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Makefile
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CC = g++
#CXXFLAGS = -I "src/utils" -Wall -fno-inline -O2 -std=c++11 -g3
#CXXFLAGS = -I "src/utils" -U__STRICT_ANSI__ -Wall -std=c++11 -O3 -DMULTI_PAIRWISE #-pg -ggdb -Bstatic #-static
CXXFLAGS = -I "src/utils" -U__STRICT_ANSI__ -Wall -std=c++11 -O3 -pthread #-DMULTI_PAIRWISE #-DCORES #-DUSE_CACHED_FILES #-DSPARSE -ggdb #-pg
ifeq ($(SPARSE), 1)
CXXFLAGS := $(CXXFLAGS)-DSPARSE
endif
ifeq ($(MULTI), 1)
CXXFLAGS := $(CXXFLAGS)-DMULTI_PAIRWISE
endif
INCLUDES =
LFLAGS =
LIBS =
METHODS_SRC = \
src/methods/SANA.cpp \
src/methods/GreedyLCCS.cpp \
src/methods/HillClimbing.cpp \
src/methods/Method.cpp \
src/methods/NoneMethod.cpp \
src/methods/RandomAligner.cpp \
src/methods/TabuSearch.cpp \
src/methods/WeightedAlignmentVoter.cpp \
src/methods/Dijkstra.cpp
UTILS_SRC = \
src/utils/NormalDistribution.cpp \
src/utils/templateUtils.cpp \
src/utils/Timer.cpp \
src/utils/utils.cpp \
src/utils/randomSeed.cpp \
src/utils/SkipList.cpp \
src/utils/SeedMatrix.cpp \
src/utils/LinearRegression.cpp \
src/utils/ParetoFront.cpp \
src/utils/Matrix.cpp
ARGUMENTS_SRC = \
src/arguments/ArgumentParser.cpp \
src/arguments/modeSelector.cpp \
src/arguments/measureSelector.cpp \
src/arguments/methodSelector.cpp \
src/arguments/graphLoader.cpp \
src/arguments/supportedArguments.cpp \
src/arguments/defaultArguments.cpp
MEASURES_SRCS = \
src/measures/EdgeCorrectness.cpp \
src/measures/EdgeDifference.cpp \
src/measures/EdgeRatio.cpp \
src/measures/TriangleCorrectness.cpp \
src/measures/MultiEdgeCorrectness.cpp \
src/measures/ExternalWeightedEdgeConservation.cpp \
src/measures/GoAverage.cpp \
src/measures/NetGO.cpp \
src/measures/InducedConservedStructure.cpp \
src/measures/InvalidMeasure.cpp \
src/measures/LargestCommonConnectedSubgraph.cpp \
src/measures/Measure.cpp \
src/measures/MeasureCombination.cpp \
src/measures/NodeCorrectness.cpp \
src/measures/ShortestPathConservation.cpp \
src/measures/SymmetricSubstructureScore.cpp \
src/measures/SymmetricEdgeCoverage.cpp \
src/measures/SquaredEdgeScore.cpp \
src/measures/EdgeExposure.cpp \
src/measures/WeightedEdgeConservation.cpp \
src/measures/MultiS3.cpp \
src/measures/localMeasures/EdgeCount.cpp \
src/measures/localMeasures/EdgeDensity.cpp \
src/measures/localMeasures/ExternalSimMatrix.cpp \
src/measures/localMeasures/GenericLocalMeasure.cpp \
src/measures/localMeasures/GoSimilarity.cpp \
src/measures/localMeasures/Graphlet.cpp \
src/measures/localMeasures/GraphletLGraal.cpp \
src/measures/localMeasures/Importance.cpp \
src/measures/localMeasures/LocalMeasure.cpp \
src/measures/localMeasures/NodeCount.cpp \
src/measures/localMeasures/NodeDensity.cpp \
src/measures/localMeasures/Sequence.cpp \
src/measures/localMeasures/GraphletCosine.cpp \
src/measures/localMeasures/GraphletNorm.cpp
METHOD_WRAPPERS_SRC = \
src/methods/wrappers/WrappedMethod.cpp \
src/methods/wrappers/HubAlignWrapper.cpp \
src/methods/wrappers/LGraalWrapper.cpp \
src/methods/wrappers/NETALWrapper.cpp \
src/methods/wrappers/MIGRAALWrapper.cpp \
src/methods/wrappers/GHOSTWrapper.cpp \
src/methods/wrappers/PISwapWrapper.cpp \
src/methods/wrappers/OptNetAlignWrapper.cpp \
src/methods/wrappers/SPINALWrapper.cpp \
src/methods/wrappers/GREATWrapper.cpp \
src/methods/wrappers/NATALIEWrapper.cpp \
src/methods/wrappers/GEDEVOWrapper.cpp \
src/methods/wrappers/MagnaWrapper.cpp \
src/methods/wrappers/WAVEWrapper.cpp \
src/methods/wrappers/PINALOGWrapper.cpp \
src/methods/wrappers/SANAPISWAPWrapper.cpp \
src/methods/wrappers/CytoGEDEVOWrapper.cpp \
SCHEDULEMETHODS_SRC = \
src/schedulemethods/Ameur.cpp \
src/schedulemethods/IteratedAmeur.cpp \
src/schedulemethods/LinearRegressionModern.cpp \
src/schedulemethods/LinearRegressionVintage.cpp \
src/schedulemethods/PBadBinarySearch.cpp \
src/schedulemethods/ScheduleMethod.cpp \
src/schedulemethods/scheduleUtils.cpp \
src/schedulemethods/StatisticalTest.cpp \
src/schedulemethods/IteratedLinearRegression.cpp
MODES_SRC = \
src/modes/AlphaEstimation.cpp \
src/modes/Experiment.cpp \
src/modes/ParameterEstimation.cpp \
src/modes/NormalMode.cpp \
src/modes/DebugMode.cpp \
src/modes/ClusterMode.cpp \
src/modes/AnalysisMode.cpp \
src/modes/SimilarityMode.cpp \
src/modes/ParetoMode.cpp
OTHER_SRC = \
src/Graph.cpp \
src/computeGraphlets.cpp \
src/Alignment.cpp \
src/complementaryProteins.cpp \
src/main.cpp \
src/report.cpp
SRCS = $(METHODS_SRC) $(OTHER_SRC) $(UTILS_SRC) $(MEASURES_SRCS) $(METHOD_WRAPPERS_SRC) $(SCHEDULEMETHODS_SRC) $(ARGUMENTS_SRC) $(MODES_SRC)
OBJDIR = _objs
OBJS = $(addprefix $(OBJDIR)/, $(SRCS:.cpp=.o))
#MAIN = sana_dbg
MAIN = sana
.PHONY: depend clean test test_all regression_test
all: $(MAIN) argumentCSV createShadow
$(MAIN): $(OBJS)
$(CC) $(CXXFLAGS) $(INCLUDES) -o $(MAIN) $(OBJS) $(LFLAGS) $(LIBS)
$(MAIN).static: $(OBJS)
$(CC) $(CXXFLAGS) -static $(INCLUDES) -o $(MAIN).static $(OBJS) $(LFLAGS) $(LIBS)
#.c.o:
# $(CC) $(CXXFLAGS) $(INCLUDES) -c $< -o $@
#$(OBJDIR)/%.o: %.c
# $(CC) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
$(OBJDIR)/%.o: %.cpp
@mkdir -p $(dir $@)
$(CC) -c $(INCLUDES) -o $@ $< $(CXXFLAGS)
# TEST_SRC is anything that ends in _UT (unit test)
TEST_SRC = $(wildcard test/*_UT.cpp)
# TEST_DEPENDS is all the OBJS without main and Gtest
_MAIN_OBJ = $(OBJDIR)/src/main.o
TEST_DEPENDS = $(filter-out $(_MAIN_OBJ), $(OBJS))
GTEST_OBJS = test/gtest/gtest-main.o test/gtest/gtest-all.o
TEST_OBJS = $(addprefix $(OBJDIR)/, $(TEST_SRC:.cpp=.o))
TEST_MAIN = unit_test
TEST_CXXFLAGS = $(CXXFLAGS) -lpthread # add pthread for Gtest
regression_test:
./regressionTest.sh
argumentCSV:
(cd src/arguments; ./create-csv.sh)
test_all: $(TEST_OBJS) $(GTEST_OBJS) $(TEST_DEPENDS)
$(CC) $(TEST_CXXFLAGS) $(INCLUDES) -o $(OBJDIR)/$(TEST_MAIN) $(TEST_OBJS) $(GTEST_OBJS) $(TEST_DEPENDS) $(LFLAGS) $(LIBS)
./$(OBJDIR)/$(TEST_MAIN)
test: $(OBJDIR)/test/$(tg).o $(GTEST_OBJS) $(TEST_DEPENDS)
$(CC) $(TEST_CXXFLAGS) $(INCLUDES) -o $(OBJDIR)/$(tg) $(OBJDIR)/test/$(tg).o $(GTEST_OBJS) $(TEST_DEPENDS) $(LFLAGS) $(LIBS)
./$(OBJDIR)/$(tg)
$(GTEST_OBJS):
cd test/gtest && make
clean: #clear_cache
$(RM) -rf cache* # mostly for pBad
$(RM) -rf $(OBJDIR)/src
$(RM) $(MAIN)
$(RM) -f src/arguments/argumentTable.csv
clear_cache:
rm -rf autogenerated
rm -rf matrices/autogenerated
rm -rf tmp
rm -rf networks/*/autogenerated
rm -rf cache_pbad
depend: $(SRCS)
makedepend $(INCLUDES) $^
# Here is the targets for making the wrappedAlgorithms
optnetalign:
cd wrappedAlgorithms/OptNetAlign/src; $(MAKE) optnetalignubuntu; chmod +x optnetalign; cp optnetalign ../
multi:
$(MAKE) 'MULTI=1'
mv sana sana.multi
createShadow: scripts/createShadowCpp/createShadow
mv scripts/createShadowCpp/createShadow .