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Commits on Mar 1, 2016

• 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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• adding utility method

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Commits on Feb 5, 2016

• Change substitution matrix to SDM for symmetry phylogeny

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• Print a summary of internal symmetry in Jmol display

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Commits on Feb 4, 2016

• Use HSDM substitution matrix instead of BLOSUM45 in MSA trees

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

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Commits on Feb 3, 2016

• Fix bugs in Phylogenetic tree display

  lafita

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

  lafita

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• New feature, show phylogenetic trees for Multiple Structure Alignemnts

  lafita

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Commits on Feb 1, 2016

• Merge branch 'master' into cesymm

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• Rename Display class following part 2 of #396

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Commits on Jan 31, 2016

• making method static

  andreasprlic

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• adding missing update

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• making method static

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• #393 step 1) all classes that are Jmol specific, should have Jmol in their name. Also, starting to break out general purpose utility methods that can be used for other viewers.

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Commits on Jan 28, 2016

• Create method to get protodomains as StructureIdentifiers

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Commits on Jan 27, 2016

• Extend CeSymmResult class

  lafita

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• Remove DemoMultipleAlignmentJmol

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• Fixing demo after latest changes

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Commits on Jan 26, 2016

• Making demos compile but not package into jar #387

  josemduarte

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• Fixing some bugs in internal symmetry

  lafita

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• Merge branch 'master' into cesymm

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• Fix display bugs

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• Adapt CeSymm methods to new Refiner interface

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• #383 updating of demo scripts to new StructureIdentifier convention

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• #383 this unit test references code from the testing framework. Disabling for now.

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Commits on Jan 25, 2016

• Adapt SymmetryGUI to latest changes

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Commits on Jan 20, 2016

• Changing many classes to use StructureIdentifier

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• Moving SCOP name guessing from AtomCache to StructureName

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Commits on Jan 14, 2016

• Add lectins as example of CECP multiple alignment

  lafita

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Commits on Jan 12, 2016

• Fixing build

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  sbliven

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• Adding license to sub-poms

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Commits on Dec 1, 2015

• Adding biojava license statements

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• Adding alpha component to rotateHue

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