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Commits on Apr 19, 2017

• Dak’s new unit test that demonstrates a problem when parsing FASTA files

  andreasprlic

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Commits on Apr 13, 2017

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

  valasatava

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Commits on Apr 4, 2017

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

  valasatava

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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

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Commits on Mar 28, 2017

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

  valasatava

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

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• hashCode added to SequenceFileProxyLoader class

  valasatava

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

  valasatava

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

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

  valasatava

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Commits on Feb 8, 2017

• Merge branch 'upstream_master'

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• Add in previously missed protein aliases...

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Commits on Nov 9, 2016

• Fix #596. Remove test for GenBank identifier parsing

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Commits on Sep 14, 2016

• Also get short name when getting other protein aliases

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Commits on Aug 25, 2016

• Merge branch 'pr/44'

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  emckee2006

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• add ability to pull gene and protein aliases from uniprot

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Commits on Aug 23, 2016

• Merge pull request #555 from andreasprlic/master

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Commits on Aug 21, 2016

• GenericInsdcHeaderFormat: Fixed formatting codes.

  andviane

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Commits on Aug 18, 2016

• making output less verbose

  andreasprlic

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• setting default log level to warn

  andreasprlic

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• making output less verbose

  andreasprlic

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Commits on Aug 16, 2016

• updating to latest version of Cobertura tests. Now can successfully run locally.

  andreasprlic

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Commits on Jul 4, 2016

• Merge pull request #525 from andreasprlic/master

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

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Commits on Jul 1, 2016

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

  

  Mohamed Ezzat

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• pmd:InefficientStringBuffering - Inefficient String Buffering

  

  Mohamed Ezzat

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Commits on Jun 30, 2016

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

  andreasprlic

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

  andreasprlic

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Commits on Jun 27, 2016

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

  lafita

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Commits on Jun 24, 2016

• Implement tests for new utility methods in sequence objects #491

  lafita

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• Method for total gapped positions and coverage in aligned sequences

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  lafita

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• Method for percentage of identity of a sequence pair #491

  lafita

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Commits on Jun 16, 2016

• squid:S2272 - "Iterator.next()" methods should throw "NoSuchElementException"

  

  Mohamed Ezzat

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Commits on Jun 15, 2016

• squid:S2063 - Comparators should be Serializable

  

  Mohamed Ezzat

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Commits on Jun 10, 2016

• squid:S2130 - Parsing should be used to convert Strings to primitives

  

  Mohamed Ezzat

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