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Commits on May 3, 2016

• [maven-release-plugin] prepare release biojava-4.2.1

  josemduarte

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• [maven-release-plugin] rollback the release of biojava-4.2.1

  josemduarte

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• [maven-release-plugin] prepare release biojava-4.2.1

  josemduarte

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• Updated MMCif Parser to handle non-numeric data in the NCS operator field.

  

  abradle

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  josemduarte

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• #459 removing javaws dependency part 2

  

  andreasprlic

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  josemduarte

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• cherry-picking: #459 removing javaws dependency

  

  andreasprlic

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Commits on Apr 29, 2016

• Added handling of '?' and other non integer string for the charge.

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  abradle

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  josemduarte

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• Refactored ChargeAdder and fixed bugs where it wasn't adding charges to all groups.

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  abradle

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Commits on Apr 27, 2016

• Fix #455. Use parsing params for AtomCache

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  sbliven

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  josemduarte

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Commits on Apr 22, 2016

• Fix #452 update ECOD javadoc

  lafita

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• Update CATH default and latest versions to 4.0.0 #453

  lafita

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• Fix bug in internal symmetry levels report

  lafita

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Commits on Apr 11, 2016

• Fixing bug in mmcif writing: ins codes were written as ascii code

  josemduarte

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Commits on Apr 6, 2016

• Fix #449 by copying SEQRES to new chains

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  sbliven

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• Switch DownloadChemCompProvider to use NIO for moving

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Commits on Mar 29, 2016

• Display only elementary axes of symmetry

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  lafita

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• Implement method to calculate coverage of a MultipleAlignment

  lafita

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• Port the getReasons method from symmetry project

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• Create two threshold parameters for CE-Symm

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• Take the best alignment of the optimization trajectory cesymm

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Commits on Mar 25, 2016

• Merge branch 'bugfixes-4.2' of github.com:biojava/biojava into bugfixes-4.2

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  andreasprlic

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• fixing a problem with reflection and changed method signatures.

  andreasprlic

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• Updating biojava-protein-comparison-tool dependencies

  sbliven

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• Setting 4.2.1-SNAPSHOT in all other poms

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  sbliven

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• Logging and documentation

  sbliven

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• Fix major bug with BIO: identifiers

  sbliven

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Commits on Mar 23, 2016

• Add parameterized constructor to NCBIQBlastService to support BLAST on the cloud service providers

  

  christiam

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  josemduarte

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• Fixes for jdk8 javadoc errors

  

  heuermh

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Commits on Mar 22, 2016

• Fix small jmol display bug for internal symmetry

  lafita

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Commits on Mar 14, 2016

• Fixed a bug where nucleotide bonds were not being generated. Added a test to ensure nucleotide bonds are being generated.

  

  Anthony Bradley

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  josemduarte

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• Setting 4.2.1-SNAPSHOT in pom

  josemduarte

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Commits on Mar 10, 2016

• [maven-release-plugin] prepare release biojava-4.2.0

  andreasprlic

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• Updating maven release plugin version

  josemduarte

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• Merge pull request #432 from sbliven/master

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  sbliven

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• Light cleanup:

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