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Commits on Aug 13, 2013

• Added GenbankCookbookTest test case.

  

  Karl Nicholas

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  Karl Nicholas

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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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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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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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  aalhossary

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• Typo correction

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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 Feb 27, 2012

• added another method to QualityFeature; also some javadoc

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  brandstaetter

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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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  grimsa

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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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