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Commits on Jan 24, 2013

• Adding a plain fasta header parser for atypical data header formats

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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 19, 2012

• Typo and format

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• Typo and format

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• fixing a warning, by closing InputStream

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Commits on Nov 13, 2012

• keeping a Deprecated stub to getConsituents() in order not t break old codes

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• Typo correction

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Commits on Nov 10, 2012

• should take distribution config from parent

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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 Apr 30, 2012

• default color is green not black

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Commits on Mar 27, 2012

• Adding CasePreservingProteinSequenceCreator, which stores the case of the input string in the ProteinSequence user collection

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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 Feb 27, 2012

• added another method to QualityFeature; also some javadoc

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Commits on Feb 26, 2012

• fixed a typo in QualityFeature

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• added a QualityFeature to hold quality information in DNASequences

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Commits on Feb 11, 2012

• NCBIQBlastService replaced with the new implementation.

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Commits on Feb 8, 2012

• adding patch from Hannes

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Commits on Jan 16, 2012

• Simplified boolean expressions.

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Commits on Jan 11, 2012

• Removed the case where length= at the end of a header would get parsed out. Requested by Hannes Brandstätter-Müller <biojava@hannes.oib.com>

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Commits on Jan 10, 2012

• Changed instances of String concatenation in StringBuffer to use append.

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Commits on Dec 15, 2011

• replacing < and > with &lt; and &gt; in order not to break HTML and enable generating .CHM files using http://jan.baresovi.cz/dr/en/javadoc-chm

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Commits on Oct 12, 2011

• Fix Bug #3305 for not closing open file

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Commits on Oct 8, 2011

• Added some documentation to functions that take 1-based indices, although there are definitely more which need documentation.

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  blivens

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• Added the ability to fetch AminoAcidCompounds by 3 letter names

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Commits on Sep 21, 2011

• moving from test section to main section

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Commits on Sep 19, 2011

• moving StringManipulationTestsHelper to org.biojava3.core.util

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Commits on Sep 2, 2011

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

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• [maven-release-plugin] prepare release biojava-3.0.2

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Commits on Aug 31, 2011

• cleaning up some javadoc warnings

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• cleaning up some javadoc

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• cleaning up some javadoc

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