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1. Commits on Jan 14, 2016

   • Merge pull request #371 from abradle/master

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   • Update gitignore to fit last commit

     

     Anthony

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   • Updated class to be serialzable for spark

     

     Anthony

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   • Fix broken tests in MultipleAlignmentScorer

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     lafita

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   • Add lectins as example of CECP multiple alignment

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   • Fix bug in transformed Atoms from MStA

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   • Merge pull request #370 from lafita/phylo

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   • Merge branch 'master' into phylo

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2. Commits on Jan 13, 2016

   • Fixing #369, also removing some warnings

     josemduarte

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   • Removing unused code

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   • Adding NMR write/read mmcif test

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   • Adding test case for #368. Fixed also TestURLBasedFileParsing

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3. Commits on Jan 12, 2016

   • Fixing #368

     josemduarte

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   • Fixing build

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     sbliven

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   • Fixing version of protein-comparison-tool module

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     sbliven

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   • Bumping remaining maven dependencies

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   • Adding license to sub-poms

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   • Updating more maven plugin versions.

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   • Updating maven plugin versions.

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   • Merge pull request #365 from sbliven/master

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     andreasprlic

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   • Merge pull request #366 from lafita/afpchain

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4. Commits on Jan 11, 2016

   • Merge pull request #358 from edlunde-dnastar/ssbonds

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   • Merge branch 'master' into ssbonds

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     Matt Larson

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   • Merge branch 'master' into ssbonds

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     Matt Larson

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   • Only build bonds within basic 1_555 symmetry. Added a marker for future implementation of the bonds between symmetry-related molecules.

     

     Matt Larson

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   • AFPChain old constructor backwards compatible & deprecated #286

     lafita

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   • Pass the algorithmName in AFPChain constructor #286

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   • Make all AFPChain memeber variables private

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   • Print warning only when Bridge information loss #360

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   • Downgrading Log4J to 2.3 for compatibility with Java 1.6

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     sbliven

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   • Rename the TestSecStrucCalc #320

     lafita

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   • Print a warning when number of beta bridges exceeds 2 #360

     lafita

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5. Commits on Jan 8, 2016

   • #360 improving class and method names

     andreasprlic

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   • Adding constructor so that path can be initialised externally

     josemduarte

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6. Commits on Jan 7, 2016

   • Merge pull request #361 from edlunde-dnastar/mmcif-seqres

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