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Commits on Mar 8, 2013

• now using making sure to only pull lgpl code

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Commits on Mar 2, 2013

• get pariwise alignment of protein sequences

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Commits on Nov 30, 2012

• [maven-release-plugin] prepare for next development iteration

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• [maven-release-plugin] prepare release biojava-3.0.5

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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

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• Adding getBioSequences(boolean ignoreCase)

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Commits on Nov 10, 2012

• should take distribution config from parent

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Commits on Nov 9, 2012

• for testing of stockholm parser

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• making sure this compiles with Maven 3.x

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• new unit test for stockholm file parsing

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• Adding test-scope dependency on forester to the alignment package

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• Replacing 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

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• 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

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• an example for how to align DNA

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• adding 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 May 22, 2012

• [maven-release-plugin] prepare for next development iteration

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• [maven-release-plugin] prepare release biojava-3.0.4

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Commits on Mar 16, 2012

• [maven-release-plugin] prepare for next development iteration

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• [maven-release-plugin] prepare release biojava-3.0.3

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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

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

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