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Commits on Jul 31, 2012

• workaround for a problem that seems openjdk specific

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• adding javadoc

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Commits on Jul 23, 2012

• PDBWW-4789 entityView is now linked to structure summary page!

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Commits on Jun 15, 2012

• now serializable

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• now serializable

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Commits on May 30, 2012

• switching the json library according to request from Olivier Sallou

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Commits on Feb 11, 2012

• NCBIQBlastService replaced with the new implementation.

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Commits on Jan 12, 2012

• Reversed conditions in if statement so null check was first. Prevents NPE.

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Commits on Jan 9, 2012

• Alternate implementation of NCBIQBlastService

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Commits on Dec 20, 2011

• adding @since 3.0.3 annotations

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• Adding a new client for submitting ProteinSequences to the Hmmer3 web service and retrieving Pfam domain annotations

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Commits on Dec 12, 2011

• Included some error catching mechanisms into NCBIQBlastService to intercept QBlast's error messages.

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Commits on Dec 8, 2011

• Fixing PAM250 default values

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• Major mods in NCBIQBlastAlignmentProperties: it is now responsible for basic sanity checks of these properties instead of NCBIQBlastService. Also added get/set methods for blastp matrix selection a…

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Commits on Dec 2, 2011

• Adjustments to getBlastFromPOsition and getBlastToPosition

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• using MEGABLAST should now work in setBlastProgram

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• added getBlastWordSize/setBlastWordSize to use WORD_SIZE values for BLAST requests

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• added getBlastExpect/setBlastExpect to use EXPECT values for BLAST requests

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Commits on Aug 30, 2011

• Simple comment addition

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• Commented out code removed, cleaning the mess...

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Commits on May 26, 2011

• Fix a problem that appeared in the NCBI QBlast service where using the FORMAT_OBJECT=ALIGNMENT tag in the URL would return no results from the getAlignementResults method...

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Commits on Feb 21, 2011

• New methods to add getting/setting EXPECT and WORD_SIZE parameters

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• More bug fixes: checking for null program or null database now works with new code

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• Bug fixes

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Commits on Jan 25, 2011

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• Improving the code...

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• Fixing BJ1.7 to BJ3 bugs

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• Fixing bugs generated from BJ1.7 to BJ3 transitions

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Commits on Jan 24, 2011

• Fixing more BJ1.7 to BJ3.0 bugs

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Commits on Jan 11, 2011

• Working on removing old legacy BJ dust... Sequence interface used instead of RichSequence. I also included the import requests for DNASequence and ProteinSequence. I need to add the logic related t…

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• Working on removing old legacy BJ dust... Sequence interface used instead of RichSequence

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Commits on Sep 30, 2010

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• Correcting a "==" inequality, using Arrays' searchBinary() method instead.

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• Various fixing to match biojava3 usage: removing usage of BioException

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