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Commits on Sep 8, 2017

• Making it clear that the soft memory cache is a singleton

  josemduarte

  committed
  2b1860b

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• Fix for new tests so that they don't pollute other tests

  josemduarte

  committed
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Commits on Jul 8, 2017

• Revert to old behavior where process(int) return null on end-of-file.

  arojnuckarin

  committed
  4f301ce

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• Attempt to fix issue #659 - Error parsing FASTA in multiple passes

  arojnuckarin

  committed
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Commits on Jun 13, 2017

• Add @since 5.0.0 annotation into AbstractReference, GenbankReference,

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  jimty0511

  committed
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Commits on Jun 7, 2017

• Added Javadoc into AbstractSequence.

  jimty0511

  committed
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• 1. Added Javadoc into AbstractReference.

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  jimty0511

  committed
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• 1. Added a new folder into main/java/org/biojava/nbio/core/sequence package

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  jimty0511

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Commits on Jun 2, 2017

• Added List<String> of comments with getter and setter into AbstractSequence.java;

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  jimty0511

  committed
  6fa0df9

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• Merge pull request #666 from psoares/master

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  josemduarte

  authored
  8fd2685

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Commits on May 31, 2017

• Fix for #663 and some code cleanup.

  psoares

  committed
  5e52308

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Commits on Apr 27, 2017

• Add methods for reading RNA sequences.

  heuermh

  committed
  0169997

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Commits on Apr 13, 2017

• Exposing alignment mappings to be able to map query sequence to target sequence

  valasatava

  committed
  c29825e

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Commits on Apr 4, 2017

• Refactoring FileDownload util to be a part of biojava-core project

  valasatava

  committed
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Commits on Apr 3, 2017

• Adding a method to check whether an array of sequences contains at least two sequences of an equal length

  valasatava

  committed
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Commits on Mar 28, 2017

• hashCode() added for all the classes where added an equals()

  valasatava

  committed
  2d90038

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• Merge branch 'sequenceEquals' of https://github.com/valasatava/biojava into sequenceEquals

  valasatava

  committed
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• hashCode added to SequenceFileProxyLoader class

  valasatava

  committed
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• adding a sequence.equals(Sequence) and hashCode class to sequences.

  valasatava

  committed
  3dadec1

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• changing equals(Sequence) method signature to equals(Object)

  andreasprlic

  committed
  7587b03

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• adding a sequence.equals(Sequence) and hashCode class to sequences.

  valasatava

  committed
  f4c9b69

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Commits on Feb 8, 2017

• Merge branch 'upstream_master'

  emckee2006

  committed
  3b3354e

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• Add in previously missed protein aliases...

  emckee2006

  committed
  246525b

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Commits on Nov 9, 2016

• Fix #596. Remove test for GenBank identifier parsing

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  sbliven

  committed
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Commits on Sep 14, 2016

• Also get short name when getting other protein aliases

  emckee2006

  committed
  9b0d208

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Commits on Aug 25, 2016

• add ability to pull gene and protein aliases from uniprot

  emckee2006

  committed
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Commits on Aug 21, 2016

• GenericInsdcHeaderFormat: Fixed formatting codes.

  andviane

  committed
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Commits on Jul 4, 2016

• Merge pull request #525 from andreasprlic/master

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  josemduarte

  authored
  2fca095

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• Merge pull request #519 from DevFactory/release--inefficient-string-buffering-fix-1

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  josemduarte

  authored
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Commits on Jul 1, 2016

• Cleanup - squid:S1858 - "toString()" should never be called on a String object

  

  Mohamed Ezzat

  committed
  082d860

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• pmd:InefficientStringBuffering - Inefficient String Buffering

  

  Mohamed Ezzat

  committed
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Commits on Jun 30, 2016

• #505 switching to https for all NCBI utils traffic.

  andreasprlic

  committed
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• #505 switching to https for all NCBI utils traffic.

  andreasprlic

  committed
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Commits on Jun 27, 2016

• Normalize percentage of identity by the length without gaps #521

  lafita

  committed
  3722ce5

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Commits on Jun 24, 2016

• Method for total gapped positions and coverage in aligned sequences

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  lafita

  committed
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