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biojava
biojava3-alignment
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Commits on Dec 15, 2014
Adding @Override and @Deprecated tags where applicable
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Commits on Dec 8, 2014
Removing logger from demo classes
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Commits on Dec 4, 2014
A few important improvements: identity matrix and gap coverage checking
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Commits on Nov 21, 2014
Removing deprecated classes for biojava 4 release
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Commits on Nov 20, 2014
Commented a gotcha (at least, it just got me):
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Merge branch 'master' of github.com:biojava/biojava
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Fixed this issue:
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Partially reverted #685b81c by deleting NeedlemanWunschQuadratic and removing it from Alignments.
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Commits on Nov 10, 2014
Added comments to SubstitutionMatrixScorer.
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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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Commits on Nov 7, 2014
Fixing #202 . Doubles the memory requirement in alignments
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Commits on Oct 28, 2014
Fixing #193
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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
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Commits on Sep 18, 2014
Adding missing log4j2.xml files and unifying config across modules #155
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Convert org.biojava3.alignment package to use slf4j
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Commits on Aug 24, 2014
updating CookbookMSA example to up-to-date uniprot IDs
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Commits on Feb 28, 2014
fixing display problem with IDs of different length
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Commits on Dec 17, 2013
Merge branch 'master' of https://github.com/biojava/biojava
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Wrote a SubstitutionMatrixScorer.
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Added getRow() and getColumn() methods to SubstitutionMatrix.
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Commits on Dec 16, 2013
Fixed issue #85.
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FractionalSimilarityScorer was actually identical to
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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
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Refactored subproblem bounds from int[4] into a Subproblem class to improve code readability
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Alignments of zero length return a null Location instead of crashing during alignment
d-cameron
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Commits on Dec 10, 2013
Added multiple test cases for various alignment bugs including #78
d-cameron
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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
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Commits on Oct 26, 2013
Stockholm Parser is stateless now (more tolerant but less robust)
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Commits on Jul 28, 2013
Made a general-purpose public method
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Commits on Mar 2, 2013
get pariwise alignment of protein sequences
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Commits on Nov 28, 2012
adding another database type constant
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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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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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Commits on Nov 24, 2012
just doc
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