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Makefile
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Makefile
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TIPars: TIPars.java
javac -classpath .:beast.jar TIPars.java;\
jar cvfm TIPars.jar MANIFEST.MF *class;\
rm -rf *class
test: TIPars
java -classpath .:beast.jar TIPars FourExamples/Try1_KC542905/NDV_fullg.tree FourExamples/Try1_KC542905/NDV_fullg.fas FourExamples/Try1_KC542905/anc_NDV_fullg.fas FourExamples/Try1_KC542905/KC542905.fas test.tree 1 label GenName
testRscript: TIPars
./tipars.rsh -t FourExamples/Try1_KC542905/NDV_fullg.tree -s FourExamples/Try1_KC542905/NDV_fullg.fas -a FourExamples/Try1_KC542905/anc_NDV_fullg.fas -q FourExamples/Try1_KC542905/KC542905.fas -o test.nex
testscript: TIPars
./tipars -t FourExamples/rm2.tree -s FourExamples/taxa_seq.fas -a FourExamples/anc_seq.fas -q FourExamples/KC542905_KM885167.fas -o test.nwk
testReadFASTA:
cd test;\
javac -classpath ..:../beast.jar testReadFASTA.java;\
echo "";\
echo "--> sample fasta file:";\
echo "";\
cat testData/sampleFASTA.fas;\
echo "";\
echo "--> file contains parsed by readFastaAlignmentFile:";\
echo "";\
java -classpath ..:../beast.jar:../TIPars.jar testReadFASTA
testTreeReader:
cd test;\
javac -classpath ..:../beast.jar:../TIPars.jar testTreeReader.java;\
java -classpath ..:../beast.jar:../TIPars.jar testTreeReader