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Commits on Dec 17, 2013

• Fixed use of assertEquals() on doubles.

  dmyersturnbull

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

  dmyersturnbull

  committed
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Commits on Dec 16, 2013

• Fixed issue #85.

  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
  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 16, 2013

• Clean up the majority of compile warnings

  emckee2006

  committed
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Commits on Nov 19, 2012

• Adding getBioSequences(boolean ignoreCase)

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  aalhossary

  committed
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Commits on Nov 9, 2012

• new unit test for stockholm file parsing

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  andreasprlic

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Commits on Oct 18, 2012

• Refactor to use forester 1.005

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  markchapman

  committed
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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

  committed
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Commits on Feb 24, 2012

• unified indentation in pom.xml; added some Test cases for DNA Alignments

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  brandstaetter

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Commits on Oct 6, 2011

• new unit test for DNA alignments

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  andreasprlic

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Commits on Oct 5, 2011

• Added missing intra-package import (Thanks to Hannes Brandstätter-Müller)

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  sbliven

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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

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Commits on Nov 2, 2010

• Modified in line with latest version of biojava3-core's Sequence interface

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  andrewyatz

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Commits on Sep 28, 2010

• extending junit tests with conversion info

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  andreasprlic

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Commits on Aug 20, 2010

• finished with linear space (anchored) alignments

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  markchapman

  committed
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Commits on Aug 12, 2010

• added alignment output formatting; outputs to CLUSTALW's ALN, FASTA, and GCG's MSF formats

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  markchapman

  committed
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Commits on Aug 11, 2010

• refactored alignment routines: granted access to all score matrices, reduced memory requirement

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  markchapman

  committed
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Commits on Jul 29, 2010

• refactored aligner, scorer, and refiner enum types

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  markchapman

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Commits on Jul 28, 2010

• improvements to memory usage during multiple sequence alignment

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  markchapman

  committed
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• improvements to memory usage during multiple sequence alignment

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  markchapman

  committed
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Commits on Jul 27, 2010

• cookbook programs

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  markchapman

  committed
  21ad1b7

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• updated tests to use SubstitutionMatrixHelper

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  markchapman

  committed
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Commits on Jul 22, 2010

• refactored AlignedSequence to have a Sequence generic type in addition to a Compound generic type

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  markchapman

  committed
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Commits on Jul 10, 2010

• added concurrent progressive multiple sequence alignment

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  markchapman

  committed
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Commits on Jul 9, 2010

• added caching of profile vectors

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  markchapman

  committed
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• refactored and commented GuideTree and GuideTreeNode, added Iterator from leaves to root

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  markchapman

  committed
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Commits on Jul 7, 2010

• implemented GuideTree as wrapper for forester's Phylogeny

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  markchapman

  committed
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• implemented profile-profile alignment

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  markchapman

  committed
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