debian/changelog

-fastml (3.1-5) UNRELEASED; urgency=medium
+fastml (3.11-1) unstable; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Use secure copyright file specification URI.
   * Trim trailing whitespace.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Sat, 20 Oct 2018 20:47:58 +0000
+  [ Andreas Tille ]
+  * New upstream version
+  * debhelper 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Fri, 19 Jul 2019 20:41:51 +0200
 
 fastml (3.1-4) unstable; urgency=medium
 

debian/compat

-11
+12

debian/control

@@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.1.5
+Build-Depends: debhelper (>= 12~)
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/fastml
 Vcs-Git: https://salsa.debian.org/med-team/fastml.git
 Homepage: http://fastml.tau.ac.il/

debian/patches/g++-6.patch

-Author: Gert Wollny <gw.fossdev@debian.org>
-Last-Update: Tue, 10 May 2016
-Bug: https://bugs.debian.org/811944
-Forwarded-Upstream: no
-Description: Replace comparisons of std::*stream 
- It is no longer possible to compare std::*stream to NULL or
- to each other, hence use .good() in the first case and compare
- the pointers in the second one. 
-
---- a/libs/phylogeny/errorMsg.cpp
-+++ b/libs/phylogeny/errorMsg.cpp
-@@ -16,7 +16,7 @@
- 	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 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){
---- a/libs/phylogeny/someUtil.cpp
-+++ b/libs/phylogeny/someUtil.cpp
-@@ -353,7 +353,7 @@
- 
- 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 +401,7 @@
- 						   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 +428,7 @@
- 						   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 +452,7 @@
- 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);
- 	}
---- a/programs/fastml/bbReport.cpp
-+++ b/programs/fastml/bbReport.cpp
-@@ -47,7 +47,7 @@
- 	//}
- 	out<<" position is: "<<_position<<endl;
- //	cerr<<"reportFileIs: "<<_reportFileName<<endl;
--	if (out == NULL) {
-+	if (!out.good()) {
- 		errorMsg::reportError("unable to open output file for reporting");
- 	}
- //	exit(555);

debian/patches/remove-template-depth.patch

@@ -7,28 +7,6 @@ Description: Remove all instances of -ftemplate-depth
  hence there is no need to set a lower value that makes the
  compilation fail. 
 
---- a/libs/phylogeny/Makefile
-+++ b/libs/phylogeny/Makefile
-@@ -88,8 +88,8 @@
- 
- #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 @@
- 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)
 --- a/libs/phylogeny/tests/Makefile
 +++ b/libs/phylogeny/tests/Makefile
 @@ -1,5 +1,5 @@
@@ -39,25 +17,25 @@ Description: Remove all instances of -ftemplate-depth
  
  # -O3
  LDFLAGS= -L.. 
---- a/programs/Makefile.generic
-+++ b/programs/Makefile.generic
-@@ -53,8 +53,8 @@
- 
- .SECONDARY: $(addsuffix _cmdline.c,$(EXEC)) $(addsuffix _cmdline.h,$(EXEC)) $(addsuffix .ggo,$(EXEC))
- 
--CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
--CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
-+CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG 
-+CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG
- 
- LDFLAGSDEBUG := $(LDFLAGS) -g 
- # sources
-@@ -197,7 +197,7 @@
- 	echo $(LIB)
- 
- 
--%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG -ftemplate-depth-25
-+%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG 
- 
- %.debug: %.o 
- 
+---- programs/Makefile.generic
+-+++ programs/Makefile.generic
+-@@ -53,8 +53,8 @@
+- 
+- .SECONDARY: $(addsuffix _cmdline.c,$(EXEC)) $(addsuffix _cmdline.h,$(EXEC)) $(addsuffix .ggo,$(EXEC))
+- 
+--CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
+--CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
+-+CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG 
+-+CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG
+- 
+- LDFLAGSDEBUG := $(LDFLAGS) -g 
+- # sources
+-@@ -197,7 +197,7 @@
+- 	echo $(LIB)
+- 
+- 
+--%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG -ftemplate-depth-25
+-+%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG 
+- 
+- %.debug: %.o 
+- 

debian/patches/series

@@ -5,4 +5,3 @@ spelling.patch
 change_to_tests_dir_only_if_existing.patch
 skip_failing_tests.patch
 remove-template-depth.patch
-g++-6.patch

libs/phylogeny/#Makefile#

+#! /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

@@ -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

-// $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/someUtil.cpp

-// $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);
 	}

programs/Makefile.generic

@@ -53,8 +53,8 @@ GENGETOPT = gengetopt
 
 .SECONDARY: $(addsuffix _cmdline.c,$(EXEC)) $(addsuffix _cmdline.h,$(EXEC)) $(addsuffix .ggo,$(EXEC))
 
-CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
-CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG -ftemplate-depth-32
+CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG 
+CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG 
 
 LDFLAGSDEBUG := $(LDFLAGS) -g 
 # sources
@@ -196,7 +196,7 @@ pl:
 	echo $(LIB)
 
 
-%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG -ftemplate-depth-25
+%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG 
 
 %.debug: %.o 
 

programs/fastml/bbReport.cpp

@@ -47,7 +47,7 @@ void BandBReport::makeReport() const {
 	//}
 	out<<" position is: "<<_position<<endl;
 //	cerr<<"reportFileIs: "<<_reportFileName<<endl;
-	if (out == NULL) {
+	if (!out.good()) {
 		errorMsg::reportError("unable to open output file for reporting");
 	}
 //	exit(555);

programs/fastml/make.dep

+fastml.o fastml.debug.o: fastml.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/logFile.h \
+ sequenceDataDiff.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h bbAlg.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h bbNodeOrderAlg.h \
+ ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ bbfindBestAVDynProg.h bbReport.h ../../libs/phylogeny/distribution.h
+bbAlg.o bbAlg.debug.o: bbAlg.cpp bbAlg.h ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \
+ ../../libs/phylogeny/definitions.h bb_options.h \
+ ../../libs/phylogeny/getopt.h bb_options_list.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/gainLossAlphabet.h bbEvaluateSpecificAV.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \
+ bbReport.h ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/computeUpAlg.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/unObservableData.h \
+ ../../libs/phylogeny/maseFormat.h
+bbComputeDownAlg.o bbComputeDownAlg.debug.o: bbComputeDownAlg.cpp bbComputeDownAlg.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbComputeUpAlg.o bbComputeUpAlg.debug.o: bbComputeUpAlg.cpp bbComputeUpAlg.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbEvaluateSpecificAV.o bbEvaluateSpecificAV.debug.o: bbEvaluateSpecificAV.cpp bbEvaluateSpecificAV.h \
+ bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/sequence.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbfindBestAVDynProg.o bbfindBestAVDynProg.debug.o: bbfindBestAVDynProg.cpp bbfindBestAVDynProg.h \
+ bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h
+bbNodeOrderAlg.o bbNodeOrderAlg.debug.o: bbNodeOrderAlg.cpp bbNodeOrderAlg.h \
+ ../../libs/phylogeny/definitions.h bb_options.h \
+ ../../libs/phylogeny/getopt.h bb_options_list.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/gainLossAlphabet.h bbComputeUpAlg.h \
+ bbComputeDownAlg.h ../../libs/phylogeny/computeMarginalAlg.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/computePijComponent.h
+bb_options.o bb_options.debug.o: bb_options.cpp bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h
+bbReport.o bbReport.debug.o: bbReport.cpp bbReport.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/amino.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/codon.h
+computeMarginalReconstruction.o computeMarginalReconstruction.debug.o: computeMarginalReconstruction.cpp \
+ computeMarginalReconstruction.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/computeDownAlg.h \
+ ../../libs/phylogeny/computeMarginalAlg.h ../../libs/phylogeny/treeIt.h
+jointNoGamma.o jointNoGamma.debug.o: jointNoGamma.cpp jointNoGamma.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h \
+ ../../libs/phylogeny/suffStatComponent.h suffStatComponentJointNoGamma.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/seqContainerTreeMap.h \
+ ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/sequenceContainer.h
+mainbb.o mainbb.debug.o: mainbb.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \
+ ../../libs/phylogeny/definitions.h bb_options_list.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/pijAccelerator.h \
+ ../../libs/phylogeny/replacementModel.h \
+ ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \
+ ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/aaJC.h \
+ ../../libs/phylogeny/amino.h ../../libs/phylogeny/codon.h bbAlg.h \
+ ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \
+ ../../libs/phylogeny/stochasticProcess.h \
+ ../../libs/phylogeny/multipleStochasticProcess.h \
+ ../../libs/phylogeny/gammaDistribution.h \
+ ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \
+ ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \
+ ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \
+ ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \
+ bbReport.h ../../libs/phylogeny/distribution.h \
+ ../../libs/phylogeny/bestAlpha.h \
+ ../../libs/phylogeny/likelihoodComputation.h \
+ ../../libs/phylogeny/computePijComponent.h \
+ ../../libs/phylogeny/suffStatComponent.h \
+ ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bblEM.h \
+ ../../libs/phylogeny/countTableComponent.h \
+ ../../libs/phylogeny/chebyshevAccelerator.h \
+ ../../libs/phylogeny/clustalFormat.h computeMarginalReconstruction.h \
+ ../../libs/phylogeny/distanceTable.h \
+ ../../libs/phylogeny/distanceMethod.h ../../libs/phylogeny/fastaFormat.h \
+ ../../libs/phylogeny/gammaDistribution.h jointNoGamma.h \
+ suffStatComponentJointNoGamma.h ../../libs/phylogeny/likeDist.h \
+ ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/molphyFormat.h \
+ ../../libs/phylogeny/nexusFormat.h ../../libs/phylogeny/nucleotide.h \
+ ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/nj.h \
+ ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \
+ ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/gtrModel.h \
+ ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/hky.h \
+ ../../libs/phylogeny/phylipFormat.h ../../libs/phylogeny/readDatMatrix.h \
+ ../../libs/phylogeny/datMatrixHolder.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/trivialAccelerator.h \
+ ../../libs/phylogeny/uniDistribution.h \
+ ../../libs/phylogeny/bestGtrModelParams.h \
+ ../../libs/phylogeny/gtrModel.h ../../libs/phylogeny/bestTamura92param.h \
+ ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/bestHKYparam.h \
+ ../../libs/phylogeny/hky.h ../../libs/phylogeny/bestAlphaAndK.h \
+ ../../libs/phylogeny/likelihoodComputation2Codon.h \
+ ../../libs/phylogeny/wYangModel.h ../../libs/phylogeny/bblEM2codon.h \
+ ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \
+ ../../libs/phylogeny/uniformDistribution.h \
+ ../../libs/phylogeny/codonUtils.h ../../libs/phylogeny/nucleotide.h \
+ ../../libs/phylogeny/amino.h ../../libs/phylogeny/fastaFormat.h \
+ ../../libs/phylogeny/clustalFormat.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/evaluateCharacterFreq.h
+sequenceDataDiff.o sequenceDataDiff.debug.o: sequenceDataDiff.cpp sequenceDataDiff.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h
+suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.debug.o: suffStatComponentJointNoGamma.cpp \
+ suffStatComponentJointNoGamma.h ../../libs/phylogeny/definitions.h

programs/indelCoder/make.dep

+indelCoder.o indelCoder.debug.o: indelCoder.cpp indelCoder.h gaps.h \
+ ../../libs/phylogeny/definitions.h character.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \
+ indelCoderOptions.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/talRandom.h indelCoderUtils.h
+indelCoderOptions.o indelCoderOptions.debug.o: indelCoderOptions.cpp indelCoderOptions.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \
+ ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \
+ ../../libs/phylogeny/Parameters.h
+indelCoderProject.o indelCoderProject.debug.o: indelCoderProject.cpp indelCoder.h gaps.h \
+ ../../libs/phylogeny/definitions.h character.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \
+ indelCoderOptions.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/talRandom.h indelCoderUtils.h \
+ ../../libs/phylogeny/Parameters.h
+indelCoderUtils.o indelCoderUtils.debug.o: indelCoderUtils.cpp indelCoderUtils.h \
+ ../../libs/phylogeny/logFile.h indelCoder.h gaps.h \
+ ../../libs/phylogeny/definitions.h character.h \
+ ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \
+ ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \
+ indelCoderOptions.h ../../libs/phylogeny/amino.h \
+ ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \
+ ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \
+ ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \
+ ../../libs/phylogeny/mulAlphabet.h \
+ ../../libs/phylogeny/gainLossAlphabet.h \
+ ../../libs/phylogeny/recognizeFormat.h \
+ ../../libs/phylogeny/sequenceContainer.h \
+ ../../libs/phylogeny/talRandom.h
+character.o character.debug.o: character.cpp character.h ../../libs/phylogeny/definitions.h \
+ gaps.h ../../libs/phylogeny/matrixUtils.h \
+ ../../libs/phylogeny/definitions.h ../../libs/phylogeny/logFile.h \
+ ../../libs/phylogeny/errorMsg.h indelCoderOptions.h
+gaps.o gaps.debug.o: gaps.cpp gaps.h ../../libs/phylogeny/definitions.h