolite names, must have same dimension as
mets.
+ Datatype: cell array of strings. Corresponds to
AbstractSBase.getName()
+
+
+
+metPubChemID
+
+Pub Chem ID for each corresponding metabolite.
+ Optional: if present, it must have same dimension as
mets.
+ Data type: cell array of strings.
+
+
+
+mets
+
+Metabolite name abbreviation; metabolite ID; order corresponds to S matrix.
+ Metabolite BiGG ids (incl. compartment code). Data type: cell array of
+ strings. Corresponds to AbstractSBase.getId().
+
+
+
+
+metSmile
+
+Optional: if present, it must have same dimension as
mets.
+
+
+
+
+
+
+
+
+
+
+
+
+osense
+
+Objective sense, i.e., to minimize or maximize the objective. This field
+ can either be defined in the mat file itself or when performing an
+ optimization function (e.g., optimizeCbModel).
+
+
+
+
+proteins
+
+Proteins associated with each reaction.
+
+
+
+
+rev
+
+A vector consisting of zeros and ones that translate to binary and determine
+ if the corresponding reaction of that index is reversible (1) or not (0).
+ Dimensions must be equal to the number of reactions. Corresponds to the
+ value Reaction.isReversible()
+
+
+
+
+rules
+
+Boolean rule for the corresponding reaction which defines gene-reaction
+ relationship.
+
+
+
+
+rxnCOG
+
+TODO: description COG
+
+
+
+
+rxnConfidenceEcoIDA
+public static final ModelField rxnConfidenceEcoIDA Cell array of strings, can any value in a range of 0 to 4. Length must be
+ equal to the number of reactions.
+
+
+
+
+rxnConfidenceScores
+public static final ModelField rxnConfidenceScores .
+
+
+
+
+rxnsboTerm
+
+The Systems Biology Ontology Term to describe the role of a reaction.
+ Length must be identical to the number of reactions. Value corresponds to
+ the attribute AbstractSBase.getSBOTerm()
+
+
+
+
+rxnGeneMat
+
+A matrix with rows corresponding to reaction list and columns corresponding
+ to gene list. Data type: sparse double. Size of this matrix must be number
+ of reactions times number of genes. No counterpart in FBC v2.
+
+
+
+
+rxnKeggID
+
+Reaction identifiers in KEGG, but sometimes also contains
ecNumbers.
+ Length must be identical to the number of reactions. Entries belong to the
+ annotation of
Reaction.
+
+
+
+rxnNames
+
+Descriptive reaction names, length of this array must be identical to the
+ number of reactions. Data type: cell array of string. Corresponds to the
+ name of a Reaction.
+
+
+
+
+rxnKeggOrthology
+
+TODO: description KEGG Orthology
+
+
+
+
+rxnECNumbers
+
+E. C. number for each reaction
+
+See Also:
+
+
+
+
+
+
+
+
+rxnReferences
+
+Cell array of strings which can contain optional information on references
+ for each specific reaction.
+ Example:
+
+
+ 'Na coupled transport of pyruvate, lactate, and short chain fatty acids, i.e., acetate, propionate, and butyrate mediated by SMCT1
+
+
+
+
+rxns
+
+Reaction BiGG ids. Corresponds to the id of Reaction.
+ Reaction name abbreviation; reaction ID; order corresponds to S matrix.
+
+
+
+
+rxnNotes
+
+Cell array of strings. Text notes (description) about reactions. Length
+ must be identical to the number of reactions.
+
+
+
+
+S
+
+Stoichiometric matrix in sparse format.
+
+
+
+
+subSystems
+
+This defines groups of reactions that belong to a common reaction subsystem.
+ Their number must hence be identical to the reaction count. Subsystems are
+ listed repeatedly in the source file.
+ If present, the size of this field must be identical to the number of
+ reactions.
+ Data type: cell array of strings.
+
+
+
+
+ub
+
+Upper reaction flux bounds for corresponding reactions
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+values
+
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+Returns:
+an array containing the constants of this enum class, in the order they are declared
+
+
+
+
+
+valueOf
+
+Returns the enum constant of this class with the specified name.
+The string must match exactly an identifier used to declare an
+enum constant in this class. (Extraneous whitespace characters are
+not permitted.)
+
+Parameters:
+name - the name of the enum constant to be returned.Returns:
+the enum constant with the specified name
+Throws:
+IllegalArgumentException NullPointerException
+
+
+
+
+getCorrectName
+
+Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies, if case can't be
+ matched
+
+Parameters:
+query - :
+ Possible model field, present in model structReturns:
+List of matching ModelField variant names
+
+
+
+
+
+getNameForPrefix
+
+Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies using struct
+ field as prefix of knwon model field
+
+
+
+
+
+
+
+
+
+
+
ReactionParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
+
+public class ReactionParser
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
boolean
+
+
+
Tries to update a resource according to pre-defined rules.
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+parse
+public void parse ()
+
+
+
+
+addResource
+public boolean addResource (String resource,
+ org.sbml.jsbml.CVTerm term,
+ String prefix) Tries to update a resource according to pre-defined rules. If the resource
+ starts with the MIRIAM name followed by a colon, its value is added to the
+ given term. This method assumes that there is a colon between catalog id
+ and resource id. If this is not the case, false will be returned.
+
+Returns:
+true if successful, false otherwise.
+
+
+
+
+
+
+
+
+
+
+
SpeciesParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
+
+public class SpeciesParser
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+parse
+public void parse ()
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+
+
+
+
+
All Classes and Interfaces Classes Enum Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io.parsers.cobra Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra.GeneParser
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra.MatlabParser
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
+
+
+
+
+
+Enum Class Hierarchy
+
+
+
+
+
JSONConverter (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+
+public class JSONConverter
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+JSONConverter
+public JSONConverter ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+getJSONDocument
+public static String getJSONDocument (org.sbml.jsbml.SBMLDocument doc)
+ throws com.fasterxml.jackson.core.JsonProcessingException,
+XMLStreamException
+Throws:
+com.fasterxml.jackson.core.JsonProcessingExceptionXMLStreamException
+
+
+
+
+getJSONModel
+public static String getJSONModel (org.sbml.jsbml.Model model)
+ throws com.fasterxml.jackson.core.JsonProcessingException,
+XMLStreamException
+Throws:
+com.fasterxml.jackson.core.JsonProcessingExceptionXMLStreamException
+
+
+
+
+
+
+
+
+
+
+
JSONParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+
+public class JSONParser
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
org.sbml.jsbml.SBMLDocument
+
+
+
Creates the ModelBuilder, SBMLDocument and reads the
+ jsonFile as a tree
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+parse
+public org.sbml.jsbml.SBMLDocument parse (File jsonFile)
+ throws IOException Creates the ModelBuilder, SBMLDocument and reads the
+ jsonFile as a tree
+
+Throws:
+IOException
+
+
+
+
+parseAnnotation
+public void parseAnnotation (org.sbml.jsbml.SBase node,
+ Object annotation)
+
+
+
+parseNotes
+public void parseNotes (org.sbml.jsbml.SBase node,
+ Object notes)
+
+
+
+parseCompartments
+public void parseCompartments (org.sbml.jsbml.util.ModelBuilder builder,
+ Map <String ,String > compartments)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Compartments (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+
+public class Compartments
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
+
+
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Compartments
+public Compartments ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Gene (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+
+public class Gene
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+
+
+
+setNotes
+public void setNotes (Object notes)
+
+
+
+
+
+
+setAnnotation
+public void setAnnotation (Object annotation)
+
+
+
+
+
+
+
+
+
+
Metabolite (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+
+public class Metabolite
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
double
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Metabolite
+public Metabolite ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+getCompartment
+public String getCompartment ()
+
+
+
+setCompartment
+public void setCompartment (String compartment)
+
+
+
+getCharge
+public int getCharge ()
+
+
+
+
+setCharge
+public void setCharge (int charge)
+
+
+
+
+
+
+
+
+
+
+getBound
+public double getBound ()
+
+
+
+
+setBound
+public void setBound (double bound)
+
+
+
+
+
+
+
+setNotes
+public void setNotes (Object notes)
+
+
+
+
+
+
+setAnnotation
+public void setAnnotation (Object annotation)
+
+
+
+
+
+
+
+
+
+
Metabolites (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
+
+public class Metabolites
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Metabolites
+public Metabolites ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+add
+public void add (String key,
+ double value)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Reaction (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+
+public class Reaction
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
double
+
+
+
+
+
+
+
+
+
+
+
+
double
+
+
+
+
+
+
double
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Reaction
+public Reaction ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+
+
+
+
+
+
+getGeneReactionRule
+public String getGeneReactionRule ()
+
+
+
+setGeneReactionRule
+public void setGeneReactionRule (String geneReactionRule)
+
+
+
+getLowerBound
+public double getLowerBound ()
+
+
+
+
+setLowerBound
+public void setLowerBound (double lowerBound)
+
+
+
+
+getUpperBound
+public double getUpperBound ()
+
+
+
+
+setUpperBound
+public void setUpperBound (double upperBound)
+
+
+
+
+getObjectiveCoefficient
+public double getObjectiveCoefficient ()
+
+
+
+
+setObjectiveCoefficient
+public void setObjectiveCoefficient (double objectiveCoefficient)
+
+
+
+
+
+
+
+setSubsystem
+public void setSubsystem (String subsystem)
+
+
+
+
+
+
+setNotes
+public void setNotes (Object notes)
+
+
+
+
+
+
+setAnnotation
+public void setAnnotation (Object annotation)
+
+
+
+
+
+
+
+
+
+
Root (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+
+public class Root
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
int
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+getDescription
+public String getDescription ()
+
+
+
+setDescription
+public void setDescription (String description)
+
+
+
+getVersion
+public int getVersion ()
+
+
+
+
+setVersion
+public void setVersion (int version)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+setNotes
+public void setNotes (Object notes)
+
+
+
+
+
+
+setAnnotation
+public void setAnnotation (Object annotation)
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+
+
+
+
+
+
+
+
Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.io.parsers.json (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.io.parsers.json
+
+
+
+
de.uni_halle.informatik.biodata.mp.io.parsers.json Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+
+
+
+
+
+
+
BundleNames (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class BundleNames
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+FIXING_MESSAGES
+public static final String FIXING_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+IO_MESSAGES
+public static final String IO_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+ANNOTATION_MESSAGES
+public static final String ANNOTATION_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+DB_MESSAGES
+public static final String DB_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+POLISHING_MESSAGES
+public static final String POLISHING_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+BIGG_ANNOTATION_MESSAGES
+public static final String BIGG_ANNOTATION_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+CLI_MESSAGES
+public static final String CLI_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+BASE_MESSAGES
+public static final String BASE_MESSAGES
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BundleNames
+public BundleNames ()
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.logging (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.logging
+
+
+
+
de.uni_halle.informatik.biodata.mp.logging Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/parameters/ADBAnnotationParameters.html b/docs/de/uni_halle/informatik/biodata/mp/parameters/ADBAnnotationParameters.html
new file mode 100644
index 00000000..9dde9a3d
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/parameters/ADBAnnotationParameters.html
@@ -0,0 +1,251 @@
+
+
+
+
+ADBAnnotationParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+
+public class ADBAnnotationParameters
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
protected boolean
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
boolean
+
+
+
+
+
+
boolean
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+annotateWithAdb
+protected boolean annotateWithAdb
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ADBAnnotationParameters
+public ADBAnnotationParameters ()
+
+
+
+
+ADBAnnotationParameters
+public ADBAnnotationParameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+annotateWithAdb
+public boolean annotateWithAdb ()
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
+
+
+
AnnotationParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+
+public class AnnotationParameters
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
boolean
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+AnnotationParameters
+public AnnotationParameters ()
+
+
+
+
+AnnotationParameters
+public AnnotationParameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+adbAnnotationParameters
+
+
+
+
+
+biggAnnotationParameters
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
BiGGAnnotationParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+
+public class BiGGAnnotationParameters
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
protected boolean
+
+
+
+
+
+
+
+
+
protected boolean
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
boolean
+
+
+
+
+
+
+
+
+
boolean
+
+
+
int
+
+
+
boolean
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+annotateWithBiGG
+protected boolean annotateWithBiGG
+
+
+
+
+includeAnyURI
+protected boolean includeAnyURI
+
+
+
+
+documentTitlePattern
+protected String documentTitlePattern
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BiGGAnnotationParameters
+public BiGGAnnotationParameters ()
+
+
+
+
+
+
+
+BiGGAnnotationParameters
+public BiGGAnnotationParameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+includeAnyURI
+public boolean includeAnyURI ()
+
+
+
+
+annotateWithBiGG
+public boolean annotateWithBiGG ()
+
+
+
+
+documentTitlePattern
+public String documentTitlePattern ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
BiGGNotesParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+
+public class BiGGNotesParameters
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
boolean
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+modelNotesFile
+protected File modelNotesFile
+
+
+
+documentNotesFile
+protected File documentNotesFile
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+BiGGNotesParameters
+public BiGGNotesParameters ()
+
+
+
+
+BiGGNotesParameters
+public BiGGNotesParameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+documentNotesFile
+public File documentNotesFile ()
+
+
+
+modelNotesFile
+public File modelNotesFile ()
+
+
+
+noModelNotes
+public boolean noModelNotes ()
+
+
+
+
+
+
+
+
+
+
+
DBParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class DBParameters
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
boolean
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+DBParameters
+public DBParameters ()
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
FixingParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+
+public class FixingParameters
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
boolean
+
+
+
boolean
+
+
+
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+FixingParameters
+public FixingParameters ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+dontFix
+public boolean dontFix ()
+
+
+
+
+fluxObjectivesPolishingParameters
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
FluxObjectivesFixingParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+
+public class FluxObjectivesFixingParameters
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+FluxObjectivesFixingParameters
+public FluxObjectivesFixingParameters ()
+
+
+
+
+FluxObjectivesFixingParameters
+
+
+
+
+
+FluxObjectivesFixingParameters
+public FluxObjectivesFixingParameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
GeneralOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface GeneralOptions
+extends de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+Nested Class Summary
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
Set this option to true if generic top-level annotations, such as 'process'
+ should not be applied.
+
+
+
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
If true, the created SBML file will be validated through the online
+ validator service at
http://sbml.org .
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+ADD_GENERIC_TERMS
+static final de.zbit.util.prefs.Option<Boolean > ADD_GENERIC_TERMS Set this option to true if generic top-level annotations, such as 'process'
+ should not be applied. Not using those terms will reduce the size of the
+ resulting output file.
+
+
+
+
+SBML_VALIDATION
+static final de.zbit.util.prefs.Option<Boolean > SBML_VALIDATION If true, the created SBML file will be validated through the online
+ validator service at
http://sbml.org . This option is only used
+ if the output is GZIP compressed.
+
+
+
+
+
+
+
+
+
+
Parameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class Parameters
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
protected boolean
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
boolean
+
+
+
+
+
+
int
+
+
+
+
+
+
+
+
+
boolean
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+sbmlValidation
+protected boolean sbmlValidation
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Parameters
+public Parameters ()
+
+
+
+
+Parameters
+public Parameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+sbmlValidation
+public boolean sbmlValidation ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
+
+
+
ParametersException (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+Serializable
+public class ParametersException
+
extends Throwable
+See Also:
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
Methods inherited from class java.lang.Throwable
+
addSuppressed , fillInStackTrace , getCause , getLocalizedMessage , getMessage , getStackTrace , getSuppressed , initCause , printStackTrace , printStackTrace , printStackTrace , setStackTrace , toString
+
+
+
+
+
+
+
+
ParametersParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.ParametersParser
+
+public class ParametersParser
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ParametersParser
+public ParametersParser ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
PolishingParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
+
+public class PolishingParameters
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+PolishingParameters
+public PolishingParameters ()
+
+
+
+
+PolishingParameters
+public PolishingParameters (boolean polishEvenIfModelInvalid)
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polishEvenIfModelInvalid
+public boolean polishEvenIfModelInvalid ()
+
+
+
+
+
+
+
+
+
+
+
SBOParameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class SBOParameters
+
extends Object
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
protected boolean
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
boolean
+
+
+
boolean
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+addGenericTerms
+protected boolean addGenericTerms
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+SBOParameters
+public SBOParameters ()
+
+
+
+
+SBOParameters
+public SBOParameters (de.zbit.util.prefs.SBProperties args)
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+addGenericTerms
+public boolean addGenericTerms ()
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.parameters (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.parameters
+
+
+
+
+
All Classes and Interfaces Interfaces Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.parameters Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Interface Hierarchy
+
+de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+
AbstractPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+
+
+All Implemented Interfaces:
+IReportStatus
+
+Direct Known Subclasses:
+AnnotationPolisher CompartmentPolisher FBCPolisher FBCReactionPolisher GeneProductsPolisher ModelPolisher ObjectivesPolisher ParametersPolisher ReactionsPolisher SBMLPolisher SpeciesPolisher UnitPolisher
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
boolean
+
+
+
+
+
+
int
+
+
+
void
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
+
+
+
AnnotationPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.Annotation annotation)
+
+
Processes the annotations of an SBML entity to potentially correct identifiers
+ and/or retrieve additional identifiers.org URLs.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (org.sbml.jsbml.Annotation annotation)
+Processes the annotations of an SBML entity to potentially correct identifiers
+ and/or retrieve additional identifiers.org URLs.
+ This method iterates over all Controlled Vocabulary (CV) Terms in the provided Annotation object.
+ For each resource URL in a CV Term,
+ it checks and possibly corrects the URL or adds new URLs from identifiers.org.
+ It then updates the CV Term with the corrected and/or additional URLs.
+
+Specified by:
+polish IPolishAnnotations Parameters:
+annotation - The Annotation object associated with an SBML entity that contains CV Terms to be processed.
+
+
+
+
+
+
+
+
+
+
+
CompartmentPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IPolishSBases <org.sbml.jsbml.Compartment>IReportStatus
+This class is responsible for polishing the properties of a compartment in an SBML model to ensure
+ compliance with standards and completeness. It handles the annotation processing, ID and name setting,
+ and ensures that necessary attributes like units and spatial dimensions are appropriately set.
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (List <org.sbml.jsbml.Compartment> compartments)
+
+
Polishes all compartments in the given SBML model.
+
+
void
+
polish (org.sbml.jsbml.Compartment compartment)
+
+
Polishes the properties of a compartment to ensure compliance with standards and completeness.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (List <org.sbml.jsbml.Compartment> compartments) Polishes all compartments in the given SBML model. This method iterates through each compartment
+ in the model, updates the progress display, and applies polishing operations defined in the
+ CompartmentPolishing class.
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Compartment>
+
+
+
+
+polish
+public void polish (org.sbml.jsbml.Compartment compartment)
+Polishes the properties of a compartment to ensure compliance with standards and completeness.
+ This method processes annotations, sets default values for missing identifiers, names, and meta identifiers,
+ and ensures that the compartment has appropriate units and other necessary attributes set.
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Compartment>
+
+
+
+
+
+
+
+
+
+
+
IPolishAnnotations (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+AnnotationPolisher
+public interface IPolishAnnotations
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.Annotation annotation)
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+void polish (org.sbml.jsbml.Annotation annotation)
+
+
+
+
+
+
+
+
+
+
+
IPolishSBaseAttributes (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+NamePolisher
+public interface IPolishSBaseAttributes
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods Default Methods
+
+
+
+
+
+
default void
+
polish (List <org.sbml.jsbml.SBase> elementsToPolish)
+
+
void
+
polish (org.sbml.jsbml.SBase elementToPolish)
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+default void polish (List <org.sbml.jsbml.SBase> elementsToPolish)
+
+
+
+polish
+void polish (org.sbml.jsbml.SBase elementToPolish)
+
+
+
+
+
+
+
+
+
+
+
IPolishSBases (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+CompartmentPolisher FBCPolisher FBCReactionPolisher GeneProductsPolisher ModelPolisher ObjectivesPolisher ParametersPolisher ReactionsPolisher SBMLPolisher SpeciesPolisher UnitPolisher
+public interface IPolishSBases<SBMLElement extends org.sbml.jsbml.SBase>
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods Default Methods
+
+
+
+
+
+
default void
+
+
+
void
+
+
+
+
+
+
+
+
+
+
+
+
+
IPolishSpeciesReferences (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods Default Methods
+
+
+
+
+
+
default void
+
polish (List <org.sbml.jsbml.SpeciesReference> elementsToPolish)
+
+
void
+
polish (org.sbml.jsbml.SpeciesReference elementToPolish)
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+default void polish (List <org.sbml.jsbml.SpeciesReference> elementsToPolish)
+
+
+
+polish
+void polish (org.sbml.jsbml.SpeciesReference elementToPolish)
+
+
+
+
+
+
+
+
+
+
+
ModelPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IPolishSBases <org.sbml.jsbml.Model>IReportStatus
+This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
+ Polishing involves enhancing the document with additional annotations, setting appropriate SBO (Systems Biology Ontology) terms,
+ and ensuring the document adheres to certain standards and conventions useful for computational models in systems biology.
+ The class supports operations such as checking the document's structure, polishing individual model components,
+ and processing external resources linked within the document.
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.Model model)
+
+
This method orchestrates the polishing of an SBML model by delegating tasks to specific polishing methods
+ for different components of the model.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (org.sbml.jsbml.Model model)
+This method orchestrates the polishing of an SBML model by delegating tasks to specific polishing methods
+ for different components of the model. It initializes a progress bar to track and display the progress of
+ the polishing process.
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Model>Parameters:
+model - The SBML Model to be polished.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
NamePolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.SBase sbase)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+NamePolisher
+public NamePolisher ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
ParametersPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (List <org.sbml.jsbml.Parameter> modelParameters)
+
+
void
+
polish (org.sbml.jsbml.Parameter p)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (List <org.sbml.jsbml.Parameter> modelParameters)
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Parameter>
+
+
+
+
+polish
+public void polish (org.sbml.jsbml.Parameter p)
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Parameter>
+
+
+
+
+
+
+
+
+
+
+
PolisherFactory (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.polishing.PolisherFactory
+
+public class PolisherFactory
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+PolisherFactory
+public PolisherFactory ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
PolishingOptions (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Superinterfaces:
+de.zbit.util.prefs.KeyProvider
+public interface PolishingOptions
+extends de.zbit.util.prefs.KeyProvider
+
+
+
+
+
+
+Nested Class Summary
+
+
Nested classes/interfaces inherited from interface de.zbit.util.prefs.KeyProvider
+
de.zbit.util.prefs.KeyProvider.Entry<T extends Object >, de.zbit.util.prefs.KeyProvider.Tools
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
static final de.zbit.util.prefs.Option<Boolean >
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+
+
+
+POLISH_EVEN_IF_MODEL_INVALID
+static final de.zbit.util.prefs.Option<Boolean > POLISH_EVEN_IF_MODEL_INVALID
+
+
+
+
+
+
+
+
+
+
ReactionsPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IPolishSBases <org.sbml.jsbml.Reaction>IReportStatus
+This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
+ It includes functionality to:
+ - Check and set SBO terms based on reaction ID patterns.
+ - Polish species references and compartments.
+ - Validate and set flux bounds and objectives.
+ - Convert gene associations from reaction notes to FBCv2 format.
+ - Check mass and atom balance of reactions.
+
+ The class operates on an SBML Reaction object and modifies it to conform to standards and conventions
+ used in systems biology models, particularly those related to flux balance constraints.
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
polish (org.sbml.jsbml.Reaction reaction)
+
+
Polishes the reaction by applying various checks and modifications to ensure it conforms to
+ the expected standards and conventions.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (List <org.sbml.jsbml.Reaction> reactions)
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+polish
+public void polish (org.sbml.jsbml.Reaction reaction)
+Polishes the reaction by applying various checks and modifications to ensure it conforms to
+ the expected standards and conventions. This includes setting SBO terms, checking compartments,
+ and ensuring proper setup of reactants and products.
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+
+
+
+
+
+
+
SBMLPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.SBMLDocument doc)
+
+
This method serves as the entry point from the ModelPolisher class to polish an SBML document.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (org.sbml.jsbml.SBMLDocument doc)
+This method serves as the entry point from the ModelPolisher class to polish an SBML document.
+ It ensures the document contains a model, performs a sanity check, polishes the model, sets the SBO term,
+ marks the progress as finished if applicable, and processes any linked resources.
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.SBMLDocument>Parameters:
+doc - The SBMLDocument containing the model to be polished.
+
+
+
+
+
+
+
+
+
+
+
SpeciesPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
polish (org.sbml.jsbml.Species species)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (List <org.sbml.jsbml.Species> species)
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Species>
+
+
+
+
+polish
+public void polish (org.sbml.jsbml.Species species)
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Species>
+
+
+
+
+
+
+
+
+
+
+
SpeciesReferencesPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.polishing.SpeciesReferencesPolisher
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.SpeciesReference sr)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+SpeciesReferencesPolisher
+public SpeciesReferencesPolisher (Integer defaultSBOterm)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
UnitPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+IPolishSBases <org.sbml.jsbml.Model>IReportStatus
+This class is responsible for ensuring that all necessary
UnitDefinitions and
Units are correctly
+ defined and present in the SBML model. It handles the creation and verification of units used in the model,
+ particularly focusing on the units related to growth, substance, time, and volume.
+
+ Additionally, this class is responsible for accurately assigning these defined units to specific components
+ such as reactions, species, and parameters within the model as needed.
+ This ensures that all these components adhere uniformly to the correct unit specifications,
+ maintaining consistency and accuracy throughout the model's unit definitions.
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
static final org.sbml.jsbml.CVTerm
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.Model model)
+
+
Ensures that all necessary UnitDefinitions and Units are present in the model.
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT
+public static final org.sbml.jsbml.CVTerm CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT
+
+
+
+
+GROWTH_UNIT_ID
+public static final String GROWTH_UNIT_ID
+See Also:
+
+
+
+
+
+
+
+
+GROWTH_UNIT_NAME
+public static final String GROWTH_UNIT_NAME
+See Also:
+
+
+
+
+
+
+
+
+CV_TERM_IS_SUBSTANCE_UNIT
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_SUBSTANCE_UNIT
+
+
+
+
+CV_TERM_IS_TIME_UNIT
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_TIME_UNIT
+
+
+
+
+CV_TERM_IS_VOLUME_UNIT
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_VOLUME_UNIT
+
+
+
+
+CV_TERM_IS_UO_SECOND
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_SECOND
+
+
+
+
+CV_TERM_IS_UO_HOUR
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_HOUR
+
+
+
+
+CV_TERM_IS_UO_MMOL
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_MMOL
+
+
+
+
+CV_TERM_IS_UO_GRAM
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_UO_GRAM
+
+
+
+
+CV_TERM_IS_VERSION_OF_UO_SECOND
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_VERSION_OF_UO_SECOND
+
+
+
+
+CV_TERM_IS_VERSION_OF_UO_MOLE
+public static final org.sbml.jsbml.CVTerm CV_TERM_IS_VERSION_OF_UO_MOLE
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (org.sbml.jsbml.Model model)
+Ensures that all necessary UnitDefinitions and Units are present in the model.
+ If any are missing, they are created and added to the model. This method also sets the model's
+ extent and substance units if they are not already set.
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Model>
+
+
+
+
+
+
+
+
+
+
+
FBCPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.Model model)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (org.sbml.jsbml.Model model)
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Model>
+
+
+
+
+
+
+
+
+
+
+
FBCReactionPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
polish (org.sbml.jsbml.Reaction reaction)
+
+
void
+
+
+
Polishes the SBO term of a flux bound parameter based on its ID.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (List <org.sbml.jsbml.Reaction> reactions)
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+polish
+public void polish (org.sbml.jsbml.Reaction reaction)
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.Reaction>
+
+
+
+
+setFluxBoundSBOTerm
+public void setFluxBoundSBOTerm (org.sbml.jsbml.Parameter bound)
+Polishes the SBO term of a flux bound parameter based on its ID.
+ If the parameter's ID matches the default flux bound pattern, it sets the SBO term to 626.
+ Otherwise, it sets the SBO term to 625.
+
+Parameters:
+bound - The parameter representing a flux bound.
+
+
+
+
+
+
+
+
+
+
+
GeneProductAssociationsProcessor (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductAssociationsProcessor
+
+public class GeneProductAssociationsProcessor
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+GeneProductAssociationsProcessor
+public GeneProductAssociationsProcessor ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+convertAssociationsToFBCV2
+public void convertAssociationsToFBCV2 (org.sbml.jsbml.Reaction reaction,
+ boolean addGenericTerms)
+
+
+
+
+
+
+
+
+
+
+
GeneProductsPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (List <org.sbml.jsbml.ext.fbc.GeneProduct> geneProducts)
+
+
void
+
polish (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (List <org.sbml.jsbml.ext.fbc.GeneProduct> geneProducts)
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.ext.fbc.GeneProduct>
+
+
+
+
+polish
+public void polish (org.sbml.jsbml.ext.fbc.GeneProduct geneProduct)
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.ext.fbc.GeneProduct>
+
+
+
+
+
+
+
+
+
+
+
ObjectivesPolisher (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
polish (org.sbml.jsbml.ext.fbc.Objective objective)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+polish
+public void polish (org.sbml.jsbml.ext.fbc.Objective objective)
+
+Specified by:
+polish IPolishSBases <org.sbml.jsbml.ext.fbc.Objective>
+
+
+
+
+
+
+
+
+
+
+
StrictnessPredicate (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+
+
+All Implemented Interfaces:
+Predicate <org.sbml.jsbml.Model>
+public class StrictnessPredicate
+
extends Object
+implements Predicate <org.sbml.jsbml.Model>
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
5) All defined FluxObjective objects must have their coefficient attribute set
+ to a double value that is not 'NaN', nor '-INF', nor 'INF'.
+
+
boolean
+
+
+
4) InitialAssignment objects may not target the Parameter objects referenced by
+ the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
+
+
boolean
+
+
+
4) InitialAssignment objects may not target the Parameter objects referenced by
+ the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
+
+
boolean
+
+
+
boolean
+
+
+
1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound',
+ with each attribute pointing to a valid Parameter object defined in the current Model.
+
+
boolean
+
+
+
boolean
+
+
+
3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value
+ that is not 'NaN', nor '-INF', nor 'INF'.
+
+
boolean
+
test (org.sbml.jsbml.Model model)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+StrictnessPredicate
+public StrictnessPredicate ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+test
+public boolean test (org.sbml.jsbml.Model model)
+
+Specified by:
+test Predicate <org.sbml.jsbml.Model>
+
+
+
+
+reactionHasValidBounds
+public boolean reactionHasValidBounds (org.sbml.jsbml.Reaction r)
+1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound',
+ with each attribute pointing to a valid Parameter object defined in the current Model.
+ 2) Each Parameter object referred to by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound'
+ must have its 'constant' attribute set to the value 'true'
+ and its 'value' attribute set to a value of type double. This value may not be 'NaN'.
+ 6) A Reaction 'lowerFluxBound' attribute may not point to a Parameter object that has a value of 'INF'.
+ 7) A Reaction 'upperFluxBound' attribute may not point to a Parameter object that has a value of '-INF'.
+ 8) For all Reaction objects, the value of a 'lowerFluxBound' attribute must be
+ less than or equal to the value of the 'upperFluxBound' attribute.
+
+
+
+
+isBoundSet
+public boolean isBoundSet (org.sbml.jsbml.Parameter bound)
+
+
+
+
+reactionSpeciesReferencesHaveValidAttributes
+public boolean reactionSpeciesReferencesHaveValidAttributes (org.sbml.jsbml.Reaction r)
+
+
+
+
+
+strictnessOfSpeciesReferences
+public boolean strictnessOfSpeciesReferences (org.sbml.jsbml.ListOf<org.sbml.jsbml.SpeciesReference> listOfSpeciesReference)
+3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value
+ that is not 'NaN', nor '-INF', nor 'INF'.
+ In addition, the value of their 'constant' attribute must be set to 'true'.
+
+
+
+
+initialAssignmentDoesNotReferenceBoundParameters
+public boolean initialAssignmentDoesNotReferenceBoundParameters (org.sbml.jsbml.InitialAssignment ia)
+4) InitialAssignment objects may not target the Parameter objects referenced by
+ the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
+
+
+
+
+initialAssignmentDoesNotReferenceSpeciesReferences
+public boolean initialAssignmentDoesNotReferenceSpeciesReferences (org.sbml.jsbml.InitialAssignment ia)
+4) InitialAssignment objects may not target the Parameter objects referenced by
+ the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
+
+
+
+
+fluxObjectiveHasValidCoefficients
+public Boolean fluxObjectiveHasValidCoefficients (org.sbml.jsbml.ext.fbc.FluxObjective fo) 5) All defined FluxObjective objects must have their coefficient attribute set
+ to a double value that is not 'NaN', nor '-INF', nor 'INF'.
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.polishing.ext.fbc (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+
+
+
+
+
Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.polishing.ext.fbc Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/polishing/package-summary.html b/docs/de/uni_halle/informatik/biodata/mp/polishing/package-summary.html
new file mode 100644
index 00000000..06736921
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/polishing/package-summary.html
@@ -0,0 +1,129 @@
+
+
+
+
+de.uni_halle.informatik.biodata.mp.polishing (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.polishing
+
+
+
+
+
All Classes and Interfaces Interfaces Classes
+
+
+
+
+
+
+
+
+
+
+
This class is responsible for polishing the properties of a compartment in an SBML model to ensure
+ compliance with standards and completeness.
+
+
+
+
+
+
+
+
+
+
+
+
This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
+
+
+
+
+
+
+
+
+
+
+
+
This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
+
+
+
+
+
+
+
+
+
+
This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly
+ defined and present in the SBML model.
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.polishing Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/reporting/DiffListener.html b/docs/de/uni_halle/informatik/biodata/mp/reporting/DiffListener.html
new file mode 100644
index 00000000..5ad8abd1
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/reporting/DiffListener.html
@@ -0,0 +1,192 @@
+
+
+
+
+DiffListener (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+PropertyChangeListener EventListener org.sbml.jsbml.util.TreeNodeChangeListener
+public class DiffListener
+
extends Object
+implements org.sbml.jsbml.util.TreeNodeChangeListener
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
nodeRemoved (org.sbml.jsbml.util.TreeNodeRemovedEvent event)
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+DiffListener
+public DiffListener ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+nodeAdded
+
+
+Specified by:
+nodeAdded in interface org.sbml.jsbml.util.TreeNodeChangeListener
+
+
+
+
+nodeRemoved
+public void nodeRemoved (org.sbml.jsbml.util.TreeNodeRemovedEvent event)
+
+Specified by:
+nodeRemoved in interface org.sbml.jsbml.util.TreeNodeChangeListener
+
+
+
+
+
+
+
+
+
+
+
+
+
+
IReportDiffs (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+AbstractAnnotator AbstractBiGGAnnotator BiGGCompartmentsAnnotator BiGGCVTermAnnotator BiGGFBCAnnotator BiGGFBCSpeciesAnnotator BiGGGeneProductAnnotator BiGGModelAnnotator BiGGPublicationsAnnotator BiGGReactionsAnnotator BiGGSBMLAnnotator BiGGSpeciesAnnotator
+public interface IReportDiffs
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
+
+
+
IReportStatus (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+AbstractAnnotator AbstractBiGGAnnotator AbstractFixer AbstractPolisher AnnotationPolisher BiGGCompartmentsAnnotator BiGGCVTermAnnotator BiGGFBCAnnotator BiGGFBCSpeciesAnnotator BiGGGeneProductAnnotator BiGGModelAnnotator BiGGPublicationsAnnotator BiGGReactionsAnnotator BiGGSBMLAnnotator BiGGSpeciesAnnotator CompartmentFixer CompartmentPolisher FBCPolisher FBCReactionPolisher FBCSpeciesFixer GeneProductsPolisher GroupsFixer ListOfObjectivesFixer ModelFixer ModelPolisher ObjectivesPolisher ParametersPolisher ReactionFixer ReactionsPolisher SBMLFixer SBMLPolisher SpeciesFixer SpeciesPolisher UnitPolisher
+public interface IReportStatus
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
+
+
+
PolisherProgressBar (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+PolisherProgressBar
+public PolisherProgressBar ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
ProgressFinalization (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public record ProgressFinalization (
String message)
+
extends Record
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
Creates an instance of a ProgressFinalization record class.
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
final boolean
+
+
+
Indicates whether some other object is "equal to" this one.
+
+
final int
+
+
+
Returns a hash code value for this object.
+
+
+
+
+
Returns the value of the message record component.
+
+
+
+
+
Returns a string representation of this record class.
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ProgressFinalization
+public ProgressFinalization (String message) Creates an instance of a ProgressFinalization record class.
+
+Parameters:
+message - the value for the message record component
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+toString
+public final String toString ()
Returns a string representation of this record class. The representation contains the name of the class, followed by the name and value of each of the record components.
+
+Specified by:
+toString Record Returns:
+a string representation of this object
+
+
+
+
+
+hashCode
+public final int hashCode ()
+Returns a hash code value for this object. The value is derived from the hash code of each of the record components.
+
+Specified by:
+hashCode Record Returns:
+a hash code value for this object
+
+
+
+
+
+equals
+public final boolean equals (Object o) Indicates whether some other object is "equal to" this one. The objects are equal if the other object is of the same class and if all the record components are equal. All components in this record class are compared with
Objects::equals(Object,Object).
+Specified by:
+equals Record Parameters:
+o - the object with which to compareReturns:
+true if this object is the same as the o argument; false otherwise.
+
+
+
+
+message
+
+Returns the value of the message record component.
+
+Returns:
+the value of the message record component
+
+
+
+
+
+
+
+
+
+
+
+
ProgressInitialization (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public record ProgressInitialization (int totalCalls)
+
extends Record
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
Creates an instance of a ProgressInitialization record class.
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
final boolean
+
+
+
Indicates whether some other object is "equal to" this one.
+
+
final int
+
+
+
Returns a hash code value for this object.
+
+
+
+
+
Returns a string representation of this record class.
+
+
int
+
+
+
Returns the value of the totalCalls record component.
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ProgressInitialization
+public ProgressInitialization (int totalCalls)
+Creates an instance of a ProgressInitialization record class.
+
+Parameters:
+totalCalls - the value for the totalCalls record component
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+toString
+public final String toString ()
Returns a string representation of this record class. The representation contains the name of the class, followed by the name and value of each of the record components.
+
+Specified by:
+toString Record Returns:
+a string representation of this object
+
+
+
+
+
+hashCode
+public final int hashCode ()
+Returns a hash code value for this object. The value is derived from the hash code of each of the record components.
+
+Specified by:
+hashCode Record Returns:
+a hash code value for this object
+
+
+
+
+
+equals
+public final boolean equals (Object o) Indicates whether some other object is "equal to" this one. The objects are equal if the other object is of the same class and if all the record components are equal. All components in this record class are compared with '=='.
+
+Specified by:
+equals Record Parameters:
+o - the object with which to compareReturns:
+true if this object is the same as the o argument; false otherwise.
+
+
+
+
+totalCalls
+public int totalCalls ()
+Returns the value of the totalCalls record component.
+
+Returns:
+the value of the totalCalls record component
+
+
+
+
+
+
+
+
+
+
+
+
ProgressObserver (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+PolisherProgressBar
+public interface ProgressObserver
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
+
+
+
+
+
+
+
ProgressUpdate (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
Creates an instance of a ProgressUpdate record class.
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
final boolean
+
+
+
Indicates whether some other object is "equal to" this one.
+
+
final int
+
+
+
Returns a hash code value for this object.
+
+
+
+
+
Returns the value of the obj record component.
+
+
+
+
+
Returns the value of the reportType record component.
+
+
+
+
+
Returns the value of the text record component.
+
+
+
+
+
Returns a string representation of this record class.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+toString
+public final String toString ()
Returns a string representation of this record class. The representation contains the name of the class, followed by the name and value of each of the record components.
+
+Specified by:
+toString Record Returns:
+a string representation of this object
+
+
+
+
+
+hashCode
+public final int hashCode ()
+Returns a hash code value for this object. The value is derived from the hash code of each of the record components.
+
+Specified by:
+hashCode Record Returns:
+a hash code value for this object
+
+
+
+
+
+equals
+public final boolean equals (Object o) Indicates whether some other object is "equal to" this one. The objects are equal if the other object is of the same class and if all the record components are equal. All components in this record class are compared with
Objects::equals(Object,Object).
+Specified by:
+equals Record Parameters:
+o - the object with which to compareReturns:
+true if this object is the same as the o argument; false otherwise.
+
+
+
+
+text
+
+Returns the value of the text record component.
+
+Returns:
+the value of the text record component
+
+
+
+
+
+obj
+
+Returns the value of the obj record component.
+
+Returns:
+the value of the obj record component
+
+
+
+
+
+reportType
+
+Returns the value of the reportType record component.
+
+Returns:
+the value of the reportType record component
+
+
+
+
+
+
+
+
+
+
+
+
ReportType (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Nested Class Summary
+
+
+
+
+
+
+Enum Constant Summary
+Enum Constants
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Returns the enum constant of this class with the specified name.
+
+
+
+
+
Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+
+
+
+
Methods inherited from class java.lang.Enum
+
clone , compareTo , describeConstable , equals , finalize , getDeclaringClass , hashCode , name , ordinal , toString , valueOf
+
+
+
+
+
+
+
+
+Enum Constant Details
+
+
+
+
+
+
+Method Details
+
+
+
+values
+
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+Returns:
+an array containing the constants of this enum class, in the order they are declared
+
+
+
+
+
+valueOf
+
+Returns the enum constant of this class with the specified name.
+The string must match exactly an identifier used to declare an
+enum constant in this class. (Extraneous whitespace characters are
+not permitted.)
+
+Parameters:
+name - the name of the enum constant to be returned.Returns:
+the enum constant with the specified name
+Throws:
+IllegalArgumentException NullPointerException
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.reporting (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.reporting
+
+
+
+
+
All Classes and Interfaces Interfaces Classes Enum Classes Record Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.reporting Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.reporting.DiffListener (implements org.sbml.jsbml.util.TreeNodeChangeListener)
+de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar (implements de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver )
+java.lang.Record
+
+
+
+
+
+
+
+
+Enum Class Hierarchy
+
+
+
+
+
Registry (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+IdentifiersOrg
+public interface Registry
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
boolean
+
+
+
+
+
+
boolean
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getNamespaceForPrefix
+
+
+
+
+
+getPrefixByNamespaceName
+
+
+
+
+
+getPatternByNamespaceName
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
RegistryURI (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+All Known Implementing Classes:
+IdentifiersOrgURI
+public interface RegistryURI
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Abstract Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
IdentifiersOrg (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+
+
+All Implemented Interfaces:
+Registry
+The
IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
+ MIRIAM is a standard for annotating computational models in biology with machine-readable information.
+
+ This class provides static methods and utilities to handle, validate,
+ and correct resource URLs based on the MIRIAM standards. It ensures that identifiers and URLs conform to recognized formats and corrects common errors in identifiers from various
+ biological databases. The class also initializes necessary resources and configurations at the start through a static block.
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
boolean
+
+
+
+
+
+
Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
+
+
boolean
+
+
+
Existing models on BiGG and Biomodels use some namespaces that were removed from identifiers.org.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+IdentifiersOrg
+public IdentifiersOrg ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+resolveBackwards
+
+Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
+ This method handles specific cases such as URLs containing "omim", "ncbigi", and "reactome".
+ It also processes general identifiers.org URLs and other alternative formats.
+
+Specified by:
+resolveBackwards Registry Parameters:
+url - The URL to be checked and potentially modified.Returns:
+An Optional
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
IdentifiersOrgRegistryParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgRegistryParser
+
+public class IdentifiersOrgRegistryParser
+
extends Object The IdentifiersOrgRegistryParser class is a singleton that provides functionality to parse the MIRIAM registry
+ from a JSON file and convert it into a Miriam object. This class ensures that only one instance
+ of the parser is created and used throughout the application.
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+IdentifiersOrgRegistryParser
+public IdentifiersOrgRegistryParser ()
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
IdentifiersOrgURI (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
int
+
+
+
boolean
+
+
+
+
+
+
+
+
+
+
+
+
int
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+IDENTIFIERS_ORG_ID_PATTERN
+public static final String IDENTIFIERS_ORG_ID_PATTERN
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+IdentifiersOrgURI
+public IdentifiersOrgURI (String url)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+hashCode
+public int hashCode ()
+
+Overrides:
+hashCode Object
+
+
+
+
+
+
+
+
+
+
+
+
+
+
IdentifiersOrgURIUtils (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
+
+public class IdentifiersOrgURIUtils
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Replaces the identifier placeholder "{$id}" in a URL pattern with a specified regex pattern.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+IdentifiersOrgURIUtils
+public IdentifiersOrgURIUtils ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+addJavaRegexCaptureGroup
+public static String addJavaRegexCaptureGroup (String pattern)
+
+
+
+removeHttpProtocolFromUrl
+public static String removeHttpProtocolFromUrl (String query)
+
+
+
+replaceIdTag
+
+Replaces the identifier placeholder "{$id}" in a URL pattern with a specified regex pattern.
+ This method is designed to facilitate the matching of URLs against a dynamic regex pattern that represents
+ an identifier within an identifiers.org namespace or its child resources.
+
+ The method first attempts to find the "{$id}" placeholder within the provided URL. If found, it splits the URL
+ around this placeholder and reassembles it with the given regex pattern in place of the placeholder. If the
+ placeholder is not found, the URL is returned as is, but quoted to ensure it is treated as a literal string in regex
+ operations.
+
+ Note: The placeholder "{$id}" can optionally be surrounded by curly braces, which are considered during the
+ replacement but do not affect the functionality.
+Parameters:
+url - The URL pattern containing the "{$id}" placeholder. This pattern represents a identifiers.org namespace or a related child namespace.pattern - The regex pattern that should replace the "{$id}" placeholder in the URL pattern.Returns:
+A string representing the URL with the "{$id}" placeholder replaced by the provided regex pattern. If no placeholder is found, the URL is returned unchanged but quoted.
+
+
+
+
+
+
+
+
+
+
+
+
Institution (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+
+public class Institution
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
long
+
+
+
+
+
+
+
+
+
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Institution
+public Institution ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getId
+public long getId ()
+
+
+
+
+setId
+public void setId (long id)
+
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+
+
+
+setHomeUrl
+public void setHomeUrl (String homeUrl)
+
+
+
+getDescription
+public String getDescription ()
+
+
+
+setDescription
+public void setDescription (String description)
+
+
+
+
+
+
+
+
+
+
+
+
+setRorId
+public void setRorId (String rorId)
+
+
+
+
+
+
+
+
+
+
Location (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+
+public class Location
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Location
+public Location ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getCountryCode
+public String getCountryCode ()
+
+
+
+setCountryCode
+public void setCountryCode (String countryCode)
+
+
+
+getCountryName
+public String getCountryName ()
+
+
+
+setCountryName
+public void setCountryName (String countryName)
+
+
+
+
+
+
+
+
+
+
Namespace (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+
+public class Namespace
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
long
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
boolean
+
+
+
boolean
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Namespace
+public Namespace ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getId
+public long getId ()
+
+
+
+
+setId
+public void setId (long id)
+
+
+
+
+
+
+
+setMirId
+public void setMirId (String mirId)
+
+
+
+
+
+
+setPrefix
+public void setPrefix (String prefix)
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+getDescription
+public String getDescription ()
+
+
+
+setDescription
+public void setDescription (String description)
+
+
+
+
+
+
+setPattern
+public void setPattern (String pattern)
+
+
+
+
+
+
+setCreated
+public void setCreated (Calendar created)
+
+
+
+
+
+
+setModified
+public void setModified (Calendar modified)
+
+
+
+
+
+
+setSampleId
+public void setSampleId (String sampleId)
+
+
+
+isNamespaceEmbeddedInLui
+public boolean isNamespaceEmbeddedInLui ()
+
+
+
+
+setNamespaceEmbeddedInLui
+public void setNamespaceEmbeddedInLui (boolean namespaceEmbeddedInLui)
+
+
+
+
+
+
+
+
+
+
+isDeprecated
+public boolean isDeprecated ()
+
+
+
+
+setDeprecated
+public void setDeprecated (boolean deprecated)
+
+
+
+
+
+
+
+setDeprecationDate
+public void setDeprecationDate (Calendar deprecationDate)
+
+
+
+
+
+
+
+
+
+
RawIdentifiersOrgRegistry (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+
+public class RawIdentifiersOrgRegistry
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+RawIdentifiersOrgRegistry
+public RawIdentifiersOrgRegistry ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+
+
+
+setApiVersion
+public void setApiVersion (String apiVersion)
+
+
+
+getErrorMessage
+public String getErrorMessage ()
+
+
+
+setErrorMessage
+public void setErrorMessage (String errorMessage)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Resource (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+
+public class Resource
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
+
+
+
long
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
boolean
+
+
+
boolean
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
void
+
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+Resource
+public Resource ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+getId
+public long getId ()
+
+
+
+
+setId
+public void setId (long id)
+
+
+
+
+
+
+
+setMirId
+public void setMirId (String mirId)
+
+
+
+
+
+
+setUrlPattern
+public void setUrlPattern (String urlPattern)
+
+
+
+
+
+
+setName
+public void setName (String name)
+
+
+
+getDescription
+public String getDescription ()
+
+
+
+setDescription
+public void setDescription (String description)
+
+
+
+isOfficial
+public boolean isOfficial ()
+
+
+
+
+setOfficial
+public void setOfficial (boolean official)
+
+
+
+
+getProviderCode
+public String getProviderCode ()
+
+
+
+setProviderCode
+public void setProviderCode (String providerCode)
+
+
+
+
+
+
+setSampleId
+public void setSampleId (String sampleId)
+
+
+
+getResourceHomeUrl
+public String getResourceHomeUrl ()
+
+
+
+setResourceHomeUrl
+public void setResourceHomeUrl (String resourceHomeUrl)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+isDeprecated
+public boolean isDeprecated ()
+
+
+
+
+setDeprecated
+public void setDeprecated (boolean deprecated)
+
+
+
+
+
+
+
+setDeprecationDate
+public void setDeprecationDate (Calendar deprecationDate)
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+
+
+
+
+
+
+
+
Classes
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+
+
+
+
+
+
+
+
Classes
+
+
+
+
+
+
The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
+
+
+
+
The IdentifiersOrgRegistryParser class is a singleton that provides functionality to parse the MIRIAM registry
+ from a JSON file and convert it into a Miriam object.
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.resolver.identifiersorg Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/de/uni_halle/informatik/biodata/mp/resolver/package-summary.html b/docs/de/uni_halle/informatik/biodata/mp/resolver/package-summary.html
new file mode 100644
index 00000000..b3ddc36a
--- /dev/null
+++ b/docs/de/uni_halle/informatik/biodata/mp/resolver/package-summary.html
@@ -0,0 +1,94 @@
+
+
+
+
+de.uni_halle.informatik.biodata.mp.resolver (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.resolver
+
+
+
+
de.uni_halle.informatik.biodata.mp.resolver Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Interface Hierarchy
+
+de.uni_halle.informatik.biodata.mp.resolver.Registry
+de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
+
+
+
+
+
ReactionNamePatterns (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+Serializable Comparable <ReactionNamePatterns >Constable
+Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
+ Each enum constant represents a specific type of reaction and is associated with a regex pattern that matches
+ reaction IDs corresponding to that type.
+
+
+
+
+
+
+Nested Class Summary
+
+
+
+
+
+
+Enum Constant Summary
+Enum Constants
+
+
+
+
+
+
Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.
+
+
+
+
Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.
+
+
+
+
Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.
+
+
+
+
Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.
+
+
+
+
Pattern for demand reactions, identified by IDs starting with 'DM_'.
+
+
+
+
Pattern for exchange reactions, identified by IDs starting with 'EX_'.
+
+
+
+
Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Instance Methods Concrete Methods
+
+
+
+
+
+
+
+
+
Retrieves the compiled Pattern object for this enum constant.
+
+
+
+
+
Returns the enum constant of this class with the specified name.
+
+
+
+
+
Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+
+
+
+
Methods inherited from class java.lang.Enum
+
clone , compareTo , describeConstable , equals , finalize , getDeclaringClass , hashCode , name , ordinal , toString , valueOf
+
+
+
+
+
+
+
+
+Enum Constant Details
+
+
+
+ATP_MAINTENANCE
+
+Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.
+
+
+
+
+BIOMASS_CASE_INSENSITIVE
+
+Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.
+
+
+
+
+BIOMASS_CASE_SENSITIVE
+
+Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.
+
+
+
+
+DEFAULT_FLUX_BOUND
+
+Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.
+
+
+
+
+DEMAND_REACTION
+
+Pattern for demand reactions, identified by IDs starting with 'DM_'.
+
+
+
+
+EXCHANGE_REACTION
+
+Pattern for exchange reactions, identified by IDs starting with 'EX_'.
+
+
+
+
+SINK_REACTION
+
+Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+values
+
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+Returns:
+an array containing the constants of this enum class, in the order they are declared
+
+
+
+
+
+valueOf
+
+Returns the enum constant of this class with the specified name.
+The string must match exactly an identifier used to declare an
+enum constant in this class. (Extraneous whitespace characters are
+not permitted.)
+
+Parameters:
+name - the name of the enum constant to be returned.Returns:
+the enum constant with the specified name
+Throws:
+IllegalArgumentException NullPointerException
+
+
+
+
+getPattern
+
+Retrieves the compiled Pattern object for this enum constant.
+
+Returns:
+The compiled Pattern object.
+
+
+
+
+
+
+
+
+
+
+
+
GPRParser (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+public class GPRParser
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
static void
+
+
+
+
stringify (org.sbml.jsbml.ext.fbc.Association association)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+GPRParser
+public GPRParser ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+setGeneProductAssociation
+public static void setGeneProductAssociation (org.sbml.jsbml.Reaction r,
+ String geneReactionRule,
+ boolean addGenericTerms)
+
+
+
+stringify
+public static String stringify (org.sbml.jsbml.ext.fbc.Association association)
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.util.ext.fbc (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.util.ext.fbc
+
+
+
+
de.uni_halle.informatik.biodata.mp.util.ext.fbc Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
+
+
+
+
+
+
+
GroupsUtils (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils
+
+public class GroupsUtils
+
extends Object A collection of helpful functions for dealing with SBML data structures.
+
+
+
+
+
+
+Field Summary
+Fields
+
+
+
+
+
+
+
+
Key to link from Reaction directly to Members referencing
+ that reaction.
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Static Methods Concrete Methods
+
+
+
+
+
+
static void
+
+
+
Establishes a link between a reaction and a subsystem member by setting the member's reference to the reaction.
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Field Details
+
+
+
+SUBSYSTEM_LINK
+public static final String SUBSYSTEM_LINK Key to link from Reaction directly to Members referencing
+ that reaction.
+
+See Also:
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+GroupsUtils
+public GroupsUtils ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+createSubsystemLink
+public static void createSubsystemLink (org.sbml.jsbml.Reaction r,
+ org.sbml.jsbml.ext.groups.Member member)
+Establishes a link between a reaction and a subsystem member by setting the member's reference to the reaction.
+ Additionally, it ensures that the reaction maintains a set of all members linked to it. If the set does not exist,
+ it is created and the member is added to it.
+
+Parameters:
+r - The reaction object to which the member should be linked.member - The subsystem member that should be linked to the reaction.
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.util.ext.groups (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.util.ext.groups
+
+
+
+
+
Classes
+
+
+
+
+
+
A collection of helpful functions for dealing with SBML data structures.
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.util.ext.groups Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Class Hierarchy
+
+java.lang.Object
+
+de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.util (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.util
+
+
+
+
+
Enum Classes
+
+
+
+
+
+
Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.util Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+Enum Class Hierarchy
+
+
+
+
+
ModelValidator (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+java.lang.Object
+
de.uni_halle.informatik.biodata.mp.validation.ModelValidator
+
+public class ModelValidator
+
extends Object
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
+
+
+
void
+
+
+
org.sbml.jsbml.SBMLErrorLog
+
validate (org.sbml.jsbml.SBMLDocument doc)
+
+
+
+
+
Methods inherited from class java.lang.Object
+
clone , equals , finalize , getClass , hashCode , notify , notifyAll , toString , wait , wait , wait
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ModelValidator
+public ModelValidator ()
+
+
+
+
+
+
+
+
+Method Details
+
+
+
+validate
+public org.sbml.jsbml.SBMLErrorLog validate (org.sbml.jsbml.SBMLDocument doc)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
ModelValidatorException (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+Serializable
+public class ModelValidatorException
+
extends Exception
+See Also:
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+Constructors
+
+
+
+
+
+
+Method Summary
+
+
All Methods Instance Methods Concrete Methods
+
+
+
Methods inherited from class java.lang.Throwable
+
addSuppressed , fillInStackTrace , getCause , getLocalizedMessage , getMessage , getStackTrace , getSuppressed , initCause , printStackTrace , printStackTrace , printStackTrace , setStackTrace , toString
+
+
+
+
+
+
+
+
+Constructor Details
+
+
+
+ModelValidatorException
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.validation (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+package de.uni_halle.informatik.biodata.mp.validation
+
+
+
+
+
All Classes and Interfaces Classes Exceptions
+
+
+
+
+
+
+
de.uni_halle.informatik.biodata.mp.validation Class Hierarchy (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
diff --git a/docs/element-list b/docs/element-list
new file mode 100644
index 00000000..2f7b886f
--- /dev/null
+++ b/docs/element-list
@@ -0,0 +1,27 @@
+de.uni_halle.informatik.biodata.mp.annotation
+de.uni_halle.informatik.biodata.mp.annotation.adb
+de.uni_halle.informatik.biodata.mp.annotation.bigg
+de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+de.uni_halle.informatik.biodata.mp.db
+de.uni_halle.informatik.biodata.mp.db.adb
+de.uni_halle.informatik.biodata.mp.db.bigg
+de.uni_halle.informatik.biodata.mp.eco
+de.uni_halle.informatik.biodata.mp.fixing
+de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
+de.uni_halle.informatik.biodata.mp.fixing.ext.groups
+de.uni_halle.informatik.biodata.mp.io
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+de.uni_halle.informatik.biodata.mp.io.parsers.json
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+de.uni_halle.informatik.biodata.mp.logging
+de.uni_halle.informatik.biodata.mp.parameters
+de.uni_halle.informatik.biodata.mp.polishing
+de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+de.uni_halle.informatik.biodata.mp.reporting
+de.uni_halle.informatik.biodata.mp.resolver
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+de.uni_halle.informatik.biodata.mp.util
+de.uni_halle.informatik.biodata.mp.util.ext.fbc
+de.uni_halle.informatik.biodata.mp.util.ext.groups
+de.uni_halle.informatik.biodata.mp.validation
diff --git a/docs/help-doc.html b/docs/help-doc.html
new file mode 100644
index 00000000..4ace43a3
--- /dev/null
+++ b/docs/help-doc.html
@@ -0,0 +1,185 @@
+
+
+
+
+API Help (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+JavaDoc Help
+
+
+
Navigation
+Starting from the
Overview page, you can browse the documentation using the links in each page, and in the navigation bar at the top of each page. The
Index and Search box allow you to navigate to specific declarations and summary pages, including:
All Packages ,
All Classes and Interfaces
+
+Search
+You can search for definitions of modules, packages, types, fields, methods, system properties and other terms defined in the API, using some or all of the name, optionally using "camelCase" abbreviations. For example:
+
+j.l.obj will match "java.lang.Object"InpStr will match "java.io.InputStream"HM.cK will match "java.util.HashMap.containsKey(Object)"
+Refer to the Javadoc Search Specification for a full description of search features.
+
+
+
Kinds of Pages
+The following sections describe the different kinds of pages in this collection.
+
+Overview
+The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.
+
+
+Package
+Each package has a page that contains a list of its classes and interfaces, with a summary for each. These pages may contain the following categories:
+
+Interfaces
+Classes
+Enum Classes
+Exceptions
+Errors
+Annotation Interfaces
+
+
+
+Class or Interface
+Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a declaration and description, member summary tables, and detailed member descriptions. Entries in each of these sections are omitted if they are empty or not applicable.
+
+Class Inheritance Diagram
+Direct Subclasses
+All Known Subinterfaces
+All Known Implementing Classes
+Class or Interface Declaration
+Class or Interface Description
+
+
+Nested Class Summary
+Enum Constant Summary
+Field Summary
+Property Summary
+Constructor Summary
+Method Summary
+Required Element Summary
+Optional Element Summary
+
+
+Enum Constant Details
+Field Details
+Property Details
+Constructor Details
+Method Details
+Element Details
+
+Note: Annotation interfaces have required and optional elements, but not methods. Only enum classes have enum constants. The components of a record class are displayed as part of the declaration of the record class. Properties are a feature of JavaFX.
+The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.
+
+
+Other Files
+Packages and modules may contain pages with additional information related to the declarations nearby.
+
+
+Tree (Class Hierarchy)
+There is a Class Hierarchy page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. Classes are organized by inheritance structure starting with java.lang.Object. Interfaces do not inherit from java.lang.Object.
+
+When viewing the Overview page, clicking on TREE displays the hierarchy for all packages.
+When viewing a particular package, class or interface page, clicking on TREE displays the hierarchy for only that package.
+
+
+
+
+
+All Packages
+The All Packages page contains an alphabetic index of all packages contained in the documentation.
+
+
+All Classes and Interfaces
+The All Classes and Interfaces page contains an alphabetic index of all classes and interfaces contained in the documentation, including annotation interfaces, enum classes, and record classes.
+
+
+
+
+
Index (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+A B C D E F G H I J L M N O P R S T U V W All Classes and Interfaces | All Packages | Constant Field Values | Serialized Form
+A
+
+A - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v =
+ 0 or g(μ ) ⋅ A ⋅ v + B ⋅ v = 0 with
+ g(μ ) being some continuous nonlinear function of μ ;
+
+AbstractADBAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
+AbstractADBAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
+AbstractAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation
+AbstractAnnotator() - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
+AbstractAnnotator(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
+AbstractBiGGAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
+AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
+AbstractFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+AbstractFixer() - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
+AbstractFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
+AbstractPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+AbstractPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+AbstractPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+adb - Variable in class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
+adbAnnotationParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+ADBAnnotationParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+ADBAnnotationParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+ADBAnnotationParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+ADBReactionsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
+ADBReactionsAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBReactionsAnnotator
+ADBSBMLAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
+ADBSBMLAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSBMLAnnotator
+ADBSpeciesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.adb
+ADBSpeciesAnnotator(AnnotateDB, ADBAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSpeciesAnnotator
+add(String, double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
+add(String, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+ADD_ADB_ANNOTATIONS - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+If set to true, annotations will be added to species and reactions from AnnotateDB also.
+
+ADD_GENERIC_TERMS - Static variable in interface de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions
+Set this option to true if generic top-level annotations, such as 'process'
+ should not be applied.
+
+addAll(Map<String, String>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+addAnnotations(GeneProduct, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+Adds annotations to a gene product based on a given
BiGGId.
+addBQB_IS_AnnotationsFromADB(Annotation, String, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
+addChild(Node) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+addChild(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+addGenericTerms - Variable in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+addGenericTerms() - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+addJavaRegexCaptureGroup(String) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
+addParent(Node) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+addParent(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+addResource(String, CVTerm, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
+Tries to update a resource according to pre-defined rules.
+
+annotate(List<Compartment>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
+annotate(List<GeneProduct>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+This method handles the annotation of gene products in a given SBML model.
+
+annotate(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBReactionsAnnotator
+annotate(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+Delegates the annotation process for each reaction in the given SBML model.
+
+annotate(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSpeciesAnnotator
+annotate(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
+Delegates annotation processing for all chemical species contained in the Model.
+
+annotate(List<SBMLElement>) - Method in interface de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases
+annotate(Compartment) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
+Annotates the compartment with BiGG and SBO terms.
+
+annotate(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+Annotates a gene product by adding relevant metadata and references.
+
+annotate(Model) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
+Annotates the Model with relevant metadata and delegates the annotation of contained elements such as
+ Compartment, Species, Reaction, and GeneProduct.
+
+annotate(Model) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGPublicationsAnnotator
+annotate(Model) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCAnnotator
+annotate(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBReactionsAnnotator
+annotate(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+Annotates a reaction by setting its name, SBO term, and additional annotations.
+
+annotate(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSBMLAnnotator
+annotate(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator
+Annotates an SBMLDocument using data from the BiGG Knowledgebase.
+
+annotate(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.adb.ADBSpeciesAnnotator
+annotate(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
+This method annotates a species with various details fetched from the BiGG Knowledgebase.
+
+annotate(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCSpeciesAnnotator
+annotate(SBMLElement) - Method in interface de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases
+ANNOTATE_WITH_BIGG - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+If set to true, the model will be annotated with data from BiGG Models
+ database.
+
+AnnotateDB - Class in de.uni_halle.informatik.biodata.mp.db.adb
+AnnotateDB() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
+AnnotateDBContract - Class in de.uni_halle.informatik.biodata.mp.db.adb
+AnnotateDBContract() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract
+AnnotateDBContract.Constants - Class in de.uni_halle.informatik.biodata.mp.db.adb
+AnnotateDBContract.Constants.Column - Class in de.uni_halle.informatik.biodata.mp.db.adb
+AnnotateDBContract.Constants.Table - Class in de.uni_halle.informatik.biodata.mp.db.adb
+AnnotateDBOptions - Interface in de.uni_halle.informatik.biodata.mp.db.adb
+This interface provides options for connecting to the ADB database.
+
+annotateWithAdb - Variable in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+annotateWithAdb() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+annotateWithBiGG - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+annotateWithBiGG() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+annotation() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+ANNOTATION_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+AnnotationException - Exception in de.uni_halle.informatik.biodata.mp.annotation
+AnnotationException(String, Exception) - Constructor for exception de.uni_halle.informatik.biodata.mp.annotation.AnnotationException
+AnnotationOptions - Interface in de.uni_halle.informatik.biodata.mp.annotation
+AnnotationParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+AnnotationParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+AnnotationParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+AnnotationPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+AnnotationPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AnnotationPolisher
+AnnotationPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.AnnotationPolisher
+AnnotationsSorter - Class in de.uni_halle.informatik.biodata.mp.annotation
+AnnotationsSorter() - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.AnnotationsSorter
+archiveFile() - Method in exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
+asString(Array) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+asString(Array, String, int) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+ATP_MAINTENANCE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Pattern for ATP maintenance reactions, which are typically denoted by IDs containing 'ATPM' in any case.
+
+author - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+
+B
+
+b - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The bound vector of metabolite concentration change rates (usually but not
+ always all zero, i.e., steady-state): S ⋅ v = b .
+
+B - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Matrix of constraints, form μ ⋅ A ⋅ v + B ⋅ v =
+ 0 or g(μ ) ⋅ A ⋅ v + B ⋅ v = 0 with
+ g(μ ) being some continuous nonlinear function of μ ;
+
+BASE_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+bigg - Variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
+BIGG_ANNOTATION_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+BIGG_GENE_ID_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+BIGG_METABOLITE - Static variable in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
+BIGG_REACTION - Static variable in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
+BiGGAnnotationException - Exception in de.uni_halle.informatik.biodata.mp.annotation.bigg
+BiGGAnnotationException(String, Exception, Object) - Constructor for exception de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGAnnotationException
+biggAnnotationParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+biGGAnnotationParameters - Variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
+BiGGAnnotationParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+BiGGAnnotationParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+BiGGAnnotationParameters(boolean, boolean, String, BiGGNotesParameters, DBParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+BiGGAnnotationParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+BiGGCompartmentsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
+
+BiGGCompartmentsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
+BiGGCompartmentsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCompartmentsAnnotator
+BiGGCVTermAnnotator <T extends org.sbml.jsbml.SBase> - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
+
+BiGGCVTermAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator
+BiGGCVTermAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator
+BiGGDB - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+This class provides a connection to the BiGG database.
+
+BiGGDB() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+BiGGDB.ForeignReaction - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+Represents a reaction from an external data source mapped to the BiGG database, including its compartment details.
+
+BiGGDBContract - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+BiGGDBContract.Constants - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+BiGGDBContract.Constants.Column - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+BiGGDBContract.Constants.Table - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+BiGGDBOptions - Interface in de.uni_halle.informatik.biodata.mp.db.bigg
+BiGGDocumentNotesProcessor - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+BiGGDocumentNotesProcessor(BiGGDB, BiGGAnnotationParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGDocumentNotesProcessor
+BiGGFBCAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+BiGGFBCAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCAnnotator
+BiGGFBCSpeciesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+BiGGFBCSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCSpeciesAnnotator
+BiGGGeneProductAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
+
+BiGGGeneProductAnnotator(BiGGGeneProductReferencesAnnotator, BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+BiGGGeneProductReferencesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+BiGGGeneProductReferencesAnnotator() - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductReferencesAnnotator
+BiGGId - Class in de.uni_halle.informatik.biodata.mp.db.bigg
+Represents a BiGG identifier used to uniquely identify various biological entities
+ such as reactions, metabolites, and genes within the BiGG database.
+
+BiGGId() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+BiGGId(String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+BiGGId(String, String, String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+BiGGModelAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+This class is responsible for annotating an SBML Model with relevant metadata and references.
+
+BiGGModelAnnotator(BiGGDB, BiGGAnnotationParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
+BiGGModelAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
+BiGGNotesParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+BiGGNotesParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+BiGGNotesParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+BiGGPublicationsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+BiGGPublicationsAnnotator(BiGGDB, BiGGAnnotationParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGPublicationsAnnotator
+BiGGReactionsAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
+
+BiGGReactionsAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+BiGGReactionsAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+BiGGSBMLAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+This class is responsible for annotating SBML models using data from the BiGG database.
+
+BiGGSBMLAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator
+BiGGSBMLAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSBMLAnnotator
+BiGGSpeciesAnnotator - Class in de.uni_halle.informatik.biodata.mp.annotation.bigg
+This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
+
+BiGGSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
+BiGGSpeciesAnnotator(BiGGDB, BiGGAnnotationParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
+BIOMASS_CASE_INSENSITIVE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Case-insensitive pattern for biomass reactions, matching IDs that include the word 'biomass' in any case.
+
+BIOMASS_CASE_SENSITIVE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Case-sensitive pattern for biomass reactions, matching IDs that specifically contain 'BIOMASS'.
+
+BundleNames - Class in de.uni_halle.informatik.biodata.mp.logging
+BundleNames() - Constructor for class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+
+C
+
+c - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The objective function vector for max(c' ⋅ v ) for corresponding
+ reactions.
+
+checkCreateOutDir(File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils
+Creates output directory or output parent directory, if necessary
+
+checkId(String) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+Necessary to check for a special whitespace (code 160) at beginning of id
+ (iCHOv1.mat, possibly other models) and to remove trailing ';'
+
+citations - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Literature references for the reactions.
+
+CLI_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+close() - Method in class de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
+close() - Method in class de.uni_halle.informatik.biodata.mp.io.DeleteOnCloseFileInputStream
+COBRAUtils - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+COBRAUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+coefficients - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+TODO
+
+Column() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column
+Column() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Column
+COMBINE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
+COMBINE_SPECIFICATION - Static variable in class de.uni_halle.informatik.biodata.mp.io.CombineArchive
+CombineArchive - Class in de.uni_halle.informatik.biodata.mp.io
+The CombineArchive class provides functionality to create a COMBINE archive from an SBML document.
+
+CombineArchive(SBMLDocument, File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.CombineArchive
+comments - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+These are human-readable notes for reactions.
+
+compareTo(IdentifiersOrgURI) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+CompartmentFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+CompartmentFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer
+compartmentId - Variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
+compartmentName - Variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
+CompartmentPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+This class is responsible for polishing the properties of a compartment in an SBML model to ensure
+ compliance with standards and completeness.
+
+CompartmentPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher
+Compartments - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+Compartments() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+confidenceScores - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Confidence score for each reaction.
+
+Constants() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants
+Constants() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
+convertAssociationsToFBCV2(Reaction, boolean) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductAssociationsProcessor
+convertGene(GeneProduct) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+convertGenes(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+convertMetabolite(Species) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+convertMetabolites(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+convertModel(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+convertReaction(Reaction) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+convertReactions(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+createGeneId(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+createMetaboliteId(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+createReactionId(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+createReactionId(String, boolean) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+Creates a BiGG ID for a reaction based on the provided string identifier.
+
+createSubsystemLink(Reaction, Member) - Static method in class de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils
+Establishes a link between a reaction and a subsystem member by setting the member's reference to the reaction.
+
+csense - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The csense field expresses equality constraints in the model.
+
+CV_TERM_DESCRIBED_BY_PUBMED_GROWTH_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_SUBSTANCE_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_TIME_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_UO_GRAM - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_UO_HOUR - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_UO_MMOL - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_UO_SECOND - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_VERSION_OF_UO_MOLE - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_VERSION_OF_UO_SECOND - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+CV_TERM_IS_VOLUME_UNIT - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+
+D
+
+DAG - Class in de.uni_halle.informatik.biodata.mp.eco
+DAG(Term) - Constructor for class de.uni_halle.informatik.biodata.mp.eco.DAG
+data() - Method in exception de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGAnnotationException
+DATA - Enum constant in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType
+DB_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+dbName() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+DBNAME - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
+DBNAME - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
+dbParameters - Variable in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+dbParameters - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+dbParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+dbParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+DBParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+DBParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+DBParameters(String, String, String, Integer, String) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+de.uni_halle.informatik.biodata.mp.annotation - package de.uni_halle.informatik.biodata.mp.annotation
+de.uni_halle.informatik.biodata.mp.annotation.adb - package de.uni_halle.informatik.biodata.mp.annotation.adb
+de.uni_halle.informatik.biodata.mp.annotation.bigg - package de.uni_halle.informatik.biodata.mp.annotation.bigg
+de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc - package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc
+de.uni_halle.informatik.biodata.mp.db - package de.uni_halle.informatik.biodata.mp.db
+de.uni_halle.informatik.biodata.mp.db.adb - package de.uni_halle.informatik.biodata.mp.db.adb
+de.uni_halle.informatik.biodata.mp.db.bigg - package de.uni_halle.informatik.biodata.mp.db.bigg
+de.uni_halle.informatik.biodata.mp.eco - package de.uni_halle.informatik.biodata.mp.eco
+de.uni_halle.informatik.biodata.mp.fixing - package de.uni_halle.informatik.biodata.mp.fixing
+de.uni_halle.informatik.biodata.mp.fixing.ext.fbc - package de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
+de.uni_halle.informatik.biodata.mp.fixing.ext.groups - package de.uni_halle.informatik.biodata.mp.fixing.ext.groups
+de.uni_halle.informatik.biodata.mp.io - package de.uni_halle.informatik.biodata.mp.io
+de.uni_halle.informatik.biodata.mp.io.parsers.cobra - package de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+de.uni_halle.informatik.biodata.mp.io.parsers.json - package de.uni_halle.informatik.biodata.mp.io.parsers.json
+de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping - package de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+de.uni_halle.informatik.biodata.mp.logging - package de.uni_halle.informatik.biodata.mp.logging
+de.uni_halle.informatik.biodata.mp.parameters - package de.uni_halle.informatik.biodata.mp.parameters
+de.uni_halle.informatik.biodata.mp.polishing - package de.uni_halle.informatik.biodata.mp.polishing
+de.uni_halle.informatik.biodata.mp.polishing.ext.fbc - package de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+de.uni_halle.informatik.biodata.mp.reporting - package de.uni_halle.informatik.biodata.mp.reporting
+de.uni_halle.informatik.biodata.mp.resolver - package de.uni_halle.informatik.biodata.mp.resolver
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg - package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping - package de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+de.uni_halle.informatik.biodata.mp.util - package de.uni_halle.informatik.biodata.mp.util
+de.uni_halle.informatik.biodata.mp.util.ext.fbc - package de.uni_halle.informatik.biodata.mp.util.ext.fbc
+de.uni_halle.informatik.biodata.mp.util.ext.groups - package de.uni_halle.informatik.biodata.mp.util.ext.groups
+de.uni_halle.informatik.biodata.mp.validation - package de.uni_halle.informatik.biodata.mp.validation
+DEFAULT_FLUX_BOUND - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Pattern for default flux bound reactions, matching IDs that typically start with a prefix followed by 'default_'.
+
+DeleteOnCloseFileInputStream - Class in de.uni_halle.informatik.biodata.mp.io
+DeleteOnCloseFileInputStream(File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.DeleteOnCloseFileInputStream
+DeleteOnCloseFileInputStream(String) - Constructor for class de.uni_halle.informatik.biodata.mp.io.DeleteOnCloseFileInputStream
+DEMAND_REACTION - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Pattern for demand reactions, identified by IDs starting with 'DM_'.
+
+description - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Human-redable information about the model, e.g., the model name.
+
+DiffListener - Class in de.uni_halle.informatik.biodata.mp.reporting
+DiffListener() - Constructor for class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
+diffReport(String, Object, Object) - Method in class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
+diffReport(String, Object, Object) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.IReportDiffs
+disabled - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The "disabled" field comes from the reconstruction tool rBioNet.
+
+doc() - Method in exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
+DOCUMENT_NOTES_FILE - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+This XHTML file defines alternative document notes and makes them
+ exchangeable.
+
+DOCUMENT_TITLE_PATTERN - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+This option allows you to define the title of the SBML document's
+ description and hence the headline when the file is displayed in a web
+ browser.
+
+documentNotesFile - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+documentNotesFile() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+documentTitlePattern - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+documentTitlePattern() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+DONT_FIX - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
+dontFix() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+
+E
+
+ecNumbers - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The Enzyme Commission codes for the reactions.
+
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication
+Indicates whether some other object is "equal to" this one.
+
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization
+Indicates whether some other object is "equal to" this one.
+
+equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization
+Indicates whether some other object is "equal to" this one.
+
+equals(Object) - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Indicates whether some other object is "equal to" this one.
+
+equals(Object) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+EXCHANGE_REACTION - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Pattern for exchange reactions, identified by IDs starting with 'EX_'.
+
+exists(Array, int) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+extractCompartmentCode(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+Extracts the compartment code from a given identifier if it matches the expected pattern.
+
+
+F
+
+FBCPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+FBCPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCPolisher
+FBCReactionPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+FBCReactionPolisher(FBCModelPlugin, PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
+FBCReactionPolisher(FBCModelPlugin, PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
+FBCSpeciesFixer - Class in de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
+FBCSpeciesFixer() - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.FBCSpeciesFixer
+findBiGGId(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+Validates the ID of a
GeneProduct against the expected BiGG ID format and attempts to retrieve a
+ corresponding
BiGGId from existing annotations if the initial ID does not conform to the BiGG format.
+findBiGGId(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding
+ BiGG ID based on existing annotations.
+
+findBiGGId(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
+Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
+
+findBiGGId(Species) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCSpeciesAnnotator
+findBiGGId(T) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator
+Abstract method to check the validity of a BiGG ID.
+
+findChild(Node, Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+findParent(Node, Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+findTerm(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+Returns the Node containing the specified Term or null, if not present
+
+finish(ProgressFinalization) - Method in class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
+finish(ProgressFinalization) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver
+fix(List<Compartment>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer
+fix(List<Group>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer
+fix(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer
+fix(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer
+fix(List<SpeciesReference>) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSpeciesReferences
+fix(List<SBMLElement>) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSBases
+fix(Compartment, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.CompartmentFixer
+fix(ListOfObjectives, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.ListOfObjectivesFixer
+fix(Group, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer
+fix(Model, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ModelFixer
+fix(Reaction, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer
+fix(SBMLDocument, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer
+fix(Species, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.FBCSpeciesFixer
+fix(Species, int) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer
+fix(SpeciesReference) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSpeciesReferences
+fix(SpeciesReference) - Method in class de.uni_halle.informatik.biodata.mp.fixing.SpeciesReferenceFixer
+fix(SBMLElement, int) - Method in interface de.uni_halle.informatik.biodata.mp.fixing.IFixSBases
+fixIdentifiersOrgUri(IdentifiersOrgURI) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+fixing() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+FIXING_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+FixingOptions - Interface in de.uni_halle.informatik.biodata.mp.fixing
+FixingParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+FixingParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+FixingParameters(boolean, FluxObjectivesFixingParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+FixingParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+FLUX_COEFFICIENTS - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
+FLUX_OBJECTIVES - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
+fluxCoefficients - Variable in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+fluxCoefficients() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+fluxObjectiveHasValidCoefficients(FluxObjective) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+5) All defined FluxObjective objects must have their coefficient attribute set
+ to a double value that is not 'NaN', nor '-INF', nor 'INF'.
+
+fluxObjectives - Variable in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+fluxObjectives() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+FluxObjectivesFixingParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+FluxObjectivesFixingParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+FluxObjectivesFixingParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+FluxObjectivesFixingParameters(List<Double>, List<String>) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.FluxObjectivesFixingParameters
+fluxObjectivesPolishingParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+ForeignReaction(String, String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
+Constructs a new ForeignReaction instance.
+
+
+G
+
+Gene - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+Gene() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+genedate - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+geneindex - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+GeneParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+GeneParser(FBCModelPlugin, int) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.GeneParser
+GeneProductAssociationsProcessor - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+GeneProductAssociationsProcessor() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductAssociationsProcessor
+GeneProductsPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+GeneProductsPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductsPolisher
+GeneralOptions - Interface in de.uni_halle.informatik.biodata.mp.parameters
+genes - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The list of all genes in the model, where each contained gene corresponds
+ to a AbstractSBase.getId().
+
+genesource - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+GENOME_ASSEMBLY_ID_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
+get() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+get() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
+getAbbreviation() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+getAllBiggIds(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves a set of unique BiGG IDs from a specified table in the database.
+
+getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getAnnotation() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getAnnotations(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
+Retrieves a set of annotated URLs based on the type and BiGG ID provided.
+
+getApiVersion() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+getBiGGIdFromResources(List<String>, String) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
+Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase.
+
+getBiggIdFromSynonym(String, String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the BiGG ID associated with a given synonym and type from the specified data source.
+
+getBiggIdsForReactionForeignId(RegistryURI) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves a collection of ForeignReaction objects for a given synonym and data source ID.
+
+getBiGGVersion() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the version date of the BiGG database.
+
+getBound() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getCharge() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getCharge(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the charge for a given component and model from the database.
+
+getChargeByCompartment(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the charge associated with a specific component in a given compartment when the model ID is unknown.
+
+getChemicalFormula(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the chemical formula for a given component within a specific model in the BiGG database.
+
+getChemicalFormulaByCompartment(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the unique chemical formula for a given component within a specific compartment.
+
+getChildren() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+getCompartment() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getCompartmentCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+getCompartmentName(BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the name of the compartment associated with the given BiGG ID from the database.
+
+getCompartments() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getComponentName(BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the name of the component associated with the given BiGG ID from the database.
+
+getComponentType(BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the type of the component associated with the given BiGG ID from the database.
+
+getConnection() - Method in class de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
+getCorrectName(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies, if case can't be
+ matched
+
+getCountryCode() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+getCountryName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+getCreated() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getDeprecationDate() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getDeprecationDate() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getDescription() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getDescription() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+getDescription() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getDescription() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getErrorMessage() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+getFileExtension() - Method in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
+getFileType(File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils
+Determines the type of the input file based on its extension or content.
+
+getFormula() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getGeneIds(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves all possible MIRIAM-compliant gene identifiers from the database based on a given label.
+
+getGeneName(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the gene name from the database based on a given label.
+
+getGeneReactionRule() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getGeneReactionRule(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves formatted gene reaction rules for a specific reaction and model from the database.
+
+getGenes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getGenomeAccesion(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the genome accession for a given model ID from the BiGG database.
+
+getHomeUrl() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getId() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getId() - Method in interface de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
+getInstitution() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getJSONDocument(SBMLDocument) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+getJSONModel(Model) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+getLabel(GeneProduct, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+Retrieves the label for a gene product based on the provided BiGGId.
+
+getLocation() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+getLocation() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getLowerBound() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getMetabolites() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getMetabolites() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getMirId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getMirId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getModified() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getName() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+getName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getName() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getNameForPrefix(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Get known model field variant name for a struct field, disregarding upper/lowercase discrepancies using struct
+ field as prefix of knwon model field
+
+getNamespaceForPrefix(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+getNamespaceForPrefix(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
+getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getNotes() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getObjectiveCoefficient() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getObservers() - Method in class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
+getObservers() - Method in class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
+getObservers() - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+getOrganism(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the organism associated with a given BiGG model abbreviation from the database.
+
+getOutputFileName(File, File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils
+Fix output file name to contain xml extension
+
+getParents() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+getPattern() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getPattern() - Method in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Retrieves the compiled Pattern object for this enum constant.
+
+getPatternByNamespaceName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+getPatternByNamespaceName(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
+getPayload() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+getPrefix() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+getPrefix() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+getPrefix() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getPrefix() - Method in interface de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
+getPrefixByNamespaceName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+getPrefixByNamespaceName(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
+getProviderCode() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getPublications(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves a list of publications associated with a given BiGG model abbreviation from the database.
+
+getReactionName(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the name of a reaction based on its BiGG ID abbreviation, ensuring the name is not empty.
+
+getReactionRules(String, String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Executes a provided SQL query to retrieve gene reaction rules from the database.
+
+getReactions() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+getResourceHomeUrl() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getResources() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getResources(BiGGId, boolean, boolean) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves a set of resource URLs for a given BiGG ID, optionally filtering to include only those containing 'identifiers.org'.
+
+getRoot() - Method in class de.uni_halle.informatik.biodata.mp.eco.DAG
+getRorId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+getSampleId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+getSampleId() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getSubsystem() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getSubsystems(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs.
+
+getSubsystemsForReaction(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID.
+
+getTaxonId(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Retrieves the taxonomic identifier (taxon ID) for a given model based on its abbreviation.
+
+getTerm() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+getTissueCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+getUpperBound() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+getURI() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+getURI() - Method in interface de.uni_halle.informatik.biodata.mp.resolver.RegistryURI
+getUrlPattern() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+getVersion() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+GPRParser - Class in de.uni_halle.informatik.biodata.mp.util.ext.fbc
+GPRParser() - Constructor for class de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
+groupAndSortAnnotations(SBase) - Method in class de.uni_halle.informatik.biodata.mp.annotation.AnnotationsSorter
+Recursively goes through all annotations in the given SBase and
+ alphabetically sort annotations after grouping them by CVTerm.Qualifier.
+
+GroupsFixer - Class in de.uni_halle.informatik.biodata.mp.fixing.ext.groups
+GroupsFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ext.groups.GroupsFixer
+GroupsUtils - Class in de.uni_halle.informatik.biodata.mp.util.ext.groups
+A collection of helpful functions for dealing with SBML data structures.
+
+GroupsUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils
+GROWTH_UNIT_ID - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+GROWTH_UNIT_NAME - Static variable in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+grRules - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Boolean gene-protein-reaction (GPR) rules in a readable format (AND/OR).
+
+
+H
+
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication
+Returns a hash code value for this object.
+
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization
+Returns a hash code value for this object.
+
+hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization
+Returns a hash code value for this object.
+
+hashCode() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Returns a hash code value for this object.
+
+hashCode() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+host() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+HOST - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
+HOST - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
+
+I
+
+IAnnotateSBases <SBMLElement extends org.sbml.jsbml.SBase> - Interface in de.uni_halle.informatik.biodata.mp.annotation
+IDENTIFIERS_ORG_ID_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+IdentifiersOrg - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+The IdentifiersOrg class serves as a central hub for managing and processing identifiers related to the MIRIAM registry.
+
+IdentifiersOrg() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+IdentifiersOrgRegistryParser - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+The IdentifiersOrgRegistryParser class is a singleton that provides functionality to parse the MIRIAM registry
+ from a JSON file and convert it into a Miriam object.
+
+IdentifiersOrgRegistryParser() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgRegistryParser
+IdentifiersOrgURI - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+IdentifiersOrgURI(String) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+IdentifiersOrgURI(String, BiGGId) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+IdentifiersOrgURI(String, Object) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+IdentifiersOrgURI(String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+IdentifiersOrgURIUtils - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg
+IdentifiersOrgURIUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
+IFixSBases <SBMLElement extends org.sbml.jsbml.SBase> - Interface in de.uni_halle.informatik.biodata.mp.fixing
+IFixSpeciesReferences - Interface in de.uni_halle.informatik.biodata.mp.fixing
+INCLUDE_ANY_URI - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+This switch allows users to specify if also those database cross-links
+ should be extracted from BiGG Models database for which currently no entry
+ in the MIRIAM exists.
+
+includeAnyURI - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+includeAnyURI() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+init(DBParameters) - Static method in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
+init(DBParameters) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+init(String, Integer, String, String, String) - Static method in class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB
+init(String, Integer, String, String, String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+initialAssignmentDoesNotReferenceBoundParameters(InitialAssignment) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+4) InitialAssignment objects may not target the Parameter objects referenced by
+ the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
+
+initialAssignmentDoesNotReferenceSpeciesReferences(InitialAssignment) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+4) InitialAssignment objects may not target the Parameter objects referenced by
+ the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
+
+initialize(ProgressInitialization) - Method in class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
+initialize(ProgressInitialization) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver
+input() - Method in class de.uni_halle.informatik.biodata.mp.io.ModelReaderException
+Institution - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+Institution() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+IO_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+IOOptions - Interface in de.uni_halle.informatik.biodata.mp.io
+IOOptions.OutputType - Enum Class in de.uni_halle.informatik.biodata.mp.io
+IPolishAnnotations - Interface in de.uni_halle.informatik.biodata.mp.polishing
+IPolishSBaseAttributes - Interface in de.uni_halle.informatik.biodata.mp.polishing
+IPolishSBases <SBMLElement extends org.sbml.jsbml.SBase> - Interface in de.uni_halle.informatik.biodata.mp.polishing
+IPolishSpeciesReferences - Interface in de.uni_halle.informatik.biodata.mp.polishing
+IProcessNotes - Interface in de.uni_halle.informatik.biodata.mp.annotation
+IReadModelsFromFile - Interface in de.uni_halle.informatik.biodata.mp.io
+IReportDiffs - Interface in de.uni_halle.informatik.biodata.mp.reporting
+IReportStatus - Interface in de.uni_halle.informatik.biodata.mp.reporting
+isBoundSet(Parameter) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+isCompartment(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+isDataSource(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+isDeprecated() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+isDeprecated() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+isDirectory(File) - Static method in class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils
+Check if file is directory by calling
File.isDirectory() on an existing file or check presence of '.' in
+ output.getName(), if this is not the case
+isEmptyString(String) - Static method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.COBRAUtils
+isMetabolite(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+isModel(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+isNamespaceEmbeddedInLui() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+isOfficial() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+isPseudoreaction(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Determines if a given reaction ID corresponds to a pseudoreaction in the database.
+
+isReaction(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+isSetAbbreviation() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+isSetCompartmentCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+isSetPrefix() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+isSetTissueCode() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+isValid(String) - Static method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+isValid(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+isValid(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
+IWriteModels - Interface in de.uni_halle.informatik.biodata.mp.io
+IWriteModelsToFile - Interface in de.uni_halle.informatik.biodata.mp.io
+
+J
+
+JSON - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
+JSON_FILE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
+JSONConverter - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json
+JSONConverter() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONConverter
+JSONParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json
+JSONParser(Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+
+L
+
+lb - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Lower reaction flux bounds for corresponding reactions
+
+linkNodes(Node, Node) - Static method in class de.uni_halle.informatik.biodata.mp.eco.Node
+ListOfObjectivesFixer - Class in de.uni_halle.informatik.biodata.mp.fixing.ext.fbc
+ListOfObjectivesFixer(FixingParameters, FBCModelPlugin, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ext.fbc.ListOfObjectivesFixer
+Location - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+Location() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+
+M
+
+MAT_FILE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
+MatlabParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+MatlabParser(SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.MatlabParser
+message() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization
+Returns the value of the message record component.
+
+MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.fixing.FixingOptions
+MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.io.IOOptions
+MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
+MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions
+MESSAGES - Static variable in interface de.uni_halle.informatik.biodata.mp.polishing.PolishingOptions
+Metabolite - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+Metabolite() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+Metabolites - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+Metabolites() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
+metCharge - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Value of charge for corresponding metabolite.
+
+metCHEBIID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+metFormulas - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Elemental formula for each metabolite.
+
+metHMDB - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+metInchiString - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Inichi String for each corresponding metabolite.
+
+metKeggID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+KEGG ID for each corresponding metabolite.
+
+metNames - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+metPubChemID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Pub Chem ID for each corresponding metabolite.
+
+mets - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Metabolite name abbreviation; metabolite ID; order corresponds to S matrix.
+
+metSmile - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+MODEL_NOTES_FILE - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+This XHTML file defines alternative model notes and makes them
+ exchangeable.
+
+ModelField - Enum Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+
+
+ModelFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+ModelFixer(FixingParameters, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ModelFixer
+modelNotesFile - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+modelNotesFile() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+ModelPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+This class provides functionality to polish an SBML (Systems Biology Markup Language) document.
+
+ModelPolisher(PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
+ModelPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
+ModelReader - Class in de.uni_halle.informatik.biodata.mp.io
+ModelReader(SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelReader
+ModelReaderException - Class in de.uni_halle.informatik.biodata.mp.io
+ModelReaderException(String, File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelReaderException
+ModelReaderException(String, Exception, File) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelReaderException
+ModelValidator - Class in de.uni_halle.informatik.biodata.mp.validation
+ModelValidator() - Constructor for class de.uni_halle.informatik.biodata.mp.validation.ModelValidator
+ModelValidatorException - Exception in de.uni_halle.informatik.biodata.mp.validation
+ModelValidatorException(Exception, File) - Constructor for exception de.uni_halle.informatik.biodata.mp.validation.ModelValidatorException
+ModelWriter - Class in de.uni_halle.informatik.biodata.mp.io
+ModelWriter(IOOptions.OutputType) - Constructor for class de.uni_halle.informatik.biodata.mp.io.ModelWriter
+ModelWriterException - Exception in de.uni_halle.informatik.biodata.mp.io
+ModelWriterException(String, Exception, SBMLDocument, File) - Constructor for exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
+ModelWriterException(String, SBMLDocument, File, File) - Constructor for exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
+
+N
+
+name - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+NamePolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+NamePolisher() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.NamePolisher
+Namespace - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+Namespace() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+NO_MODEL_NOTES - Static variable in interface de.uni_halle.informatik.biodata.mp.annotation.AnnotationOptions
+If set to true, no web content will be inserted in the SBML container nor
+ into the model within the SBML file.
+
+Node - Class in de.uni_halle.informatik.biodata.mp.eco
+Node(Term) - Constructor for class de.uni_halle.informatik.biodata.mp.eco.Node
+nodeAdded(TreeNode) - Method in class de.uni_halle.informatik.biodata.mp.io.UpdateListener
+Handles the event when a new node is added to the TreeNode structure.
+
+nodeAdded(TreeNode) - Method in class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
+nodeRemoved(TreeNodeRemovedEvent) - Method in class de.uni_halle.informatik.biodata.mp.io.UpdateListener
+nodeRemoved(TreeNodeRemovedEvent) - Method in class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
+noModelNotes() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGNotesParameters
+notes - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+notesParameters - Variable in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+notesParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+
+O
+
+obj() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Returns the value of the obj record component.
+
+ObjectivesPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+ObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.ObjectivesPolisher
+ObjectivesPolisher(FBCModelPlugin, PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.ObjectivesPolisher
+organism - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+osense - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Objective sense, i.e., to minimize or maximize the objective.
+
+output() - Method in exception de.uni_halle.informatik.biodata.mp.io.ModelWriterException
+OUTPUT_TYPE - Static variable in interface de.uni_halle.informatik.biodata.mp.io.IOOptions
+Decides whether the output file should directly be compressed and if
+ so, which archive type should be used.
+
+outputFile() - Method in exception de.uni_halle.informatik.biodata.mp.validation.ModelValidatorException
+outputType - Variable in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+outputType() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+
+P
+
+parameters - Variable in class de.uni_halle.informatik.biodata.mp.annotation.adb.AbstractADBAnnotator
+Parameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+Parameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+Parameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+ParametersException - Class in de.uni_halle.informatik.biodata.mp.parameters
+ParametersException(String, Parameters) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ParametersException
+ParametersParser - Class in de.uni_halle.informatik.biodata.mp.parameters
+ParametersParser() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.ParametersParser
+ParametersPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+ParametersPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ParametersPolisher
+parse() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.GeneParser
+parse() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
+parse() - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
+parse(File) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.MatlabParser
+parse(File) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+Creates the ModelBuilder, SBMLDocument and reads the
+ jsonFile as a tree
+
+parse(InputStream) - Method in class de.uni_halle.informatik.biodata.mp.parameters.ParametersParser
+parse(InputStream) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgRegistryParser
+parseAnnotation(SBase, Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+parseCompartments(ModelBuilder, Map<String, String>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+parseGene(Model, Gene, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+parseGeneReactionRules(Reaction, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+Parses gene reaction rules for a given reaction based on the BiGG database identifier.
+
+parseMetabolite(Model, Metabolite, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+parseNotes(SBase, Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+parseReaction(ModelBuilder, Reaction, String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.JSONParser
+passwd() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+PASSWD - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
+PASSWD - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
+polish(String) - Method in class de.uni_halle.informatik.biodata.mp.polishing.NamePolisher
+polish(List<Compartment>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher
+Polishes all compartments in the given SBML model.
+
+polish(List<GeneProduct>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductsPolisher
+polish(List<Parameter>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ParametersPolisher
+polish(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
+polish(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
+polish(List<SBase>) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBaseAttributes
+polish(List<Species>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
+polish(List<SpeciesReference>) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSpeciesReferences
+polish(List<SBMLElement>) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBases
+polish(Annotation) - Method in class de.uni_halle.informatik.biodata.mp.polishing.AnnotationPolisher
+Processes the annotations of an SBML entity to potentially correct identifiers
+ and/or retrieve additional identifiers.org URLs.
+
+polish(Annotation) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishAnnotations
+polish(Compartment) - Method in class de.uni_halle.informatik.biodata.mp.polishing.CompartmentPolisher
+Polishes the properties of a compartment to ensure compliance with standards and completeness.
+
+polish(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.GeneProductsPolisher
+polish(Objective) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.ObjectivesPolisher
+polish(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCPolisher
+polish(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
+This method orchestrates the polishing of an SBML model by delegating tasks to specific polishing methods
+ for different components of the model.
+
+polish(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+Ensures that all necessary UnitDefinitions and Units are present in the model.
+
+polish(Parameter) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ParametersPolisher
+polish(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
+polish(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
+Polishes the reaction by applying various checks and modifications to ensure it conforms to
+ the expected standards and conventions.
+
+polish(SBase) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBaseAttributes
+polish(SBase) - Method in class de.uni_halle.informatik.biodata.mp.polishing.NamePolisher
+polish(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher
+This method serves as the entry point from the ModelPolisher class to polish an SBML document.
+
+polish(Species) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
+polish(SpeciesReference) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSpeciesReferences
+polish(SpeciesReference) - Method in class de.uni_halle.informatik.biodata.mp.polishing.SpeciesReferencesPolisher
+polish(SBMLElement) - Method in interface de.uni_halle.informatik.biodata.mp.polishing.IPolishSBases
+POLISH_EVEN_IF_MODEL_INVALID - Static variable in interface de.uni_halle.informatik.biodata.mp.polishing.PolishingOptions
+PolisherFactory - Class in de.uni_halle.informatik.biodata.mp.polishing
+PolisherFactory() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.PolisherFactory
+PolisherProgressBar - Class in de.uni_halle.informatik.biodata.mp.reporting
+PolisherProgressBar() - Constructor for class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
+polishEvenIfModelInvalid() - Method in class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
+polishing() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+POLISHING_MESSAGES - Static variable in class de.uni_halle.informatik.biodata.mp.logging.BundleNames
+PolishingOptions - Interface in de.uni_halle.informatik.biodata.mp.polishing
+polishingParameters - Variable in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+PolishingParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+PolishingParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
+PolishingParameters(boolean) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
+PolishingParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.PolishingParameters
+port() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+PORT - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
+PORT - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
+PostgresConnectionPool - Class in de.uni_halle.informatik.biodata.mp.db
+PostgresConnectionPool(String, int, String, String, String) - Constructor for class de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool
+processNotes(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGDocumentNotesProcessor
+ProgressFinalization - Record Class in de.uni_halle.informatik.biodata.mp.reporting
+ProgressFinalization(String) - Constructor for record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization
+Creates an instance of a ProgressFinalization record class.
+
+ProgressInitialization - Record Class in de.uni_halle.informatik.biodata.mp.reporting
+ProgressInitialization(int) - Constructor for record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization
+Creates an instance of a ProgressInitialization record class.
+
+ProgressObserver - Interface in de.uni_halle.informatik.biodata.mp.reporting
+ProgressUpdate - Record Class in de.uni_halle.informatik.biodata.mp.reporting
+ProgressUpdate(String, Object, ReportType) - Constructor for record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Creates an instance of a ProgressUpdate record class.
+
+propertyChange(PropertyChangeEvent) - Method in class de.uni_halle.informatik.biodata.mp.io.UpdateListener
+Responds to property change events, specifically focusing on changes to the ID property of tree nodes.
+
+propertyChange(PropertyChangeEvent) - Method in class de.uni_halle.informatik.biodata.mp.reporting.DiffListener
+proteins - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Proteins associated with each reaction.
+
+Publication - Record Class in de.uni_halle.informatik.biodata.mp.db.bigg
+Publication(String, String) - Constructor for record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication
+Creates an instance of a Publication record class.
+
+
+R
+
+RawIdentifiersOrgRegistry - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+RawIdentifiersOrgRegistry() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+RDF_MEDIATYPE - Static variable in class de.uni_halle.informatik.biodata.mp.io.CombineArchive
+Reaction - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+Reaction() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+ReactionFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+ReactionFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.ReactionFixer
+reactionHasValidBounds(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+1) Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound',
+ with each attribute pointing to a valid Parameter object defined in the current Model.
+
+reactionId - Variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB.ForeignReaction
+ReactionNamePatterns - Enum Class in de.uni_halle.informatik.biodata.mp.util
+Defines an enumeration for regex patterns that are used to categorize reactions based on their ID strings.
+
+ReactionParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+ReactionParser(ModelBuilder, int, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ReactionParser
+reactionSpeciesReferencesHaveValidAttributes(Reaction) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+
+
+ReactionsPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+This class provides methods to polish and validate SBML reactions according to specific rules and patterns.
+
+ReactionsPolisher(PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
+ReactionsPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ReactionsPolisher
+read(File) - Method in interface de.uni_halle.informatik.biodata.mp.io.IReadModelsFromFile
+read(File) - Method in class de.uni_halle.informatik.biodata.mp.io.ModelReader
+REF_SEQ_ACCESSION_NUMBER_PATTERN - Static variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGModelAnnotator
+referenceId() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication
+Returns the value of the referenceId record component.
+
+referenceType() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication
+Returns the value of the referenceType record component.
+
+registry - Variable in class de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator
+registry - Variable in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+Registry - Interface in de.uni_halle.informatik.biodata.mp.resolver
+RegistryURI - Interface in de.uni_halle.informatik.biodata.mp.resolver
+removeHttpProtocolFromUrl(String) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
+replaceIdTag(String, String) - Static method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURIUtils
+Replaces the identifier placeholder "{$id}" in a URL pattern with a specified regex pattern.
+
+reportType() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Returns the value of the reportType record component.
+
+ReportType - Enum Class in de.uni_halle.informatik.biodata.mp.reporting
+resolveBackwards(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+Checks and processes a given resource URL to ensure it conforms to expected formats and corrections.
+
+resolveBackwards(String) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
+Resource - Class in de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping
+Resource() - Constructor for class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+rev - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+A vector consisting of zeros and ones that translate to binary and determine
+ if the corresponding reaction of that index is reversible (1) or not (0).
+
+Root - Class in de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping
+Root() - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+rules - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Boolean rule for the corresponding reaction which defines gene-reaction
+ relationship.
+
+rxnCOG - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+TODO: description COG
+
+rxnConfidenceEcoIDA - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Cell array of strings, can any value in a range of 0 to 4.
+
+rxnConfidenceScores - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+.
+
+rxnECNumbers - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+E.
+
+rxnGeneMat - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+A matrix with rows corresponding to reaction list and columns corresponding
+ to gene list.
+
+rxnKeggID - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+
+
+rxnKeggOrthology - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+TODO: description KEGG Orthology
+
+rxnNames - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Descriptive reaction names, length of this array must be identical to the
+ number of reactions.
+
+rxnNotes - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Cell array of strings.
+
+rxnReferences - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Cell array of strings which can contain optional information on references
+ for each specific reaction.
+
+rxns - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Reaction BiGG ids.
+
+rxnsboTerm - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+The Systems Biology Ontology Term to describe the role of a reaction.
+
+
+S
+
+S - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Stoichiometric matrix in sparse format.
+
+SBML - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
+SBML_FILE - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
+SBML_VALIDATION - Static variable in interface de.uni_halle.informatik.biodata.mp.parameters.GeneralOptions
+If true, the created SBML file will be validated through the online
+ validator service at
http://sbml.org .
+SBMLFileUtils - Class in de.uni_halle.informatik.biodata.mp.io
+SBMLFileUtils() - Constructor for class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils
+SBMLFileUtils.FileType - Enum Class in de.uni_halle.informatik.biodata.mp.io
+Possible FileTypes of input file
+
+SBMLFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+SBMLFixer(FixingParameters) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer
+SBMLFixer(FixingParameters, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SBMLFixer
+sbmlPolisher(SBMLDocument, PolishingParameters, SBOParameters) - Static method in class de.uni_halle.informatik.biodata.mp.polishing.PolisherFactory
+SBMLPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+SBMLPolisher(PolishingParameters, SBOParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher
+SBMLPolisher(PolishingParameters, SBOParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SBMLPolisher
+sbmlValidation - Variable in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+sbmlValidation() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+sboParameters() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+SBOParameters - Class in de.uni_halle.informatik.biodata.mp.parameters
+SBOParameters() - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+SBOParameters(SBProperties) - Constructor for class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+set(Map<String, Double>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolites
+set(Map<String, String>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Compartments
+setAbbreviation(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+
+ Only contain upper and lower case letters, numbers, and underscores
+ /[0-9a-zA-Z][a-zA-Z0-9_]+/, only ASCII and don't start with numbers
+ When converting old BIGG IDs to BIGG2 IDs, replace a dash with two
+ underscores.
+
+setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setAnnotation(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setApiVersion(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+setBound(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setCharge(int) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setChildren(List<Node>) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+setCompartment(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setCompartmentCode(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+One or two characters in length, and contain only lower case letters and
+ numbers, and must begin with a lower case letter.
+
+setCompartments(Compartments) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setCountryCode(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+setCountryName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Location
+setCreated(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setDeprecated(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setDeprecated(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setDeprecationDate(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setDeprecationDate(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setDescription(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setErrorMessage(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+setFluxBoundSBOTerm(Parameter) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.FBCReactionPolisher
+Polishes the SBO term of a flux bound parameter based on its ID.
+
+setFormula(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setGeneProductAssociation(Reaction, String, boolean) - Static method in class de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
+setGeneReactionRule(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setGenes(List<Gene>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setGPLabelName(GeneProduct, String) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductAnnotator
+Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database.
+
+setHomeUrl(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+setId(long) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+setId(long) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setId(long) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setId(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setInstitution(Institution) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setLocation(Location) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+setLocation(Location) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setLowerBound(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setMetabolites(Metabolites) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setMetabolites(List<Metabolite>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setMirId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setMirId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setModified(Calendar) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setName(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setName(Reaction, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+Sets the name of the reaction based on the provided BiGGId.
+
+setName(Species, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGSpeciesAnnotator
+Updates the name of the species based on data retrieved from the BiGG Knowledgebase.
+
+setNamespaceEmbeddedInLui(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Gene
+setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Metabolite
+setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setNotes(Object) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setObjectiveCoefficient(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setOfficial(boolean) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setParents(List<Node>) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+setPattern(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setPayload(Map<String, List<Namespace>>) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.RawIdentifiersOrgRegistry
+setPrefix(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+
+ R: reaction
+ M: metabolite /[RM]/
+ NOTE: Do we want to have the id entity use R and M, and just remove
+ them when constructing the model, or have them just as
+ [abbreviation]_[compartment code] and add the prefix when they are put
+ into SBML models? Also SBML id's use capital letters (/[RM]/).
+
+setPrefix(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setProviderCode(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setReactions(List<Reaction>) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+setResourceHomeUrl(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setResources(List<Resource>) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setRorId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Institution
+setSampleId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Namespace
+setSampleId(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setSBOTerm(Reaction, BiGGId) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGReactionsAnnotator
+Sets the SBO term for a reaction based on the given BiGGId.
+
+setSubsystem(String) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setTerm(Term) - Method in class de.uni_halle.informatik.biodata.mp.eco.Node
+setTissueCode(String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+One or two characters in length, and contain only upper case letters and
+ numbers, and must begin with an upper case letter.
+
+setUpperBound(double) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Reaction
+setUrlPattern(String) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping.Resource
+setVersion(int) - Method in class de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping.Root
+singleParamStatement(String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB
+Executes a SQL query with a single parameter and returns the result as an Optional.
+
+SINK_REACTION - Enum constant in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Pattern for sink reactions, which are reactions that remove metabolites from the system, identified by IDs starting with 'SK_' or 'SINK_'.
+
+SpeciesFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+SpeciesFixer(List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SpeciesFixer
+SpeciesParser - Class in de.uni_halle.informatik.biodata.mp.io.parsers.cobra
+SpeciesParser(Model, int, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.SpeciesParser
+SpeciesPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+SpeciesPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
+SpeciesPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SpeciesPolisher
+SpeciesReferenceFixer - Class in de.uni_halle.informatik.biodata.mp.fixing
+SpeciesReferenceFixer() - Constructor for class de.uni_halle.informatik.biodata.mp.fixing.SpeciesReferenceFixer
+SpeciesReferencesPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+SpeciesReferencesPolisher(Integer) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.SpeciesReferencesPolisher
+STATUS - Enum constant in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType
+statusReport(String, Object) - Method in class de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator
+statusReport(String, Object) - Method in class de.uni_halle.informatik.biodata.mp.fixing.AbstractFixer
+statusReport(String, Object) - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+statusReport(String, Object) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.IReportStatus
+strictnessOfSpeciesReferences(ListOf<SpeciesReference>) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+3) SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value
+ that is not 'NaN', nor '-INF', nor 'INF'.
+
+StrictnessPredicate - Class in de.uni_halle.informatik.biodata.mp.polishing.ext.fbc
+
+
+StrictnessPredicate() - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+stringify(Association) - Static method in class de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser
+SUBSYSTEM_LINK - Static variable in class de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils
+Key to link from Reaction directly to Members referencing
+ that reaction.
+
+subSystems - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+This defines groups of reactions that belong to a common reaction subsystem.
+
+
+T
+
+Table() - Constructor for class de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Table
+Table() - Constructor for class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Table
+test(Model) - Method in class de.uni_halle.informatik.biodata.mp.polishing.ext.fbc.StrictnessPredicate
+text() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Returns the value of the text record component.
+
+toBiGGId() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+Generates a BiGG ID for this object based on its properties.
+
+toBiGGId(String, String, String, String) - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+Constructs a BiGG ID using the provided components.
+
+toString() - Method in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId
+toString() - Method in record class de.uni_halle.informatik.biodata.mp.db.bigg.Publication
+Returns a string representation of this record class.
+
+toString() - Method in class de.uni_halle.informatik.biodata.mp.eco.DAG
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.AnnotationParameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.FixingParameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.Parameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.parameters.SBOParameters
+toString() - Method in class de.uni_halle.informatik.biodata.mp.polishing.AbstractPolisher
+toString() - Method in class de.uni_halle.informatik.biodata.mp.polishing.ModelPolisher
+toString() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressFinalization
+Returns a string representation of this record class.
+
+toString() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization
+Returns a string representation of this record class.
+
+toString() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressUpdate
+Returns a string representation of this record class.
+
+toString() - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI
+totalCalls() - Method in record class de.uni_halle.informatik.biodata.mp.reporting.ProgressInitialization
+Returns the value of the totalCalls record component.
+
+traverse(Node, int, StringBuilder) - Method in class de.uni_halle.informatik.biodata.mp.eco.DAG
+TYPE_GENE_PRODUCT - Static variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
+TYPE_REACTION - Static variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
+TYPE_SPECIES - Static variable in class de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants
+
+U
+
+ub - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Upper reaction flux bounds for corresponding reactions
+
+UnitPolisher - Class in de.uni_halle.informatik.biodata.mp.polishing
+This class is responsible for ensuring that all necessary UnitDefinitions and Units are correctly
+ defined and present in the SBML model.
+
+UnitPolisher(PolishingParameters, Registry) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+UnitPolisher(PolishingParameters, Registry, List<ProgressObserver>) - Constructor for class de.uni_halle.informatik.biodata.mp.polishing.UnitPolisher
+UNKNOWN - Enum constant in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
+update(ProgressUpdate) - Method in class de.uni_halle.informatik.biodata.mp.reporting.PolisherProgressBar
+update(ProgressUpdate) - Method in interface de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver
+update(GeneProduct) - Method in class de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGGeneProductReferencesAnnotator
+Updates the reference of a gene product in the geneProductReferences map using the gene product's ID.
+
+UpdateListener - Class in de.uni_halle.informatik.biodata.mp.io
+The UpdateListener class implements the TreeNodeChangeListener to monitor and respond to changes
+ within an SBML model's structure.
+
+UpdateListener() - Constructor for class de.uni_halle.informatik.biodata.mp.io.UpdateListener
+Constructs an UpdateListener instance and initializes the geneIdToAssociation map.
+
+user() - Method in class de.uni_halle.informatik.biodata.mp.parameters.DBParameters
+USER - Static variable in interface de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBOptions
+USER - Static variable in interface de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBOptions
+
+V
+
+validate(File) - Method in class de.uni_halle.informatik.biodata.mp.validation.ModelValidator
+validate(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.validation.ModelValidator
+validRegistryUrlPrefix(RegistryURI) - Method in class de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg
+Existing models on BiGG and Biomodels use some namespaces that were removed from identifiers.org.
+
+validRegistryUrlPrefix(RegistryURI) - Method in interface de.uni_halle.informatik.biodata.mp.resolver.Registry
+valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
+Returns the enum constant of this class with the specified name.
+
+valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Returns the enum constant of this class with the specified name.
+
+valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
+Returns the enum constant of this class with the specified name.
+
+valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType
+Returns the enum constant of this class with the specified name.
+
+valueOf(String) - Static method in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Returns the enum constant of this class with the specified name.
+
+values() - Static method in enum class de.uni_halle.informatik.biodata.mp.io.IOOptions.OutputType
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+values() - Static method in enum class de.uni_halle.informatik.biodata.mp.io.parsers.cobra.ModelField
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+values() - Static method in enum class de.uni_halle.informatik.biodata.mp.io.SBMLFileUtils.FileType
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+values() - Static method in enum class de.uni_halle.informatik.biodata.mp.reporting.ReportType
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+values() - Static method in enum class de.uni_halle.informatik.biodata.mp.util.ReactionNamePatterns
+Returns an array containing the constants of this enum class, in
+the order they are declared.
+
+
+W
+
+write() - Method in class de.uni_halle.informatik.biodata.mp.io.CombineArchive
+write(SBMLDocument) - Method in interface de.uni_halle.informatik.biodata.mp.io.IWriteModels
+write(SBMLDocument) - Method in class de.uni_halle.informatik.biodata.mp.io.ModelWriter
+write(SBMLDocument, File) - Method in interface de.uni_halle.informatik.biodata.mp.io.IWriteModelsToFile
+write(SBMLDocument, File) - Method in class de.uni_halle.informatik.biodata.mp.io.ModelWriter
+
+A B C D E F G H I J L M N O P R S T U V W All Classes and Interfaces | All Packages | Constant Field Values | Serialized Form
+
+
Overview (lib 2.1 API)
+
+JavaScript is disabled on your browser.
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version 2
+only ("GPL2"), with the following clarification and special exception.
+
+ Linking this OpenJDK Code statically or dynamically with other code
+ is making a combined work based on this library. Thus, the terms
+ and conditions of GPL2 cover the whole combination.
+
+ As a special exception, Oracle gives you permission to link this
+ OpenJDK Code with certain code licensed by Oracle as indicated at
+ http://openjdk.java.net/legal/exception-modules-2007-05-08.html
+ ("Designated Exception Modules") to produce an executable,
+ regardless of the license terms of the Designated Exception Modules,
+ and to copy and distribute the resulting executable under GPL2,
+ provided that the Designated Exception Modules continue to be
+ governed by the licenses under which they were offered by Oracle.
+
+As such, it allows licensees and sublicensees of Oracle's GPL2 OpenJDK Code
+to build an executable that includes those portions of necessary code that
+Oracle could not provide under GPL2 (or that Oracle has provided under GPL2
+with the Classpath exception). If you modify or add to the OpenJDK code,
+that new GPL2 code may still be combined with Designated Exception Modules
+if the new code is made subject to this exception by its copyright holder.
diff --git a/docs/legal/LICENSE b/docs/legal/LICENSE
new file mode 100644
index 00000000..8b400c7a
--- /dev/null
+++ b/docs/legal/LICENSE
@@ -0,0 +1,347 @@
+The GNU General Public License (GPL)
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software--to make sure the
+software is free for all its users. This General Public License applies to
+most of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+When we speak of free software, we are referring to freedom, not price. Our
+General Public Licenses are designed to make sure that you have the freedom to
+distribute copies of free software (and charge for this service if you wish),
+that you receive source code or can get it if you want it, that you can change
+the software or use pieces of it in new free programs; and that you know you
+can do these things.
+
+To protect your rights, we need to make restrictions that forbid anyone to deny
+you these rights or to ask you to surrender the rights. These restrictions
+translate to certain responsibilities for you if you distribute copies of the
+software, or if you modify it.
+
+For example, if you distribute copies of such a program, whether gratis or for
+a fee, you must give the recipients all the rights that you have. You must
+make sure that they, too, receive or can get the source code. And you must
+show them these terms so they know their rights.
+
+We protect your rights with two steps: (1) copyright the software, and (2)
+offer you this license which gives you legal permission to copy, distribute
+and/or modify the software.
+
+Also, for each author's protection and ours, we want to make certain that
+everyone understands that there is no warranty for this free software. If the
+software is modified by someone else and passed on, we want its recipients to
+know that what they have is not the original, so that any problems introduced
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+
+Finally, any free program is threatened constantly by software patents. We
+wish to avoid the danger that redistributors of a free program will
+individually obtain patent licenses, in effect making the program proprietary.
+To prevent this, we have made it clear that any patent must be licensed for
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+
+The precise terms and conditions for copying, distribution and modification
+follow.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+0. This License applies to any program or other work which contains a notice
+placed by the copyright holder saying it may be distributed under the terms of
+this General Public License. The "Program", below, refers to any such program
+or work, and a "work based on the Program" means either the Program or any
+derivative work under copyright law: that is to say, a work containing the
+Program or a portion of it, either verbatim or with modifications and/or
+translated into another language. (Hereinafter, translation is included
+without limitation in the term "modification".) Each licensee is addressed as
+"you".
+
+Activities other than copying, distribution and modification are not covered by
+this License; they are outside its scope. The act of running the Program is
+not restricted, and the output from the Program is covered only if its contents
+constitute a work based on the Program (independent of having been made by
+running the Program). Whether that is true depends on what the Program does.
+
+1. You may copy and distribute verbatim copies of the Program's source code as
+you receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice and
+disclaimer of warranty; keep intact all the notices that refer to this License
+and to the absence of any warranty; and give any other recipients of the
+Program a copy of this License along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and you may
+at your option offer warranty protection in exchange for a fee.
+
+2. You may modify your copy or copies of the Program or any portion of it, thus
+forming a work based on the Program, and copy and distribute such modifications
+or work under the terms of Section 1 above, provided that you also meet all of
+these conditions:
+
+ a) You must cause the modified files to carry prominent notices stating
+ that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in whole or
+ in part contains or is derived from the Program or any part thereof, to be
+ licensed as a whole at no charge to all third parties under the terms of
+ this License.
+
+ c) If the modified program normally reads commands interactively when run,
+ you must cause it, when started running for such interactive use in the
+ most ordinary way, to print or display an announcement including an
+ appropriate copyright notice and a notice that there is no warranty (or
+ else, saying that you provide a warranty) and that users may redistribute
+ the program under these conditions, and telling the user how to view a copy
+ of this License. (Exception: if the Program itself is interactive but does
+ not normally print such an announcement, your work based on the Program is
+ not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If identifiable
+sections of that work are not derived from the Program, and can be reasonably
+considered independent and separate works in themselves, then this License, and
+its terms, do not apply to those sections when you distribute them as separate
+works. But when you distribute the same sections as part of a whole which is a
+work based on the Program, the distribution of the whole must be on the terms
+of this License, whose permissions for other licensees extend to the entire
+whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest your
+rights to work written entirely by you; rather, the intent is to exercise the
+right to control the distribution of derivative or collective works based on
+the Program.
+
+In addition, mere aggregation of another work not based on the Program with the
+Program (or with a work based on the Program) on a volume of a storage or
+distribution medium does not bring the other work under the scope of this
+License.
+
+3. You may copy and distribute the Program (or a work based on it, under
+Section 2) in object code or executable form under the terms of Sections 1 and
+2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable source
+ code, which must be distributed under the terms of Sections 1 and 2 above
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+ b) Accompany it with a written offer, valid for at least three years, to
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+4. You may not copy, modify, sublicense, or distribute the Program except as
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+sublicense or distribute the Program is void, and will automatically terminate
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+5. You are not required to accept this License, since you have not signed it.
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+conditions of this License. If you cannot distribute so as to satisfy
+simultaneously your obligations under this License and any other pertinent
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+For example, if a patent license would not permit royalty-free redistribution
+of the Program by all those who receive copies directly or indirectly through
+you, then the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply and
+the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or
+other property right claims or to contest validity of any such claims; this
+section has the sole purpose of protecting the integrity of the free software
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+people have made generous contributions to the wide range of software
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+distribute software through any other system and a licensee cannot impose that
+choice.
+
+This section is intended to make thoroughly clear what is believed to be a
+consequence of the rest of this License.
+
+8. If the distribution and/or use of the Program is restricted in certain
+countries either by patents or by copyrighted interfaces, the original
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+geographical distribution limitation excluding those countries, so that
+distribution is permitted only in or among countries not thus excluded. In
+such case, this License incorporates the limitation as if written in the body
+of this License.
+
+9. The Free Software Foundation may publish revised and/or new versions of the
+General Public License from time to time. Such new versions will be similar in
+spirit to the present version, but may differ in detail to address new problems
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+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any later
+version", you have the option of following the terms and conditions either of
+that version or of any later version published by the Free Software Foundation.
+If the Program does not specify a version number of this License, you may
+choose any version ever published by the Free Software Foundation.
+
+10. If you wish to incorporate parts of the Program into other free programs
+whose distribution conditions are different, write to the author to ask for
+permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this.
+Our decision will be guided by the two goals of preserving the free status of
+all derivatives of our free software and of promoting the sharing and reuse of
+software generally.
+
+NO WARRANTY
+
+11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
+THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE
+STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE
+PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE,
+YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL
+ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE
+PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR
+INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
+BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER
+OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
+
+How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible
+use to the public, the best way to achieve this is to make it free software
+which everyone can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach
+them to the start of each source file to most effectively convey the exclusion
+of warranty; and each file should have at least the "copyright" line and a
+pointer to where the full notice is found.
+
+ One line to give the program's name and a brief idea of what it does.
+
+ Copyright (C)
+
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the Free
+ Software Foundation; either version 2 of the License, or (at your option)
+ any later version.
+
+ This program is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+ more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this when it
+starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author Gnomovision comes
+ with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free
+ software, and you are welcome to redistribute it under certain conditions;
+ type 'show c' for details.
+
+The hypothetical commands 'show w' and 'show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may be
+called something other than 'show w' and 'show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your school,
+if any, to sign a "copyright disclaimer" for the program, if necessary. Here
+is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ 'Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ signature of Ty Coon, 1 April 1989
+
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General Public
+License instead of this License.
+
+
+"CLASSPATH" EXCEPTION TO THE GPL
+
+Certain source files distributed by Oracle America and/or its affiliates are
+subject to the following clarification and special exception to the GPL, but
+only where Oracle has expressly included in the particular source file's header
+the words "Oracle designates this particular file as subject to the "Classpath"
+exception as provided by Oracle in the LICENSE file that accompanied this code."
+
+ Linking this library statically or dynamically with other modules is making
+ a combined work based on this library. Thus, the terms and conditions of
+ the GNU General Public License cover the whole combination.
+
+ As a special exception, the copyright holders of this library give you
+ permission to link this library with independent modules to produce an
+ executable, regardless of the license terms of these independent modules,
+ and to copy and distribute the resulting executable under terms of your
+ choice, provided that you also meet, for each linked independent module,
+ the terms and conditions of the license of that module. An independent
+ module is a module which is not derived from or based on this library. If
+ you modify this library, you may extend this exception to your version of
+ the library, but you are not obligated to do so. If you do not wish to do
+ so, delete this exception statement from your version.
diff --git a/docs/legal/jquery.md b/docs/legal/jquery.md
new file mode 100644
index 00000000..d468b318
--- /dev/null
+++ b/docs/legal/jquery.md
@@ -0,0 +1,72 @@
+## jQuery v3.6.1
+
+### jQuery License
+```
+jQuery v 3.6.1
+Copyright OpenJS Foundation and other contributors, https://openjsf.org/
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+******************************************
+
+The jQuery JavaScript Library v3.6.1 also includes Sizzle.js
+
+Sizzle.js includes the following license:
+
+Copyright JS Foundation and other contributors, https://js.foundation/
+
+This software consists of voluntary contributions made by many
+individuals. For exact contribution history, see the revision history
+available at https://github.com/jquery/sizzle
+
+The following license applies to all parts of this software except as
+documented below:
+
+====
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+====
+
+All files located in the node_modules and external directories are
+externally maintained libraries used by this software which have their
+own licenses; we recommend you read them, as their terms may differ from
+the terms above.
+
+*********************
+
+```
diff --git a/docs/legal/jqueryUI.md b/docs/legal/jqueryUI.md
new file mode 100644
index 00000000..8bda9d7a
--- /dev/null
+++ b/docs/legal/jqueryUI.md
@@ -0,0 +1,49 @@
+## jQuery UI v1.13.2
+
+### jQuery UI License
+```
+Copyright jQuery Foundation and other contributors, https://jquery.org/
+
+This software consists of voluntary contributions made by many
+individuals. For exact contribution history, see the revision history
+available at https://github.com/jquery/jquery-ui
+
+The following license applies to all parts of this software except as
+documented below:
+
+====
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+====
+
+Copyright and related rights for sample code are waived via CC0. Sample
+code is defined as all source code contained within the demos directory.
+
+CC0: http://creativecommons.org/publicdomain/zero/1.0/
+
+====
+
+All files located in the node_modules and external directories are
+externally maintained libraries used by this software which have their
+own licenses; we recommend you read them, as their terms may differ from
+the terms above.
+
+```
diff --git a/docs/member-search-index.js b/docs/member-search-index.js
new file mode 100644
index 00000000..c2ff2d7f
--- /dev/null
+++ b/docs/member-search-index.js
@@ -0,0 +1 @@
+memberSearchIndex = [{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","c":"ModelField","l":"A"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.adb","c":"AbstractADBAnnotator","l":"AbstractADBAnnotator(AnnotateDB, ADBAnnotationParameters)","u":"%3Cinit%3E(de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB,de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters)"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","c":"AbstractAnnotator","l":"AbstractAnnotator()","u":"%3Cinit%3E()"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","c":"AbstractAnnotator","l":"AbstractAnnotator(List)","u":"%3Cinit%3E(java.util.List)"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","c":"AbstractBiGGAnnotator","l":"AbstractBiGGAnnotator(BiGGDB, BiGGAnnotationParameters, 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\ No newline at end of file
diff --git a/docs/script.js b/docs/script.js
new file mode 100644
index 00000000..73cd8faa
--- /dev/null
+++ b/docs/script.js
@@ -0,0 +1,132 @@
+/*
+ * Copyright (c) 2013, 2020, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+var moduleSearchIndex;
+var packageSearchIndex;
+var typeSearchIndex;
+var memberSearchIndex;
+var tagSearchIndex;
+function loadScripts(doc, tag) {
+ createElem(doc, tag, 'search.js');
+
+ createElem(doc, tag, 'module-search-index.js');
+ createElem(doc, tag, 'package-search-index.js');
+ createElem(doc, tag, 'type-search-index.js');
+ createElem(doc, tag, 'member-search-index.js');
+ createElem(doc, tag, 'tag-search-index.js');
+}
+
+function createElem(doc, tag, path) {
+ var script = doc.createElement(tag);
+ var scriptElement = doc.getElementsByTagName(tag)[0];
+ script.src = pathtoroot + path;
+ scriptElement.parentNode.insertBefore(script, scriptElement);
+}
+
+function show(tableId, selected, columns) {
+ if (tableId !== selected) {
+ document.querySelectorAll('div.' + tableId + ':not(.' + selected + ')')
+ .forEach(function(elem) {
+ elem.style.display = 'none';
+ });
+ }
+ document.querySelectorAll('div.' + selected)
+ .forEach(function(elem, index) {
+ elem.style.display = '';
+ var isEvenRow = index % (columns * 2) < columns;
+ elem.classList.remove(isEvenRow ? oddRowColor : evenRowColor);
+ elem.classList.add(isEvenRow ? evenRowColor : oddRowColor);
+ });
+ updateTabs(tableId, selected);
+}
+
+function updateTabs(tableId, selected) {
+ document.getElementById(tableId + '.tabpanel')
+ .setAttribute('aria-labelledby', selected);
+ document.querySelectorAll('button[id^="' + tableId + '"]')
+ .forEach(function(tab, index) {
+ if (selected === tab.id || (tableId === selected && index === 0)) {
+ tab.className = activeTableTab;
+ tab.setAttribute('aria-selected', true);
+ tab.setAttribute('tabindex',0);
+ } else {
+ tab.className = tableTab;
+ tab.setAttribute('aria-selected', false);
+ tab.setAttribute('tabindex',-1);
+ }
+ });
+}
+
+function switchTab(e) {
+ var selected = document.querySelector('[aria-selected=true]');
+ if (selected) {
+ if ((e.keyCode === 37 || e.keyCode === 38) && selected.previousSibling) {
+ // left or up arrow key pressed: move focus to previous tab
+ selected.previousSibling.click();
+ selected.previousSibling.focus();
+ e.preventDefault();
+ } else if ((e.keyCode === 39 || e.keyCode === 40) && selected.nextSibling) {
+ // right or down arrow key pressed: move focus to next tab
+ selected.nextSibling.click();
+ selected.nextSibling.focus();
+ e.preventDefault();
+ }
+ }
+}
+
+var updateSearchResults = function() {};
+
+function indexFilesLoaded() {
+ return moduleSearchIndex
+ && packageSearchIndex
+ && typeSearchIndex
+ && memberSearchIndex
+ && tagSearchIndex;
+}
+
+// Workaround for scroll position not being included in browser history (8249133)
+document.addEventListener("DOMContentLoaded", function(e) {
+ var contentDiv = document.querySelector("div.flex-content");
+ window.addEventListener("popstate", function(e) {
+ if (e.state !== null) {
+ contentDiv.scrollTop = e.state;
+ }
+ });
+ window.addEventListener("hashchange", function(e) {
+ history.replaceState(contentDiv.scrollTop, document.title);
+ });
+ contentDiv.addEventListener("scroll", function(e) {
+ var timeoutID;
+ if (!timeoutID) {
+ timeoutID = setTimeout(function() {
+ history.replaceState(contentDiv.scrollTop, document.title);
+ timeoutID = null;
+ }, 100);
+ }
+ });
+ if (!location.hash) {
+ history.replaceState(contentDiv.scrollTop, document.title);
+ }
+});
diff --git a/docs/search.js b/docs/search.js
new file mode 100644
index 00000000..db3b2f4a
--- /dev/null
+++ b/docs/search.js
@@ -0,0 +1,354 @@
+/*
+ * Copyright (c) 2015, 2020, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+var noResult = {l: "No results found"};
+var loading = {l: "Loading search index..."};
+var catModules = "Modules";
+var catPackages = "Packages";
+var catTypes = "Classes and Interfaces";
+var catMembers = "Members";
+var catSearchTags = "Search Tags";
+var highlight = "$& ";
+var searchPattern = "";
+var fallbackPattern = "";
+var RANKING_THRESHOLD = 2;
+var NO_MATCH = 0xffff;
+var MIN_RESULTS = 3;
+var MAX_RESULTS = 500;
+var UNNAMED = "";
+function escapeHtml(str) {
+ return str.replace(//g, ">");
+}
+function getHighlightedText(item, matcher, fallbackMatcher) {
+ var escapedItem = escapeHtml(item);
+ var highlighted = escapedItem.replace(matcher, highlight);
+ if (highlighted === escapedItem) {
+ highlighted = escapedItem.replace(fallbackMatcher, highlight)
+ }
+ return highlighted;
+}
+function getURLPrefix(ui) {
+ var urlPrefix="";
+ var slash = "/";
+ if (ui.item.category === catModules) {
+ return ui.item.l + slash;
+ } else if (ui.item.category === catPackages && ui.item.m) {
+ return ui.item.m + slash;
+ } else if (ui.item.category === catTypes || ui.item.category === catMembers) {
+ if (ui.item.m) {
+ urlPrefix = ui.item.m + slash;
+ } else {
+ $.each(packageSearchIndex, function(index, item) {
+ if (item.m && ui.item.p === item.l) {
+ urlPrefix = item.m + slash;
+ }
+ });
+ }
+ }
+ return urlPrefix;
+}
+function createSearchPattern(term) {
+ var pattern = "";
+ var isWordToken = false;
+ term.replace(/,\s*/g, ", ").trim().split(/\s+/).forEach(function(w, index) {
+ if (index > 0) {
+ // whitespace between identifiers is significant
+ pattern += (isWordToken && /^\w/.test(w)) ? "\\s+" : "\\s*";
+ }
+ var tokens = w.split(/(?=[A-Z,.()<>[\/])/);
+ for (var i = 0; i < tokens.length; i++) {
+ var s = tokens[i];
+ if (s === "") {
+ continue;
+ }
+ pattern += $.ui.autocomplete.escapeRegex(s);
+ isWordToken = /\w$/.test(s);
+ if (isWordToken) {
+ pattern += "([a-z0-9_$<>\\[\\]]*?)";
+ }
+ }
+ });
+ return pattern;
+}
+function createMatcher(pattern, flags) {
+ var isCamelCase = /[A-Z]/.test(pattern);
+ return new RegExp(pattern, flags + (isCamelCase ? "" : "i"));
+}
+var watermark = 'Search';
+$(function() {
+ var search = $("#search-input");
+ var reset = $("#reset-button");
+ search.val('');
+ search.prop("disabled", false);
+ reset.prop("disabled", false);
+ search.val(watermark).addClass('watermark');
+ search.blur(function() {
+ if ($(this).val().length === 0) {
+ $(this).val(watermark).addClass('watermark');
+ }
+ });
+ search.on('click keydown paste', function() {
+ if ($(this).val() === watermark) {
+ $(this).val('').removeClass('watermark');
+ }
+ });
+ reset.click(function() {
+ search.val('').focus();
+ });
+ search.focus()[0].setSelectionRange(0, 0);
+});
+$.widget("custom.catcomplete", $.ui.autocomplete, {
+ _create: function() {
+ this._super();
+ this.widget().menu("option", "items", "> :not(.ui-autocomplete-category)");
+ },
+ _renderMenu: function(ul, items) {
+ var rMenu = this;
+ var currentCategory = "";
+ rMenu.menu.bindings = $();
+ $.each(items, function(index, item) {
+ var li;
+ if (item.category && item.category !== currentCategory) {
+ ul.append("" + item.category + " ");
+ currentCategory = item.category;
+ }
+ li = rMenu._renderItemData(ul, item);
+ if (item.category) {
+ li.attr("aria-label", item.category + " : " + item.l);
+ li.attr("class", "result-item");
+ } else {
+ li.attr("aria-label", item.l);
+ li.attr("class", "result-item");
+ }
+ });
+ },
+ _renderItem: function(ul, item) {
+ var label = "";
+ var matcher = createMatcher(escapeHtml(searchPattern), "g");
+ var fallbackMatcher = new RegExp(fallbackPattern, "gi")
+ if (item.category === catModules) {
+ label = getHighlightedText(item.l, matcher, fallbackMatcher);
+ } else if (item.category === catPackages) {
+ label = getHighlightedText(item.l, matcher, fallbackMatcher);
+ } else if (item.category === catTypes) {
+ label = (item.p && item.p !== UNNAMED)
+ ? getHighlightedText(item.p + "." + item.l, matcher, fallbackMatcher)
+ : getHighlightedText(item.l, matcher, fallbackMatcher);
+ } else if (item.category === catMembers) {
+ label = (item.p && item.p !== UNNAMED)
+ ? getHighlightedText(item.p + "." + item.c + "." + item.l, matcher, fallbackMatcher)
+ : getHighlightedText(item.c + "." + item.l, matcher, fallbackMatcher);
+ } else if (item.category === catSearchTags) {
+ label = getHighlightedText(item.l, matcher, fallbackMatcher);
+ } else {
+ label = item.l;
+ }
+ var li = $("
").appendTo(li);
+ if (item.category === catSearchTags && item.h) {
+ if (item.d) {
+ div.html(label + " (" + item.h + ") "
+ + item.d + " (" + item.h + ") ");
+ }
+ } else {
+ if (item.m) {
+ div.html(item.m + "/" + label);
+ } else {
+ div.html(label);
+ }
+ }
+ return li;
+ }
+});
+function rankMatch(match, category) {
+ if (!match) {
+ return NO_MATCH;
+ }
+ var index = match.index;
+ var input = match.input;
+ var leftBoundaryMatch = 2;
+ var periferalMatch = 0;
+ // make sure match is anchored on a left word boundary
+ if (index === 0 || /\W/.test(input[index - 1]) || "_" === input[index]) {
+ leftBoundaryMatch = 0;
+ } else if ("_" === input[index - 1] || (input[index] === input[index].toUpperCase() && !/^[A-Z0-9_$]+$/.test(input))) {
+ leftBoundaryMatch = 1;
+ }
+ var matchEnd = index + match[0].length;
+ var leftParen = input.indexOf("(");
+ var endOfName = leftParen > -1 ? leftParen : input.length;
+ // exclude peripheral matches
+ if (category !== catModules && category !== catSearchTags) {
+ var delim = category === catPackages ? "/" : ".";
+ if (leftParen > -1 && leftParen < index) {
+ periferalMatch += 2;
+ } else if (input.lastIndexOf(delim, endOfName) >= matchEnd) {
+ periferalMatch += 2;
+ }
+ }
+ var delta = match[0].length === endOfName ? 0 : 1; // rank full match higher than partial match
+ for (var i = 1; i < match.length; i++) {
+ // lower ranking if parts of the name are missing
+ if (match[i])
+ delta += match[i].length;
+ }
+ if (category === catTypes) {
+ // lower ranking if a type name contains unmatched camel-case parts
+ if (/[A-Z]/.test(input.substring(matchEnd)))
+ delta += 5;
+ if (/[A-Z]/.test(input.substring(0, index)))
+ delta += 5;
+ }
+ return leftBoundaryMatch + periferalMatch + (delta / 200);
+
+}
+function doSearch(request, response) {
+ var result = [];
+ searchPattern = createSearchPattern(request.term);
+ fallbackPattern = createSearchPattern(request.term.toLowerCase());
+ if (searchPattern === "") {
+ return this.close();
+ }
+ var camelCaseMatcher = createMatcher(searchPattern, "");
+ var fallbackMatcher = new RegExp(fallbackPattern, "i");
+
+ function searchIndexWithMatcher(indexArray, matcher, category, nameFunc) {
+ if (indexArray) {
+ var newResults = [];
+ $.each(indexArray, function (i, item) {
+ item.category = category;
+ var ranking = rankMatch(matcher.exec(nameFunc(item)), category);
+ if (ranking < RANKING_THRESHOLD) {
+ newResults.push({ranking: ranking, item: item});
+ }
+ return newResults.length <= MAX_RESULTS;
+ });
+ return newResults.sort(function(e1, e2) {
+ return e1.ranking - e2.ranking;
+ }).map(function(e) {
+ return e.item;
+ });
+ }
+ return [];
+ }
+ function searchIndex(indexArray, category, nameFunc) {
+ var primaryResults = searchIndexWithMatcher(indexArray, camelCaseMatcher, category, nameFunc);
+ result = result.concat(primaryResults);
+ if (primaryResults.length <= MIN_RESULTS && !camelCaseMatcher.ignoreCase) {
+ var secondaryResults = searchIndexWithMatcher(indexArray, fallbackMatcher, category, nameFunc);
+ result = result.concat(secondaryResults.filter(function (item) {
+ return primaryResults.indexOf(item) === -1;
+ }));
+ }
+ }
+
+ searchIndex(moduleSearchIndex, catModules, function(item) { return item.l; });
+ searchIndex(packageSearchIndex, catPackages, function(item) {
+ return (item.m && request.term.indexOf("/") > -1)
+ ? (item.m + "/" + item.l) : item.l;
+ });
+ searchIndex(typeSearchIndex, catTypes, function(item) {
+ return request.term.indexOf(".") > -1 ? item.p + "." + item.l : item.l;
+ });
+ searchIndex(memberSearchIndex, catMembers, function(item) {
+ return request.term.indexOf(".") > -1
+ ? item.p + "." + item.c + "." + item.l : item.l;
+ });
+ searchIndex(tagSearchIndex, catSearchTags, function(item) { return item.l; });
+
+ if (!indexFilesLoaded()) {
+ updateSearchResults = function() {
+ doSearch(request, response);
+ }
+ result.unshift(loading);
+ } else {
+ updateSearchResults = function() {};
+ }
+ response(result);
+}
+$(function() {
+ $("#search-input").catcomplete({
+ minLength: 1,
+ delay: 300,
+ source: doSearch,
+ response: function(event, ui) {
+ if (!ui.content.length) {
+ ui.content.push(noResult);
+ } else {
+ $("#search-input").empty();
+ }
+ },
+ autoFocus: true,
+ focus: function(event, ui) {
+ return false;
+ },
+ position: {
+ collision: "flip"
+ },
+ select: function(event, ui) {
+ if (ui.item.category) {
+ var url = getURLPrefix(ui);
+ if (ui.item.category === catModules) {
+ url += "module-summary.html";
+ } else if (ui.item.category === catPackages) {
+ if (ui.item.u) {
+ url = ui.item.u;
+ } else {
+ url += ui.item.l.replace(/\./g, '/') + "/package-summary.html";
+ }
+ } else if (ui.item.category === catTypes) {
+ if (ui.item.u) {
+ url = ui.item.u;
+ } else if (ui.item.p === UNNAMED) {
+ url += ui.item.l + ".html";
+ } else {
+ url += ui.item.p.replace(/\./g, '/') + "/" + ui.item.l + ".html";
+ }
+ } else if (ui.item.category === catMembers) {
+ if (ui.item.p === UNNAMED) {
+ url += ui.item.c + ".html" + "#";
+ } else {
+ url += ui.item.p.replace(/\./g, '/') + "/" + ui.item.c + ".html" + "#";
+ }
+ if (ui.item.u) {
+ url += ui.item.u;
+ } else {
+ url += ui.item.l;
+ }
+ } else if (ui.item.category === catSearchTags) {
+ url += ui.item.u;
+ }
+ if (top !== window) {
+ parent.classFrame.location = pathtoroot + url;
+ } else {
+ window.location.href = pathtoroot + url;
+ }
+ $("#search-input").focus();
+ }
+ }
+ });
+});
diff --git a/docs/serialized-form.html b/docs/serialized-form.html
new file mode 100644
index 00000000..ae4258c5
--- /dev/null
+++ b/docs/serialized-form.html
@@ -0,0 +1,189 @@
+
+
+
+
+Serialized Form (lib 2.1 API)
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\
+ ');
+ background-size:100% 100%;
+ width:7px;
+ height:7px;
+ margin-left:2px;
+ margin-bottom:4px;
+}
+main a[href*="://"]:hover::after,
+main a[href*="://"]:focus::after {
+ background-image:url('data:image/svg+xml; utf8, \
+ \
+ ');
+}
+
+/*
+ * Styles for user-provided tables.
+ *
+ * borderless:
+ * No borders, vertical margins, styled caption.
+ * This style is provided for use with existing doc comments.
+ * In general, borderless tables should not be used for layout purposes.
+ *
+ * plain:
+ * Plain borders around table and cells, vertical margins, styled caption.
+ * Best for small tables or for complex tables for tables with cells that span
+ * rows and columns, when the "striped" style does not work well.
+ *
+ * striped:
+ * Borders around the table and vertical borders between cells, striped rows,
+ * vertical margins, styled caption.
+ * Best for tables that have a header row, and a body containing a series of simple rows.
+ */
+
+table.borderless,
+table.plain,
+table.striped {
+ margin-top: 10px;
+ margin-bottom: 10px;
+}
+table.borderless > caption,
+table.plain > caption,
+table.striped > caption {
+ font-weight: bold;
+ font-size: smaller;
+}
+table.borderless th, table.borderless td,
+table.plain th, table.plain td,
+table.striped th, table.striped td {
+ padding: 2px 5px;
+}
+table.borderless,
+table.borderless > thead > tr > th, table.borderless > tbody > tr > th, table.borderless > tr > th,
+table.borderless > thead > tr > td, table.borderless > tbody > tr > td, table.borderless > tr > td {
+ border: none;
+}
+table.borderless > thead > tr, table.borderless > tbody > tr, table.borderless > tr {
+ background-color: transparent;
+}
+table.plain {
+ border-collapse: collapse;
+ border: 1px solid black;
+}
+table.plain > thead > tr, table.plain > tbody tr, table.plain > tr {
+ background-color: transparent;
+}
+table.plain > thead > tr > th, table.plain > tbody > tr > th, table.plain > tr > th,
+table.plain > thead > tr > td, table.plain > tbody > tr > td, table.plain > tr > td {
+ border: 1px solid black;
+}
+table.striped {
+ border-collapse: collapse;
+ border: 1px solid black;
+}
+table.striped > thead {
+ background-color: #E3E3E3;
+}
+table.striped > thead > tr > th, table.striped > thead > tr > td {
+ border: 1px solid black;
+}
+table.striped > tbody > tr:nth-child(even) {
+ background-color: #EEE
+}
+table.striped > tbody > tr:nth-child(odd) {
+ background-color: #FFF
+}
+table.striped > tbody > tr > th, table.striped > tbody > tr > td {
+ border-left: 1px solid black;
+ border-right: 1px solid black;
+}
+table.striped > tbody > tr > th {
+ font-weight: normal;
+}
+/**
+ * Tweak font sizes and paddings for small screens.
+ */
+@media screen and (max-width: 1050px) {
+ #search-input {
+ width: 300px;
+ }
+}
+@media screen and (max-width: 800px) {
+ #search-input {
+ width: 200px;
+ }
+ .top-nav,
+ .bottom-nav {
+ font-size: 11px;
+ padding-top: 6px;
+ }
+ .sub-nav {
+ font-size: 11px;
+ }
+ .about-language {
+ padding-right: 16px;
+ }
+ ul.nav-list li,
+ .sub-nav .nav-list-search {
+ padding: 6px;
+ }
+ ul.sub-nav-list li {
+ padding-top: 5px;
+ }
+ main {
+ padding: 10px;
+ }
+ .summary section[class$="-summary"], .details section[class$="-details"],
+ .class-uses .detail, .serialized-class-details {
+ padding: 0 8px 5px 8px;
+ }
+ body {
+ -webkit-text-size-adjust: none;
+ }
+}
+@media screen and (max-width: 500px) {
+ #search-input {
+ width: 150px;
+ }
+ .top-nav,
+ .bottom-nav {
+ font-size: 10px;
+ }
+ .sub-nav {
+ font-size: 10px;
+ }
+ .about-language {
+ font-size: 10px;
+ padding-right: 12px;
+ }
+}
diff --git a/docs/tag-search-index.js b/docs/tag-search-index.js
new file mode 100644
index 00000000..bf10aaf6
--- /dev/null
+++ b/docs/tag-search-index.js
@@ -0,0 +1 @@
+tagSearchIndex = [{"l":"Constant Field Values","h":"","u":"constant-values.html"},{"l":"Serialized Form","h":"","u":"serialized-form.html"}];updateSearchResults();
\ No newline at end of file
diff --git a/docs/type-search-index.js b/docs/type-search-index.js
new file mode 100644
index 00000000..0eac9f23
--- /dev/null
+++ b/docs/type-search-index.js
@@ -0,0 +1 @@
+typeSearchIndex = [{"p":"de.uni_halle.informatik.biodata.mp.annotation.adb","l":"AbstractADBAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","l":"AbstractAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"AbstractBiGGAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"AbstractFixer"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"AbstractPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"ADBAnnotationParameters"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.adb","l":"ADBReactionsAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.adb","l":"ADBSBMLAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.adb","l":"ADBSpeciesAnnotator"},{"l":"All Classes and Interfaces","u":"allclasses-index.html"},{"p":"de.uni_halle.informatik.biodata.mp.db.adb","l":"AnnotateDB"},{"p":"de.uni_halle.informatik.biodata.mp.db.adb","l":"AnnotateDBContract"},{"p":"de.uni_halle.informatik.biodata.mp.db.adb","l":"AnnotateDBOptions"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","l":"AnnotationException"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","l":"AnnotationOptions"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"AnnotationParameters"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"AnnotationPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","l":"AnnotationsSorter"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGAnnotationException"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"BiGGAnnotationParameters"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGCompartmentsAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGCVTermAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDB"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDBContract"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDBOptions"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGDocumentNotesProcessor"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc","l":"BiGGFBCAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc","l":"BiGGFBCSpeciesAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc","l":"BiGGGeneProductAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc","l":"BiGGGeneProductReferencesAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGId"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGModelAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"BiGGNotesParameters"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGPublicationsAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGReactionsAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGSBMLAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.annotation.bigg","l":"BiGGSpeciesAnnotator"},{"p":"de.uni_halle.informatik.biodata.mp.logging","l":"BundleNames"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","l":"COBRAUtils"},{"p":"de.uni_halle.informatik.biodata.mp.db.adb","l":"AnnotateDBContract.Constants.Column"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDBContract.Constants.Column"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"CombineArchive"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"CompartmentFixer"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"CompartmentPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping","l":"Compartments"},{"p":"de.uni_halle.informatik.biodata.mp.db.adb","l":"AnnotateDBContract.Constants"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDBContract.Constants"},{"p":"de.uni_halle.informatik.biodata.mp.eco","l":"DAG"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"DBParameters"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"DeleteOnCloseFileInputStream"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"DiffListener"},{"p":"de.uni_halle.informatik.biodata.mp.polishing.ext.fbc","l":"FBCPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.polishing.ext.fbc","l":"FBCReactionPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.fixing.ext.fbc","l":"FBCSpeciesFixer"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"SBMLFileUtils.FileType"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"FixingOptions"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"FixingParameters"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"FluxObjectivesFixingParameters"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDB.ForeignReaction"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping","l":"Gene"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","l":"GeneParser"},{"p":"de.uni_halle.informatik.biodata.mp.polishing.ext.fbc","l":"GeneProductAssociationsProcessor"},{"p":"de.uni_halle.informatik.biodata.mp.polishing.ext.fbc","l":"GeneProductsPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"GeneralOptions"},{"p":"de.uni_halle.informatik.biodata.mp.util.ext.fbc","l":"GPRParser"},{"p":"de.uni_halle.informatik.biodata.mp.fixing.ext.groups","l":"GroupsFixer"},{"p":"de.uni_halle.informatik.biodata.mp.util.ext.groups","l":"GroupsUtils"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","l":"IAnnotateSBases"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg","l":"IdentifiersOrg"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg","l":"IdentifiersOrgRegistryParser"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg","l":"IdentifiersOrgURI"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg","l":"IdentifiersOrgURIUtils"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"IFixSBases"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"IFixSpeciesReferences"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping","l":"Institution"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"IOOptions"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"IPolishAnnotations"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"IPolishSBaseAttributes"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"IPolishSBases"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"IPolishSpeciesReferences"},{"p":"de.uni_halle.informatik.biodata.mp.annotation","l":"IProcessNotes"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"IReadModelsFromFile"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"IReportDiffs"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"IReportStatus"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"IWriteModels"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"IWriteModelsToFile"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json","l":"JSONConverter"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json","l":"JSONParser"},{"p":"de.uni_halle.informatik.biodata.mp.fixing.ext.fbc","l":"ListOfObjectivesFixer"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping","l":"Location"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","l":"MatlabParser"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping","l":"Metabolite"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping","l":"Metabolites"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","l":"ModelField"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"ModelFixer"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"ModelPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"ModelReader"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"ModelReaderException"},{"p":"de.uni_halle.informatik.biodata.mp.validation","l":"ModelValidator"},{"p":"de.uni_halle.informatik.biodata.mp.validation","l":"ModelValidatorException"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"ModelWriter"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"ModelWriterException"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"NamePolisher"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping","l":"Namespace"},{"p":"de.uni_halle.informatik.biodata.mp.eco","l":"Node"},{"p":"de.uni_halle.informatik.biodata.mp.polishing.ext.fbc","l":"ObjectivesPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"IOOptions.OutputType"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"Parameters"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"ParametersException"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"ParametersParser"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"ParametersPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"PolisherFactory"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"PolisherProgressBar"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"PolishingOptions"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"PolishingParameters"},{"p":"de.uni_halle.informatik.biodata.mp.db","l":"PostgresConnectionPool"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"ProgressFinalization"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"ProgressInitialization"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"ProgressObserver"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"ProgressUpdate"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"Publication"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping","l":"RawIdentifiersOrgRegistry"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping","l":"Reaction"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"ReactionFixer"},{"p":"de.uni_halle.informatik.biodata.mp.util","l":"ReactionNamePatterns"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","l":"ReactionParser"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"ReactionsPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.resolver","l":"Registry"},{"p":"de.uni_halle.informatik.biodata.mp.resolver","l":"RegistryURI"},{"p":"de.uni_halle.informatik.biodata.mp.reporting","l":"ReportType"},{"p":"de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.mapping","l":"Resource"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.json.mapping","l":"Root"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"SBMLFileUtils"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"SBMLFixer"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"SBMLPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.parameters","l":"SBOParameters"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"SpeciesFixer"},{"p":"de.uni_halle.informatik.biodata.mp.io.parsers.cobra","l":"SpeciesParser"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"SpeciesPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.fixing","l":"SpeciesReferenceFixer"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"SpeciesReferencesPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.polishing.ext.fbc","l":"StrictnessPredicate"},{"p":"de.uni_halle.informatik.biodata.mp.db.adb","l":"AnnotateDBContract.Constants.Table"},{"p":"de.uni_halle.informatik.biodata.mp.db.bigg","l":"BiGGDBContract.Constants.Table"},{"p":"de.uni_halle.informatik.biodata.mp.polishing","l":"UnitPolisher"},{"p":"de.uni_halle.informatik.biodata.mp.io","l":"UpdateListener"}];updateSearchResults();
\ No newline at end of file
diff --git a/gradle.properties b/gradle.properties
new file mode 100644
index 00000000..f6e25a95
--- /dev/null
+++ b/gradle.properties
@@ -0,0 +1,2 @@
+org.gradle.console=verbose
+org.gradle.caching=true
\ No newline at end of file
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
new file mode 100644
index 00000000..de03b8d9
--- /dev/null
+++ b/gradle/libs.versions.toml
@@ -0,0 +1,35 @@
+[versions]
+jackson = "2.17.1"
+slf4j = "2.0.16"
+jupiter = "5.10.2"
+testContainers = "1.20.1"
+
+[libraries]
+sysbio = { module = "de.zbit.SysBio:SysBio", version = "1390" }
+jsbml = { module = "org.sbml.jsbml:jsbml", version = "1.6.1"}
+biojavaOntology = { module = "org.biojava:biojava-ontology", version = "7.1.1"}
+combineArchive = { module = "de.uni-rostock.sbi:CombineArchive", version = "1.4.1"}
+jtidy = { module = "net.sf.jtidy:jtidy", version = "r938" }
+matlab = { module = 'us.hebi.matlab.mat:mfl-core', version = '0.5.15' }
+
+postgres = { module = "org.postgresql:postgresql", version = "42.7.3" }
+hikariCP = { module = "com.zaxxer:HikariCP", version = "5.1.0"}
+jacksonCore = { module = "com.fasterxml.jackson.core:jackson-core", version.ref = "jackson"}
+jacksonDatabinding = { module = "com.fasterxml.jackson.core:jackson-databind", version.ref = "jackson" }
+commonsIO = { module = 'commons-io:commons-io', version = '2.16.1' }
+commonsLang = { module = 'org.apache.commons:commons-lang3', version = '3.15.0' }
+
+slf4j = { module = "org.slf4j:slf4j-api", version.ref = "slf4j" }
+julToSlf4j = { module = "org.slf4j:jul-to-slf4j", version.ref = "slf4j" }
+jclOverSlf4j = { module = "org.slf4j:jcl-over-slf4j", version.ref = "slf4j" }
+log4jOverSlf4j = { module = "org.slf4j:log4j-over-slf4j", version.ref = "slf4j" }
+osgiOverSlf4j = { module = "org.slf4j:osgi-over-slf4j", version.ref = "slf4j" }
+logback = { module = 'ch.qos.logback:logback-classic', version = '1.5.7' }
+
+jupiter = { module = "org.junit.jupiter:junit-jupiter-api", version.ref = "jupiter" }
+jupiterEngine = { module = "org.junit.jupiter:junit-jupiter-engine", version.ref = "jupiter"}
+junitPlatformLauncher = { module = 'org.junit.platform:junit-platform-launcher', version = '1.10.2' }
+
+testContainers = { module = "org.testcontainers:testcontainers", version.ref = "testContainers" }
+testContainersJupiter = {module = "org.testcontainers:junit-jupiter", version.ref = "testContainers" }
+
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index f3d88b1c..d64cd491 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index dd44a242..9355b415 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,7 @@
-#Wed Feb 05 04:01:03 CET 2020
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.1.1-all.zip
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
-zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
index 2fe81a7d..1aa94a42 100755
--- a/gradlew
+++ b/gradlew
@@ -1,7 +1,7 @@
-#!/usr/bin/env sh
+#!/bin/sh
#
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
@@ -17,78 +17,111 @@
#
##############################################################################
-##
-## Gradle start up script for UN*X
-##
+#
+# Gradle start up script for POSIX generated by Gradle.
+#
+# Important for running:
+#
+# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+# noncompliant, but you have some other compliant shell such as ksh or
+# bash, then to run this script, type that shell name before the whole
+# command line, like:
+#
+# ksh Gradle
+#
+# Busybox and similar reduced shells will NOT work, because this script
+# requires all of these POSIX shell features:
+# * functions;
+# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+# * compound commands having a testable exit status, especially «case»;
+# * various built-in commands including «command», «set», and «ulimit».
+#
+# Important for patching:
+#
+# (2) This script targets any POSIX shell, so it avoids extensions provided
+# by Bash, Ksh, etc; in particular arrays are avoided.
+#
+# The "traditional" practice of packing multiple parameters into a
+# space-separated string is a well documented source of bugs and security
+# problems, so this is (mostly) avoided, by progressively accumulating
+# options in "$@", and eventually passing that to Java.
+#
+# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+# see the in-line comments for details.
+#
+# There are tweaks for specific operating systems such as AIX, CygWin,
+# Darwin, MinGW, and NonStop.
+#
+# (3) This script is generated from the Groovy template
+# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+# within the Gradle project.
+#
+# You can find Gradle at https://github.com/gradle/gradle/.
+#
##############################################################################
# Attempt to set APP_HOME
+
# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+ APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
+ [ -h "$app_path" ]
+do
+ ls=$( ls -ld "$app_path" )
+ link=${ls#*' -> '}
+ case $link in #(
+ /*) app_path=$link ;; #(
+ *) app_path=$APP_HOME$link ;;
+ esac
done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
warn () {
echo "$*"
-}
+} >&2
die () {
echo
echo "$*"
echo
exit 1
-}
+} >&2
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
+case "$( uname )" in #(
+ CYGWIN* ) cygwin=true ;; #(
+ Darwin* ) darwin=true ;; #(
+ MSYS* | MINGW* ) msys=true ;; #(
+ NONSTOP* ) nonstop=true ;;
esac
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
# Determine the Java command to use to start the JVM.
if [ -n "$JAVA_HOME" ] ; then
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
# IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
+ JAVACMD=$JAVA_HOME/jre/sh/java
else
- JAVACMD="$JAVA_HOME/bin/java"
+ JAVACMD=$JAVA_HOME/bin/java
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -97,87 +130,120 @@ Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+ JAVACMD=java
+ if ! command -v java >/dev/null 2>&1
+ then
+ die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
+ fi
fi
# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+ case $MAX_FD in #(
+ max*)
+ # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+ # shellcheck disable=SC2039,SC3045
+ MAX_FD=$( ulimit -H -n ) ||
+ warn "Could not query maximum file descriptor limit"
+ esac
+ case $MAX_FD in #(
+ '' | soft) :;; #(
+ *)
+ # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+ # shellcheck disable=SC2039,SC3045
+ ulimit -n "$MAX_FD" ||
+ warn "Could not set maximum file descriptor limit to $MAX_FD"
+ esac
fi
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
+# Collect all arguments for the java command, stacking in reverse order:
+# * args from the command line
+# * the main class name
+# * -classpath
+# * -D...appname settings
+# * --module-path (only if needed)
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
# For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
+if "$cygwin" || "$msys" ; then
+ APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+ CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+ JAVACMD=$( cygpath --unix "$JAVACMD" )
+
# Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
+ for arg do
+ if
+ case $arg in #(
+ -*) false ;; # don't mess with options #(
+ /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
+ [ -e "$t" ] ;; #(
+ *) false ;;
+ esac
+ then
+ arg=$( cygpath --path --ignore --mixed "$arg" )
fi
- i=`expr $i + 1`
+ # Roll the args list around exactly as many times as the number of
+ # args, so each arg winds up back in the position where it started, but
+ # possibly modified.
+ #
+ # NB: a `for` loop captures its iteration list before it begins, so
+ # changing the positional parameters here affects neither the number of
+ # iterations, nor the values presented in `arg`.
+ shift # remove old arg
+ set -- "$@" "$arg" # push replacement arg
done
- case $i in
- 0) set -- ;;
- 1) set -- "$args0" ;;
- 2) set -- "$args0" "$args1" ;;
- 3) set -- "$args0" "$args1" "$args2" ;;
- 4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
fi
-# Escape application args
-save () {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=`save "$@"`
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+# and any embedded shellness will be escaped.
+# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+# treated as '${Hostname}' itself on the command line.
+
+set -- \
+ "-Dorg.gradle.appname=$APP_BASE_NAME" \
+ -classpath "$CLASSPATH" \
+ org.gradle.wrapper.GradleWrapperMain \
+ "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+ die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+# set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+ printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+ xargs -n1 |
+ sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+ tr '\n' ' '
+ )" '"$@"'
exec "$JAVACMD" "$@"
diff --git a/gradlew.bat b/gradlew.bat
index 24467a14..6689b85b 100644
--- a/gradlew.bat
+++ b/gradlew.bat
@@ -14,7 +14,7 @@
@rem limitations under the License.
@rem
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
@rem ##########################################################################
@rem
@rem Gradle startup script for Windows
@@ -25,10 +25,14 @@
if "%OS%"=="Windows_NT" setlocal
set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
@@ -37,7 +41,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if %ERRORLEVEL% equ 0 goto execute
echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -51,7 +55,7 @@ goto fail
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -61,38 +65,26 @@ echo location of your Java installation.
goto fail
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
:execute
@rem Setup the command line
set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
:end
@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
:fail
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
rem the _cmd.exe /c_ return code!
-if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
:mainEnd
if "%OS%"=="Windows_NT" endlocal
diff --git a/lib/build.gradle b/lib/build.gradle
new file mode 100644
index 00000000..72bf5462
--- /dev/null
+++ b/lib/build.gradle
@@ -0,0 +1,173 @@
+import groovy.json.JsonOutput
+import groovy.json.JsonSlurper
+import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+
+plugins {
+ id "java"
+ id "maven-publish"
+}
+
+group = "de.uni-halle.informatik.biodata"
+version = "2.1"
+
+sourceSets {
+ main {
+ java {
+ srcDirs = ["src/main/java"]
+ }
+ resources {
+ srcDirs = ["src/main/resources"]
+ }
+ }
+ test {
+ java {
+ srcDirs = ["src/test/java"]
+ }
+ resources {
+ srcDirs = ["src/test/resources"]
+ }
+ }
+}
+
+dependencies {
+ implementation(libs.sysbio)
+ implementation(libs.jsbml) {
+ exclude group: "org.apache.logging.log4j", module: "log4j-core"
+ exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
+ exclude group: "org.apache.commons", module: "logging"
+ }
+ implementation(libs.biojavaOntology) {
+ exclude group: "org.apache.logging.log4j", module: "log4j-core"
+ exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
+ }
+ implementation(libs.combineArchive)
+ implementation(libs.matlab)
+
+ // JDBC connection pool
+ implementation(libs.hikariCP)
+ // JSON processor
+ implementation(libs.jacksonCore)
+ // data binding for Jackson
+ implementation(libs.jacksonDatabinding)
+ implementation(libs.commonsLang)
+ // Java port of HTML Tidy, for cleaning up malformed HTML
+ implementation(libs.jtidy)
+ // official JDBC driver for PostgreSQL
+ implementation(libs.postgres)
+
+ testImplementation(libs.logback)
+ // Test implementation dependencies
+ // API for writing tests with JUnit 5
+ testImplementation(libs.jupiter)
+ // runtime engine for executing tests with JUnit 5
+ testRuntimeOnly(libs.jupiterEngine)
+ testRuntimeOnly(libs.junitPlatformLauncher)
+
+ // for integration testing with Docker containers
+ testImplementation(libs.testContainers)
+ // integration of Testcontainers with JUnit Jupiter
+ testImplementation(libs.testContainersJupiter)
+}
+
+
+tasks.withType(JavaCompile).configureEach {
+ options.compilerArgs << '-Xlint:deprecation'
+}
+
+tasks.withType(Jar).configureEach {
+ dependsOn test
+ duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+ destinationDirectory = file("$rootDir/target")
+ manifest {
+ attributes(
+ "Version": project.version,
+ "Implementation-Title": "ModelPolisher",
+ "Implementation-Version": project.version,
+ "Specification-Vendor": "Martin-Luther-Universität Halle-Wittenberg, BioDatA Arbeitsgruppe",
+ "Specification-Title": "ModelPolisher",
+ "Implementation-Vendor-Id": "de.uni-halle.informatik.biodata",
+ "Implementation-Vendor": "Martin-Luther-Universität Halle-Wittenberg, BioDatA Arbeitsgruppe"
+ )
+ }
+
+ into("META-INF/maven/${project.group}/${rootProject.name}") {
+ from { generatePomFileForModelPolisherLibraryPublication }
+ rename { it.replace('pom-default.xml', 'pom.xml') }
+ }
+
+ archiveFileName = "${rootProject.name}-${project.version}.jar"
+
+ from sourceSets.main.output
+}
+
+
+publishing {
+ publications {
+ modelPolisherLibrary(MavenPublication) {
+ from components.java
+
+ artifactId = 'ModelPolisher'
+ }
+ }
+ // https://reposilite.com/guide/gradle
+ repositories {
+ maven {
+ name = "reposilite"
+ url = "https://biodata.informatik.uni-halle.de/maven/releases"
+ credentials(PasswordCredentials)
+ authentication {
+ basic(BasicAuthentication)
+ }
+ }
+ }
+}
+
+tasks.named('test') {
+ useJUnitPlatform()
+ environment "TESTCONTAINERS_RYUK_DISABLED", "true"
+ testLogging {
+ showStandardStreams = true
+ events "passed", "skipped", "failed"
+ exceptionFormat TestExceptionFormat.FULL
+ showCauses true
+ showExceptions true
+ showStackTraces true
+ }
+}
+
+tasks.javadoc {
+ classpath = sourceSets.main.runtimeClasspath
+ source = sourceSets.main.allJava
+ options.addBooleanOption('Xdoclint:none', true)
+ file(new File(rootProject.projectDir.toString() + "/docs")).mkdirs()
+ destinationDir = new File(rootProject.projectDir.toString() + "/docs")
+}
+
+// get latest version of IdentifiersOrg registry
+tasks.register('downloadIdentifiersOrg') {
+ doLast {
+ def registryUrl = 'https://registry.api.identifiers.org/resolutionApi/getResolverDataset'
+ def parentDir = file('src/main/resources/de/uni_halle/informatik/biodata/mp/resolver/identifiersorg')
+ def registryFile = file("${parentDir}/IdentifiersOrg-Registry.json")
+
+ if (!parentDir.exists()) {
+ parentDir.mkdirs()
+ }
+
+ def registry = new URL(registryUrl).text
+ def jsonParser = new JsonSlurper()
+ def parsedJson = jsonParser.parseText(registry)
+ def prettyJson = JsonOutput.prettyPrint(JsonOutput.toJson(parsedJson))
+ registryFile.text = prettyJson
+ }
+}
+
+// ensure downloadIdentifiersOrg task is executed before processResources task
+// processResources is inbuilt in the Java plugin and
+// copies resources from src/main/resources to build/resources/main
+processResources.dependsOn(downloadIdentifiersOrg)
+
+clean.doFirst {
+ file(".gradle").deleteDir()
+ file("target").deleteDir()
+}
\ No newline at end of file
diff --git a/lib/de/zbit/SysBio/1390/SysBio-1390.jar b/lib/de/zbit/SysBio/1390/SysBio-1390.jar
deleted file mode 100644
index 41eddc08..00000000
Binary files a/lib/de/zbit/SysBio/1390/SysBio-1390.jar and /dev/null differ
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AbstractAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AbstractAnnotator.java
new file mode 100644
index 00000000..90d4401f
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AbstractAnnotator.java
@@ -0,0 +1,37 @@
+package de.uni_halle.informatik.biodata.mp.annotation;
+
+import de.uni_halle.informatik.biodata.mp.reporting.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public abstract class AbstractAnnotator implements IReportStatus, IReportDiffs {
+
+ private final List observers;
+
+ public AbstractAnnotator() {
+ observers = new ArrayList<>();
+ }
+
+ public AbstractAnnotator(List observers) {
+ this.observers = observers;
+ }
+
+ @Override
+ public void statusReport(String text, Object element) {
+ for (var o : observers) {
+ o.update(new ProgressUpdate(text, element, ReportType.STATUS));
+ }
+ }
+
+ @Override
+ public void diffReport(String elementType, Object element1, Object element2) {
+ for (var o : observers) {
+ o.update(new ProgressUpdate(elementType, List.of(element1, element2), ReportType.DATA));
+ }
+ }
+ public List getObservers() {
+ return observers;
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationException.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationException.java
new file mode 100644
index 00000000..1feabc48
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationException.java
@@ -0,0 +1,8 @@
+package de.uni_halle.informatik.biodata.mp.annotation;
+
+public class AnnotationException extends Exception{
+
+ public AnnotationException(String msg, Exception e) {
+ super(msg, e);
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationOptions.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationOptions.java
new file mode 100644
index 00000000..49150d5e
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationOptions.java
@@ -0,0 +1,74 @@
+package de.uni_halle.informatik.biodata.mp.annotation;
+
+import de.zbit.util.ResourceManager;
+import de.zbit.util.prefs.KeyProvider;
+import de.zbit.util.prefs.Option;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+
+import java.io.File;
+import java.util.ResourceBundle;
+
+public interface AnnotationOptions extends KeyProvider {
+
+ ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.ANNOTATION_MESSAGES);
+
+ /**
+ * If set to true, annotations will be added to species and reactions from AnnotateDB also.
+ */
+ @SuppressWarnings("unchecked")
+ Option ADD_ADB_ANNOTATIONS =
+ new Option<>("ADD_ADB_ANNOTATIONS", Boolean.class, MESSAGES.getString("ADD_ADB_ANNOTATIONS_DESC"),
+ Boolean.FALSE);
+ /**
+ * If set to true, the model will be annotated with data from BiGG Models
+ * database. If set to false, the resulting model will not receive annotation
+ * or correction from BiGG Models database
+ */
+ @SuppressWarnings("unchecked")
+ Option ANNOTATE_WITH_BIGG =
+ new Option<>("ANNOTATE_WITH_BIGG", Boolean.class, MESSAGES.getString("ANNOTATE_WITH_BIGG_DESC"),
+ Boolean.FALSE);
+
+ /**
+ * This XHTML file defines alternative model notes and makes them
+ * exchangeable.
+ */
+ Option MODEL_NOTES_FILE = new Option<>("MODEL_NOTES_FILE", File.class,
+ MESSAGES.getString("MODEL_NOTES_DESC"));
+
+ /**
+ * If set to true, no web content will be inserted in the SBML container nor
+ * into the model within the SBML file.
+ */
+ @SuppressWarnings("unchecked")
+ Option NO_MODEL_NOTES =
+ new Option<>("NO_MODEL_NOTES", Boolean.class, MESSAGES.getString("NO_MODEL_NOTES_DESC"),
+ Boolean.FALSE);
+
+ /**
+ * This switch allows users to specify if also those database cross-links
+ * should be extracted from BiGG Models database for which currently no entry
+ * in the MIRIAM exists. If set to true, ModelPolisher also includes URIs that
+ * do not contain the pattern identifiers.org.
+ */
+ @SuppressWarnings("unchecked")
+ Option INCLUDE_ANY_URI =
+ new Option<>("INCLUDE_ANY_URI", Boolean.class, MESSAGES.getString("INCLUDE_ANY_URI_DESC"),
+ Boolean.FALSE);
+
+ /**
+ * This XHTML file defines alternative document notes and makes them
+ * exchangeable.
+ */
+ Option DOCUMENT_NOTES_FILE =
+ new Option<>("DOCUMENT_NOTES_FILE", File.class, MESSAGES.getString("DOC_NOTES_DESC"));
+
+ /**
+ * This option allows you to define the title of the SBML document's
+ * description and hence the headline when the file is displayed in a web
+ * browser.
+ */
+ @SuppressWarnings("unchecked")
+ Option DOCUMENT_TITLE_PATTERN = new Option<>("DOCUMENT_TITLE_PATTERN", String.class,
+ MESSAGES.getString("DOC_TITLE_PATTERN_DESC"), "[biggId] - [organism]");
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationsSorter.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationsSorter.java
new file mode 100644
index 00000000..c2937d14
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/AnnotationsSorter.java
@@ -0,0 +1,86 @@
+package de.uni_halle.informatik.biodata.mp.annotation;
+
+import de.zbit.util.ResourceManager;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBase;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.swing.tree.TreeNode;
+import java.util.*;
+
+import static java.text.MessageFormat.format;
+
+public class AnnotationsSorter {
+ private static final Logger logger = LoggerFactory.getLogger(AnnotationsSorter.class);
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.ANNOTATION_MESSAGES);
+
+
+ /**
+ * Recursively goes through all annotations in the given {@link SBase} and
+ * alphabetically sort annotations after grouping them by {@link org.sbml.jsbml.CVTerm.Qualifier}.
+ *
+ * @param sbase:
+ * {@link SBase} to start the merging process at, corresponding to an instance of {@link SBMLDocument} here,
+ * though also used to pass current {@link SBase} during recursion
+ */
+ public void groupAndSortAnnotations(SBase sbase) {
+ if (sbase.isSetAnnotation()) {
+ SortedMap> miriam = new TreeMap<>();
+ boolean doMerge = hashMIRIAMuris(sbase, miriam);
+ if (doMerge) {
+ sbase.getAnnotation().unsetCVTerms();
+ for (Map.Entry> entry : miriam.entrySet()) {
+ logger.debug(format(MESSAGES.getString("MERGING_MIRIAM_RESOURCES"), entry.getKey(),
+ sbase.getClass().getSimpleName(), sbase.getId()));
+ sbase.addCVTerm(new CVTerm(entry.getKey(), entry.getValue().toArray(new String[0])));
+ }
+ }
+ }
+ for (int i = 0; i < sbase.getChildCount(); i++) {
+ TreeNode node = sbase.getChildAt(i);
+ if (node instanceof SBase) {
+ groupAndSortAnnotations((SBase) node);
+ }
+ }
+ }
+
+ /**
+ * Evaluates and merges CVTerm annotations for a given SBase element. This method checks each CVTerm associated with
+ * the SBase and determines if there are multiple CVTerms with the same Qualifier that need merging. It also corrects
+ * invalid qualifiers based on the type of SBase (Model or other biological elements).
+ *
+ * @param sbase The SBase element whose annotations are to be evaluated and potentially merged.
+ * @param miriam A sorted map that groups CVTerm resources by their qualifiers.
+ * @return true if there are CVTerms with the same qualifier that need to be merged, false otherwise.
+ */
+ private boolean hashMIRIAMuris(SBase sbase, SortedMap> miriam) {
+ boolean doMerge = false;
+ for (int i = 0; i < sbase.getCVTermCount(); i++) {
+ CVTerm term = sbase.getCVTerm(i);
+ CVTerm.Qualifier qualifier = term.getQualifier();
+ if (miriam.containsKey(qualifier)) {
+ doMerge = true;
+ } else {
+ if (sbase instanceof Model) {
+ if (!qualifier.isModelQualifier()) {
+ logger.debug(format(MESSAGES.getString("CORRECTING_INVALID_QUALIFIERS"),
+ qualifier.getElementNameEquivalent(), sbase.getId()));
+ qualifier = CVTerm.Qualifier.getModelQualifierFor(qualifier.getElementNameEquivalent());
+ }
+ } else if (!qualifier.isBiologicalQualifier()) {
+ logger.debug(format(MESSAGES.getString("CORRECTING_INVALID_MODEL_QUALIFIER"),
+ qualifier.getElementNameEquivalent(), sbase.getClass().getSimpleName(), sbase.getId()));
+ qualifier = CVTerm.Qualifier.getBiologicalQualifierFor(qualifier.getElementNameEquivalent());
+ }
+ miriam.put(qualifier, new TreeSet<>());
+ }
+ miriam.get(qualifier).addAll(term.getResources());
+ }
+ return doMerge;
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/IAnnotateSBases.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/IAnnotateSBases.java
new file mode 100644
index 00000000..b0c453f1
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/IAnnotateSBases.java
@@ -0,0 +1,18 @@
+package de.uni_halle.informatik.biodata.mp.annotation;
+
+import org.sbml.jsbml.SBase;
+
+import java.sql.SQLException;
+import java.util.List;
+
+public interface IAnnotateSBases {
+
+ default void annotate(List elementsToAnnotate) throws SQLException, AnnotationException {
+ for (var element: elementsToAnnotate) {
+ annotate(element);
+ }
+ }
+
+ void annotate(SBMLElement elementToAnnotate) throws SQLException, AnnotationException;
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/IProcessNotes.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/IProcessNotes.java
new file mode 100644
index 00000000..7139760a
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/IProcessNotes.java
@@ -0,0 +1,4 @@
+package de.uni_halle.informatik.biodata.mp.annotation;
+
+public interface IProcessNotes {
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBReactionsAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBReactionsAnnotator.java
new file mode 100644
index 00000000..9f0157f4
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBReactionsAnnotator.java
@@ -0,0 +1,36 @@
+package de.uni_halle.informatik.biodata.mp.annotation.adb;
+
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import org.sbml.jsbml.Reaction;
+
+import java.sql.SQLException;
+import java.util.*;
+
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.BIGG_REACTION;
+
+public class ADBReactionsAnnotator extends AbstractADBAnnotator implements IAnnotateSBases {
+
+ public ADBReactionsAnnotator(AnnotateDB adb, ADBAnnotationParameters parameters) {
+ super(adb, parameters);
+ }
+
+ @Override
+ public void annotate(List reactions) throws SQLException {
+ for (Reaction reaction : reactions) {
+ annotate(reaction);
+ }
+ }
+
+ @Override
+ public void annotate(Reaction reaction) throws SQLException {
+ String id = reaction.getId();
+ var reactionId = BiGGId.createReactionId(id);
+ addBQB_IS_AnnotationsFromADB(reaction.getAnnotation(), BIGG_REACTION, reactionId);
+ if ((reaction.getCVTermCount() > 0) && !reaction.isSetMetaId()) {
+ reaction.setMetaId(reaction.getId());
+ }
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBSBMLAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBSBMLAnnotator.java
new file mode 100644
index 00000000..3d7efc53
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBSBMLAnnotator.java
@@ -0,0 +1,24 @@
+package de.uni_halle.informatik.biodata.mp.annotation.adb;
+
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+
+import java.sql.SQLException;
+
+public class ADBSBMLAnnotator extends AbstractADBAnnotator implements IAnnotateSBases {
+
+ public ADBSBMLAnnotator(AnnotateDB adb, ADBAnnotationParameters parameters) {
+ super(adb, parameters);
+ }
+
+ @Override
+ public void annotate(SBMLDocument doc) throws SQLException {
+ Model model = doc.getModel();
+
+ new ADBSpeciesAnnotator(adb, parameters).annotate(model.getListOfSpecies());
+ new ADBReactionsAnnotator(adb, parameters).annotate(model.getListOfReactions());
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBSpeciesAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBSpeciesAnnotator.java
new file mode 100644
index 00000000..b66e5b7a
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/ADBSpeciesAnnotator.java
@@ -0,0 +1,36 @@
+package de.uni_halle.informatik.biodata.mp.annotation.adb;
+
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import org.sbml.jsbml.Species;
+
+import java.sql.SQLException;
+import java.util.*;
+
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.BIGG_METABOLITE;
+
+public class ADBSpeciesAnnotator extends AbstractADBAnnotator implements IAnnotateSBases {
+
+ public ADBSpeciesAnnotator(AnnotateDB adb, ADBAnnotationParameters parameters) {
+ super(adb, parameters);
+ }
+
+ @Override
+ public void annotate(List species) throws SQLException {
+ for (Species s : species) {
+ annotate(s);
+ }
+ }
+
+ @Override
+ public void annotate(Species species) throws SQLException {
+ String id = species.getId();
+ var metaboliteId = BiGGId.createMetaboliteId(id);
+ addBQB_IS_AnnotationsFromADB(species.getAnnotation(), BIGG_METABOLITE, metaboliteId);
+ if ((species.getCVTermCount() > 0) && !species.isSetMetaId()) {
+ species.setMetaId(species.getId());
+ }
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/AbstractADBAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/AbstractADBAnnotator.java
new file mode 100644
index 00000000..dd6f0ee5
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/adb/AbstractADBAnnotator.java
@@ -0,0 +1,42 @@
+package de.uni_halle.informatik.biodata.mp.annotation.adb;
+
+import de.uni_halle.informatik.biodata.mp.parameters.ADBAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import org.sbml.jsbml.Annotation;
+import org.sbml.jsbml.CVTerm;
+
+import java.sql.SQLException;
+import java.util.*;
+
+public abstract class AbstractADBAnnotator {
+
+ protected final AnnotateDB adb;
+ protected final ADBAnnotationParameters parameters;
+
+ public AbstractADBAnnotator(AnnotateDB adb, ADBAnnotationParameters parameters) {
+ super();
+ this.adb = adb;
+ this.parameters = parameters;
+ }
+
+ protected void addBQB_IS_AnnotationsFromADB(Annotation annotation, String type, BiGGId biggId) throws SQLException {
+ CVTerm cvTerm = annotation.getListOfCVTerms().stream()
+ .filter(term -> term.getQualifier() == CVTerm.Qualifier.BQB_IS)
+ .findFirst()
+ .orElse(new CVTerm(CVTerm.Qualifier.BQB_IS));
+
+ Set annotations = adb.getAnnotations(type, biggId.toBiGGId());
+
+ annotations.removeAll(new HashSet<>(cvTerm.getResources()));
+ List sortedAnnotations = new ArrayList<>(annotations);
+ Collections.sort(sortedAnnotations);
+ for (String a : sortedAnnotations) {
+ cvTerm.addResource(a);
+ }
+
+ if (cvTerm.getResourceCount() == 0) {
+ annotation.removeCVTerm(cvTerm);
+ }
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/AbstractBiGGAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/AbstractBiGGAnnotator.java
new file mode 100644
index 00000000..80c81a1f
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/AbstractBiGGAnnotator.java
@@ -0,0 +1,98 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.uni_halle.informatik.biodata.mp.annotation.AbstractAnnotator;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.resolver.RegistryURI;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI;
+import org.sbml.jsbml.Reaction;
+import org.sbml.jsbml.Species;
+import org.sbml.jsbml.ext.fbc.GeneProduct;
+
+import java.sql.SQLException;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Stream;
+
+
+public abstract class AbstractBiGGAnnotator extends AbstractAnnotator {
+
+ protected final BiGGDB bigg;
+ protected final Registry registry;
+ protected final BiGGAnnotationParameters biGGAnnotationParameters;
+
+ public AbstractBiGGAnnotator(BiGGDB bigg, BiGGAnnotationParameters biGGAnnotationParameters, Registry registry) {
+ super();
+ this.bigg = bigg;
+ this.registry = registry;
+ this.biGGAnnotationParameters = biGGAnnotationParameters;
+ }
+
+ public AbstractBiGGAnnotator(BiGGDB bigg, BiGGAnnotationParameters biGGAnnotationParameters, Registry registry, List observers) {
+ super(observers);
+ this.bigg = bigg;
+ this.registry = registry;
+ this.biGGAnnotationParameters = biGGAnnotationParameters;
+ }
+
+ /**
+ * Attempts to extract a BiGG ID that conforms to the BiGG ID specification from the BiGG knowledgebase. This method
+ * processes annotations for biological entities such as {@link Species}, {@link Reaction}, or {@link GeneProduct}.
+ * Each entity's annotations are provided as a list of URIs, which are then parsed to retrieve the BiGG ID.
+ *
+ * @param resources A list of URIs containing annotations for the biological entity.
+ * @param type The type of the biological entity, which can be one of the following:
+ * {@link BiGGDBContract.Constants#TYPE_SPECIES}, {@link BiGGDBContract.Constants#TYPE_REACTION}, or
+ * {@link BiGGDBContract.Constants#TYPE_GENE_PRODUCT}.
+ * @return An {@link Optional } containing the BiGG ID if it could be successfully retrieved, otherwise {@link Optional#empty()}.
+ */
+ public Optional getBiGGIdFromResources(List resources, String type) throws SQLException {
+ var identifiersOrgUrisStream = resources.stream()
+ .filter(registry::isValid)
+ .map(IdentifiersOrgURI::new)
+ .filter(registry::validRegistryUrlPrefix);
+
+ var resolvedIdentifiersOrgUrisStream = resources.stream()
+ .filter(r -> !registry.isValid(r))
+ .map(registry::resolveBackwards)
+ .filter(Optional::isPresent)
+ .map(Optional::get)
+ .filter(registry::validRegistryUrlPrefix);
+
+ var uris = Stream.concat(identifiersOrgUrisStream, resolvedIdentifiersOrgUrisStream).toList();
+ for (var uri : uris) {
+ if (registry.identifiesBiGG(uri.getPrefix())) {
+ return Optional.of(new BiGGId(uri.getId()));
+ } else {
+ var biggId = getBiggIdFromParts(uri, type);
+ if (biggId.isPresent()) {
+ return biggId;
+ }
+ }
+ }
+ return Optional.empty();
+ }
+
+ /**
+ * Attempts to retrieve a BiGG identifier from the BiGG Knowledgebase using a given prefix and identifier. This method
+ * is used for specific biological entities such as species, reactions, or gene products.
+ *
+ * @param type The type of biological entity for which the ID is being retrieved. Valid types are defined in
+ * {@link BiGGDBContract.Constants} and include TYPE_SPECIES, TYPE_REACTION, and TYPE_GENE_PRODUCT.
+ * @return An {@link Optional} containing the BiGG ID if found, otherwise {@link Optional#empty()}.
+ */
+ private Optional getBiggIdFromParts(RegistryURI uri, String type) throws SQLException {
+ if (bigg.isDataSource(uri.getPrefix())) {
+ Optional id = bigg.getBiggIdFromSynonym(uri.getPrefix(), uri.getId(), type);
+ if (id.isPresent()) {
+ return id;
+ }
+ }
+ return Optional.empty();
+ }
+
+}
\ No newline at end of file
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGAnnotationException.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGAnnotationException.java
new file mode 100644
index 00000000..de8348f2
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGAnnotationException.java
@@ -0,0 +1,17 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.uni_halle.informatik.biodata.mp.annotation.AnnotationException;
+
+public class BiGGAnnotationException extends AnnotationException {
+
+ private final Object data;
+
+ public BiGGAnnotationException(String msg, Exception e, Object o) {
+ super(msg, e);
+ this.data = o;
+ }
+
+ public Object data() {
+ return data;
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGCVTermAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGCVTermAnnotator.java
new file mode 100644
index 00000000..e6e2fc1a
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGCVTermAnnotator.java
@@ -0,0 +1,124 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import org.sbml.jsbml.*;
+
+import java.sql.SQLException;
+import java.util.List;
+
+/**
+ * Abstract class providing a framework for annotating SBML elements with Controlled Vocabulary (CV) Terms.
+ * This class defines the basic structure and operations for adding annotations to SBML elements based on BiGG IDs.
+ * It includes methods to check the validity of BiGG IDs, add annotations to SBML elements, and specifically handle
+ * annotations for Species and Reactions using data from BiGG and other databases.
+ */
+public abstract class BiGGCVTermAnnotator extends AbstractBiGGAnnotator {
+
+ public BiGGCVTermAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry) {
+ super(bigg, parameters, registry);
+ }
+
+ public BiGGCVTermAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ }
+
+
+ /**
+ * Abstract method to check the validity of a BiGG ID. Implementations should return an Optional containing
+ * the BiGG ID if it is valid, or an empty Optional if not.
+ *
+ * @return Optional containing the valid BiGG ID or empty if the ID is invalid.
+ */
+ protected abstract BiGGId findBiGGId(T element) throws SQLException;
+
+// /**
+// * Adds annotations to an SBML node (either a Species or a Reaction) using a given BiGGId.
+// * This method first checks if the node is an instance of Species or Reaction and throws an IllegalArgumentException if not.
+// * It then removes any existing CVTerm with the qualifier BQB_IS, prepares a new CVTerm if none existed,
+// * and collects annotations from various sources (BiGG database, AnnotateDB) based on whether the node is a Species or Reaction.
+// * These annotations are filtered to remove any that already exist on the node, sorted, and then added to the node.
+// * Finally, it ensures that the node has a metaId set if it has any CVTerms.
+// *
+// * @param node The SBML node to annotate, which should be either a Species or a Reaction.
+// * @param biggId The BiGGId used for fetching annotations.
+// * @throws IllegalArgumentException If the node is neither a Species nor a Reaction.
+// */
+// void addAnnotations(T node, BiGGId biggId) throws IllegalArgumentException {
+//
+// // TODO: ???
+// CVTerm cvTerm = null;
+// for (CVTerm term : node.getAnnotation().getListOfCVTerms()) {
+// if (term.getQualifier() == Qualifier.BQB_IS) {
+// cvTerm = term;
+// node.removeCVTerm(term);
+// break;
+// }
+// }
+// if (cvTerm == null) {
+// cvTerm = new CVTerm(Qualifier.BQB_IS);
+// }
+//
+// Set annotations = new HashSet<>();
+//
+// if (node instanceof Reaction) {
+// boolean isBiGGReaction = MemorizedQuery.isReaction(biggId.getAbbreviation());
+// // using BiGG Database
+// if (isBiGGReaction) {
+// annotations.add(new IdentifiersOrgURI("bigg.reaction", biggId).getURI());
+//
+// Set biggAnnotations = bigg.getResources(biggId, parameters.includeAnyURI(), true)
+// .stream()
+// .map(IdentifiersOrgURI::getURI)
+// .collect(Collectors.toSet());
+// annotations.addAll(biggAnnotations);
+//
+// // using AnnotateDB
+// if (MemorizedQuery.isReaction(biggId.getAbbreviation()) && adb != null) {
+// Set adbAnnotations = AnnotateDB.getAnnotations(BIGG_REACTION, biggId.toBiGGId());
+// annotations.addAll(adbAnnotations);
+// }
+// }
+//
+//
+// } else {
+// boolean isBiGGMetabolite = MemorizedQuery.isMetabolite(biggId.getAbbreviation());
+// // using BiGG Database
+// if (isBiGGMetabolite) {
+// annotations.add(new IdentifiersOrgURI("bigg.metabolite", biggId).getURI());
+//
+// Set biggAnnotations = bigg.getResources(biggId, parameters.includeAnyURI(), false)
+// .stream().map(IdentifiersOrgURI::getURI).collect(Collectors.toSet());
+// annotations.addAll(biggAnnotations);
+//
+// // using AnnotateDB
+// if (adb != null) {
+// Set adb_annotations = AnnotateDB.getAnnotations(BIGG_METABOLITE, biggId.toBiGGId());
+// annotations.addAll(adb_annotations);
+// }
+// }
+//
+// }
+// // don't add resources that are already present
+// Set existingAnnotations =
+// cvTerm.getResources().stream()
+// .map(resource -> resource.replaceAll("http://identifiers.org", "https://identifiers.org"))
+// .collect(Collectors.toSet());
+// annotations.removeAll(existingAnnotations);
+// // adding annotations to cvTerm
+// List sortedAnnotations = new ArrayList<>(annotations);
+// Collections.sort(sortedAnnotations);
+// for (String annotation : sortedAnnotations) {
+// cvTerm.addResource(annotation);
+// }
+// if (cvTerm.getResourceCount() > 0) {
+// node.addCVTerm(cvTerm);
+// }
+// if ((node.getCVTermCount() > 0) && !node.isSetMetaId()) {
+// node.setMetaId(node.getId());
+// }
+// }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGCompartmentsAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGCompartmentsAnnotator.java
new file mode 100644
index 00000000..faddae0f
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGCompartmentsAnnotator.java
@@ -0,0 +1,58 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import org.sbml.jsbml.*;
+
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+
+import java.sql.SQLException;
+import java.util.List;
+
+/**
+ * This class is responsible for annotating a specific compartment within an SBML model using data from the BiGG database.
+ * It allows for the addition of both BiGG and SBO annotations to a compartment, and can also set the compartment's name
+ * based on information retrieved from the BiGG database.
+ */
+public class BiGGCompartmentsAnnotator extends AbstractBiGGAnnotator implements IAnnotateSBases {
+
+
+ public BiGGCompartmentsAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry) {
+ super(bigg, parameters, registry);
+ }
+
+ public BiGGCompartmentsAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ }
+
+ @Override
+ public void annotate(List compartments) throws SQLException {
+ for (Compartment compartment : compartments) {
+ statusReport("Annotating Compartments (2/5) ", compartment);
+ annotate(compartment);
+ }
+ }
+
+ /**
+ * Annotates the compartment with BiGG and SBO terms. If the compartment's name is not set or is set to "default",
+ * it updates the name based on the BiGG database. This method only processes compartments that are recognized
+ * within the BiGG Knowledgebase.
+ */
+ @Override
+ public void annotate(Compartment compartment) throws SQLException {
+ BiGGId biggId = new BiGGId(compartment.getId());
+ if (bigg.isCompartment(biggId.getAbbreviation())) {
+ compartment.addCVTerm(
+ new CVTerm(CVTerm.Qualifier.BQB_IS,
+ new IdentifiersOrgURI("bigg.compartment", biggId).getURI()));
+ compartment.setSBOTerm(SBO.getCompartment()); // physical compartment
+ if (!compartment.isSetName() || compartment.getName().equals("default")) {
+ bigg.getCompartmentName(biggId).ifPresent(compartment::setName);
+ }
+ }
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGDocumentNotesProcessor.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGDocumentNotesProcessor.java
new file mode 100644
index 00000000..dcdec85d
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGDocumentNotesProcessor.java
@@ -0,0 +1,153 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.zbit.util.ResourceManager;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+
+import javax.xml.stream.XMLStreamException;
+import java.io.*;
+import java.sql.SQLException;
+import java.util.*;
+
+import static java.text.MessageFormat.format;
+
+public class BiGGDocumentNotesProcessor {
+
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.BIGG_ANNOTATION_MESSAGES);
+
+ private final BiGGAnnotationParameters parameters;
+ private final BiGGDB bigg;
+
+ public BiGGDocumentNotesProcessor(BiGGDB bigg, BiGGAnnotationParameters parameters) {
+ this.parameters = parameters;
+ this.bigg = bigg;
+ }
+
+
+ public void processNotes(SBMLDocument doc) throws BiGGAnnotationException, SQLException {
+ var model = doc.getModel();
+ try {
+ // Process replacements for placeholders in the model notes
+ Map replacements = processReplacements(model);
+ appendNotes(doc, replacements);
+ } catch (IOException | XMLStreamException e) {
+ throw new BiGGAnnotationException(MESSAGES.getString("FAILED_WRITE_NOTES"), e, doc);
+ }
+ }
+
+
+ /**
+ * Processes and replaces placeholders in the document title pattern and model notes with actual values from the model.
+ * This method retrieves the model ID and organism information from the BiGG database, and uses these along with
+ * other parameters to populate a map of replacements. These replacements are used later to substitute placeholders
+ * in the SBMLDocument notes.
+ *
+ * @return A map of placeholder strings and their corresponding replacement values.
+ */
+ private Map processReplacements(Model model) throws SQLException {
+ // Retrieve the model ID
+ String id = model.getId();
+ // Attempt to retrieve the organism name associated with the model ID; use an empty string if not available
+ String organism = bigg.getOrganism(id).orElse("");
+ // Retrieve and process the document title pattern by replacing placeholders
+ String name = parameters.documentTitlePattern();
+ name = name.replace("[biggId]", id);
+ name = name.replace("[organism]", organism);
+ // Initialize a map to hold the replacement values
+ Map replacements = new HashMap<>();
+ replacements.put("${organism}", organism);
+ replacements.put("${title}", name);
+ replacements.put("${bigg_id}", id);
+ replacements.put("${year}", Integer.toString(Calendar.getInstance().get(Calendar.YEAR)));
+ replacements.put("${bigg.timestamp}", bigg.getBiGGVersion().map(date -> format("{0,date}", date)).orElse(""));
+ replacements.put("${species_table}", "");
+ return replacements;
+ }
+
+
+ /**
+ * This method appends notes to the SBMLDocument and its model by replacing placeholders in the notes files.
+ * It handles both model-specific notes and document-wide notes.
+ *
+ * @param doc The SBMLDocument to which the notes will be appended.
+ * @param replacements A map containing the placeholder text and their replacements.
+ * @throws IOException If there is an error reading the notes files or writing to the document.
+ * @throws XMLStreamException If there is an error processing the XML content of the notes.
+ */
+ private void appendNotes(SBMLDocument doc, Map replacements) throws IOException, XMLStreamException {
+ String modelNotesFile = "ModelNotes.html";
+ String documentNotesFile = "SBMLDocumentNotes.html";
+
+ // Determine the files to use for model and document notes based on user settings
+ if (parameters.notesParameters().noModelNotes()) {
+ modelNotesFile = null;
+ documentNotesFile = null;
+ } else {
+ if (parameters.notesParameters().modelNotesFile() != null) {
+ File modelNotes = parameters.notesParameters().modelNotesFile();
+ modelNotesFile = modelNotes != null ? modelNotes.getAbsolutePath() : null;
+ }
+ if (parameters.notesParameters().documentNotesFile() != null) {
+ File documentNotes = parameters.notesParameters().documentNotesFile();
+ documentNotesFile = documentNotes != null ? documentNotes.getAbsolutePath() : null;
+ }
+ }
+
+ // Append document notes if the title placeholder is present and the notes file is specified
+ if (replacements.containsKey("${title}") && (documentNotesFile != null)) {
+ doc.appendNotes(parseNotes(documentNotesFile, replacements));
+ }
+
+ // Append model notes if the notes file is specified
+ if (modelNotesFile != null) {
+ doc.getModel().appendNotes(parseNotes(modelNotesFile, replacements));
+ }
+ }
+
+
+ /**
+ * Parses the notes from a specified location and replaces placeholder tokens with actual values.
+ * This method first attempts to read the resource from the classpath. If the resource is not found,
+ * it falls back to reading from the filesystem. It processes the content line by line, starting to
+ * append lines to the result after encountering a `` tag and stopping after a `` tag.
+ * Any placeholders in the format `${placeholder}` found within the body are replaced with corresponding
+ * values provided in the `replacements` map.
+ *
+ * @param location The relative path to the resource from this class.
+ * @param replacements A map of placeholder tokens to their actual values to be replaced in the notes.
+ * @return A string containing the processed notes with placeholders replaced by actual values.
+ * @throws IOException If an I/O error occurs while reading the file.
+ */
+ private String parseNotes(String location, Map replacements) throws IOException {
+ StringBuilder sb = new StringBuilder();
+ try (InputStream is = getClass().getResourceAsStream(location);
+ InputStreamReader isReader = new InputStreamReader((is != null) ? is : new FileInputStream(location));
+ BufferedReader br = new BufferedReader(isReader)) {
+ String line;
+ boolean start = false;
+ while (br.ready() && ((line = br.readLine()) != null)) {
+ if (line.matches("\\s* {
+
+ public static final String REF_SEQ_ACCESSION_NUMBER_PATTERN = "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$";
+ public static final String GENOME_ASSEMBLY_ID_PATTERN = "^GC[AF]_[0-9]{9}\\.[0-9]+$";
+
+ public BiGGModelAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry) {
+ super(bigg, parameters, registry);
+ }
+ public BiGGModelAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ }
+
+
+ /**
+ * Annotates the {@link Model} with relevant metadata and delegates the annotation of contained elements such as
+ * {@link Compartment}, {@link Species}, {@link Reaction}, and {@link GeneProduct}.
+ *
+ * Steps:
+ * 1. Retrieves the model's ID and uses it to fetch and add a taxonomy annotation if available.
+ * 2. Checks if the model exists in the database and adds specific BiGG database annotations.
+ * 3. Sets the model's MetaId to its ID if MetaId is not already set and the model has at least one CVTerm.
+ */
+ @Override
+ public void annotate(Model model) throws SQLException {
+ // Retrieve the model ID
+ String id = model.getId();
+ // Attempt to retrieve the organism name associated with the model ID; use an empty string if not available
+ String organism = bigg.getOrganism(id).orElse("");
+ if (!model.isSetName()) {
+ model.setName(organism);
+ }
+
+ addTaxonomyAnnotation(model, model.getId());
+
+ // annotation indicating the model's identity within BiGG
+ model.addCVTerm(
+ new CVTerm(CVTerm.Qualifier.BQM_IS,
+ new IdentifiersOrgURI("bigg.model", model.getId()).getURI()));
+
+ // Retrieve the genomic accession number for the model
+ String accession = bigg.getGenomeAccesion(model.getId());
+ addNCBIReferenceAnnotation(model, accession);
+
+ // Set the model's MetaId to its ID if MetaId is not set and there are existing CVTerms
+ if (!model.isSetMetaId() && (model.getCVTermCount() > 0)) {
+ model.setMetaId(model.getId());
+ }
+ }
+
+
+ private void addTaxonomyAnnotation(Model model, String modelId) throws SQLException {
+ // Attempt to fetch and add a taxonomy annotation using the model's ID
+ bigg.getTaxonId(modelId).ifPresent(
+ taxonId -> model.addCVTerm(
+ new CVTerm(CVTerm.Qualifier.BQB_HAS_TAXON,
+ new IdentifiersOrgURI("taxonomy", taxonId).getURI())));
+ }
+
+
+ private void addNCBIReferenceAnnotation(Model model, String accession) {
+ // Prepare a pattern matcher for RefSeq accession numbers
+ Matcher refseqMatcher = Pattern.compile(REF_SEQ_ACCESSION_NUMBER_PATTERN).matcher(accession);
+ // Create a CVTerm for versioning annotation
+ CVTerm term = new CVTerm(CVTerm.Qualifier.BQB_IS_VERSION_OF);
+ // Check if the accession matches the RefSeq pattern
+ if (refseqMatcher.matches()) {
+ // Add a RefSeq resource to the CVTerm
+ term.addResource(new IdentifiersOrgURI("refseq", accession).getURI());
+ } else {
+ // Check if non-MIRIAM URIs are allowed
+ if (biGGAnnotationParameters.includeAnyURI()) {
+ // Prepare a pattern matcher for genome assembly accession numbers
+ Matcher genomeAssemblyMatcher = Pattern.compile(GENOME_ASSEMBLY_ID_PATTERN).matcher(accession);
+ if (genomeAssemblyMatcher.matches()) {
+ // Add a genome assembly resource to the CVTerm, resolving non-MIRIAM way due to known issues
+ term.addResource("https://www.ncbi.nlm.nih.gov/assembly/" + accession);
+ } else {
+ // Add a nucleotide resource to the CVTerm for other cases
+ term.addResource("https://www.ncbi.nlm.nih.gov/nuccore/" + accession);
+ }
+ }
+ }
+ // Add the CVTerm to the model if it contains any resources
+ if (term.getResourceCount() > 0) {
+ model.addCVTerm(term);
+ }
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGPublicationsAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGPublicationsAnnotator.java
new file mode 100644
index 00000000..2c30ca53
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGPublicationsAnnotator.java
@@ -0,0 +1,36 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.Publication;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.Model;
+
+import java.sql.SQLException;
+import java.util.List;
+
+public class BiGGPublicationsAnnotator extends AbstractBiGGAnnotator implements IAnnotateSBases {
+
+ public BiGGPublicationsAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+
+ }
+
+ @Override
+ public void annotate(Model model) throws SQLException {
+ List publications = bigg.getPublications(model.getId());
+ statusReport("Annotating Publications (1/5) ", model);
+
+ String[] resources = publications.stream()
+ .map(publication -> new IdentifiersOrgURI(publication.referenceType(), publication.referenceId()))
+ .map(IdentifiersOrgURI::getURI)
+ .toArray(String[]::new);
+
+ model.addCVTerm(new CVTerm(CVTerm.Qualifier.BQM_IS_DESCRIBED_BY, resources));
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGReactionsAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGReactionsAnnotator.java
new file mode 100644
index 00000000..828be5b9
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGReactionsAnnotator.java
@@ -0,0 +1,309 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.zbit.util.ResourceManager;
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.parameters.SBOParameters;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI;
+import de.uni_halle.informatik.biodata.mp.util.ext.fbc.GPRParser;
+import de.uni_halle.informatik.biodata.mp.util.ext.groups.GroupsUtils;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.CVTerm.Qualifier;
+import org.sbml.jsbml.Compartment;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Reaction;
+import org.sbml.jsbml.ext.groups.Group;
+import org.sbml.jsbml.ext.groups.GroupsConstants;
+import org.sbml.jsbml.ext.groups.GroupsModelPlugin;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+/**
+ * This class provides functionality to annotate a reaction in an SBML model using BiGG database identifiers.
+ * It extends the {@link BiGGCVTermAnnotator} class, allowing it to manage controlled vocabulary (CV) terms
+ * associated with the reaction. The class handles various aspects of reaction annotation including setting
+ * the reaction's name, SBO term, and additional annotations. It also processes gene reaction rules and
+ * subsystem information associated with the reaction.
+ */
+public class BiGGReactionsAnnotator extends BiGGCVTermAnnotator implements IAnnotateSBases {
+
+ private static final Logger logger = LoggerFactory.getLogger(BiGGReactionsAnnotator.class);
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.BIGG_ANNOTATION_MESSAGES);
+
+ private static boolean triggeredSubsystemWarning = false;
+
+ private final SBOParameters sboParameters;
+
+ public BiGGReactionsAnnotator(BiGGDB bigg, BiGGAnnotationParameters biGGAnnotationParameters, SBOParameters sboParameters, Registry registry) {
+ super(bigg, biGGAnnotationParameters, registry);
+ this.sboParameters = sboParameters;
+ }
+
+ public BiGGReactionsAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ this.sboParameters = sboParameters;
+ }
+
+
+ /**
+ * Delegates the annotation process for each reaction in the given SBML model.
+ * This method iterates over all reactions in the model, updates the progress display,
+ * and invokes the annotation for each reaction.
+ */
+ @Override
+ public void annotate(List reactions) throws SQLException {
+ for (Reaction reaction : reactions) {
+ annotate(reaction);
+ }
+ }
+
+ /**
+ * Annotates a reaction by setting its name, SBO term, and additional annotations. It also processes gene reaction rules
+ * and subsystem information associated with the reaction. This method retrieves a BiGG ID for the reaction, either from
+ * the reaction's ID directly or through associated annotations. If a valid BiGG ID is found, it proceeds with the
+ * annotation and parsing processes.
+ */
+ @Override
+ public void annotate(Reaction reaction) throws SQLException {
+ statusReport("Annotating Reactions (4/5) ", reaction);
+ // Attempt to retrieve a BiGG ID for the reaction, either directly from the reaction ID or through associated annotations
+ var biggId = findBiGGId(reaction);
+ setName(reaction, biggId); // Set the reaction's name based on the BiGG ID
+ setSBOTerm(reaction, biggId); // Assign the appropriate SBO term based on the BiGG ID
+ addAnnotations(reaction, biggId); // Add additional annotations related to the BiGG ID
+ parseGeneReactionRules(reaction, biggId); // Parse and process gene reaction rules associated with the BiGG ID
+ parseSubsystems(reaction, biggId); // Convert subsystem information into corresponding groups based on the BiGG ID
+ }
+
+ /**
+ * This method checks if the ID of the reaction is a valid BiGG ID and attempts to retrieve a corresponding
+ * BiGG ID based on existing annotations. It first checks if the reaction ID matches the expected BiGG ID format
+ * and verifies its existence in the database. If the ID does not match or is not found, it then attempts to
+ * extract a BiGG ID from the reaction's annotations. This involves parsing the CVTerms associated with the reaction,
+ * extracting URLs, validating them, and then querying the BiGG database for corresponding reaction IDs that match
+ * the reaction's compartment.
+ *
+ * @return An {@link Optional} containing the BiGG ID if found or created successfully, otherwise {@link Optional#empty()}
+ */
+ @Override
+ public BiGGId findBiGGId(Reaction reaction) throws SQLException {
+ String id = reaction.getId();
+ // Check if the reaction ID matches the expected BiGG ID format and exists in the database
+ boolean isBiGGid = bigg.isReaction(id);
+ if (!isBiGGid) {
+ // Extract BiGG IDs from annotations if the direct ID check fails
+ var ids = reaction.getAnnotation().getListOfCVTerms()
+ .stream()
+ .filter(cvTerm -> cvTerm.getQualifier() == Qualifier.BQB_IS)
+ .flatMap(term -> term.getResources().stream())
+ .map(registry::resolveBackwards)
+ .flatMap(Optional::stream)
+ .map(bigg::getBiggIdsForReactionForeignId)
+ .flatMap(Collection::stream)
+ .filter(foreignReaction -> matchingCompartments(reaction, foreignReaction))
+ .map(fr -> fr.reactionId)
+ .collect(Collectors.toSet());
+ // Select the first valid ID from the set, if available
+ id = ids.stream()
+ .findFirst()
+ .orElse(id);
+ }
+ return BiGGId.createReactionId(id);
+ }
+
+ /**
+ * Determines if the reaction's compartment matches the compartment information of a foreign reaction from the BiGG database.
+ *
+ * This method checks various conditions to ensure that the compartments are correctly matched:
+ * 1. If the reaction does not have a compartment set and the foreign reaction also lacks compartment details, it returns true.
+ * 2. If the reaction does not have a compartment set but the foreign reaction does, it returns false.
+ * 3. If the reaction has a compartment set, it checks if the compartment ID matches the foreign reaction's compartment ID.
+ * 4. If the reaction has a named compartment instance set, it checks if the name matches the foreign reaction's compartment name.
+ *
+ * @param foreignReaction The foreign reaction object containing compartment details to compare against the reaction.
+ * @return true if the compartments match according to the conditions above, false otherwise.
+ */
+ private boolean matchingCompartments(Reaction reaction, BiGGDB.ForeignReaction foreignReaction) {
+ if (!reaction.isSetCompartment()
+ && null == foreignReaction.compartmentId
+ && null == foreignReaction.compartmentName) {
+ return true;
+ } else if (!reaction.isSetCompartment()
+ && (null != foreignReaction.compartmentId
+ || null != foreignReaction.compartmentName)) {
+ return false;
+ } else if (reaction.isSetCompartmentInstance()
+ && reaction.getCompartmentInstance().isSetName()
+ && foreignReaction.compartmentName != null) {
+ String reactionCompartmentName = reaction.getCompartmentInstance().getName().toLowerCase();
+ String foreignReactionCompartmentName = foreignReaction.compartmentName.toLowerCase();
+ return reactionCompartmentName.equals(foreignReactionCompartmentName)
+ || reactionCompartmentName.contains(foreignReactionCompartmentName)
+ || foreignReactionCompartmentName.contains(reactionCompartmentName);
+ } else if (reaction.isSetCompartment()) {
+ return reaction.getCompartment().equals(foreignReaction.compartmentId);
+ }
+ else
+ return false;
+ }
+
+ /**
+ * Sets the name of the reaction based on the provided BiGGId. It retrieves the reaction name
+ * using the abbreviation from the BiGGId, polishes the name, and updates the reaction's name
+ * if the new name is different from the current name.
+ *
+ * @param biggId The BiGGId object containing the abbreviation used to fetch and potentially update the reaction's name.
+ */
+ public void setName(Reaction reaction, BiGGId biggId) throws SQLException {
+ String abbreviation = biggId.getAbbreviation();
+ bigg.getReactionName(abbreviation).ifPresent(reaction::setName);
+ }
+
+ /**
+ * Sets the SBO term for a reaction based on the given BiGGId.
+ * If the reaction does not already have an SBO term set, it determines the appropriate SBO term
+ * based on whether the reaction is a pseudoreaction or a generic process. Pseudoreactions are assigned
+ * an SBO term of 631, while generic processes are assigned an SBO term of 375 unless the configuration
+ * specifies to omit generic terms.
+ *
+ * @param biggId The BiGGId object containing the abbreviation used to check if the reaction is a pseudoreaction.
+ */
+ public void setSBOTerm(Reaction reaction, BiGGId biggId) throws SQLException {
+ String abbreviation = biggId.getAbbreviation();
+ if (!reaction.isSetSBOTerm()) {
+ if (bigg.isPseudoreaction(abbreviation)) {
+ reaction.setSBOTerm(631);
+ }
+ }
+ }
+
+ void addAnnotations(Reaction node, BiGGId biggId) throws SQLException {
+ CVTerm cvTerm = null;
+ for (CVTerm term : node.getAnnotation().getListOfCVTerms()) {
+ if (term.getQualifier() == Qualifier.BQB_IS) {
+ cvTerm = term;
+ node.removeCVTerm(term);
+ break;
+ }
+ }
+ if (cvTerm == null) {
+ cvTerm = new CVTerm(Qualifier.BQB_IS);
+ }
+
+ Set annotations = new HashSet<>();
+ boolean isBiGGReaction = bigg.isReaction(biggId.getAbbreviation());
+ // using BiGG Database
+ if (isBiGGReaction) {
+ annotations.add(new IdentifiersOrgURI("bigg.reaction", biggId).getURI());
+
+ Set biggAnnotations = bigg.getResources(biggId, biGGAnnotationParameters.includeAnyURI(), true)
+ .stream()
+ .map(IdentifiersOrgURI::getURI)
+ .collect(Collectors.toSet());
+ annotations.addAll(biggAnnotations);
+ }
+
+
+ // don't add resources that are already present
+ Set existingAnnotations =
+ cvTerm.getResources().stream()
+ .map(resource -> resource.replaceAll("http://identifiers.org", "https://identifiers.org"))
+ .collect(Collectors.toSet());
+ annotations.removeAll(existingAnnotations);
+ // adding annotations to cvTerm
+ List sortedAnnotations = new ArrayList<>(annotations);
+ Collections.sort(sortedAnnotations);
+ for (String annotation : sortedAnnotations) {
+ cvTerm.addResource(annotation);
+ }
+ if (cvTerm.getResourceCount() > 0) {
+ node.addCVTerm(cvTerm);
+ }
+ if ((node.getCVTermCount() > 0) && !node.isSetMetaId()) {
+ node.setMetaId(node.getId());
+ }
+ }
+
+ /**
+ * Parses gene reaction rules for a given reaction based on the BiGG database identifier.
+ * This method retrieves gene reaction rules associated with the reaction's abbreviation
+ * from the BiGG database and applies gene-protein-reaction (GPR) parsing to the reaction.
+ * It considers whether generic terms should be omitted based on the current parameters.
+ *
+ * @param biggId The BiGG database identifier for the reaction, used to fetch and parse gene reaction rules.
+ */
+ public void parseGeneReactionRules(Reaction reaction, BiGGId biggId) throws SQLException {
+ String abbreviation = biggId.getAbbreviation();
+ List geneReactionRules = bigg.getGeneReactionRule(abbreviation, reaction.getModel().getId());
+ for (String geneReactionRule : geneReactionRules) {
+ GPRParser.setGeneProductAssociation(reaction, geneReactionRule, sboParameters.addGenericTerms());
+ }
+ }
+
+
+ /**
+ * Retrieves subsystem information from the BiGG Knowledgebase and converts it into corresponding groups using the
+ * {@link GroupsModelPlugin}. It then links the reaction to the appropriate group based on the subsystem information.
+ * If the model is not from BiGG, it logs a warning and uses a different method to fetch subsystems.
+ * It also ensures that subsystems are unique by converting them to lowercase and removing duplicates.
+ * If multiple subsystems are found for a non-BiGG model, the method returns early to avoid ambiguity.
+ * Each subsystem is then either fetched from a cache or a new group is created and added to the model.
+ * Finally, the reaction is linked to the group.
+ *
+ * @param biggId the {@link BiGGId} associated with the reaction, used to fetch subsystem information
+ */
+ private void parseSubsystems(Reaction reaction, BiGGId biggId) throws SQLException {
+ Model model = reaction.getModel();
+ boolean isBiGGModel = bigg.isModel(model.getId());
+ List subsystems;
+ if (isBiGGModel) {
+ subsystems = bigg.getSubsystems(model.getId(), biggId.getAbbreviation());
+ } else {
+ if (!triggeredSubsystemWarning) {
+ triggeredSubsystemWarning = true;
+ logger.debug(MESSAGES.getString("SUBSYSTEM_MODEL_NOT_BIGG"));
+ }
+ subsystems = bigg.getSubsystemsForReaction(biggId.getAbbreviation());
+ }
+ if (subsystems.isEmpty()) {
+ return;
+ } else {
+ // filter out duplicates only differing in case - relevant for #getSubsystemsForReaction results
+ subsystems = subsystems.stream().map(String::toLowerCase).distinct().collect(Collectors.toList());
+ // Code already allows for multiple results from one query. If we have no BiGG model id, this might lead to
+ // ambiguous, incorrect results
+ if (!isBiGGModel && subsystems.size() > 1) {
+ return;
+ }
+ }
+ String groupKey = "GROUP_FOR_NAME";
+ if (model.getUserObject(groupKey) == null) {
+ model.putUserObject(groupKey, new HashMap());
+ }
+ @SuppressWarnings("unchecked")
+ Map groupForName = (Map) model.getUserObject(groupKey);
+ for (String subsystem : subsystems) {
+ Group group;
+ if (groupForName.containsKey(subsystem)) {
+ group = groupForName.get(subsystem);
+ } else {
+ GroupsModelPlugin groupsModelPlugin = (GroupsModelPlugin) model.getPlugin(GroupsConstants.shortLabel);
+ group = groupsModelPlugin.createGroup("g" + (groupsModelPlugin.getGroupCount() + 1));
+ group.setName(subsystem);
+ group.setKind(Group.Kind.partonomy);
+ group.setSBOTerm(633); // subsystem
+ groupForName.put(subsystem, group);
+ }
+ GroupsUtils.createSubsystemLink(reaction, group.createMember());
+ }
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSBMLAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSBMLAnnotator.java
new file mode 100644
index 00000000..3d3acb85
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSBMLAnnotator.java
@@ -0,0 +1,71 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import java.sql.SQLException;
+import java.util.List;
+
+import de.uni_halle.informatik.biodata.mp.annotation.AnnotationException;
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.parameters.SBOParameters;
+import de.uni_halle.informatik.biodata.mp.annotation.AnnotationsSorter;
+import de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc.BiGGFBCAnnotator;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.SBMLDocument;
+
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+
+
+/**
+ * This class is responsible for annotating SBML models using data from the BiGG database.
+ * It handles the addition of annotations related to compartments, species, reactions, and gene products.
+ *
+ * @author Thomas Zajac
+ * This code runs only, if ANNOTATE_WITH_BIGG is true
+ */
+public class BiGGSBMLAnnotator extends AbstractBiGGAnnotator implements IAnnotateSBases {
+
+ private final SBOParameters sboParameters;
+
+ public BiGGSBMLAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry) {
+ super(bigg, parameters, registry);
+ this.sboParameters = sboParameters;
+ }
+
+ public BiGGSBMLAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ this.sboParameters = sboParameters;
+ }
+
+
+ /**
+ * Annotates an SBMLDocument using data from the BiGG Knowledgebase. This method processes various components of the
+ * SBML model such as compartments, species, reactions, and gene products by adding relevant annotations from BiGG.
+ * It also handles the addition of publications and notes related to the model.
+ *
+ * @param doc The SBMLDocument that contains the model to be annotated.
+ */
+ @Override
+ public void annotate(SBMLDocument doc) throws SQLException, AnnotationException {
+ Model model = doc.getModel();
+
+ new BiGGModelAnnotator(bigg, biGGAnnotationParameters, registry, getObservers()).annotate(model);
+
+ // Annotate various components of the model
+ new BiGGPublicationsAnnotator(bigg, biGGAnnotationParameters, registry, getObservers()).annotate(model);
+
+ new BiGGCompartmentsAnnotator(bigg, biGGAnnotationParameters, registry, getObservers()).annotate(model.getListOfCompartments());
+
+ new BiGGSpeciesAnnotator(bigg, biGGAnnotationParameters, sboParameters, registry, getObservers()).annotate(model.getListOfSpecies());
+
+ new BiGGReactionsAnnotator(bigg, biGGAnnotationParameters, sboParameters, registry).annotate(model.getListOfReactions());
+
+ new BiGGFBCAnnotator(bigg, biGGAnnotationParameters, registry, getObservers()).annotate(model);
+
+ new BiGGDocumentNotesProcessor(bigg, biGGAnnotationParameters).processNotes(doc);
+
+ new AnnotationsSorter().groupAndSortAnnotations(doc);
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotator.java
new file mode 100644
index 00000000..c85df34a
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/BiGGSpeciesAnnotator.java
@@ -0,0 +1,163 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg;
+
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.parameters.SBOParameters;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI;
+import org.sbml.jsbml.*;
+import org.sbml.jsbml.CVTerm.Qualifier;
+
+import java.sql.SQLException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+import static de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.TYPE_SPECIES;
+import static java.text.MessageFormat.format;
+
+/**
+ * This class provides functionality to annotate a species in an SBML model using BiGG database identifiers.
+ * It extends the {@link BiGGCVTermAnnotator} class, allowing it to manage controlled vocabulary (CV) terms
+ * associated with the species. The class handles various aspects of species annotation including setting
+ * the species' name, SBO term, and additional annotations. It also sets the chemical formula and charge
+ * for the species using FBC (Flux Balance Constraints) extensions.
+ */
+public class BiGGSpeciesAnnotator extends BiGGCVTermAnnotator implements IAnnotateSBases {
+
+ private final SBOParameters sboParameters;
+
+ protected BiGGSpeciesAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry) {
+ super(bigg, parameters, registry);
+ this.sboParameters = sboParameters;
+ }
+ protected BiGGSpeciesAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, SBOParameters sboParameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ this.sboParameters = sboParameters;
+ }
+
+ /**
+ * Delegates annotation processing for all chemical species contained in the {@link Model}.
+ * This method iterates over each species in the model and applies specific annotations.
+ */
+ @Override
+ public void annotate(List species) throws SQLException {
+ for (Species s : species) {
+ statusReport("Annotating Species (3/5) ", s);
+ annotate(s);
+ }
+ }
+
+ /**
+ * This method annotates a species with various details fetched from the BiGG Knowledgebase. It performs the following:
+ * 1. Sets the species name based on the BiGGId. If the species does not have a name, it uses the BiGGId as the name.
+ * 2. Assigns an SBO (Systems Biology Ontology) term to the species based on the BiGGId.
+ * 3. Adds additional annotations to the species, such as database cross-references.
+ *
+ * The BiGGId used for these operations is either derived from the species' URI list or directly from its ID if available.
+ */
+ @Override
+ public void annotate(Species species) throws SQLException {
+ // Retrieve the BiGGId for the species, either from its URI list or its direct ID
+ var biGGId = findBiGGId(species);
+ setName(species, biGGId); // Set the species name based on the BiGGId
+ addAnnotations(species, biGGId); // Add database cross-references and other annotations
+ }
+
+
+ /**
+ * Validates the species ID and attempts to retrieve a corresponding BiGGId based on existing annotations.
+ * This method first tries to create a BiGGId from the species ID. If the species ID does not correspond to a known
+ * BiGGId in the database, it then searches through the species' annotations to find a valid BiGGId.
+ *
+ * @return An {@link Optional} containing the BiGGId if a valid one is found or created, otherwise {@link Optional#empty()}
+ */
+ @Override
+ public BiGGId findBiGGId(Species species) throws SQLException {
+ // Attempt to create a BiGGId from the species ID
+ var metaboliteId = BiGGId.createMetaboliteId(species.getId());
+
+ // Check if the created BiGGId is valid, if not, try to find a BiGGId from annotations
+ boolean isBiGGid = bigg.isMetabolite(metaboliteId.getAbbreviation());
+
+ if (!isBiGGid) {
+ // Collect all resources from CVTerms that qualify as BQB_IS
+ // Attempt to retrieve a BiGGId from the collected resources
+ List resources = species.getAnnotation().getListOfCVTerms()
+ .stream()
+ .filter(cvTerm -> cvTerm.getQualifier() == Qualifier.BQB_IS)
+ .flatMap(term -> term.getResources().stream())
+ .toList();
+ var biggIdFromResources = getBiGGIdFromResources(resources, TYPE_SPECIES);
+ if (biggIdFromResources.isPresent()) {
+ return biggIdFromResources.get();
+ }
+ }
+ return metaboliteId;
+ }
+
+
+ /**
+ * Updates the name of the species based on data retrieved from the BiGG Knowledgebase.
+ * The species name is set only if it has not been previously set or if the current name
+ * follows a default format that combines the BiGGId abbreviation and
+ * compartment code. This method relies on the availability of a valid {@link BiGGId} for the species.
+ *
+ * @param biggId The {@link BiGGId} associated with the species, used to fetch the component name from the BiGG database.
+ */
+ public void setName(Species species, BiGGId biggId) throws SQLException {
+ if (!species.isSetName()
+ || species.getName().equals(format("{0}_{1}", biggId.getAbbreviation(), biggId.getCompartmentCode()))) {
+ bigg.getComponentName(biggId).ifPresent(species::setName);
+ }
+ }
+
+
+ void addAnnotations(Species species, BiGGId biggId) throws IllegalArgumentException, SQLException {
+
+ CVTerm cvTerm = null;
+ for (CVTerm term : species.getAnnotation().getListOfCVTerms()) {
+ if (term.getQualifier() == Qualifier.BQB_IS) {
+ cvTerm = term;
+ species.removeCVTerm(term);
+ break;
+ }
+ }
+ if (cvTerm == null) {
+ cvTerm = new CVTerm(Qualifier.BQB_IS);
+ }
+
+ Set annotations = new HashSet<>();
+
+ boolean isBiGGMetabolite = bigg.isMetabolite(biggId.getAbbreviation());
+ // using BiGG Database
+ if (isBiGGMetabolite) {
+ if (cvTerm.getResources().stream().noneMatch(resource -> resource.contains("bigg.metabolite"))) {
+ annotations.add(new IdentifiersOrgURI("bigg.metabolite", biggId).getURI());
+ }
+ Set biggAnnotations = bigg.getResources(biggId, biGGAnnotationParameters.includeAnyURI(), false)
+ .stream()
+ .map(IdentifiersOrgURI::getURI)
+ .collect(Collectors.toSet());
+ annotations.addAll(biggAnnotations);
+ }
+
+ // don't add resources that are already present
+ annotations.removeAll(new HashSet<>(cvTerm.getResources()));
+ // adding annotations to cvTerm
+ List sortedAnnotations = new ArrayList<>(annotations);
+ Collections.sort(sortedAnnotations);
+ for (String annotation : sortedAnnotations) {
+ cvTerm.addResource(annotation);
+ }
+ if (cvTerm.getResourceCount() > 0) {
+ species.addCVTerm(cvTerm);
+ }
+ if ((species.getCVTermCount() > 0) && !species.isSetMetaId()) {
+ species.setMetaId(species.getId());
+ }
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGFBCAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGFBCAnnotator.java
new file mode 100644
index 00000000..cfc9d65f
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGFBCAnnotator.java
@@ -0,0 +1,38 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc;
+
+import de.uni_halle.informatik.biodata.mp.annotation.AnnotationException;
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.fbc.FBCConstants;
+import org.sbml.jsbml.ext.fbc.FBCModelPlugin;
+
+import java.sql.SQLException;
+import java.util.List;
+
+public class BiGGFBCAnnotator extends AbstractBiGGAnnotator implements IAnnotateSBases {
+
+ public BiGGFBCAnnotator(BiGGDB bigg, BiGGAnnotationParameters parameters, Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ }
+
+ @Override
+ public void annotate(Model model) throws SQLException, AnnotationException {
+// // Calculate the change in the number of gene products to update the progress bar accordingly
+// int changed = fbcModelPlugin.getNumGeneProducts() - initialGeneProducts;
+// if (changed > 0) {
+// long current = progress.getCallNumber();
+// // Adjust the total number of calls for the progress bar by subtracting the placeholder count
+// progress.setNumberOfTotalCalls(progress.getNumberOfTotalCalls() + changed - 50);
+// progress.setCallNr(current);
+// }
+ FBCModelPlugin fbcModelPlugin = (FBCModelPlugin) model.getPlugin(FBCConstants.shortLabel);
+ new BiGGFBCSpeciesAnnotator(bigg, biGGAnnotationParameters, registry).annotate(model.getListOfSpecies());
+ new BiGGGeneProductAnnotator(new BiGGGeneProductReferencesAnnotator(), bigg, biGGAnnotationParameters, registry, getObservers())
+ .annotate(fbcModelPlugin.getListOfGeneProducts());
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGFBCSpeciesAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGFBCSpeciesAnnotator.java
new file mode 100644
index 00000000..f0b205b0
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGFBCSpeciesAnnotator.java
@@ -0,0 +1,122 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc;
+
+import de.zbit.util.ResourceManager;
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.annotation.bigg.AbstractBiGGAnnotator;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.Species;
+import org.sbml.jsbml.ext.fbc.FBCConstants;
+import org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin;
+import org.sbml.jsbml.validator.SyntaxChecker;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.Optional;
+import java.util.ResourceBundle;
+
+import static de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.TYPE_SPECIES;
+import static java.text.MessageFormat.format;
+
+public class BiGGFBCSpeciesAnnotator extends AbstractBiGGAnnotator implements IAnnotateSBases {
+
+ private static final Logger logger = LoggerFactory.getLogger(BiGGFBCSpeciesAnnotator.class);
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.BIGG_ANNOTATION_MESSAGES);
+
+
+ public BiGGFBCSpeciesAnnotator(BiGGDB bigg, BiGGAnnotationParameters biGGAnnotationParameters, Registry registry) {
+ super(bigg, biGGAnnotationParameters, registry);
+ }
+
+ @Override
+ public void annotate(Species species) throws SQLException {
+ var biGGId = findBiGGId(species);
+ setFormulaFromBiGGId(species, biGGId); // Set the chemical formula and charge
+
+ setCharge(species, biGGId);
+
+ }
+
+ public BiGGId findBiGGId(Species species) throws SQLException {
+ // Attempt to create a BiGGId from the species ID
+ var metaboliteId = BiGGId.createMetaboliteId(species.getId());
+
+ // Check if the created BiGGId is valid, if not, try to find a BiGGId from annotations
+ boolean isBiGGid = bigg.isMetabolite(metaboliteId.getAbbreviation());
+
+ if (!isBiGGid) {
+ // Collect all resources from CVTerms that qualify as BQB_IS
+ // Attempt to retrieve a BiGGId from the collected resources
+ var biggIdFromResources = getBiGGIdFromResources(
+ species.getAnnotation().getListOfCVTerms()
+ .stream()
+ .filter(cvTerm -> cvTerm.getQualifier() == CVTerm.Qualifier.BQB_IS)
+ .flatMap(term -> term.getResources().stream())
+ .toList(),
+ TYPE_SPECIES);
+ if (biggIdFromResources.isPresent()) {
+ return biggIdFromResources.get();
+ }
+ }
+ return metaboliteId;
+ }
+
+ /**
+ * Sets the chemical formula and charge for a species based on the provided BiGGId.
+ * This method first checks if the species belongs to a BiGG model and retrieves the compartment code.
+ * It then attempts to set the chemical formula if it has not been set already. The formula is fetched
+ * from the BiGG database either based on the model ID or the compartment code if the model ID fetch fails.
+ * If the formula is successfully retrieved, it is set using the FBCSpeciesPlugin.
+ * Similarly, the charge is fetched and set if the species does not already have a charge set.
+ * If a charge is fetched and if it contradicts an existing charge, log a warning and unset the existing charge.
+ *
+ * @param biggId: {@link BiGGId} from species id
+ */
+ private void setFormulaFromBiGGId(Species species, BiGGId biggId) throws SQLException {
+ boolean isBiGGModel = species.getModel() !=null && bigg.isModel(species.getModel().getId());
+
+ String compartmentCode = biggId.getCompartmentCode();
+ var fbcSpecPlug = (FBCSpeciesPlugin) species.getPlugin(FBCConstants.shortLabel);
+
+ boolean compartmentNonEmpty = compartmentCode != null && !compartmentCode.isEmpty();
+ if (!fbcSpecPlug.isSetChemicalFormula()) {
+ Optional chemicalFormula = Optional.empty();
+ if (isBiGGModel) {
+ chemicalFormula = bigg.getChemicalFormula(biggId.getAbbreviation(), species.getModel().getId());
+ }
+ if ((!isBiGGModel || chemicalFormula.isEmpty()) && compartmentNonEmpty) {
+ chemicalFormula = bigg.getChemicalFormulaByCompartment(biggId.getAbbreviation(), compartmentCode);
+ }
+ chemicalFormula.filter(SyntaxChecker::isValidChemicalFormula).ifPresent(fbcSpecPlug::setChemicalFormula);
+ }
+ }
+
+ private void setCharge(Species species, BiGGId biggId) throws SQLException {
+ boolean isBiGGModel = species.getModel() !=null && bigg.isModel(species.getModel().getId());
+ String compartmentCode = biggId.getCompartmentCode();
+ boolean compartmentNonEmpty = compartmentCode != null && !compartmentCode.isEmpty();
+ var fbcSpecPlug = (FBCSpeciesPlugin) species.getPlugin(FBCConstants.shortLabel);
+
+ Optional chargeFromBiGG = Optional.empty();
+ if (isBiGGModel) {
+ chargeFromBiGG = bigg.getCharge(biggId.getAbbreviation(), species.getModel().getId());
+ } else if (compartmentNonEmpty) {
+ chargeFromBiGG = bigg.getChargeByCompartment(biggId.getAbbreviation(), biggId.getCompartmentCode());
+ }
+ if (fbcSpecPlug.isSetCharge()) {
+ chargeFromBiGG
+ .filter(charge -> charge != fbcSpecPlug.getCharge())
+ .ifPresent(charge ->
+ logger.debug(format(MESSAGES.getString("CHARGE_CONTRADICTION"),
+ charge, fbcSpecPlug.getCharge(), species.getId())));
+ fbcSpecPlug.unsetCharge();
+ }
+ chargeFromBiGG.filter(charge -> charge != 0).ifPresent(fbcSpecPlug::setCharge);
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.java
new file mode 100644
index 00000000..83182ecf
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGGeneProductAnnotator.java
@@ -0,0 +1,205 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc;
+
+import de.zbit.util.ResourceManager;
+import de.uni_halle.informatik.biodata.mp.annotation.IAnnotateSBases;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import de.uni_halle.informatik.biodata.mp.parameters.BiGGAnnotationParameters;
+import de.uni_halle.informatik.biodata.mp.annotation.bigg.BiGGCVTermAnnotator;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGId;
+import de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDB;
+import de.uni_halle.informatik.biodata.mp.resolver.Registry;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrg;
+import de.uni_halle.informatik.biodata.mp.reporting.ProgressObserver;
+import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.CVTerm.Qualifier;
+import org.sbml.jsbml.ext.fbc.GeneProduct;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.List;
+import java.util.Optional;
+import java.util.ResourceBundle;
+import java.util.stream.Collectors;
+
+import static de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.TYPE_GENE_PRODUCT;
+import static java.text.MessageFormat.format;
+
+/**
+ * Provides functionality to annotate gene products in an SBML model using data from the BiGG database.
+ * This class extends {@link BiGGCVTermAnnotator} and specifically handles the annotation of {@link GeneProduct} instances.
+ * It includes methods to validate gene product IDs, retrieve and set labels, and add annotations based on BiGG IDs.
+ */
+public class BiGGGeneProductAnnotator extends BiGGCVTermAnnotator implements IAnnotateSBases {
+
+ private static final Logger logger = LoggerFactory.getLogger(BiGGGeneProductAnnotator.class);
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.BIGG_ANNOTATION_MESSAGES);
+ public static final String BIGG_GENE_ID_PATTERN = "^(G_)?([a-zA-Z][a-zA-Z0-9_]+)(?:_([a-z][a-z0-9]?))?(?:_([A-Z][A-Z0-9]?))?$";
+
+ /**
+ * Instance of gene product to annotate
+ */
+ private final BiGGGeneProductReferencesAnnotator gprAnnotator;
+
+ public BiGGGeneProductAnnotator(BiGGGeneProductReferencesAnnotator gprAnnotator, BiGGDB bigg, BiGGAnnotationParameters parameters,
+ Registry registry, List observers) {
+ super(bigg, parameters, registry, observers);
+ this.gprAnnotator = gprAnnotator;
+ }
+
+
+ /**
+ * This method handles the annotation of gene products in a given SBML model. It checks if the model has the FBC plugin
+ * set and then proceeds to annotate each gene product found within the model. The progress bar is updated to reflect
+ * the number of gene products being annotated.
+ */
+ @Override
+ public void annotate(List geneProducts) throws SQLException {
+ // Iterate over each gene product and annotate it
+ for (GeneProduct geneProduct : geneProducts) {
+ statusReport("Annotating Gene Products (5/5) ", geneProduct);
+ annotate(geneProduct);
+ }
+
+ }
+
+ /**
+ * Annotates a gene product by adding relevant metadata and references.
+ * This method first checks the gene product's ID for validity and retrieves a corresponding BiGGId if available.
+ * It then attempts to get a label for the gene product. If no label is found, the method returns early.
+ * If a label is present, it updates the gene product reference in the association, adds annotations using the BiGGId,
+ * and sets the gene product's metaId if it has any CV terms. Finally, it sets the gene product's label name.
+ */
+ @Override
+ public void annotate(GeneProduct geneProduct) throws SQLException {
+ var biggId = findBiGGId(geneProduct);
+
+ String label = getLabel(geneProduct, biggId);
+ if (label.isEmpty()) {
+ return;
+ }
+
+ gprAnnotator.update(geneProduct);
+ addAnnotations(geneProduct, biggId);
+ if (geneProduct.getCVTermCount() > 0) {
+ geneProduct.setMetaId(biggId.toBiGGId());
+ }
+ setGPLabelName(geneProduct, label);
+ }
+
+
+
+ /**
+ * Validates the ID of a {@link GeneProduct} against the expected BiGG ID format and attempts to retrieve a
+ * corresponding {@link BiGGId} from existing annotations if the initial ID does not conform to the BiGG format.
+ * The method first checks if the gene product's ID matches the BiGG ID pattern. If it does not match, it then
+ * tries to find a valid BiGG ID from the gene product's annotations. If a valid BiGG ID is found among the annotations,
+ * it updates the ID; otherwise, it retains the original ID.
+ *
+ * @return An {@link Optional} containing the validated or retrieved BiGG ID, or an empty Optional if no valid ID is found.
+ */
+ @Override
+ public BiGGId findBiGGId(GeneProduct geneProduct) throws SQLException {
+ String id = geneProduct.getId();
+ boolean isBiGGid = id.matches(BIGG_GENE_ID_PATTERN);
+ if (!isBiGGid) {
+ // Collect all resources from CVTerms that qualify as BQB_IS into a list
+ List resources = geneProduct.getAnnotation().getListOfCVTerms().stream()
+ .filter(cvTerm -> cvTerm.getQualifier() == Qualifier.BQB_IS)
+ .flatMap(term -> term.getResources().stream())
+ .collect(Collectors.toList());
+ // Attempt to update the ID with a valid BiGG ID from the resources, if available
+ Optional biGGIdFromResources = getBiGGIdFromResources(resources, TYPE_GENE_PRODUCT);
+ if (biGGIdFromResources.isPresent()) {
+ return biGGIdFromResources.get();
+ }
+ }
+ // Create and return a BiGGId object based on the validated or updated ID
+ return BiGGId.createGeneId(id);
+ }
+
+
+ /**
+ * Retrieves the label for a gene product based on the provided BiGGId. If the gene product has a label set and it is not "None",
+ * that label is returned. If no label is set but the gene product has an ID, the BiGGId is converted to a string and returned.
+ * If neither condition is met, an empty string is returned.
+ *
+ * @param biggId An Optional containing the BiGGId of the gene product, which may be used to generate a label if the gene product's own label is not set.
+ * @return An {@code Optional} containing the label of the gene product, or an empty string if no appropriate label is found.
+ */
+ public String getLabel(GeneProduct geneProduct, BiGGId biggId) {
+ if (geneProduct.isSetLabel() && !geneProduct.getLabel().equalsIgnoreCase("None")) {
+ return geneProduct.getLabel();
+ } else if (geneProduct.isSetId()) {
+ return biggId.toBiGGId();
+ } else {
+ return "";
+ }
+ }
+
+
+ /**
+ * Updates the label of a gene product and sets its name based on the retrieved gene name from the BiGG database.
+ * If the current label is set to "None", it updates the label to the provided one. It then attempts to fetch
+ * the gene name corresponding to this label from the BiGG database. If a gene name is found, it checks if the
+ * current gene product name is different from the fetched name. If they differ, it logs a warning and updates
+ * the gene product name. If no gene name is found, it logs this as a fine-level message.
+ *
+ * @param label The label to set or use for fetching the gene name. This label should correspond to a {@link BiGGId}
+ * or be derived from {@link GeneProduct#getId()}.
+ */
+ public void setGPLabelName(GeneProduct geneProduct, String label) throws SQLException {
+ // Check if the current label is "None" and update it if so
+ if (geneProduct.getLabel().equalsIgnoreCase("None")) {
+ geneProduct.setLabel(label);
+ }
+ // Attempt to fetch the gene name from the BiGG database using the label
+ bigg.getGeneName(label).ifPresent(geneName -> {
+ // Log if no gene name is associated with the label
+ if (geneName.isEmpty()) {
+ logger.debug(format(MESSAGES.getString("NO_GENE_FOR_LABEL"), geneProduct.getName()));
+ } else {
+ // Log a warning if the gene product name is set and differs from the fetched gene name
+ if (geneProduct.isSetName() && !geneProduct.getName().equals(geneName)) {
+ logger.debug(format(MESSAGES.getString("UPDATE_GP_NAME"), geneProduct.getName(), geneName));
+ }
+ // Update the gene product name with the fetched gene name
+ geneProduct.setName(geneName);
+ }
+ });
+ }
+
+
+ /**
+ * Adds annotations to a gene product based on a given {@link BiGGId}. This method differentiates between
+ * annotations that specify what the gene product 'is' and what it 'is encoded by'. Resources are fetched
+ * from the BiGG database using the abbreviation from the provided BiGGId. Each resource URL is checked and
+ * parsed to determine the appropriate category ('is' or 'is encoded by') based on predefined prefixes.
+ *
+ * @param biggId The {@link BiGGId} associated with the gene product, typically derived from a species ID.
+ */
+ public void addAnnotations(GeneProduct geneProduct, BiGGId biggId) throws SQLException {
+ CVTerm termIs = new CVTerm(Qualifier.BQB_IS);
+ CVTerm termEncodedBy = new CVTerm(Qualifier.BQB_IS_ENCODED_BY);
+ // Retrieve gene IDs from BiGG database and categorize them based on their prefix
+ bigg.getGeneIds(biggId.getAbbreviation()).forEach(
+ uri -> {
+ switch (IdentifiersOrg.fixIdentifiersOrgUri(uri).getPrefix()) {
+ case "interpro":
+ case "pdb":
+ case "uniprot":
+ termIs.addResource(uri.getURI());
+ break;
+ default:
+ termEncodedBy.addResource(uri.getURI());
+ }
+ });
+ // Add the CVTerm to the gene product if resources are present
+ if (termIs.getResourceCount() > 0) {
+ geneProduct.addCVTerm(termIs);
+ }
+ if (termEncodedBy.getResourceCount() > 0) {
+ geneProduct.addCVTerm(termEncodedBy);
+ }
+ }
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGGeneProductReferencesAnnotator.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGGeneProductReferencesAnnotator.java
new file mode 100644
index 00000000..f78be07b
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/annotation/bigg/ext/fbc/BiGGGeneProductReferencesAnnotator.java
@@ -0,0 +1,84 @@
+package de.uni_halle.informatik.biodata.mp.annotation.bigg.ext.fbc;
+
+import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.Reaction;
+import org.sbml.jsbml.ext.fbc.*;
+
+import javax.swing.tree.TreeNode;
+import java.util.HashMap;
+import java.util.Map;
+
+public class BiGGGeneProductReferencesAnnotator {
+
+ /**
+ * A static map that holds references to all gene products within a model, facilitating quick updates.
+ */
+ private final Map geneProductReferences = new HashMap<>();
+
+
+ /**
+ * Initializes the geneProductReferences map by traversing through all reactions and their associated gene products.
+ * It handles both direct gene product references and nested logical operators that might contain gene product references.
+ *
+ * @param reactions The list of reactions to scan for gene product associations.
+ */
+ private void init(ListOf reactions) {
+ for (Reaction r : reactions) {
+ for (int childIdx = 0; childIdx < r.getChildCount(); childIdx++) {
+ TreeNode child = r.getChildAt(childIdx);
+ if (child instanceof GeneProductAssociation) {
+ Association association = ((GeneProductAssociation) child).getAssociation();
+ if (association instanceof GeneProductRef gpr) {
+ geneProductReferences.put(gpr.getGeneProduct(), gpr);
+ } else if (association instanceof LogicalOperator) {
+ updateFromNestedAssociations(association);
+ }
+ }
+ }
+ }
+ }
+
+
+ /**
+ * Updates the reference of a gene product in the geneProductReferences map using the gene product's ID.
+ * If the gene product ID starts with "G_", it strips this prefix before updating.
+ * If the map is initially empty, it initializes the map with the current model's reactions.
+ *
+ * @param gp The GeneProduct whose reference needs to be updated.
+ */
+ public void update(GeneProduct gp) {
+ if (geneProductReferences.isEmpty()) {
+ init(gp.getModel().getListOfReactions());
+ }
+ String id = gp.getId();
+ if (id.startsWith("G_")) {
+ id = id.split("G_")[1];
+ }
+ if (geneProductReferences.containsKey(id)) {
+ GeneProductRef gpr = geneProductReferences.get(id);
+ gpr.setGeneProduct(gp.getId());
+ }
+ }
+
+
+ /**
+ * Recursively processes nested associations to map gene products to their references.
+ * This method traverses through each child of the given association. If the child is a
+ * LogicalOperator, it recursively processes it. If the child is a GeneProductRef, it
+ * adds it to the geneProductReferences map.
+ *
+ * @param association The association to process, which can contain nested associations.
+ */
+ private void updateFromNestedAssociations(Association association) {
+ for (int idx = 0; idx < association.getChildCount(); idx++) {
+ TreeNode child = association.getChildAt(idx);
+ if (child instanceof LogicalOperator) {
+ updateFromNestedAssociations((Association) child);
+ } else {
+ // This child is assumed to be a GeneProductRef
+ GeneProductRef gpr = (GeneProductRef) child;
+ geneProductReferences.put(gpr.getGeneProduct(), gpr);
+ }
+ }
+ }
+}
diff --git a/src/main/java/edu/ucsd/sbrg/db/PostgreSQLConnector.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/PostgresConnectionPool.java
similarity index 57%
rename from src/main/java/edu/ucsd/sbrg/db/PostgreSQLConnector.java
rename to lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/PostgresConnectionPool.java
index 927d8bed..ebc0271c 100644
--- a/src/main/java/edu/ucsd/sbrg/db/PostgreSQLConnector.java
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/PostgresConnectionPool.java
@@ -1,58 +1,31 @@
-package edu.ucsd.sbrg.db;
+package de.uni_halle.informatik.biodata.mp.db;
-import static java.text.MessageFormat.format;
+import com.zaxxer.hikari.HikariConfig;
+import com.zaxxer.hikari.HikariDataSource;
+import org.sbml.jsbml.util.StringTools;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.Properties;
-import java.util.StringJoiner;
-import java.util.logging.Logger;
-
-import org.sbml.jsbml.util.StringTools;
-import com.zaxxer.hikari.HikariConfig;
-import com.zaxxer.hikari.HikariDataSource;
+import static java.text.MessageFormat.format;
-/**
- * Created by mephenor on 05.05.17.
- */
-class PostgreSQLConnector {
+public class PostgresConnectionPool {
- /**
- * A {@link Logger} for this class.
- */
- private static final transient Logger logger = Logger.getLogger(PostgreSQLConnector.class.getName());
- /**
- *
- */
- private HikariDataSource dataSource;
+ private static final Logger logger = LoggerFactory.getLogger(PostgresConnectionPool.class);
+ private final HikariDataSource dataSource;
- /**
- * @return
- * @throws SQLException
- */
public Connection getConnection() throws SQLException {
return dataSource.getConnection();
}
-
- /**
- *
- */
public void close() {
dataSource.close();
}
-
-
- /**
- * @param host
- * @param port
- * @param user
- * @param password
- * @param dbName
- */
- PostgreSQLConnector(String host, int port, String user, String password, String dbName) {
+ public PostgresConnectionPool(String host, int port, String user, String password, String dbName) {
password = password == null ? "" : password;
Properties properties = new Properties();
properties.setProperty("dataSourceClassName", "org.postgresql.ds.PGSimpleDataSource");
@@ -60,10 +33,11 @@ public void close() {
properties.setProperty("dataSource.password", password);
properties.setProperty("dataSource.databaseName", dbName);
properties.setProperty("dataSource.serverName", host);
+ properties.setProperty("dataSource.portNumber", Integer.toString(port));
HikariConfig config = new HikariConfig(properties);
config.setMaximumPoolSize(16);
config.setReadOnly(true);
dataSource = new HikariDataSource(config);
- logger.fine(format("{0}@{1}:{2}, password={3}", user, host, port, StringTools.fill(password.length(), '*')));
+ logger.debug(format("{0}@{1}:{2}, password={3}", user, host, port, StringTools.fill(password.length(), '*')));
}
}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDB.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDB.java
new file mode 100644
index 00000000..81086864
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDB.java
@@ -0,0 +1,117 @@
+package de.uni_halle.informatik.biodata.mp.db.adb;
+
+import de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool;
+import de.uni_halle.informatik.biodata.mp.parameters.DBParameters;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.Set;
+import java.util.TreeSet;
+
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.BIGG_METABOLITE;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.BIGG_REACTION;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column.NAMESPACE;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column.SOURCE_NAMESPACE;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column.SOURCE_TERM;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column.TARGET_NAMESPACE;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column.TARGET_TERM;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Column.URLPATTERN;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.METABOLITE_PREFIX;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.REACTION_PREFIX;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Table.ADB_COLLECTION;
+import static de.uni_halle.informatik.biodata.mp.db.adb.AnnotateDBContract.Constants.Table.MAPPING_VIEW;
+
+/**
+ * @author Kaustubh Trivedi
+ */
+public class AnnotateDB {
+
+ private static final Logger logger = LoggerFactory.getLogger(AnnotateDB.class);
+ private static PostgresConnectionPool connectionPool;
+
+ public AnnotateDB () {}
+
+ public static void init(DBParameters parameters) {
+ String dbName = parameters.dbName();
+ String host = parameters.host();
+ String passwd = parameters.passwd();
+ Integer port = parameters.port();
+ String user = parameters.user();
+ boolean run = iStrNotNullOrEmpty(dbName);
+ run &= iStrNotNullOrEmpty(host);
+ run &= port != null;
+ run &= iStrNotNullOrEmpty(user);
+ if (run) {
+ init(host, port, user, passwd, dbName);
+ }
+ }
+
+ private static boolean iStrNotNullOrEmpty(String string) {
+ return !(string == null || string.isEmpty());
+ }
+
+ public static void init(String host, Integer port, String user, String passwd, String dbName) {
+ if (null == connectionPool) {
+ logger.debug("Initialize AnnotateDB");
+ connectionPool = new PostgresConnectionPool(host, port, user, passwd, dbName);
+
+ Runtime.getRuntime().addShutdownHook(new Thread(connectionPool::close));
+ }
+ }
+
+
+ /**
+ * Retrieves a set of annotated URLs based on the type and BiGG ID provided.
+ * This method queries the database to find matching annotations and constructs URLs using the retrieved data.
+ *
+ * @param type The type of the BiGG ID, which can be either a metabolite or a reaction.
+ * @param biggId The BiGG ID for which annotations are to be retrieved. The ID may be modified if it starts
+ * with specific prefixes or ends with an underscore.
+ * @return A sorted set of URLs that are annotations for the given BiGG ID. If the type is neither metabolite
+ * nor reaction, or if an SQL exception occurs, an empty set is returned.
+ */
+ public Set getAnnotations(String type, String biggId) throws SQLException {
+ TreeSet annotations = new TreeSet<>();
+ // Check if the type is valid for querying annotations
+ if (!type.equals(BIGG_METABOLITE) && !type.equals(BIGG_REACTION)) {
+ return annotations;
+ }
+ // Adjust the BiGG ID if it starts with a known prefix
+ if (type.equals(BIGG_METABOLITE) && biggId.startsWith(METABOLITE_PREFIX)) {
+ biggId = biggId.substring(2);
+ } else if (type.equals(BIGG_REACTION) && biggId.startsWith(REACTION_PREFIX)) {
+ biggId = biggId.substring(2);
+ }
+ // Remove trailing underscore from the BiGG ID if present
+ if (biggId.endsWith("_")) {
+ biggId = biggId.substring(0, biggId.length() - 2);
+ }
+ // SQL query to fetch annotations
+ String query = "SELECT m." + TARGET_TERM + ", ac." + URLPATTERN + " FROM " + MAPPING_VIEW + " m, " + ADB_COLLECTION
+ + " ac WHERE m." + SOURCE_NAMESPACE + " = ? AND m." + SOURCE_TERM + " = ? AND ac." + NAMESPACE + " = m."
+ + TARGET_NAMESPACE + " AND ac.urlpattern != '{$id}'";
+ try (Connection connection = connectionPool.getConnection();
+ PreparedStatement pStatement = connection.prepareStatement(query)) {
+ pStatement.setString(1, type);
+ pStatement.setString(2, biggId);
+ int i = 0;
+ try (ResultSet resultSet = pStatement.executeQuery()) {
+ // Process each result and construct the URL
+ while (resultSet.next()) {
+ i++;
+ String uri = resultSet.getString(URLPATTERN);
+ String id = resultSet.getString(TARGET_TERM);
+ uri = uri.replace("{$id}", id);
+ annotations.add(uri);
+ }
+ logger.debug("Added {} annotations from ADB for {} with ID {}", i, type, biggId);
+ }
+ }
+ return annotations;
+ }
+
+}
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDBContract.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDBContract.java
new file mode 100644
index 00000000..dcbd4e4c
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDBContract.java
@@ -0,0 +1,37 @@
+package de.uni_halle.informatik.biodata.mp.db.adb;
+
+public final class AnnotateDBContract {
+
+ public static abstract class Constants {
+
+ public static class Table {
+
+ static final String MAPPING_VIEW = "mapping_view";
+ static final String ADB_COLLECTION = "adb_collection";
+ }
+
+ public static class Column {
+
+ static final String ID = "id";
+ static final String SOURCE_NAMESPACE = "source_namespace";
+ static final String SOURCE_MIRIAM = "source_miriam";
+ static final String SOURCE_TERM = "source_term";
+ static final String QUALIFIER = "qualifier";
+ static final String TARGET_NAMESPACE = "target_namespace";
+ static final String TARGET_MIRIAM = "target_miriam";
+ static final String TARGET_TERM = "target_term";
+ static final String EVIDENCE_SOURCE = "evidence_source";
+ static final String EVIDENCE_VERSION = "evidence_version";
+ static final String EVIDENCE = "evidence";
+ static final String NAMESPACE = "namespace";
+ static final String URLPATTERN = "urlpattern";
+ }
+
+ // Other constants
+ public static final String BIGG_METABOLITE = "bigg.metabolite";
+ public static final String BIGG_REACTION = "bigg.reaction";
+ static final String METABOLITE_PREFIX = "M_";
+ static final String REACTION_PREFIX = "R_";
+ static final String GENE_PREFIX = "G_";
+ }
+}
diff --git a/src/main/java/edu/ucsd/sbrg/db/ADBOptions.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDBOptions.java
similarity index 80%
rename from src/main/java/edu/ucsd/sbrg/db/ADBOptions.java
rename to lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDBOptions.java
index e5e1809c..13f76f24 100644
--- a/src/main/java/edu/ucsd/sbrg/db/ADBOptions.java
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/adb/AnnotateDBOptions.java
@@ -1,12 +1,14 @@
-package edu.ucsd.sbrg.db;
+package de.uni_halle.informatik.biodata.mp.db.adb;
import de.zbit.util.prefs.KeyProvider;
import de.zbit.util.prefs.Option;
/**
+ * This interface provides options for connecting to the ADB database.
+ *
* @author Kaustubh Trivedi
*/
-public interface ADBOptions extends KeyProvider {
+public interface AnnotateDBOptions extends KeyProvider {
/**
*
diff --git a/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/bigg/BiGGDB.java b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/bigg/BiGGDB.java
new file mode 100644
index 00000000..1f2ecd70
--- /dev/null
+++ b/lib/src/main/java/de/uni_halle/informatik/biodata/mp/db/bigg/BiGGDB.java
@@ -0,0 +1,891 @@
+/*
+ * $Id$
+ * $URL$
+ * ---------------------------------------------------------------------
+ * This file is part of the program NetBuilder.
+ * Copyright (C) 2013 by the University of California, San Diego.
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation. A copy of the license
+ * agreement is provided in the file named "LICENSE.txt" included with
+ * this software distribution and also available online as
+ * .
+ * ---------------------------------------------------------------------
+ */
+package de.uni_halle.informatik.biodata.mp.db.bigg;
+
+import de.zbit.util.ResourceManager;
+import de.zbit.util.Utils;
+import de.uni_halle.informatik.biodata.mp.logging.BundleNames;
+import de.uni_halle.informatik.biodata.mp.parameters.DBParameters;
+import de.uni_halle.informatik.biodata.mp.db.PostgresConnectionPool;
+import de.uni_halle.informatik.biodata.mp.polishing.NamePolisher;
+import de.uni_halle.informatik.biodata.mp.resolver.RegistryURI;
+import de.uni_halle.informatik.biodata.mp.resolver.identifiersorg.IdentifiersOrgURI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.Date;
+import java.sql.*;
+import java.util.*;
+import java.util.stream.Collectors;
+
+import static de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Column.*;
+import static de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.*;
+import static de.uni_halle.informatik.biodata.mp.db.bigg.BiGGDBContract.Constants.Table.*;
+import static java.text.MessageFormat.format;
+
+/**
+ * This class provides a connection to the BiGG database.
+ *
+ * @author Andreas Dräger
+ */
+@SuppressWarnings("ALL")
+public class BiGGDB {
+
+ private static final Logger logger = LoggerFactory.getLogger(BiGGDB.class);
+ private static final ResourceBundle MESSAGES = ResourceManager.getBundle(BundleNames.DB_MESSAGES);
+
+ private static PostgresConnectionPool connectionPool;
+
+ private static Set BiGGDBCompartments = new HashSet<>();
+ private static Set BiGGDBDataSources = new HashSet<>();
+ private static Set BiGGDBMetabolites = new HashSet<>();
+ private static Set BiGGDBModels = new HashSet<>();
+ private static Set BiGGDBReactions = new HashSet<>();
+
+
+ public BiGGDB () {}
+
+ private static boolean iStrNotNullOrEmpty(String string) {
+ return !(string == null || string.isEmpty());
+ }
+
+ public static void init(DBParameters parameters) {
+ String dbName = parameters.dbName();
+ String host = parameters.host();
+ String passwd = parameters.passwd();
+ Integer port = parameters.port();
+ String user = parameters.user();
+ boolean run = iStrNotNullOrEmpty(dbName);
+ run &= iStrNotNullOrEmpty(host);
+ run &= null != port;
+ run &= iStrNotNullOrEmpty(user);
+ if (run) {
+ init(host, port, user, passwd, dbName);
+ }
+ }
+
+ public static void init(String host, Integer port, String user, String passwd, String dbName) {
+
+ if (null == connectionPool) {
+ logger.debug("Initialize BiGG DB");
+ connectionPool = new PostgresConnectionPool(host, port, user, passwd, dbName);
+
+ Runtime.getRuntime().addShutdownHook(new Thread(connectionPool::close));
+ }
+ }
+
+ /**
+ * Retrieves the version date of the BiGG database.
+ *
+ * This method queries the database to fetch the date and time of the last update
+ * from the DATABASE_VERSION table. It returns an {@link Optional} containing the
+ * date if the query is successful and the date exists, otherwise it returns an empty {@link Optional}.
+ *
+ * @return {@link Optional} The date of the last database update, or an empty {@link Optional} if not available.
+ */
+ public Optional getBiGGVersion() throws SQLException {
+ Optional date = Optional.empty();
+ String query = "SELECT " + DATE_TIME + " FROM " + DATABASE_VERSION;
+ try (Connection connection = connectionPool.getConnection();
+ PreparedStatement pStatement = connection.prepareStatement(query);
+ ResultSet resultSet = pStatement.executeQuery();) {
+ if (resultSet.next()) {
+ date = Optional.of(resultSet.getDate(1));
+ }
+ }
+ return date;
+ }
+
+
+ /**
+ * Retrieves a list of distinct subsystems associated with a specific model and reaction BiGG IDs.
+ * This method executes a SQL query to fetch subsystems from the database where both the model and reaction
+ * match the provided BiGG IDs. Only subsystems with a non-zero length are considered.
+ *
+ * @param modelBiGGid The BiGG ID of the model.
+ * @param reactionBiGGid The BiGG ID of the reaction.
+ * @return A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
+ */
+ public List getSubsystems(String modelBiGGid, String reactionBiGGid) throws SQLException {
+ String query = "SELECT DISTINCT mr." + SUBSYSTEM + " FROM " + REACTION + " r, " + MODEL + " m, " + MODEL_REACTION
+ + " mr WHERE m." + BIGG_ID + " = ? AND r." + BIGG_ID + " = ? AND m." + ID + " = mr." + MODEL_ID + " AND r." + ID
+ + " = mr." + REACTION_ID + " AND LENGTH(mr." + SUBSYSTEM + ") > 0";
+ List list = new LinkedList<>();
+ try (Connection connection = connectionPool.getConnection();
+ PreparedStatement pStatement = connection.prepareStatement(query)) {
+ pStatement.setString(1, modelBiGGid);
+ pStatement.setString(2, reactionBiGGid);
+ try (ResultSet resultSet = pStatement.executeQuery()) {
+ while (resultSet.next()) {
+ list.add(resultSet.getString(1));
+ }
+ }
+ }
+ return list;
+ }
+
+
+ /**
+ * Retrieves a list of distinct subsystems associated with a specific reaction BiGG ID.
+ * This method executes a SQL query to fetch subsystems from the database where the reaction
+ * matches the provided BiGG ID. Only subsystems with a non-zero length are considered.
+ *
+ * @param reactionBiGGid The BiGG ID of the reaction for which subsystems are to be retrieved.
+ * @return A List of subsystem names as strings. Returns an empty list if no subsystems are found or if an error occurs.
+ */
+ public List getSubsystemsForReaction(String reactionBiGGid) throws SQLException {
+ String query = "SELECT DISTINCT mr." + SUBSYSTEM + " FROM " + REACTION + " r, " + MODEL_REACTION + " mr WHERE r."
+ + BIGG_ID + " = ? AND r." + ID + " = mr." + REACTION_ID + " AND LENGTH(mr." + SUBSYSTEM + ") > 0";
+ List list = new LinkedList<>();
+ try (Connection connection = connectionPool.getConnection();
+ PreparedStatement pStatement = connection.prepareStatement(query)) {
+ pStatement.setString(1, reactionBiGGid);
+ try (ResultSet resultSet = pStatement.executeQuery()) {
+ while (resultSet.next()) {
+ list.add(resultSet.getString(1));
+ }
+ }
+ }
+ return list;
+ }
+
+
+ /**
+ * Retrieves the unique chemical formula for a given component within a specific compartment.
+ * This method queries the database to find the distinct chemical formula associated with the specified
+ * component and compartment IDs. It ensures that the formula is unique for the given parameters.
+ * If multiple distinct formulas are found, it logs a warning indicating ambiguity.
+ *
+ * @param componentId The BiGG ID of the component for which the chemical formula is to be retrieved.
+ * @param compartmentId The BiGG ID of the compartment where the component is located.
+ * @return An {@link Optional} containing the chemical formula if exactly one unique formula is found,
+ * otherwise an empty {@link Optional} if none or multiple formulas are found.
+ */
+ public Optional getChemicalFormulaByCompartment(String componentId, String compartmentId) throws SQLException {
+ String query = "SELECT DISTINCT mcc." + FORMULA + " FROM " + MCC + " mcc, " + COMPARTMENTALIZED_COMPONENT + " cc, "
+ + COMPONENT + " c, " + COMPARTMENT + " co WHERE c." + BIGG_ID + " = ? AND c." + ID + " = cc." + COMPONENT_ID
+ + " AND co." + BIGG_ID + " = ? AND co." + ID + " = cc." + COMPARTMENT_ID + " and cc." + ID + " = mcc."
+ + COMPARTMENTALIZED_COMPONENT_ID + " AND mcc." + FORMULA + " <> '' ORDER BY mcc." + FORMULA;
+ Set results = runFormulaQuery(query, componentId, compartmentId);
+ if (results.size() == 1) {
+ return Optional.of(results.iterator().next());
+ } else {
+ if (results.size() > 1) {
+ logger.debug(format(MESSAGES.getString("FORMULA_COMPARTMENT_AMBIGUOUS"), componentId, compartmentId));
+ }
+ return Optional.empty();
+ }
+ }
+
+
+ /**
+ * Executes a database query to retrieve distinct chemical formulas based on the provided SQL query.
+ * This method is designed to handle queries that fetch chemical formulas for a specific component
+ * within either a compartment or a model, depending on the IDs provided.
+ *
+ * @param query The SQL query string that retrieves distinct chemical formulas.
+ * @param componentId The BiGG ID of the component for which the formula is being retrieved.
+ * @param compartmentOrModelId The BiGG ID of either the compartment or the model associated with the component.
+ * @return A set of unique chemical formulas as strings. If no valid formulas are found, returns an empty set.
+ */
+ private Set runFormulaQuery(String query, String componentId, String compartmentOrModelId) throws SQLException {
+ Set results = new HashSet<>();
+ try (Connection connection = connectionPool.getConnection()) {
+ try (PreparedStatement pStatement = connection.prepareStatement(query)) {
+ pStatement.setString(1, componentId);
+ pStatement.setString(2, compartmentOrModelId);
+ try (ResultSet resultSet = pStatement.executeQuery()) {
+ while (resultSet.next()) {
+ results.add(resultSet.getString(1));
+ }
+ }
+ }
+ }
+ return results.stream().filter(formula -> formula != null && !formula.isEmpty()).collect(Collectors.toSet());
+ }
+
+
+ /**
+ * Retrieves the chemical formula for a given component within a specific model in the BiGG database.
+ * This method executes a SQL query to find distinct chemical formulas associated with the component and model IDs provided.
+ * If exactly one unique formula is found, it is returned. If none or multiple formulas are found, an empty Optional is returned.
+ * In case of multiple formulas, a log entry is made indicating the ambiguity.
+ *
+ * @param componentId The BiGG ID of the component for which the formula is being retrieved.
+ * @param modelId The BiGG ID of the model in which the component is present.
+ * @return An {@link Optional} containing the chemical formula if exactly one is found, otherwise empty.
+ */
+ public Optional getChemicalFormula(String componentId, String modelId) throws SQLException {
+ String query = "SELECT DISTINCT mcc." + FORMULA + "\n FROM " + COMPONENT + " c,\n" + COMPARTMENTALIZED_COMPONENT
+ + " cc,\n" + MODEL + " m,\n" + MCC + " mcc\n WHERE c." + ID + " = cc." + COMPONENT_ID + " AND\n cc." + ID
+ + " = mcc." + COMPARTMENTALIZED_COMPONENT_ID + " AND\n c." + BIGG_ID + " = ? AND\n m." + BIGG_ID + " = ? AND\n m."
+ + ID + " = mcc." + MODEL_ID + " AND mcc." + FORMULA + " <> ''";
+ Set
+
-*Authors:* [Andreas Dräger](https://github.com/draeger/), [Thomas J. Zajac](https://github.com/mephenor/), [Matthias König](https://github.com/matthiaskoenig), [Kaustubh Trivedi](https://github.com/codekaust)
-
-[](https://travis-ci.org/draeger-lab/ModelPolisher)
-[](https://github.com/draeger-lab/ModelPolisher/releases/)
+[](https://github.com/draeger-lab/ModelPolisher/releases/)
[](https://doi.org/10.1371/journal.pone.0149263)
[](http://opensource.org/licenses/MIT)
-ModelPolisher accesses the [BiGG Models knowledgebase](http://bigg.ucsd.edu) to annotate and autocomplete [SBML](http://sbml.org) models.
-Thereby, the program mainly relies on [BiGG identifiers](https://github.com/SBRG/bigg_models/wiki/BiGG-Models-ID-Specification-and-Guidelines) for model components.
-Moreover, it fixes some apparent errors in the models and uses mappings from [AnnotateDB](https://github.com/matthiaskoenig/annotatedb) to further add annotations.
+ModelPolisher is a simple single-purpose automated curation tool for SBML models.
-ModelPolisher is primarily a command-line based tool. You can run ModelPolisher locally [using `Docker`](#using-docker) or using your installation of BiGG Models database (see https://github.com/SBRG/bigg_models).
+- improve the adherence to [FAIR]((https://doi.org/10.1038%2FSDATA.2016.18)) data standards as practiced in the SBML modelling community
+- implement non-binding best practices as defined by the [SBML specification](https://sbml.org/documents/specifications/) documents
+- add [MIRIAM]((https://doi.org/10.1038%2Fnbt1156))-style semantic annotations to models, using the [BiGG Models knowledgebase](http://bigg.ucsd.edu) and [AnnotateDB](https://github.com/matthiaskoenig/annotatedb)
-Note: If you run into trouble with larger files, especially `_java.lang.OutOfMemoryError: GC overhead limit exceeded_`, please use the JVM `Xmx` flag (e.g., `java -Xmx4G -jar ModelPolisher-VERSION.jar` ).
+You can find documentation on what ModelPolisher does in [our Wiki](https://github.com/draeger-lab/ModelPolisher/wiki).
-# Table of Contents
+Furthermore, it can, on a best effort basis, attempt to perform minimal fixes on a model to make it valid with regards to the [SBMLValidator](https://sbml.org/jsbml/files/doc/api/1.6.1/org/sbml/jsbml/validator/SBMLValidator.html).
-* [How to cite ModelPolisher?](#cite-ModelPolisher)
-* [How to build?](#build-instructions)
-* [How to run ModelPolisher?](#run-ModelPolisher)
- * [Using Docker](#using-docker)
- * [Using ModelPolisher jar](#using-jar)
-* [Licenses](#licenses)
+Currently supported versions of the SBML standard are:
-# How to cite ModelPolisher?
+- Version 3 Level 1
+ - FBC Version 2
-The online version of ModelPolisher is described in this article: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149263
+You can use ModelPolisher as a tool via its [Python API client](https://github.com/draeger-lab/MPClient) to our HTTP server, using Docker, or as a Standalone JAR.
-The article ["BiGG Models: A platform for integrating, standardizing and sharing genome-scale models"](https://nar.oxfordjournals.org/content/44/D1/D515) describes BiGG Models knowledge-base including ModelPolisher.
+ModelPolisher can also be used as a Java library, building on the [JSBML](https://sbml.org/software/jsbml/) project.
-# How to build?
+# Table of Contents
-NOTE: You may run ModelPolisher, without building, using Docker (preferred). See [here](#using-docker).
+* [Performance](#performance)
+* [Using ModelPolisher as a Tool](#using-modelpolisher-as-a-tool)
+ * [Parameters](#parameters)
+ * [Using the Python API package](#using-the-python-api-client-package)
+ * [Using Docker](#using-docker)
+ * [Using ModelPolisher Jar](#using-modepolisher-jar)
+* [Using ModelPolisher as a Java library](#using-modelpolisher-as-a-java-library)
+* [How to cite ModelPolisher](#how-to-cite-ModelPolisher)
+* [Licenses](#licenses)
-ModelPolisher uses `gradle` to build. Make sure you have `gradle (version >= 5.0)` installed in your system before following the procedure below.
+# Performance
+An evaluation of running ModelPolisher on all models in the BiGG Database, on 3000 models available on Biomodels and on newly generated models using [CarveMe](https://github.com/cdanielmachado/carveme) with regards to [MEMOTE](https://memote.readthedocs.io/en/latest/) scores will be published shortly.
-First clone this github project and go to directory `