Merge pull request #31 from draeger-lab/development

Development

.gitignore

@@ -1,3 +1,8 @@
+/.settings
 /target
 *.log
-*.gen
+*.gen
+.project
+.classpath
+.properties
+/bin/

pom.xml

@@ -74,7 +74,8 @@
 				<artifactId>maven-compiler-plugin</artifactId>
 				<version>3.7.0</version>
 			</plugin>
-			<!-- To create your executable file call mvn jfx:jar. The jar-file will be placed at target/jfx/app -->
+			<!-- To create your executable file call mvn jfx:jar. The jar-file will 
+				be placed at target/jfx/app -->
 			<plugin>
 				<groupId>com.zenjava</groupId>
 				<artifactId>javafx-maven-plugin</artifactId>
@@ -83,6 +84,15 @@
 					<vendor>draeger-lab</vendor>
 					<mainClass>de.sbtab.main.SBTabMain</mainClass>
 				</configuration>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>jar</goal>
+						</goals>
+						<inherited>false</inherited>
+					</execution>
+				</executions>
 			</plugin>
 			<!--allows us to run tests that use either the “old” JUnit (3 or 4) or 
 				JUnit 5 -->

src/main/java/de/sbtab/controller/SBTabController.java

@@ -1,6 +1,15 @@
 package de.sbtab.controller;
 
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Writer;
+import java.util.Properties;
+import java.util.prefs.Preferences;
 
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
@@ -14,6 +23,39 @@ public class SBTabController {
 
   private static final transient Logger LOGGER = LogManager.getLogger(SBTabController.class);
   private static SBMLDocument doc;
+  private static String filePath = null;
+
+  public static String getFilePath() {
+    return filePath;
+  }
+
+  public static SBMLDocument getDoc() {
+    return doc;
+  }
+
+  /**
+   * Set Properties for the programm, at the moment only the file path is saved. 
+   */
+  public static void setProperties(){
+    Writer writer = null;
+    try
+    {
+      writer = new FileWriter( ".properties" );
+      Properties theProperties = new Properties( System.getProperties() );
+      if(filePath != null){
+        theProperties.setProperty( "FilePath", new File(filePath).getParent());
+      }
+      else{
+        theProperties.setProperty( "FilePath", System.getProperty("user.home"));
+      }
+      theProperties.store( writer, "Properties of STabEditor" );
+    }
+    catch ( IOException e )
+    {
+      e.printStackTrace();
+    }
+  }
+
   /**
    * Save SBML document to a {@link File}.
    * 
@@ -50,14 +92,16 @@ public Void call() {
    * 
    * @param path
    *            absolute path to {@link SBMLDocument}
-   * @return 
+   * @return
    */
   public static SBMLDocument read(String filePath) {
     Task<Void> task = new Task<Void>() {
       @Override
       public Void call() {
         try {
+          SBTabController.filePath = filePath;
           doc = SBMLReader.read(new File(filePath));
+          setProperties();
         } catch (Exception e) {
           e.printStackTrace();
         }
@@ -68,20 +112,47 @@ public Void call() {
     th.setDaemon(true);
     th.start();
     try {
-    	th.join();
+      th.join();
     } catch (InterruptedException e) {
-    	e.printStackTrace();
+      e.printStackTrace();
     }
     return doc;
   }
+  /**
+   * Validator of SBML-Files
+   * @param doc is the input SBML-File
+   * @return boolean true for valid Document else false plus Logger errors
+   */
   public static boolean validate(SBMLDocument doc) {
-    if(doc.checkConsistencyOffline() == 0) {
+	  // the number of Errors of a SBMLFile
+	  int numErrors = doc.checkConsistencyOffline();
+    if(numErrors == 0) {
       return true;
     }else {
-      for(int i = 0; i < doc.checkConsistencyOffline(); i++) {
+    	//get each error and show it
+      for(int i = 0; i < numErrors; i++) {
         LOGGER.error(doc.getError(i));
       }
       return false;
     }
   }
+  /**
+   * Number of Errors in Document
+   * @param doc
+   * @return Number of Errors
+   */
+  public static int numErrors(SBMLDocument doc) {
+	  return doc.checkConsistencyOffline();
+  }
+  /**
+   * Testmethod to get a String-Type Error Code
+   * @param doc
+   * @return String-Error
+   */
+  public static String errorToString(SBMLDocument doc) {
+	  int numErrors = doc.checkConsistencyOffline();
+	  String StringError = null;
+	  StringError = doc.getError(0).toString();
+	  return StringError;
+  }
 }

src/main/java/de/sbtab/controller/SBTabDocument.java

@@ -6,6 +6,7 @@
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.util.TreeNodeChangeListener;
+import org.sbml.jsbml.AbstractTreeNode;
 import org.sbml.jsbml.util.TreeNodeRemovedEvent;
 
 public class SBTabDocument<T> implements TreeNodeChangeListener {
@@ -21,41 +22,31 @@ public class SBTabDocument<T> implements TreeNodeChangeListener {
 	/**
 	 * Constructor for Document
 	 *
-	 * @param Doc
+	 * @param doc
 	 * 
-	 * @param version
+	 * @param pathDoc
 	 */
-	public SBTabDocument(T Doc, String version) {
+	public SBTabDocument(T doc, String pathDoc) {
 		try {
-			File temp = File.createTempFile("temp-file-name", ".tmp");			
-			String absolutePath = temp.getAbsolutePath();
-			pathtempDoc = absolutePath.substring(0, absolutePath.lastIndexOf(File.separator));
+			tempDoc = doc;
+			pathtempDoc = pathDoc;
 
-//			TidySBMLWriter.write(Doc, pathtempDoc, "temp-file-name", version);			
+//			File temp = File.createTempFile("temp-file-name", ".tmp");			
+//			String absolutePath = temp.getAbsolutePath();
+//			pathtempDoc = absolutePath.substring(0, absolutePath.lastIndexOf(File.separator));			
+//			TidySBMLWriter.write(doc, pathtempDoc, "temp-file-name", version);			
 //			tempDoc = SBMLReader.read(new File(tempfilePath));	
 
-//			((AbstractTreeNode) tempDoc).addTreeNodeChangeListener(this);
-
+			if (tempDoc instanceof AbstractTreeNode) {
+				((AbstractTreeNode) tempDoc).addTreeNodeChangeListener(this);
+			}			
 		} catch (Exception e) {
 			e.printStackTrace();
 		}
 
 		changed = false;
 	}
 
-	/**
-	 * Edit a temporary document
-	 * 
-	 * @param x
-	 */
-	public void edit(String x) {
-		try {
-			changed = true;
-
-		} catch (Exception e) {
-			LOGGER.error("Unable to edit sbml file", e);
-		}
-	}
 
 	@Override
 	public void propertyChange(PropertyChangeEvent evt) {

src/main/java/de/sbtab/controller/SBTabElement.java

@@ -0,0 +1,8 @@
+package de.sbtab.controller;
+
+/**
+ * Defines wrapper element for JSBML data node
+ * */
+public interface SBTabElement{
+	void initialize();
+}

src/main/java/de/sbtab/controller/SBTabReactionWrapper.java

@@ -5,39 +5,53 @@
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
 
-public class SBTabReactionWrapper {
+public class SBTabReactionWrapper implements SBTabElement {
 	private Reaction reaction;
-    private StringProperty reactionName;
-    private StringProperty reactionId;
-    private StringProperty reactionSBOTerm;
-
-    public SBTabReactionWrapper(Reaction reaction) {
-    	setReaction(reaction);
-    	initialize(reaction);
-    }
-
-    public void initialize(Reaction reaction) {
-    	// TODO: figure out what fields do we need to work with
-    	reactionName = new SimpleStringProperty(reaction.getName());
-    	reactionId = new SimpleStringProperty(reaction.getId());
-    	reactionSBOTerm = new SimpleStringProperty(reaction.getSBOTermID());
-    }
-
-    private void setReaction(Reaction reaction) {
+	private StringProperty reactionName;
+	private StringProperty reactionId;
+	private StringProperty reactionSBOTerm;
+
+	public SBTabReactionWrapper(Reaction reaction) {
+		if (reaction != null) {
+			setReaction(reaction);
+			initialize();
+		}
+	}
+
+	public void initialize() {
+		// TODO: figure out what fields do we need to work with
+		reactionName = new SimpleStringProperty(reaction.getName());		
+		reactionId = new SimpleStringProperty(reaction.getId());
+		reactionSBOTerm = new SimpleStringProperty(reaction.getSBOTermID());
+	}
+
+	private void setReaction(Reaction reaction) {
 		this.reaction = reaction;
 	}
 
 	public Reaction getReaction() {
 		return reaction;
 	}
+
+	public void setReactionName(StringProperty reactionName){
+		this.reactionName = reactionName;
+	}
 
 	public StringProperty getReactionName() {
 		return reactionName;
 	}
+
+	public void setReactionId(StringProperty reactionId){
+		this.reactionId = reactionId;
+	}
 
 	public StringProperty getReactionId() {
 		return reactionId;
 	}
+
+	public void setSBOTerm(StringProperty reactionSBOTerm){
+		this.reactionSBOTerm = reactionSBOTerm;
+	}
 
 	public StringProperty getSBOTerm() {
 		return reactionSBOTerm;

src/main/java/de/sbtab/main/SBTabMain.java

@@ -2,10 +2,21 @@
 
 import de.sbtab.view.SBTabMainView;
 import javafx.application.Application;
+import org.sbml.jsbml.SBMLDocument;
 
 public class SBTabMain {
 
 	public static void main(String[] args) {
-		Application.launch(SBTabMainView.class, args);
+		//Application.launch(SBTabMainView.class, args);
+		SBTabMainView GUI = new SBTabMainView();
+        Thread t = new Thread(GUI);
+        t.start();
+	}
+
+	public static void mainOnFile(SBMLDocument doc) {
+		//Application.launch(SBTabMainView.class, args);
+		SBTabMainView GUI = new SBTabMainView(doc);
+        Thread t = new Thread(GUI);
+        t.start();
 	}
 }