reorg this project.

beyondpie · Apr 10, 2020 · e570bce · e570bce
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diff --git a/.gitignore b/.gitignore
@@ -55,3 +55,4 @@
 /dev/testCMAKE/build/testRead
 /dev/testCMAKE/testRead
 /data/.DS_Store
+.DS_Store
diff --git a/README.md b/README.md
diff --git a/README.org b/README.org
@@ -0,0 +1,25 @@
+* GIFT
+An algorithm called [[http://bioinfo.au.tsinghua.edu.cn/software/GIFT/ ][GIFT]] is used to infer the chemogenmic information based on
+drug-protein interactions. Here chemogenomic information means the interactions
+between the chemical substructures and protein domains. An Expection-Maximum
+algorithm is then derived.   
+
+Note: the updated version is maintained on GitHub.
+
+** How to install
+*** C++ Version [Recommend]
+- Download and install [[http://www.boost.org/][Boost C++ Library]]
+- Download and install [[http://www.gnu.org/software/gsl/][GSL-GNU]] Scientific Library.
+- Make sure append the boost and gsl include dir to the makefile *CFLAGS*.
+
+Then use make command directly,
+#+BEGIN_SRC shell
+make install
+#+END_SRC
+
+The binary file will be installed under the dirctory *bin*
+
+*** Matlab Version
+Please check the codes under *matlab_version* directory.
+** How to usage GIFT
+Please check the GIFT_UserManual under *doc* directory.
diff --git a/doc/GIFT.tex b/doc/GIFT.tex
diff --git a/code/v_1/src_cpp/makefile → makefile b/code/v_1/src_cpp/makefile → makefile
@@ -7,17 +7,21 @@ GCC = g++
 CFLAGS = -lboost_thread -lgsl -lgslcblas -lstdc++ -Wall -O3 
 OBJDIR = obj
 SRCDIR = src
-BIN = bin
+BINDIR = bin
 SRCS = $(notdir $(wildcard $(SRCDIR)/*.cpp))
 OBJS = $(patsubst %.cpp, $(OBJDIR)/%.o, $(SRCS))
-TARGET = $(BIN)/$(NAME)
+TARGET = $(BINDIR)/$(NAME)
 
 $(TARGET):$(OBJS)
+	-mkdir -p ${BINDIR}
 	$(GCC) -g $(CFLAGS) -o $@ $^
 $(OBJDIR)/%.o : $(SRCDIR)/%.cpp
+	-mkdir -p ${OBJDIR}
 	$(GCC) -c -o $@ $<
 
+.PHONY: install
+install: ${TARGET}
+
 .PHONY: clean
 clean:
 	-rm $(TARGET) $(OBJDIR)/*.o
-
diff --git a/code/v_1/src_matlab/AssociationMethod.m → matlab_version/AssociationMethod.m b/code/v_1/src_matlab/AssociationMethod.m → matlab_version/AssociationMethod.m
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diff --git a/code/v_1/src_matlab/ExampleScript_GIFT.m → matlab_version/ExampleScript_GIFT.m b/code/v_1/src_matlab/ExampleScript_GIFT.m → matlab_version/ExampleScript_GIFT.m
diff --git a/code/v_1/src_matlab/GetHash.m → matlab_version/GetHash.m b/code/v_1/src_matlab/GetHash.m → matlab_version/GetHash.m
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diff --git a/code/v_1/src_matlab/LoglikehoodEM.m → matlab_version/LoglikehoodEM.m b/code/v_1/src_matlab/LoglikehoodEM.m → matlab_version/LoglikehoodEM.m
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diff --git a/code/v_1/src_matlab/SubDomainEM.m → matlab_version/SubDomainEM.m b/code/v_1/src_matlab/SubDomainEM.m → matlab_version/SubDomainEM.m
diff --git a/code/v_1/src_matlab/devEM.m → matlab_version/devEM.m b/code/v_1/src_matlab/devEM.m → matlab_version/devEM.m
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diff --git a/code/v_1/src_matlab/write_matrix_int_txt.m → matlab_version/write_matrix_int_txt.m b/code/v_1/src_matlab/write_matrix_int_txt.m → matlab_version/write_matrix_int_txt.m
diff --git a/code/v_1/src_matlab/write_matrix_txt.m → matlab_version/write_matrix_txt.m b/code/v_1/src_matlab/write_matrix_txt.m → matlab_version/write_matrix_txt.m
diff --git a/code/v_1/src_cpp/EM_Boost.cpp → src/EM_Boost.cpp b/code/v_1/src_cpp/EM_Boost.cpp → src/EM_Boost.cpp
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diff --git a/code/v_1/src_cpp/PreInfer.h → src/PreInfer.h b/code/v_1/src_cpp/PreInfer.h → src/PreInfer.h
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