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1. Commits on Sep 8, 2016

   • Remove some unimplemented methods in phylo

     lafita

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   • Merge alignment and phylo modules #413

     lafita

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2. 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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3. Commits on Jul 1, 2016

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

     

     Mohamed Ezzat

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4. Commits on Jun 16, 2016

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

     

     Mohamed Ezzat

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5. Commits on Jun 15, 2016

   • squid:S2063 - Comparators should be Serializable

     

     Mohamed Ezzat

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6. Commits on Apr 24, 2016

   • squid:S2178 - Short-circuit logic should be used in boolean contexts

     

     Mohamed Ezzat

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7. Commits on Mar 10, 2016

   • Light cleanup:

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     sbliven

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   • Running spacestotabs on recent changes

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     sbliven

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8. Commits on Mar 9, 2016

   • Merge branch 'master' into removeLoadChemCompInfo

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     josemduarte

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   • Removing unnecessary casts

     sbliven

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   • More whitespace fixes

     sbliven

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   • Removing unused imports

     sbliven

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   • Converting initial spaces to tabs.

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     sbliven

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   • Remove trailing whitespace globally from .java files

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     sbliven

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   • Update to remove docstring

     abradle

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   • Merge remote-tracking branch 'upstream/master' into removeLoadChemCompInfo

     josemduarte

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   • Merge pull request #427 from abradle/master

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     josemduarte

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9. Commits on Mar 8, 2016

   • Fixing a few bugs that arose after loadChemCompInfo removal, #426

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     josemduarte

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   • Create a test for issue #288 sub-optimal MSA

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     lafita

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10. Commits on Mar 7, 2016

    • Updates to make serializable for Spark

      abradle

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11. Commits on Jan 15, 2016

    • Fix typo in GuideTreeTest

      lafita

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    • Fix broken GuideTreeTest

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      lafita

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12. Commits on Nov 17, 2015

    • Generalize the GuideTree calculation using phylo

      lafita

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13. Commits on Nov 12, 2015

    • Merge commit '248cc08c7fbbdc02249bcac0f10481127b7d3ac7'

      josemduarte

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14. Commits on Oct 6, 2015

    • Converting all line endings to Unix.

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      sbliven

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15. Commits on Sep 16, 2015

    • Massive refactoring: moved alignment data structures from biojava-alignment to biojava-core.

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      paolopavan

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16. Commits on Mar 18, 2015

    • Added a more complex test for NeedlemanWunsch using an alignment done by hand.

      

      dmyersturnbull

      authored and

      sbliven

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17. Commits on Jan 30, 2015

    • Refactoring of all package names according to #245 #242 #240

      andreasprlic

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18. Commits on Jan 29, 2015

    • Ran Optimize Imports across the whole project.

      andreasprlic

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    • Major refactoring of package names in accordance with #245 #242 #240

      andreasprlic

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