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[jalview.git] / src / jalview / analysis / CrossRef.java

2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-14	gmungoc	JAL-2598 Sequence.getSequence return a copy of the...	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2557 removal of Sequence.sequenceFeatures	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-10-03	Jim Procter	JAL-2210 hack to remove EMBL from Protein crossrefs...	blob \| commitdiff \| diff to current
2016-10-03	Jim Procter	JAL-2210 explicit ‘doNotAdd’ list to prevent sequences...	blob \| commitdiff \| diff to current
2016-10-02	Jim Procter	JAL-2210 two pass attempt to import retrieved sequences...	blob \| commitdiff \| diff to current
2016-10-02	Jim Procter	JAL-2210 try to merge all sequences referenced by a...	blob \| commitdiff \| diff to current
2016-10-02	Jim Procter	JAL-2210 comments	blob \| commitdiff \| diff to current
2016-10-02	Jim Procter	JAL-2210 discover candidate dataset sequences for an...	blob \| commitdiff \| diff to current
2016-10-01	Jim Procter	JAL-2210 factored out code for processing cross-referen...	blob \| commitdiff \| diff to current
2016-10-01	Jim Procter	JAL-2210 refactor code to remove from a list of dbrefs...	blob \| commitdiff \| diff to current
2016-09-30	Jim Procter	JAL-2210 some DBRef xref/ref correspondences may add...	blob \| commitdiff \| diff to current
2016-09-30	Jim Procter	JAL-2210 CrossRef.findInDataset should search for prese...	blob \| commitdiff \| diff to current
2016-08-29	Jim Procter	JAL-2154 filter out dbrefs that already match primary...	blob \| commitdiff \| diff to current
2016-08-29	Jim Procter	JAL-2154 refactor if (for easier breakpoint) and formatting	blob \| commitdiff \| diff to current
2016-08-26	Jim Procter	JAL-2154 check that xref is a coding xref before adding...	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	JAL-2154 copy and paste error	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	Merge branch 'refactor/JAL-2106_sourceDbRef_revision...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-08-22	Jim Procter	JAL-2154 verify recovered xref sequence not already...	blob \| commitdiff \| diff to current
2016-08-22	Jim Procter	JAL-2154 regression warning - should never recover...	blob \| commitdiff \| diff to current
2016-08-16	Jim Procter	JAL-2154 make sure any new sequences via DBRefEntry...	blob \| commitdiff \| diff to current
2016-08-16	Jim Procter	JAL-2154 always resolve dataset sequences when creating...	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2154 make sure codon mappings between sequences...	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2154 todo	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2154 use convenience method	blob \| commitdiff \| diff to current
2016-07-07	gmungoc	JAL-2110 field 'cf' moved to stack	blob \| commitdiff \| diff to current
2016-07-06	gmungoc	JAL-2110 ensuring mapped dbrefs between protein and cds	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	JAL-2110 bug fix / test for searchDataset mappings...	blob \| commitdiff \| diff to current
2016-07-01	gmungoc	JAL-2110 bug fixing and tidying for get cross-refs	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 make indirect xref searches work by not filter...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 warning message when routine finds non-ds...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 clarify javadoc	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 refactor to split SequenceFetcher from x-ref...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 use SequenceI.isProtein()	blob \| commitdiff \| diff to current
2016-06-22	Jim Procter	JAL-2110 remove hardwired detection of search context...	blob \| commitdiff \| diff to current
2016-06-14	gmungoc	JAL-2110 fixes to dbref resolution and mappings, use...	blob \| commitdiff \| diff to current
2016-06-09	gmungoc	JAL-2110 work in progress	blob \| commitdiff \| diff to current
2016-06-03	gmungoc	JAL-2110 random stuff	blob \| commitdiff \| diff to current
2016-05-20	gmungoc	JAL-2110 unit tests for and minor refactoring of CrossRef	blob \| commitdiff \| diff to current
2016-04-29	gmungoc	JAL-2051 better checking of retrieved / duplicated...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...	blob \| commitdiff \| diff to current
2016-03-21	gmungoc	JAL-2029 further fixes to get correct xrefs and xrefs...	blob \| commitdiff \| diff to current
2016-03-21	gmungoc	JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings	blob \| commitdiff \| diff to current
2016-03-11	gmungoc	JAL-1705 refactoring etc for fetching Ensembl --> Uniprot	blob \| commitdiff \| diff to current
2016-02-19	gmungoc	JAL-1705 refactor show products, set initial split...	blob \| commitdiff \| diff to current
2016-02-12	gmungoc	JAL-1705 various refactoring towards Uniprot-to-Ensembl...	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-27	gmungoc	JAL-1705 add exon name to features and render on peptid...	blob \| commitdiff \| diff to current
2016-01-23	gmungoc	JAL-1705 compute peptide variants from dna; add "conseq...	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1705 get xrefs only for dna/peptide; code tidy	blob \| commitdiff \| diff to current
2015-11-30	gmungoc	JAL-1421 generics loop syntax; 'bug?' comment added	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1693 make exon alignment for get-xref splitframe...	blob \| commitdiff \| diff to current
2015-03-30	gmungoc	JAL-1264 remove broken applet build dependencies	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-06-13	jprocter	javatidy	blob \| commitdiff \| diff to current
2012-06-12	jprocter	JAL-1115 refactor base collection for Alignment from...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-06-19	jprocter	debug	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2009-02-06	jprocter	fix occasional nullpointer ref when seq ID retrieval...	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-19	jprocter	better check for molecule type when identifying interna...	blob \| commitdiff \| diff to current
2008-08-06	jprocter	extra checks for datasetsequence for when getDbRefs...	blob \| commitdiff \| diff to current
2007-11-16	jprocter	refactor abstract sequence fetching and DBSource machin...	blob \| commitdiff \| diff to current
2007-11-12	jprocter	crossrefs have properly updated pdbId lists	blob \| commitdiff \| diff to current
2007-09-07	jprocter	formatting and ensure that dataset is actually searched...	blob \| commitdiff \| diff to current
2007-08-01	jprocter	null pointer exception bug fix	blob \| commitdiff \| diff to current
2007-07-25	jprocter	fix crossRef retrieval so either protein OR nucleotide	blob \| commitdiff \| diff to current
2007-07-13	jprocter	methods for traversing database reference space	blob \| commitdiff \| diff to current

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