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Commits on Dec 15, 2014

• Adding @Override and @Deprecated tags where applicable

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  sbliven

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Commits on Dec 8, 2014

• First implementation of interface clustering based on contact overlap

  josemduarte

  committed
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Commits on Nov 20, 2014

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

  dmyersturnbull

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• Fixed this issue:

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  dmyersturnbull

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Commits on Nov 12, 2014

• Another fix for #193

  josemduarte

  committed
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Commits on Nov 5, 2014

• changed CompoundNotFoundException into IllegalArgumentException, removed MalFormedUrlException, added RemoteException when failing to fetch the uniprot entry

  parit

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• corrected the fetch url, not writing into cache when cache directory not specified and breaking correctly after fetching the entry xml

  parit

  committed
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Commits on Nov 3, 2014

• added uniprot id pattern matching to fail-fast on wrong uniprot ids, added retrying netwrok request if id is not available immediately, bubbling-up the error codes in case uniprot servers are down

  

  Parit Bansal

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Commits on Oct 28, 2014

• Fixing #193

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  josemduarte

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• More #111

  josemduarte

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Commits on Oct 4, 2014

• Merge pull request #180 from josemduarte/master

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  andreasprlic

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Commits on Oct 1, 2014

• Remove compile warnings

  emckee2006

  committed
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• Merge pull request #182 from emckee2006/master

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  emckee2006

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• Enhance UniprotProxySequenceReader to be able to parse Uniprot when XML

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  emckee2006

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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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  josemduarte

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Commits on Sep 18, 2014

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

  josemduarte

  committed
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Commits on Sep 17, 2014

• Merge pull request #166 from benjamintboyle/master

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  josemduarte

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Commits on Sep 16, 2014

• Convert core src/test/java to slf4j #155

  benjamintboyle

  committed
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• Convert core.util package to use slf4j

  benjamintboyle

  committed
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• Fixed logging issue with updated slf4j #155

  benjamintboyle

  committed
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• Converted core.sequence.loader package from print and printStackTrace

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  benjamintboyle

  committed
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• Converted all core.sequence.io print and printStackTrace to slf4j #155

  benjamintboyle

  committed
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Commits on Sep 12, 2014

• Converting core.sequence to use slf4j instead of println #155

  benjamintboyle

  committed
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Commits on Sep 11, 2014

• - add isValidSequence method into CompoundSet interface. Implemented.

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  Jacek Grzebyta

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Commits on Sep 9, 2014

• fixed misspell in property name: "java.io.tempdir"->"java.io.tmpdir"

  

  Jacek Grzebyta

  committed
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Commits on Sep 1, 2014

• fixed misspell in log4j2.xml file

  

  Jacek Grzebyta

  committed
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• replaced "/tmp" path by more generic: System.getProperty("java.io.tempdir")

  

  Jacek Grzebyta

  committed
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Commits on Aug 29, 2014

• add slf4j logger to parsers

  

  Jacek Grzebyta

  committed
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• add log4j 2 config file

  

  Jacek Grzebyta

  committed
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• Merge biojava/biojava branch

  

  Jacek Grzebyta

  committed
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• - add junit tests for GenbankProxySequenceReader and another LocationParserTest

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  Jacek Grzebyta

  committed
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• add understanding non-standard DNA nucleotides

  

  Jacek Grzebyta

  committed
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Commits on Aug 24, 2014

• updating CookbookMSA example to up-to-date uniprot IDs

  andreasprlic

  committed
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• adding better error log if a obsolete UniProt sequence is parsed.

  andreasprlic

  committed
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Commits on Aug 23, 2014

• fixing access to local files. test better done via classpath

  andreasprlic

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