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Commits on Sep 24, 2013

• [maven-release-plugin] prepare release biojava-3.0.7

  andreasprlic

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• [maven-release-plugin] rollback the release of biojava-3.0.7

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• [maven-release-plugin] prepare release biojava-3.0.7

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• [maven-release-plugin] rollback the release of biojava-3.0.7

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• [maven-release-plugin] prepare release biojava-3.0.7

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• [maven-release-plugin] rollback the release of biojava-3.0.7

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

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• [maven-release-plugin] prepare release biojava-3.0.7

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• [maven-release-plugin] rollback the release of biojava-3.0.7

  

  tomcat

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• [maven-release-plugin] prepare release biojava-3.0.7

  

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Commits on Jul 28, 2013

• Made a general-purpose public method

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  dmyersturnbull

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Commits on Jul 15, 2013

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

  

  Andreas Prlic

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• [maven-release-plugin] prepare release biojava-3.0.6

  

  Andreas Prlic

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Commits on Mar 8, 2013

• now using making sure to only pull lgpl code

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  andreasprlic

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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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  aalhossary

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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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  aalhossary

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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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  andreasprlic

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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

• Show description for 6eb094b
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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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  markchapman

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Commits on Jul 3, 2012

• demo for how to load amino acid substitution matrices

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  andreasprlic

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• an example for how to align DNA

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