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Commits on Feb 28, 2014

• fixing display problem with IDs of different length

  andreasprlic

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Commits on Dec 17, 2013

• 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

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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

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Commits on Dec 11, 2013

• 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

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Commits on Jul 28, 2013

• Made a general-purpose public method

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  dmyersturnbull

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Commits on Mar 2, 2013

• get pariwise alignment of protein sequences

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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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Commits on Nov 27, 2012

• Proper fixation of the bug, adding INFINITY as a constant, and documentation

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  aalhossary

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Commits on Nov 26, 2012

• correcting a bug that takes place at the end of the file (if you reach it ;) )

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  aalhossary

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Commits on Nov 24, 2012

• just doc

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  aalhossary

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Commits on Nov 19, 2012

• Changing return of parse() into List in stead of Vector

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  aalhossary

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• Adding getBioSequences(boolean ignoreCase)

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  aalhossary

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Commits on Nov 9, 2012

• Replacing System.lineSeparator() calls with the backwards-compatible getProperty("line.separator")

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  sbliven

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Commits on Nov 7, 2012

• Changing parseFile(xxx) function set into parse(xxx) and adding parseNext(int)

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  aalhossary

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Commits on Nov 6, 2012

• Show description for 6eb094b
  aalhossary

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• Added Stockholm Parser beta, and some test files.

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  aalhossary

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Commits on Oct 18, 2012

• Refactor to use forester 1.005

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  markchapman

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Commits on Jul 3, 2012

• demo for how to load amino acid substitution matrices

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  andreasprlic

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• an example for how to align DNA

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  andreasprlic

  committed
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• adding the cookbook example as a demo

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  andreasprlic

  committed
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Commits on Jul 2, 2012

• adding patch by Don Naki

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  andreasprlic

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Commits on Mar 8, 2012

• added sanity check to Alignments, throws IllegalArgumentException if compound sets mismatch (instead of just failing silently)

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  brandstaetter

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Commits on Jan 10, 2012

• fixing recursion

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  andreasprlic

  committed
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Commits on Oct 8, 2011

• Minor documentation changes

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  sbliven

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Commits on Aug 3, 2011

• fixing patch provided by Tariq

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  andreasprlic

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Commits on Jul 6, 2011

• Contributing new framework for loading amino acid substitution matrices from the AAINDEX database.

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  andreasprlic

  committed
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