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Commits on Apr 22, 2014

• adding new constructor

  andreasprlic

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Commits on Mar 20, 2014

• for the fix for #91 to work I believe we need to be more careful with CompoundSets

  andreasprlic

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Commits on Mar 18, 2014

• Merge pull request #16 from biojava/master

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  emckee2006

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Commits on Feb 12, 2014

• adding a http user agent, so Uniprot gets better feedback who is scripting them

  andreasprlic

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• adding a http user agent, so Uniprot gets better feedback who is scripting them

  andreasprlic

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Commits on Feb 10, 2014

• ProteinSequence was using parentSequence as a DNA Sequence. However,

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  emckee2006

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• Remove warnings

  emckee2006

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Commits on Dec 30, 2013

• Wrote a method IOUtils.print(String, File).

  dmyersturnbull

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Commits on Oct 23, 2013

• Convert %i (which formatter doesn't like) to %d for integers

  emckee2006

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Commits on Oct 16, 2013

• Clean up the majority of compile warnings

  emckee2006

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Commits on Oct 13, 2013

• moving test to correct location

  andreasprlic

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• fixing a check that seems wrong

  andreasprlic

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Commits on Oct 12, 2013

• Update test to use proper assert for tests

  emckee2006

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Commits on Oct 11, 2013

• Add a test of the Genbank Functionality

  emckee2006

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• Remove external dependancy on commons-lang3

  emckee2006

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• Add a fairly basic genbank writer (mostly ported from BioPython), expose

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  emckee2006

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Commits on Sep 23, 2013

• #53 adding junit test to reproduce error and adding patch as proposed by

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Commits on Aug 12, 2013

• Fixed bug created in SequenceFile when converted to BufferedReader from

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  Karl Nicholas

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  Karl Nicholas

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Commits on Aug 11, 2013

• More work on Genbank files, bringing them inline with interfaces.

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  Karl Nicholas

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  Karl Nicholas

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• Added GenbankParser and changed other Genbank code to use it.

  

  Karl Nicholas

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  Karl Nicholas

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Commits on Aug 8, 2013

• Added a GenbankProxySequenceReader class that takes an accessionid and

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  Karl Nicholas

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  Karl Nicholas

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Commits on Aug 4, 2013

• Updated GenbankReader and files to properly handle AbstractSequence and

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  Karl Nicholas

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  Karl Nicholas

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Commits on Jul 31, 2013

• Added simple Genbank reader. Update CommandPrompt to use the Genbank

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  Karl Nicholas

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  Karl Nicholas

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Commits on Jun 18, 2013

• Fixed negative permutations.

  dmyersturnbull

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Commits on Jun 17, 2013

• Added methods for cyclic permutations.

  dmyersturnbull

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Commits on Jun 1, 2013

• Accept lower-case amino acid single-letter codes.

  dmyersturnbull

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• Accept lower-case amino acid single-letter codes.

  dmyersturnbull

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Commits on Apr 27, 2013

• more clean up

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  aalhossary

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• clean up

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Commits on Apr 23, 2013

• Added process(int max) which tries to parse maximum max records from the

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  aalhossary

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• better use of StringBuilder

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• First commit trial using Git. Just some documentation decoration.

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Commits on Jan 24, 2013

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

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  aalhossary

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Commits on Nov 19, 2012

• Typo and format

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  aalhossary

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• Typo and format

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