Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...
[jalview.git] / src / jalview / analysis / CrossRef.java
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-03 Jim ProcterJAL-2210 hack to remove EMBL from Protein crossrefs...
2016-10-03 Jim ProcterJAL-2210 explicit ‘doNotAdd’ list to prevent sequences...
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences...
2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a...
2016-10-02 Jim ProcterJAL-2210 comments
2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an...
2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referen...
2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs...
2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add...
2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for prese...
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary...
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding...
2016-08-25 Jim ProcterJAL-2154 copy and paste error
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already...
2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover...
2016-08-16 Jim ProcterJAL-2154 make sure any new sequences via DBRefEntry...
2016-08-16 Jim ProcterJAL-2154 always resolve dataset sequences when creating...
2016-08-04 Jim ProcterJAL-2154 make sure codon mappings between sequences...
2016-08-04 Jim ProcterJAL-2154 todo
2016-08-04 Jim ProcterJAL-2154 use convenience method
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings...
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter...
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds...
2016-06-23 Jim ProcterJAL-2110 clarify javadoc
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref...
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein()
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context...
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use...
2016-06-09 gmungocJAL-2110 work in progress
2016-06-03 gmungocJAL-2110 random stuff
2016-05-20 gmungocJAL-2110 unit tests for and minor refactoring of CrossRef
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated...
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs...
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot
2016-02-19 gmungocJAL-1705 refactor show products, set initial split...
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl...
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid...
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq...
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe...
2015-03-30 gmungocJAL-1264 remove broken applet build dependencies
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-06-13 jprocterjavatidy
2012-06-12 jprocterJAL-1115 refactor base collection for Alignment from...
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-04-30 jprocterjalview 2.5 release banner
2009-06-19 jprocterdebug
2009-06-08 jprocterapply gpl development license
2009-02-06 jprocterfix occasional nullpointer ref when seq ID retrieval...
2008-09-04 jproctermerge from 2_4_Release branch
2008-08-19 jprocterbetter check for molecule type when identifying interna...
2008-08-06 jprocterextra checks for datasetsequence for when getDbRefs...
2007-11-16 jprocterrefactor abstract sequence fetching and DBSource machin...
2007-11-12 jproctercrossrefs have properly updated pdbId lists
2007-09-07 jprocterformatting and ensure that dataset is actually searched...
2007-08-01 jprocternull pointer exception bug fix
2007-07-25 jprocterfix crossRef retrieval so either protein OR nucleotide
2007-07-13 jproctermethods for traversing database reference space