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Commits on Nov 21, 2014

• Removing deprecated classes for biojava 4 release

  josemduarte

  committed
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• Removing warnings, some #111 and #155

  josemduarte

  committed
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Commits on Nov 20, 2014

• Commented a gotcha (at least, it just got me):

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  dmyersturnbull

  committed
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• Merge branch 'master' of github.com:biojava/biojava

  dmyersturnbull

  committed
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• Fixed this issue:

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  dmyersturnbull

  committed
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• Partially reverted #685b81c by deleting NeedlemanWunschQuadratic and removing it from Alignments.

  dmyersturnbull

  committed
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Commits on Nov 10, 2014

• Added comments to SubstitutionMatrixScorer.

  dmyersturnbull

  committed
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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 i…

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  dmyersturnbull

  committed
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Commits on Nov 7, 2014

• Better test

  josemduarte

  committed
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• Adding test for #202

  josemduarte

  committed
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• Fixing #202 . Doubles the memory requirement in alignments

  josemduarte

  committed
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Commits on Oct 28, 2014

• Fixing #193

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  josemduarte

  committed
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Commits on Oct 6, 2014

• trying to catch PDB ID 1A34 where the code fails to detect a short RNA sequence.

  pwrose

  committed
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Commits on Sep 18, 2014

• Adding missing log4j2.xml files and unifying config across modules #155

  josemduarte

  committed
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• Convert org.biojava3.alignment package to use slf4j

  benjamintboyle

  committed
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Commits on Aug 24, 2014

• updating CookbookMSA example to up-to-date uniprot IDs

  andreasprlic

  committed
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Commits on Feb 28, 2014

• fixing display problem with IDs of different length

  andreasprlic

  committed
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Commits on Dec 17, 2013

• Fixed use of assertEquals() on doubles.

  dmyersturnbull

  committed
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• Merge branch 'master' of https://github.com/biojava/biojava

  dmyersturnbull

  committed
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• Wrote a SubstitutionMatrixScorer.

  dmyersturnbull

  committed
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• Added getRow() and getColumn() methods to SubstitutionMatrix.

  dmyersturnbull

  committed
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Commits on Dec 16, 2013

• Fixed issue #85.

  dmyersturnbull

  committed
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• FractionalSimilarityScorer was actually identical to

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  dmyersturnbull

  committed
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• Refactored alignment to allow anchored compounds for all global alignments

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  d-cameron

  committed
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Commits on Dec 11, 2013

• Additional GuanUberbacher test coverage

  d-cameron

  committed
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• Bug fix: Cut query positions are no longer outside the bounds of the subproblem

  d-cameron

  committed
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• Refactored subproblem bounds from int[4] into a Subproblem class to improve code readability

  d-cameron

  committed
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• Alignments of zero length return a null Location instead of crashing during alignment

  d-cameron

  committed
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Commits on Dec 10, 2013

• Added multiple test cases for various alignment bugs including #78

  d-cameron

  committed
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• Compounds not included in the scoring matrix will default to the alternative case of the compound if it exists in the scoring matrix instead of the min matrix value

  d-cameron

  committed
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Commits on Oct 26, 2013

• Stockholm Parser is stateless now (more tolerant but less robust)

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  aalhossary

  committed
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Commits on Oct 16, 2013

• Clean up the majority of compile warnings

  emckee2006

  committed
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Commits on Jul 28, 2013

• Made a general-purpose public method

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  dmyersturnbull

  committed
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Commits on Mar 2, 2013

• get pariwise alignment of protein sequences

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  andreasprlic

  committed
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Commits on Nov 28, 2012

• adding another database type constant

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  aalhossary

  committed
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