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onbiojava-4.2.1

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Commits on May 3, 2016

• #459 removing javaws dependency part 2

  

  andreasprlic

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  josemduarte

  committed
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• cherry-picking: #459 removing javaws dependency

  

  andreasprlic

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  josemduarte

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Commits on Mar 29, 2016

• Display only elementary axes of symmetry

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  lafita

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• Port the getReasons method from symmetry project

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  lafita

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Commits on Mar 25, 2016

• Logging and documentation

  sbliven

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Commits on Mar 22, 2016

• Fix small jmol display bug for internal symmetry

  lafita

  committed
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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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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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• Automatically adding missing @Override

  sbliven

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• Converting initial spaces to tabs.

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  sbliven

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• Removing OpenAstexViewerImpl

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  sbliven

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• Removing template messages

  sbliven

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• Remove trailing whitespace globally from .java files

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Commits on Mar 8, 2016

• Merge branch 'master' into removeLoadChemCompInfo

  josemduarte

  committed
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• Merge remote-tracking branch 'biojava/master'

  sbliven

  committed
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• Removing loadChemCompInfo, some tests don't pass yet

  josemduarte

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Commits on Mar 7, 2016

• Final CeSymm display options before release

  lafita

  committed
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Commits on Mar 4, 2016

• Fix #385. Support BIO: identifiers

  sbliven

  committed
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Commits on Mar 3, 2016

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

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  andreasprlic

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• Use homologous structure derived matrix HSDM for msa tree building

  lafita

  committed
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• Correct significance criteria for internal symmetry

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  lafita

  committed
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Commits on Mar 1, 2016

• fixing broken demo

  andreasprlic

  committed
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• this example was using the wrong Parameter class. fixed

  andreasprlic

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Commits on Feb 10, 2016

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

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  andreasprlic

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• adding utility method

  andreasprlic

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Commits on Feb 5, 2016

• Change substitution matrix to SDM for symmetry phylogeny

  lafita

  committed
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• Print a summary of internal symmetry in Jmol display

  lafita

  committed
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Commits on Feb 4, 2016

• Use HSDM substitution matrix instead of BLOSUM45 in MSA trees

  lafita

  committed
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• Change all references to Subunits to Repeats for consistency in CeSymm

  lafita

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Commits on Feb 3, 2016

• Fix bugs in Phylogenetic tree display

  lafita

  committed
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• Superimpose freely at the end in case more than one symmetry level

  lafita

  committed
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