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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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   • Merge remote-tracking branch 'upstream/master'

     josemduarte

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   • Merge pull request #311 from lafita/cesymm

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     andreasprlic

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   • Use C-alpha Atoms in AltLocs Test

     lafita

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   • Fix StructureToolsTest to pass according to changes

     lafita

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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

   • Make getRepresentative Atoms consistent

     lafita

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   • Fixing issue in getAlignedResIndex, now the mapping will work for

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     josemduarte

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   • 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 31, 2015

   • fix for #306 - now checks provided URL if it contains the string ".cif" and switches to mmCif parsing accordingly.

     andreasprlic

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   • #308 adding a test that demonstrates that fetching mmCIF files from remote URLs is broken. Also tests for correct parsing of compressed files.

     andreasprlic

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   • Minor fix

     josemduarte

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5. 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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6. Commits on Jul 28, 2015

   • Some cosmetics

     josemduarte

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7. Commits on Jul 27, 2015

   • Merge pull request #304 from sbliven/master

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     andreasprlic

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   • Adding some more non-deposited files tests, #305.

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     josemduarte

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   • Reverting parser change: removing pure non-poly chains is a bad idea.

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     josemduarte

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   • More parsing fixes, #305

     josemduarte

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8. Commits on Jul 24, 2015

   • Merge remote-tracking branch 'upstream/master'

     josemduarte

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   • Better parsing of COMPND lines in PDB files, #305

     josemduarte

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   • Fixing tests: order of AbstractScoresCache.getScores wasn't guaranteed

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     josemduarte

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   • Fix bug with flexible MultipleAlignments

     lafita

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9. Commits on Jul 23, 2015

   • Rename and move Tests for consistency

     lafita

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

     lafita

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   • Remove the 3D transformations in MultipleAlignment

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     lafita

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   • Updating SCOPe to version 2.05

     sbliven

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   • Factor out Subunits definition in quaternary symmetry

     lafita

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   • Adding sortBlocks method

     sbliven

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10. Commits on Jul 22, 2015

    • Calc.transform() documentation and testing

      lafita

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11. Commits on Jul 20, 2015

    • Unify Vecmath to JAMA conversion methods in Calc

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      lafita

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    • 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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