| Merge pull request #209 from josemduarte/master |
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almost 12 years ago
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| Making sure that tests in aa-prop run. They weren't running at all - fixed a few bugs - removed unnecessary files - renamed tests to xxxxTest.java so that surefire picks them up - made sure that resource files are not rewritten by tests |
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almost 12 years ago
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| Merge pull request #30 from biojava/master |
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almost 12 years ago
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| Merge pull request #208 from dmyersturnbull/master |
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almost 12 years ago
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| Adding .gitignore |
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almost 12 years ago
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| Merge pull request #207 from sbliven/master |
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almost 12 years ago
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| Commented a gotcha (at least, it just got me): SimpleGapPenalty penalty = new SimpleGapPenalty(); penalty.setOpenPenalty((short) 10); penalty.getOpenPenalty(); // returns -10, not 10 |
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almost 12 years ago
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| Merge branch 'master' of github.com:biojava/biojava |
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almost 12 years ago
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| Fixed this issue: NucleotideCompound A = new DNASequence("A").getCompoundAt(1); NucleotideCompound a = new DNASequence("a").getCompoundAt(1); SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<>(DNACompoundSet.getDNACompoundSet(), (short)1, (short)0); System.out.println(matrix.getValue(A, a)); // prints 1 System.out.println(matrix.getValue(a, A)); // prints 1 System.out.println(matrix.getValue(a, a)); // prints 0!!! System.out.println(matrix.getValue(A, A)); // prints 0!!! The simple solution: compoundsEquivalent should always return true if the two are equal. Added a test for this. |
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almost 12 years ago
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| Partially reverted #685b81c by deleting NeedlemanWunschQuadratic and removing it from Alignments. |
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almost 12 years ago
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| Merge pull request #29 from biojava/master |
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almost 12 years ago
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| Adding array version of CrystalCell#transfToOriginCell |
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almost 12 years ago
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| Merge 'main/master' with 'sbliven/master' |
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almost 12 years ago
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| Reverting vecmath to 1.3.1 |
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almost 12 years ago
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| Reverting 8faf1889, which intoduced Java 1.7-specific code |
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almost 12 years ago
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| Another fix for #193 |
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almost 12 years ago
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| Merge pull request #203 from josemduarte/master |
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almost 12 years ago
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| Modifying CrystalTransform toString method |
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almost 12 years ago
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| Added comments to SubstitutionMatrixScorer. |
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almost 12 years ago
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| Added a quadratic-space global alignment class. Made Alignments.getPairwiseAligner() return the expected global alignment algorithm. Made Alignments methods throw an UnsupportedOperationException instead of returning null. |
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almost 12 years ago
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| Making sure that the parent pom sets the jdk version for all children |
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about 12 years ago
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| Better test |
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about 12 years ago
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| Adding test for #202 |
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about 12 years ago
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| Fixing #202 . Doubles the memory requirement in alignments |
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about 12 years ago
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| Adding CrystalCell methods & tests |
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about 12 years ago
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| Merge pull request #200 from parit/uniprotRMI |
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about 12 years ago
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| Merge pull request #2 from josemduarte/fixToTest |
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about 12 years ago
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| Merging local changes to master |
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about 12 years ago
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| Fixing test to fail only if CompoundNotFound, otherwise will go to error |
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about 12 years ago
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| changed CompoundNotFoundException into IllegalArgumentException, removed MalFormedUrlException, added RemoteException when failing to fetch the uniprot entry |
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about 12 years ago
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