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Commits on Jul 10, 2015

• Merge remote-tracking branch 'upstream/master'

  josemduarte

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• New method to get compounds, made getParentChains public

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Commits on Jul 9, 2015

• Review GUI code for MultipleAlignments

  lafita

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• Show ligands in the MultipleAlignment display

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Commits on Jul 8, 2015

• Merge remote-tracking branch 'main/master' into minor

  lafita

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• Create test for XML conversion and parsing of MultipleAlignments

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• Implement XML Converter and Parser for MultipleAlignments

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  lafita

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Commits on Jul 7, 2015

• Merge pull request #295 from lafita/minor

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  andreasprlic

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• Add more examples for the MultipleAlignment algorithm

  lafita

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• Review MC Optimization code

  lafita

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Commits on Jul 6, 2015

• Rename MC optimizer to a shorter name

  lafita

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Commits on Jul 1, 2015

• Create Multiple Alignment GUI

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Commits on Jun 30, 2015

• MultipleAlignment code revision

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  lafita

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• Some fixes to error handling, logging and javadoc

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Commits on Jun 26, 2015

• Important bug fix in the insertGap() move of MC

  lafita

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• Smooth probability function in MC optimization

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• Merge branch 'master' into minor

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• Merge pull request #290 from lafita/multaln

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• Undo CLI changes for Multiple Structure Alignment

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Commits on Jun 25, 2015

• Clean Demos for Multiple Alignments

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• Support flexible alignments in the MC optimization

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• Fixing #289

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• Create templates for MultipleAlignment CLI #278

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• Better exception handling, some more logging and removing warnings

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• fixing #287 as well as some performance improvements when parsing mmcif files.

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• fixing #287 as well as some performance improvements when parsing mmcif files.

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Commits on Jun 23, 2015

• Set AFPChain constructor algorithm name to unknown

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  lafita

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• Fix updateSuperposition() bug with Transformation Matrices

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Commits on Jun 22, 2015

• Create Test templates for MultipleAlignment

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• Fix AFPChainConversionTest failure

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Commits on Jun 19, 2015

• Improvements in CEMC score and algorithm

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  lafita

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Commits on Jun 18, 2015

• Update CEMC algorithm to support gaps

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• Implement MultipleAlignmentScorer methods: RMSD, Avg-TMscore, CEMC

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• Fix Bugs in MultipleAlignment DS

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Commits on Jun 17, 2015

• Merge branch 'minor' of https://github.com/biojava/biojava.git into biojava-minor

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