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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
  9e1c80c

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

  dmyersturnbull

  committed
  3773af1

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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
  3d919c4

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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
  ec9ff19

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

  d-cameron

  committed
  9dfeb09

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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

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Commits on Oct 16, 2013

• Clean up the majority of compile warnings

  emckee2006

  committed
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Commits on Sep 24, 2013

• [maven-release-plugin] prepare for next development iteration

  andreasprlic

  committed
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• [maven-release-plugin] prepare release biojava-3.0.7

  andreasprlic

  committed
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• [maven-release-plugin] rollback the release of biojava-3.0.7

  andreasprlic

  committed
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• [maven-release-plugin] prepare release biojava-3.0.7

  andreasprlic

  committed
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• [maven-release-plugin] rollback the release of biojava-3.0.7

  andreasprlic

  committed
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• [maven-release-plugin] prepare release biojava-3.0.7

  andreasprlic

  committed
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• [maven-release-plugin] rollback the release of biojava-3.0.7

  andreasprlic

  committed
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• [maven-release-plugin] prepare for next development iteration

  andreasprlic

  committed
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• [maven-release-plugin] prepare release biojava-3.0.7

  andreasprlic

  committed
  1762f68

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• [maven-release-plugin] rollback the release of biojava-3.0.7

  

  tomcat

  authored and

  tomcat

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• [maven-release-plugin] prepare release biojava-3.0.7

  

  tomcat

  authored and

  tomcat

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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 Jul 15, 2013

• [maven-release-plugin] prepare for next development iteration

  

  Andreas Prlic

  committed
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• [maven-release-plugin] prepare release biojava-3.0.6

  

  Andreas Prlic

  committed
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Commits on Mar 8, 2013

• now using making sure to only pull lgpl code

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  andreasprlic

  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 30, 2012

• [maven-release-plugin] prepare for next development iteration

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  andreasprlic

  committed
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• [maven-release-plugin] prepare release biojava-3.0.5

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  andreasprlic

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Commits on Nov 28, 2012

• adding another database type constant

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  aalhossary

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