Merge pull request #1 from ClimerLab/cleaning-code

Removed dead code

Author: kpsmithjr

Makefile

@@ -42,7 +42,7 @@ EXE = csfs
 _COMMONOBJ = ConfigParser.o Cut.o CutCreator.o CutSet.o Individual.o Marker.o \
              CSFS.o CSFS_Data.o CSFS_Utils.o RelaxationSolver.o SparseSolver.o Solution.o Timer.o \
              VariableEqualities.o
-CSFSOBJ    = main.o CutAndSolveController.o CutAndSolveWorker.o CutfileReader.o Parallel.o $(_COMMONOBJ)
+CSFSOBJ    = main.o CutAndSolveController.o CutAndSolveWorker.o Parallel.o $(_COMMONOBJ)
 
 
 #---------------------------------------------------------------------------------------------------
@@ -94,10 +94,9 @@ $(OBJDIR)/Cut.o: $(addprefix $(SRCDIR)/, Cut.cpp Cut.h)
 	$(CXX) $(CXXFLAGS) -c -o $@ $<
 
 $(OBJDIR)/CutAndSolveController.o:	$(addprefix $(SRCDIR)/, CutAndSolveController.cpp CutAndSolveController.h) \
-                               			$(addprefix $(OBJDIR)/, CutCreator.o CutfileReader.o \
-													   															 	CSFS.o Parallel.o \
-                                                       			RelaxationSolver.o Solution.o \
-                                                       			VariableEqualities.o)
+                               			$(addprefix $(OBJDIR)/, CutCreator.o CSFS.o \
+																														Parallel.o RelaxationSolver.o \
+																														Solution.o VariableEqualities.o)
 	$(MPICXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
 
 $(OBJDIR)/CutAndSolveWorker.o: $(addprefix $(SRCDIR)/, CutAndSolveWorker.cpp CutAndSolveWorker.h) \
@@ -112,16 +111,6 @@ $(OBJDIR)/CutSet.o: $(addprefix $(SRCDIR)/, CutSet.cpp CutSet.h) \
                     $(addprefix $(OBJDIR)/, Cut.o)
 	$(CXX) $(CXXFLAGS) -c -o $@ $<
 
-$(OBJDIR)/CutfileReader.o: $(addprefix $(SRCDIR)/, CutfileReader.cpp CutfileReader.h) \
-                           $(addprefix $(OBJDIR)/, Cut.o Individual.o Marker.o CSFS_Data.o \
-                                                   VariableEqualities.o)
-	$(CXX) $(CXXFLAGS) -c -o $@ $<
-
-$(OBJDIR)/CutfileWriter.o: $(addprefix $(SRCDIR)/, CutfileWriter.cpp CutfileWriter.h) \
-                           $(addprefix $(OBJDIR)/, CutSet.o Individual.o Marker.o CSFS_Data.o \
-                                                   VariableEqualities.o)
-	$(CXX) $(CXXFLAGS) -c -o $@ $<
-
 $(OBJDIR)/Individual.o: $(addprefix $(SRCDIR)/, Individual.cpp Individual.h)
 	$(CXX) $(CXXFLAGS) -c -o $@ $<
 

src/CSFS_Data.cpp

@@ -27,9 +27,6 @@ CSFS_Data::CSFS_Data(const std::string &configFile) :	timer(true),
 																										numHeadRows(parser.getSizeT("NUM_HEAD_ROWS")),
 																										numHeadCols(parser.getSizeT("NUM_HEAD_COLS")),
 																										logfileName(determineLogfileName()),
-																										inputCutfileName(parser.getString("CUTS_FILE")),
-																										inputCutfileProvided(inputCutfileName.empty() ? false : true),
-																										outputCutfileName(determineOutputCutfileName()),
 														           							numBins(parser.getSizeT("NUM_BINS")),
 																										numStates(numBins * numActualExprs),
 																										numIndiv(numCase + numCtrl),

src/CSFS_Data.h

@@ -51,9 +51,6 @@ class CSFS_Data
 	const std::size_t numHeadCols;
 
 	const std::string logfileName;
-	const std::string inputCutfileName;
-	const bool inputCutfileProvided;
-	const std::string outputCutfileName;	
 
 	const std::size_t numBins;
   const std::size_t numStates;