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Commits on Dec 18, 2014

• Merge remote-tracking branch 'biojava/master'

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Commits on Dec 17, 2014

• Fixing an altLoc bug in mmcif parsing: parent chain wasn't set

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Commits on Dec 15, 2014

• Fix #219

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• Adding @Override and @Deprecated tags where applicable

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Commits on Dec 13, 2014

• Fixed issue in test

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Commits on Dec 10, 2014

• Fixed important bug: ChainImpl.clone wasn't deep copying seqres groups

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Commits on Dec 9, 2014

• Merge remote-tracking branch 'emmebi/master'

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Commits on Dec 4, 2014

• Merged entity heuristics stuff into the existing Compound code

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• Fixed a few imporant issues with Compound mmCIF parsing

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• Bug fix for last commit, plus more minor interface changes and removed

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• Some cleanup and a minor interface change in Compound

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• Full implementation of entity finder

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• Better testing for entities

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• First implementation of entities

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Commits on Nov 13, 2014

• Adding array version of CrystalCell#transfToOriginCell

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Commits on Nov 7, 2014

• Adding CrystalCell methods & tests

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Commits on Oct 28, 2014

• Fixing #193

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Commits on Oct 7, 2014

• another fix for parsong PAU and XAU bio assemblies

  pwrose

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• need to change integer definition of bio assembly to string to support "PAU" and "XAU" biological units (e.g. 1A34). Also smarter logging.

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Commits on Oct 5, 2014

• Implementing #181

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Commits on Oct 4, 2014

• Now PDB_DIR doesn't have to be writable

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Commits on Oct 1, 2014

• Making tests use split dir layout

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• SIFTS dir now also goes to PDB_CACHE_DIR instead of PDB_DIR

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• Redoing exception handling in test by using junit4's "expected" #111

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• More consolidation on PDB_DIR/PDB_CACHE_DIR reading

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Commits on Sep 28, 2014

• Improving and unifying the setting of PDB_DIR and PDB_CACHE_DIR

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Commits on Sep 22, 2014

• manually resolving merge conflict

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Commits on Sep 20, 2014

• Full fix for #148, all tests pass

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• Towards fixing #148, compiles but some tests don't pass yet

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Commits on Sep 19, 2014

• Fix problems exposed by using mmCIF files (towards #173)

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• Fix #172. ResidueNumbers use the old chain IDs when read from mmCIF

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Commits on Sep 18, 2014

• Adding missing log4j2.xml files and unifying config across modules #155

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Commits on Sep 17, 2014

• Solving issue #145

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• Solving issue #160

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Commits on Aug 30, 2014

• #155 and some #111

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