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1. Commits on Apr 19, 2017

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

     andreasprlic

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2. Commits on Apr 13, 2017

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

     valasatava

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3. Commits on Apr 4, 2017

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

     valasatava

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4. 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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5. 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

     valasatava

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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)

     andreasprlic

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

     valasatava

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6. Commits on Feb 8, 2017

   • Merge branch 'upstream_master'

     emckee2006

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   • Add in previously missed protein aliases...

     emckee2006

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7. Commits on Nov 9, 2016

   • Fix #596. Remove test for GenBank identifier parsing

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     sbliven

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8. Commits on Sep 14, 2016

   • Also get short name when getting other protein aliases

     emckee2006

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9. 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

     emckee2006

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10. Commits on Aug 23, 2016

    • Merge pull request #555 from andreasprlic/master

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      sbliven

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11. Commits on Aug 21, 2016

    • GenericInsdcHeaderFormat: Fixed formatting codes.

      andviane

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12. 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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13. Commits on Aug 16, 2016

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

      andreasprlic

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14. Commits on Jul 4, 2016

    • Merge pull request #525 from andreasprlic/master

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      josemduarte

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

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      josemduarte

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15. 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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16. 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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17. Commits on Jun 27, 2016

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

      lafita

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18. 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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19. Commits on Jun 16, 2016

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

      

      Mohamed Ezzat

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20. Commits on Jun 15, 2016

    • squid:S2063 - Comparators should be Serializable

      

      Mohamed Ezzat

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21. Commits on Jun 10, 2016

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

      

      Mohamed Ezzat

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