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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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Commits on Nov 19, 2012
Changing return of parse() into List in stead of Vector
Show description for 376f82ecommittedAdding getBioSequences(boolean ignoreCase)
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Commits on Nov 9, 2012
for testing of stockholm parser
Show description for 73503bdcommittednew unit test for stockholm file parsing
Show description for 3f87f06committedReplacing System.lineSeparator() calls with the backwards-compatible getProperty("line.separator")
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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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Commits on Nov 6, 2012
- committed
Added Stockholm Parser beta, and some test files.
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Commits on Oct 18, 2012
Refactor to use forester 1.005
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Commits on Jul 3, 2012
demo for how to load amino acid substitution matrices
Show description for 652cebbcommittedan example for how to align DNA
Show description for ea5b48ccommittedadding the cookbook example as a demo
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Commits on Jul 2, 2012
adding patch by Don Naki
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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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Commits on Feb 24, 2012
unified indentation in pom.xml; added some Test cases for DNA Alignments
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Commits on Jan 10, 2012
fixing recursion
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Commits on Oct 8, 2011
Minor documentation changes
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Commits on Oct 6, 2011
new unit test for DNA alignments
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Commits on Oct 5, 2011
adding a unit test that aligns a DNA sequence
Show description for 2f68ad6committedAdded missing intra-package import (Thanks to Hannes Brandstätter-Müller)
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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
Show description for 4073df3committedfix compiler warnings
Show description for 2004079committedfix CruiseControl javadoc warnings
Show description for 9870db5committedrefactoring 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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