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Commits on Dec 15, 2014

• Adding @Override and @Deprecated tags where applicable

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Commits on Nov 21, 2014

• Removing warnings, some #111 and #155

  josemduarte

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Commits on Sep 21, 2014

• Fix logger class name #155

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Commits on Sep 19, 2014

• Convert org.biojava3.genome to slf4j #155

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Commits on Jul 9, 2014

• Merge pull request #135 from kevinwu1/master

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  andreasprlic

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Commits on Jul 7, 2014

• Fix character length differences

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  kevinwu1

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Commits on Jul 2, 2014

• Fix character length differences

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  kevinwu1

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• Fixes character length differences

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  kevinwu1

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Commits on Jun 27, 2014

• Merge branch 'master' of github.com:biojava/biojava

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• Thanks to Roman Sutormin for making this code available. This resolves #134

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Commits on Jun 13, 2014

• little bit more javadoc

  andreasprlic

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Commits on Feb 22, 2014

• fixing wrong order of CDS and transcription start coordinate parsing

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Commits on Feb 21, 2014

• #93 adding a parser for karyotype info from UCSC

  andreasprlic

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Commits on Feb 12, 2014

• making sure all rows have the same length

  andreasprlic

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Commits on Jan 30, 2014

• adding ensemble gene id

  andreasprlic

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Commits on Jan 29, 2014

• adding retrieval of omim ids

  andreasprlic

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• adding support for parsing gene names and chromosome locations for human genes

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Commits on Nov 27, 2013

• Update method comment to indicate legal calling sequences for using

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  emckee2006

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• Add a test case based on Daniel Cameron's example of failing FeatureList

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  emckee2006

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Commits on Oct 16, 2013

• Clean up the majority of compile warnings

  emckee2006

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Commits on Apr 27, 2013

• using temporary file instead of updating

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  aalhossary

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• using temp file for File tmp = File

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Commits on Sep 6, 2012

• Fixed the compile error in Feature.java

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  CarmeloFoti

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Commits on Sep 4, 2012

• Removed the Log4j dependencies from the GFF3 parser.

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  CarmeloFoti

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Commits on Aug 23, 2012

• Added indexes into FeatureList and GFF3Reader classes.

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  CarmeloFoti

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Commits on Aug 10, 2012

• fix for unit test failures, use proper temp directory for test output files

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  heuermh

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Commits on Mar 15, 2012

• previous commit, "deleted genome.parsers.fastq and associated test classes (duplicated, they are in their own package, sequencing)" missed removing unit tests

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  heuermh

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• deleted genome.parsers.fastq and associated test classes (duplicated, they are in their own package, sequencing)

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  brandstaetter

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Commits on Mar 12, 2012

• undid more unnecessary reformatting that made the code harder to read in the Fastq test cases, also removed some unnecessary import statements

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  brandstaetter

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• undid some unnecessary reformatting that made the code harder to read in FastqBuilderTest.java

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  brandstaetter

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• moved fastq classes from biojava3.sequencing.io.fastq to biojava3.genome.parsers.fastq

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  brandstaetter

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Commits on Jan 16, 2012

• Simplified boolean expressions.

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  rthornton

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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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  aalhossary

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Commits on Aug 30, 2011

• Ignore unit test output

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  sbliven

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Commits on Jan 24, 2011

• Added FeatureHelper which allows you to build indexes based on a feature attribute value. This is then used in GeneFeatureHelper when parsing a gmod gff3 file to quickly find the features that belo…

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