Commit 05b00510 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.11

parent f8fc59f5

libs/phylogeny/#Makefile#

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#! /usr/local/bin/gmake

# $Id: Makefile 11759 2013-09-24 13:45:40Z elilevy $

# makfile for yaep5







# use LOGREP=t or DOUBLEREP=t to activate logRep or doubleRep respectively (or setenv DOUBLEREP in the shell)

#DOUBLEREP=t

#LOGREP=t





Libsources= AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp				\

   allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp			\

   bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp			\

   bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp	\

   chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp			\

   computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp				\

   computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp			\

   computeSubstitutionCounts.cpp											\

   computePosteriorExpectationOfSubstitutions.cpp							\

   computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp			\

   ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp	\

   distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp				\

   fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp					\

   fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp 	\

   fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp				\

   generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp	\

   generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp		\

   granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp \

   likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp						\

   likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp				\

   molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp				\

   nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp			\

   pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp		\

   replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp			\

   sequence.cpp sequenceContainer.cpp simulateTree.cpp					\

   siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp				\

   splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp			\

   talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp			\

   uniformDistribution.cpp cmdline2EvolObjs.cpp						\

   generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp					\

   givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp					\

   posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp			\

   logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp					\

   replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp		\

   C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp			\

   betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp				\

   samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp				\

   likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp			\

   fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp				\

   tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp			\

   simulateCodonsJumps.cpp													\

   simulateJumpsAbstract.cpp												\

   ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp\

   extremeValDistribution.cpp \

   gammaDistributionFixedCategories.cpp  generalGammaDistributionPlusInvariant.cpp  gammaDistributionPlusInvariant.cpp   \

   distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp 					\

   optGammaMixtureLS.cpp mixtureDistribution.cpp  suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp \

   wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp	\

	threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp	\

	bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp\

	gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp



# do not use: fromInstructionFile.cpp, simulateSequnce.cpp  split.save.cpp





# LibCsources= cmdline.c

# LibCsources += getopt.c getopt1.c 



EXEC = 

#TEST_EXEC_SUB = split_test splitMap_test bootstrap_test

TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB))

LIB = libEvolTree.a

DEBUGLIB = $(LIB:.a=Debug.a)

DOUBLEREPLIB = $(LIB:.a=DoubleRep.a)





#CC=g++

CXX=g++

CC=$(CXX)



#requres 2.13, but may work with 2.11

GENGETOPT = gengetopt

# osX/tiger

#GENGETOPT = /opt/local/bin/gengetopt



.SECONDARY: semphy_cmdline.c semphy_cmdline.h



#LDFLAGS=  



CPPFLAGS=  -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32AGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS

#CPPFLAGSDOU=  $(CPPFLAGS) 

#-pg





#CPPFLAGS+= -I/usr/include/g++-v3

#CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK



# sources

sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC))



.PHONY: tests lib test debug %.debug

.PHONY:  dat DOUBLEREP doubleRep



all: lib $(EXEC)



test: all tests

	+cd tests; make -k test



#ifdef DOUBLEREP

#CPPFLAGS+= -DLOGREP

#CPPFLAGSDEBUG += -DLOGREP

#LDFLAGSDEBUG +=  -DLOGREP

#endif



ifdef DOUBLEREP

CPPFLAGS+= -DDOUBLEREP

CPPFLAGSDEBUG += -DDOUBLEREP

LDFLAGSDEBUG +=  -DDOUBLEREP

endif



debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32

debug:  $(DEBUGLIB)

pl:

	@echo "lib  ="$(LIB)

	@echo "debug="$(DEBUGLIB)

#debug: all 

#	cp libEvolTree.a libEvolTreeDebug.a



# <<<<<<< Makefile

# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25

# % debug: LIB = libEvolTreeDebug.a

# %.debug: %

# 	@echo "made \""$(*)"\" in debug mode"



# =======

#>>>>>>> 2.34



lib: $(LIB)



$(LIB): $(Libsources:.cpp=.o) $(LibCsources:.c=.o)

	ar rv $@ $?

	ranlib $@



tags: *.cpp *.h

	etags --members --language=c++ $^ 



$(EXEC) $(TEST_EXEC): $(LIB)

tests: $(TEST_EXEC)



-include make.dep



install:

	cd ../fast; make -f Makefile.lib install_do





clean:

	-rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) *.o





ifneq ($(wildcard make.dep), make.dep)

 make.dep: depend

endif



depend makedep: _make.dep

	@mv -f _make.dep make.dep 



_make.dep: $(sources)

	@echo making depend

#	$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@' 

	@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@' 

_fast:

	cd ../fast;make -f Makefile.lib -k all



fast.% _fast.%:

	cd ../fast;make -f Makefile.lib -k $(*)





simulateSequnce: simulateSequnce_cmdline.o





evolObjsTest.ggo: evolObjs.header evolObjs.args

	cat $^ > $@





# commandline (gengetopts)

%_cmdline.h %_cmdline.c: %.ggo

	$(GENGETOPT)  -i$< -F$(*)_cmdline



%.dat.q: %.dat

	awk 'BEGIN{RS="[\n\r]+";};{print "\" "$$0" \"\r"}' $< >  $@

#	cat $@



DAT = cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q



dat: $(DAT)



cleandat:

	rm $(DAT)



datMatrixHolder.o: $(DAT)



.PRECIOUS: $(DAT)



debug: LIB = $(DEBUGLIB)



%.debug: CPPFLAGS = $(CPPFLAGSDEBUG)

%.debug: %

	@echo "made \""$(*)"\" in debug mode"





%.debug.o: %.c

	$(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@



%.debug.o: %.cpp

	$(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@



$(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)

	ar rv $@ $?

	ranlib $@



#doubleRep: LOGREP=t

#doubleRep: CPPFLAGS+= -DLOGREP

doubleRep: DOUBLEREP=t

doubleRep: CPPFLAGS+= -DDOUBLEREP

doubleRep: $(DOUBLEREPLIB)



%.doubleRep.o: %.c

	$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@



%.doubleRep.o: %.cpp

	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@



$(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o)

	ar rv $@ $?

	ranlib $@



# DO NOT DELETE

libs/phylogeny/Makefile

+4 −4
Original line number Diff line number Diff line
@@ -88,8 +88,8 @@ GENGETOPT = gengetopt 


#LDFLAGS=  



CPPFLAGS=  -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32

CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS

CPPFLAGS=  -O3 -Wall -Wno-sign-compare -I. -DLOG 

CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -DVERBOS

#CPPFLAGSDOU=  $(CPPFLAGS) 

#-pg
@@ -120,7 +120,7 @@ CPPFLAGSDEBUG += -DDOUBLEREP 
LDFLAGSDEBUG +=  -DDOUBLEREP

endif



debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32

debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG 

debug:  $(DEBUGLIB)

pl:

	@echo "lib  ="$(LIB)
@@ -129,7 +129,7 @@ pl: 
#	cp libEvolTree.a libEvolTreeDebug.a



# <<<<<<< Makefile

# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25

# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG 

# % debug: LIB = libEvolTreeDebug.a

# %.debug: %

# 	@echo "made \""$(*)"\" in debug mode"

libs/phylogeny/errorMsg.cpp

+3 −3
Original line number Diff line number Diff line 
// $Id: errorMsg.cpp 6066 2009-04-14 19:11:10Z itaymay $

// $Id: errorMsg.cpp 15479 2016-10-10 16:25:21Z elilevy $



// version 1.01

// last modified 1 Jan 2004
@@ -16,7 +16,7 @@ void errorMsg::reportError(const vector<string>& textToPrint, const int exitCode 
	for (int i =0 ; i < textToPrint.size() ; ++i) {

		LOG(1,<<textToPrint[i]<<endl);

		cerr<<textToPrint[i]<<endl;

		if (_errorOut != NULL && *_errorOut != cerr)  {

		if (_errorOut != NULL && _errorOut != &cerr)  {

			(*_errorOut)<<textToPrint[i]<<endl;

		}

	}
@@ -31,7 +31,7 @@ void errorMsg::reportError(const vector<string>& textToPrint, const int exitCode 
void errorMsg::reportError(const string& textToPrint, const int exitCode) {

	LOG(1,<<endl<<textToPrint<<endl);

	cerr<<endl<<textToPrint<<endl;

	if (_errorOut != NULL && *_errorOut != cerr)  {

	if (_errorOut != NULL && _errorOut != &cerr)  {

		(*_errorOut)<<textToPrint<<endl;

	}

	if (errno!=0){

libs/phylogeny/make.dep

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+820 −0

File added.

Preview size limit exceeded, changes collapsed.

libs/phylogeny/someUtil.cpp

+11 −7
Original line number Diff line number Diff line 
// $Id: someUtil.cpp 11906 2013-12-26 10:12:24Z itaymay $

// $Id: someUtil.cpp 15479 2016-10-10 16:25:21Z elilevy $



#include "someUtil.h"

#include "errorMsg.h"
@@ -226,13 +226,17 @@ bool isCharInString(const string& stringToCheck, const char charToCheck) { 
string double2string(const double x, const int lenght, bool round){

	

	// first getting the integer part:

	//Itay: fixing bug regarding negative floats 

	double x_abs = fabs(x);

	int theIntegerPart = static_cast<int>(x_abs);

	double theRemainingPart = fabs(x_abs-theIntegerPart);

	int integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght));

	if (round)

	if (round) {

		integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght)+0.5);

		if (integerRepresentingTheRemainingPart == pow(10.0,lenght)) {

			integerRepresentingTheRemainingPart = 0;

			theIntegerPart++;

		}

	}



	string part1 = int2string(theIntegerPart);

	string part2 = int2string(integerRepresentingTheRemainingPart);
@@ -353,7 +357,7 @@ MDOUBLE string2double(const string& inString) { 


bool checkThatFileExist(const string& fileName) {

	ifstream file1(fileName.c_str());

	if (file1==NULL) return false;

	if (!file1.good()) return false;

	file1.close();

	return true;

}
@@ -401,7 +405,7 @@ string* searchStringInFile(const string& string2find, 
						   const string& inFileName) {

	ifstream f;

	f.open(inFileName.c_str());

	if (f==NULL) {

	if (!f.good()) {

		string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; 

		errorMsg::reportError(tmp);

	}
@@ -428,7 +432,7 @@ string* searchStringInFile(const string& string2find, 
						   const string& inFileName) {// return the string that is AFTER the string to search.

	ifstream f;

	f.open(inFileName.c_str());

	if (f==NULL) {

	if (!f.good()) {

		string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; 

		errorMsg::reportError(tmp);

	}
@@ -452,7 +456,7 @@ string* searchStringInFile(const string& string2find, 
bool doesWordExistInFile(const string& string2find,const string& inFileName) {

	ifstream f;

	f.open(inFileName.c_str());

	if (f==NULL) {

	if (!f.good()) {

		string tmp = "Unable to open file name: "+inFileName+" in function searchStringInFile"; 

		errorMsg::reportError(tmp);

	}