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1. Commits on Aug 14, 2015

   • Merging from master to biojava-ffx integration branch.

     jacob-litman

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2. Commits on Aug 4, 2015

   • Updated POMs in preparation for hosting as separate Maven repository; a few comments and log messages also got slightly refactored. Everything seems ready for public Biojava-FFX integration (with t…

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     Jacob Litman

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   • Allow non-refined result, only self-alignment

     lafita

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   • Fix demo issues

     lafita

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3. Commits on Aug 3, 2015

   • Add Demo for CeSymm

     lafita

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   • Port CeSymm for internal symmetry detection code to BioJava

     lafita

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4. Commits on Jul 29, 2015

   • Extended the interface-implementation paradigm to Bonds and SSBonds. Renamed chain.getParent() and chain.setParent() to chain.getStructure() and chain.setStructure() to deconflict with other APIs. …

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     Jacob Litman

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5. Commits on Jul 24, 2015

   • Fix bug with flexible MultipleAlignments

     lafita

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6. Commits on Jul 23, 2015

   • Remove the 3D transformations in MultipleAlignment

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     lafita

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7. Commits on Jul 22, 2015

   • Calc.transform() documentation and testing

     lafita

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8. Commits on Jul 20, 2015

   • Fix bug in jama to vecmath conversion

     lafita

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   • Core length used as the the min block length

     lafita

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9. Commits on Jul 17, 2015

   • Include getters for some Jmol member variables (frame and alignment)

     lafita

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10. Commits on Jul 16, 2015

    • Organize MultipleAlignment code in a util package

      lafita

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    • Test all String output Writer methods of MultipleAlignment

      lafita

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11. Commits on Jul 9, 2015

    • Review GUI code for MultipleAlignments

      lafita

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    • Show ligands in the MultipleAlignment display

      lafita

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12. Commits on Jul 8, 2015

    • Static methods for Jmol display methods, for consistency

      lafita

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

      lafita

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    • Save and Load MultipleAlignment through the GUI

      lafita

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    • Implement XML Converter and Parser for MultipleAlignments

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      lafita

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13. 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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14. Commits on Jul 1, 2015

    • Create Multiple Alignment GUI

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      lafita

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15. Commits on Jun 26, 2015

    • These two static API methods needs to stay public.

      andreasprlic

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

      lafita

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    • Smooth probability function in MC optimization

      lafita

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    • Merge pull request #290 from lafita/multaln

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      sbliven

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16. Commits on Jun 25, 2015

    • Clean Demos for Multiple Alignments

      lafita

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    • Create templates for MultipleAlignment CLI #278

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      lafita

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    • [maven-release-plugin] prepare for next development iteration

      andreasprlic

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    • [maven-release-plugin] prepare release biojava-4.1.0

      andreasprlic

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17. 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

      lafita

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