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Commits on Mar 15, 2018

• Converting junit3 to 4, thanks intellij

  josemduarte

  committed
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Commits on Mar 14, 2018

• Merge pull request #749 from josemduarte/removeV4deprecations

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  josemduarte

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  763f7ec

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• Add license to all files

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  sbliven

  committed
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Commits on Mar 12, 2018

• Removing deprecations from v4

  josemduarte

  committed
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Commits on Sep 8, 2017

• Fixing phosphosite urls and changing default url timeout to 30s

  josemduarte

  committed
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Commits on Apr 26, 2017

• Changing all line ending to unix (to match .gitattributes)

  sbliven

  committed
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Commits on Nov 30, 2016

• addressing requested changes re. throwing exceptions.

  andreasprlic

  committed
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• moving to Java 7

  andreasprlic

  committed
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• now also accepting old header line

  andreasprlic

  committed
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• #610 switching test to junit version 4

  andreasprlic

  committed
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Commits on Nov 29, 2016

• creating local dir, if it does not exist.

  andreasprlic

  committed
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• fix for #610

  andreasprlic

  committed
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Commits on Aug 18, 2016

• making output less verbose

  andreasprlic

  committed
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• setting default log level to warn

  andreasprlic

  committed
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Commits on Aug 8, 2016

• new utility classes to detect if a Group is polymeric, an amino acid, or a nucleotide group.

  andreasprlic

  committed
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Commits on Jun 15, 2016

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

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  andreasprlic

  committed
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• some formatting improvements.

  andreasprlic

  committed
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• Merge branch 'bugfixes-4.2'

  sbliven

  committed
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Commits on Jun 14, 2016

• merging in latest ptm modifications from master branch

  pwrose

  committed
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• Updating ptm list.

  pwrose

  committed
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• Added list of chromophores to ptm_list.xml file, updated unit tests

  pwrose

  committed
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Commits on Jun 10, 2016

• Reverting some changes to be compliant with the "old" way of doing chain IDs.

  andreasprlic

  committed
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• Merge pull request #502 from andreasprlic/master

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  josemduarte

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  3509775

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• merging in updated ptm_list.xml

  andreasprlic

  committed
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• merging in updated ptm_list.xml

  andreasprlic

  committed
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• merging in updated ptm_list.xml

  andreasprlic

  committed
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• distance have to be looked up by element name, not atom name

  andreasprlic

  committed
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• Adds a new definitions file so the code can correctly detect Metal bonds. Slightly more efficient representation of standard amino acids.

  andreasprlic

  committed
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• merging in fixes related to PTMs into bug fix branch

  andreasprlic

  committed
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• update for 2VH3 TY2

  andreasprlic

  committed
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• updating legacy chemical component and atom names to current naming conventions.

  andreasprlic

  committed
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• distance have to be looked up by element name, not atom name

  andreasprlic

  committed
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Commits on Jun 9, 2016

• Adds a new definitions file so the code can correctly detect Metal bonds. Slightly more efficient representation of standard amino acids.

  andreasprlic

  committed
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Commits on Jun 5, 2016

• squid:S2131 - Primitives should not be boxed just for String conversion

  

  Mohamed Ezzat

  committed
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Commits on Jun 1, 2016

• Allowing detection of PTMs that interact with Terbium, as reported by @epeisach . Also less verbose PTM junit test.

  andreasprlic

  committed
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