diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..c120555 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,4 @@ + +script: + - make + - ./snap HMM/thale DNA/thale.dna.gz diff --git a/Zoe/depend b/Zoe/depend index f6961e8..068b79e 100644 --- a/Zoe/depend +++ b/Zoe/depend @@ -1,40 +1,39 @@ zoeCDS.o: zoeCDS.c zoeCDS.h zoeDNA.h zoeFastaFile.h zoeTools.h \ - zoeProtein.h zoeFeature.h zoeFeatureTable.h + zoeProtein.h zoeFeature.h zoeFeatureTable.h zoeCounter.o: zoeCounter.c zoeCounter.h zoeDNA.h zoeFastaFile.h \ - zoeTools.h zoeProtein.h zoeFeature.h zoeMath.h zoeModel.h + zoeTools.h zoeProtein.h zoeFeature.h zoeMath.h zoeModel.h zoeDNA.o: zoeDNA.c zoeDNA.h zoeFastaFile.h zoeTools.h zoeProtein.h \ - zoeFeature.h + zoeFeature.h zoeDistribution.o: zoeDistribution.c zoeDistribution.h zoeMath.h \ - zoeTools.h + zoeTools.h zoeDuration.o: zoeDuration.c zoeDuration.h zoeDistribution.h zoeMath.h \ - zoeTools.h zoeFeature.h + zoeTools.h zoeFeature.h zoeFastaFile.o: zoeFastaFile.c zoeFastaFile.h zoeTools.h zoeFeature.o: zoeFeature.c zoeFeature.h zoeTools.h zoeFeatureFactory.o: zoeFeatureFactory.c zoeFeatureFactory.h zoeDNA.h \ - zoeFastaFile.h zoeTools.h zoeProtein.h zoeFeature.h zoeScanner.h \ - zoeMath.h zoeModel.h zoeFeatureTable.h zoeCDS.h + zoeFastaFile.h zoeTools.h zoeProtein.h zoeFeature.h zoeScanner.h \ + zoeMath.h zoeModel.h zoeFeatureTable.h zoeCDS.h zoeFeatureTable.o: zoeFeatureTable.c zoeFeatureTable.h zoeCDS.h zoeDNA.h \ - zoeFastaFile.h zoeTools.h zoeProtein.h zoeFeature.h + zoeFastaFile.h zoeTools.h zoeProtein.h zoeFeature.h zoeHMM.o: zoeHMM.c zoeHMM.h zoeDuration.h zoeDistribution.h zoeMath.h \ - zoeTools.h zoeFeature.h zoeState.h zoeModel.h zoeDNA.h zoeFastaFile.h \ - zoeProtein.h zoePhasePref.h zoeTransition.h + zoeTools.h zoeFeature.h zoeState.h zoeModel.h zoeDNA.h zoeFastaFile.h \ + zoeProtein.h zoePhasePref.h zoeTransition.h zoeIsochore.o: zoeIsochore.c zoeHMM.h zoeDuration.h zoeDistribution.h \ - zoeMath.h zoeTools.h zoeFeature.h zoeState.h zoeModel.h zoeDNA.h \ - zoeFastaFile.h zoeProtein.h zoePhasePref.h zoeTransition.h \ - zoeIsochore.h + zoeMath.h zoeTools.h zoeFeature.h zoeState.h zoeModel.h zoeDNA.h \ + zoeFastaFile.h zoeProtein.h zoePhasePref.h zoeTransition.h zoeIsochore.h zoeMath.o: zoeMath.c zoeMath.h zoeTools.h zoeModel.o: zoeModel.c zoeModel.h zoeDNA.h zoeFastaFile.h zoeTools.h \ - zoeProtein.h zoeFeature.h zoeMath.h + zoeProtein.h zoeFeature.h zoeMath.h zoePhasePref.o: zoePhasePref.c zoePhasePref.h zoeMath.h zoeTools.h \ - zoeFeature.h + zoeFeature.h zoeProtein.o: zoeProtein.c zoeProtein.h zoeFastaFile.h zoeTools.h zoeScanner.o: zoeScanner.c zoeScanner.h zoeDNA.h zoeFastaFile.h \ - zoeTools.h zoeProtein.h zoeFeature.h zoeMath.h zoeModel.h + zoeTools.h zoeProtein.h zoeFeature.h zoeMath.h zoeModel.h zoeState.o: zoeState.c zoeState.h zoeFeature.h zoeTools.h zoeTools.o: zoeTools.c zoeTools.h zoeTransition.o: zoeTransition.c zoeTransition.h zoeMath.h zoeTools.h \ - zoeFeature.h + zoeFeature.h zoeTrellis.o: zoeTrellis.c zoeTrellis.h zoeCDS.h zoeDNA.h zoeFastaFile.h \ - zoeTools.h zoeProtein.h zoeFeature.h zoeFeatureFactory.h zoeScanner.h \ - zoeMath.h zoeModel.h zoeFeatureTable.h zoeHMM.h zoeDuration.h \ - zoeDistribution.h zoeState.h zoePhasePref.h zoeTransition.h + zoeTools.h zoeProtein.h zoeFeature.h zoeFeatureFactory.h zoeScanner.h \ + zoeMath.h zoeModel.h zoeFeatureTable.h zoeHMM.h zoeDuration.h \ + zoeDistribution.h zoeState.h zoePhasePref.h zoeTransition.h diff --git a/Zoe/zoe-loop b/Zoe/zoe-loop new file mode 100755 index 0000000..3a7856b Binary files /dev/null and b/Zoe/zoe-loop differ diff --git a/Zoe/zoe-loop.o b/Zoe/zoe-loop.o new file mode 100644 index 0000000..f5529a4 Binary files /dev/null and b/Zoe/zoe-loop.o differ diff --git a/Zoe/zoeCDS.o b/Zoe/zoeCDS.o new file mode 100644 index 0000000..0f24607 Binary files /dev/null and b/Zoe/zoeCDS.o differ diff --git a/Zoe/zoeCounter.o b/Zoe/zoeCounter.o new file mode 100644 index 0000000..7ce7bbd Binary files /dev/null and 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