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|
CPPFLAGS= -g -Wall -Wno-sign-compare -I.. -DLOG -O0
CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I.. -DLOG
# -O3
LDFLAGS= -L..
LDLIBS= -lEvolTree
CC=g++
CXX=g++
.PHONY: test tests run all clean
TESTS= split_test splitMap_test \
given2seqTheDistBetweenThem-3 \
given2seqEstimateTheDistBetweenThem \
checkTreeLikelihoodGivenBranches \
given2seqEstimateTheDistBetweenThemGamma \
given2seqEstimateTheDistanceK2P \
doubleRep readTreeWithComments
# Test fails: bootstrap_test
#./bootstrap_test > bootstrap_test.out.tmp
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#
# WARN: Tree with no branch length! Create Flat tree with all branches= 0.3
#diff bootstrap_test.out.tmp bootstrap_test.out.standard
#25c25
#< ((Baboon:0.3,Human:0.3):0.3[1],(Rat:0.3,(Langur:0.3,Cow:0.3):0.3[0.4]):0.3[0.8],Horse:0.3);
#---
#> ((Baboon:1e-06,Human:1e-06):1e-06[1],(Rat:1e-06,(Langur:1e-06,Cow:1e-06):1e-06[0.4]):1e-06[0.8],Horse:1e-06);
#44c44
#< ((Baboon:0.3,Human:0.3):0.3[1],(Rat:0.3,(Langur:0.3,Cow:0.3):0.3[0.2]):0.3[0.8],Horse:0.3);
#---
#> ((Baboon:1e-06,Human:1e-06):1e-06[1],(Rat:1e-06,(Langur:1e-06,Cow:1e-06):1e-06[0.2]):1e-06[0.8],Horse:1e-06);
#
# This test does not build: computeNJtreeJCmodel
# Its probably easy to fix for a C++ expert which I'm not.
#g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. computeNJtreeJCmodel.cpp ../libEvolTree.a -lEvolTree -o computeNJtreeJCmodel
#computeNJtreeJCmodel.cpp: In function 'int main(int, char**)':
#computeNJtreeJCmodel.cpp:38:36: error: no matching function for call to 'jcDistance::jcDistance(int)'
# jcDistance likeDist1(myAlph.size());
# ^
#In file included from computeNJtreeJCmodel.cpp:15:0:
#../jcDistance.h:20:11: note: candidate: jcDistance::jcDistance()
# explicit jcDistance() {}
# ^
#../jcDistance.h:20:11: note: candidate expects 0 arguments, 1 provided
#../jcDistance.h:17:7: note: candidate: jcDistance::jcDistance(const jcDistance&)
# class jcDistance : public distanceMethod {
# ^
#../jcDistance.h:17:7: note: no known conversion for argument 1 from 'int' to 'const jcDistance&'
#<builtin>: recipe for target 'computeNJtreeJCmodel' failed
#make[5]: *** [computeNJtreeJCmodel] Error 1
#
# This test fails with rounding errors: optimizeBranchesJC_EM_gamma \
#./optimizeBranchesJC_EM_gamma > optimizeBranchesJC_EM_gamma.out.tmp
#diff optimizeBranchesJC_EM_gamma.out.tmp optimizeBranchesJC_EM_gamma.out.standard
#4,5c4,5
#< end L, after bbl = -2179.45593639
#< (Aal:0.059123756765,(Ese:0.066031306941,(Ttt:0.017925964110,Mtr:0.051557201876):0.069475675657):0.041343951589,(Eco:0.106659060114,(Dvi:0.123977612881,Meu:0.040982968534):0.105961225843):0.033195707855);
#---
#> end L, after bbl = -2179.45590941
#> (Aal:0.059126005932,(Ese:0.066030633739,(Ttt:0.017928742924,Mtr:0.051557833141):0.069475141702):0.041343973825,(Eco:0.106662142475,(Dvi:0.124009000428,Meu:0.040988634764):0.105976705171):0.033194854881);
#
# This test fails with rounding errors: optimizeBranchesJC_EM
#./optimizeBranchesJC_EM > optimizeBranchesJC_EM.out.tmp
#diff optimizeBranchesJC_EM.out.tmp optimizeBranchesJC_EM.out.standard
#4,5c4,5
#< end L, after bbl = -2219.50592652
#< (Aal:0.055487180117,(Ese:0.060837044471,(Ttt:0.018202243293,Mtr:0.048145476102):0.062911273468):0.037594602635,(Eco:0.092932645284,(Dvi:0.108154575121,Meu:0.042029680173):0.089340773079):0.033011606765);
#---
#> end L, after bbl = -2219.50591327
#> (Aal:0.055486320897,(Ese:0.060836383576,(Ttt:0.018202550909,Mtr:0.048144922650):0.062910979704):0.037581468483,(Eco:0.092932108224,(Dvi:0.108160657949,Meu:0.042026386196):0.089296640074):0.033019500657);
#
# This test fails with rounding errors: optimizeBranchesJC_EM_gam_estimate_alp \
#./optimizeBranchesJC_EM_gam_estimate_alp > optimizeBranchesJC_EM_gam_estimate_alp.out.tmp
#diff optimizeBranchesJC_EM_gam_estimate_alp.out.tmp optimizeBranchesJC_EM_gam_estimate_alp.out.standard
#5,6c5,6
#< best Alpha: 0.501705
#< (Aal:0.059680,(Ese:0.068325,(Ttt:0.017213,Mtr:0.052726):0.072593):0.043673,(Eco:0.114733,(Dvi:0.133443,Meu:0.039593):0.117925):0.033169);
#---
#> best Alpha: 0.501635
#> (Aal:0.059683,(Ese:0.068312,(Ttt:0.017214,Mtr:0.052743):0.072642):0.043677,(Eco:0.114730,(Dvi:0.133475,Meu:0.039589):0.117996):0.033172);
#
# This test fails with rounding errors: optimize_HKY_param
#./optimize_HKY_param > optimize_HKY_param.out.tmp
#diff optimize_HKY_param.out.tmp optimize_HKY_param.out.standard
#9,10c9,10
#< best HKY parameter: 1.5
#< (Aal:0.052947,(Ese:0.061028,(Ttt:0.015761,Mtr:0.050387):0.065489):0.039154,(Eco:0.095918,(Dvi:0.107884,Meu:0.044735):0.093191):0.034441);
#---
#> best HKY parameter: 1.5181
#> (Aal:0.052945,(Ese:0.061027,(Ttt:0.015761,Mtr:0.050395):0.065493):0.039148,(Eco:0.095915,(Dvi:0.107929,Meu:0.044734):0.093162):0.034430);
#
#ludouble_test DistanceTableFromTree
OTHER_TESTS= exhaustiveSearch
all: test
run: $(addsuffix .out.tmp,$(TESTS))
libEvolDebug=../libEvolTreeDebug.a
DEBUGEXEC = $(addsuffix .debug,$(TESTS))
$(DEBUGEXEC): $(libEvolDebug)
$(TESTS): ../libEvolTree.a
test: $(addsuffix .test,$(TESTS))
alltest: $(addsuffix .test,$(TESTS) $(OTHER_TESTS))
%.test: %.out.tmp %.out.standard
diff $^
readTreeWithComments.out.tmp: readTreeWithComments treeWithComments.tree
./$^>$@
%.out.tmp: %
./$(*) > $@
tests: $(TESTS)
%.debug.o: %.c
$(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@
%.debug.o: %.cpp
$(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@
debug: $(DEBUGEXEC)
clean:
-rm -f $(TESTS) *.out.tmp *.o
|
