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onbiojava-3.0.2

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Commits on Aug 3, 2011

• fixing patch provided by Tariq

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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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Commits on Jan 31, 2011

• making access methods public

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Commits on Nov 23, 2010

• common code moved to IOUtils in core

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Commits on Nov 19, 2010

• update to latest drawing code

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  andreasprlic

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• fix compiler warnings

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  markchapman

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• fix CruiseControl javadoc warnings

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• refactoring to integrate anchored and standard alignment

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Commits on Nov 3, 2010

• Sequence.getReverse() has been changed to getInverse() to avoid confusion.

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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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Commits on Oct 21, 2010

• now with nicer web display

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Commits on Sep 28, 2010

• extending junit tests with conversion info

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• fixing a junit test

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• now conservation also works with Accession IDs

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• adding new StringFormat

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• adding display of sequence conservation for pairwise alignments

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Commits on Aug 20, 2010

• finished with linear space (anchored) alignments

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Commits on Aug 17, 2010

• moved common aligner code into AlignerHelper; almost finished with linear space (anchored) alignments

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Commits on Aug 13, 2010

• making access to aligners public

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  andreasprlic

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• updates to alignment routines including a bug fix for local alignment

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  markchapman

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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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Commits on Aug 11, 2010

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

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  markchapman

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Commits on Jul 29, 2010

• refactored aligner, scorer, and refiner enum types

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Commits on Jul 28, 2010

• improvements to memory usage during multiple sequence alignment

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• improvements to memory usage during multiple sequence alignment

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Commits on Jul 27, 2010

• improvements to memory usage during multiple sequence alignment

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• updates in preparation for Myers-Miller linear space alignment

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• cookbook programs

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• changed private methods to default, removed MSAEmulation, and worked around class cast warning

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• updated tests to use SubstitutionMatrixHelper

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  markchapman

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• simple access to common substitution matrices

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Commits on Jul 22, 2010

• added distance and similarity methods to Scorer interface

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  markchapman

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

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Commits on Jul 21, 2010

• arranged in 3 access levels, added enums for refinement and more alternatives

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• updates for rescore refinement

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