git://source.jalview.org / jalview.git / history
? search:
summary | shortlog | log | commit | commitdiff | tree
first ⋅ prev ⋅ next
Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / analysis / CrossRef.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-02-03 Jim ProcterJAL-2305 comments re testFindXrefSequences_withFetch... commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... commit | commitdiff
2019-02-04 hansonrrefactoring for DBMODList commit | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... commit | commitdiff
2018-06-22 gmungocJAL-3032 avoid assignments on the same line as synchronized commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-10-03 Jim ProcterJAL-2210 hack to remove EMBL from Protein crossrefs... commit | commitdiff
2016-10-03 Jim ProcterJAL-2210 explicit ‘doNotAdd’ list to prevent sequences... commit | commitdiff
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences... commit | commitdiff
2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a... commit | commitdiff
2016-10-02 Jim ProcterJAL-2210 comments commit | commitdiff
2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an... commit | commitdiff
2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referen... commit | commitdiff
2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs... commit | commitdiff
2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add... commit | commitdiff
2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for prese... commit | commitdiff
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary... commit | commitdiff
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting commit | commitdiff
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding... commit | commitdiff
2016-08-25 Jim ProcterJAL-2154 copy and paste error commit | commitdiff
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... commit | commitdiff
2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already... commit | commitdiff
2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover... commit | commitdiff
2016-08-16 Jim ProcterJAL-2154 make sure any new sequences via DBRefEntry... commit | commitdiff
2016-08-16 Jim ProcterJAL-2154 always resolve dataset sequences when creating... commit | commitdiff
2016-08-04 Jim ProcterJAL-2154 make sure codon mappings between sequences... commit | commitdiff
2016-08-04 Jim ProcterJAL-2154 todo commit | commitdiff
2016-08-04 Jim ProcterJAL-2154 use convenience method commit | commitdiff
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack commit | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings... commit | commitdiff
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs commit | commitdiff
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter... commit | commitdiff
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds... commit | commitdiff
2016-06-23 Jim ProcterJAL-2110 clarify javadoc commit | commitdiff
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref... commit | commitdiff
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein() commit | commitdiff
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context... commit | commitdiff
2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use... commit | commitdiff
2016-06-09 gmungocJAL-2110 work in progress commit | commitdiff
2016-06-03 gmungocJAL-2110 random stuff commit | commitdiff
2016-05-20 gmungocJAL-2110 unit tests for and minor refactoring of CrossRef commit | commitdiff
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated... commit | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... commit | commitdiff
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs... commit | commitdiff
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings commit | commitdiff
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot commit | commitdiff
2016-02-19 gmungocJAL-1705 refactor show products, set initial split... commit | commitdiff
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl... commit | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge commit | commitdiff
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid... commit | commitdiff
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... commit | commitdiff
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy commit | commitdiff
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... commit | commitdiff
2015-03-30 gmungocJAL-1264 remove broken applet build dependencies commit | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-06-13 jprocterjavatidy commit | commitdiff
2012-06-12 jprocterJAL-1115 refactor base collection for Alignment from... commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2010-09-23 jprocterapply jalview code style commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-06-19 jprocterdebug commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2009-02-06 jprocterfix occasional nullpointer ref when seq ID retrieval... commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2008-08-19 jprocterbetter check for molecule type when identifying interna... commit | commitdiff
2008-08-06 jprocterextra checks for datasetsequence for when getDbRefs... commit | commitdiff
2007-11-16 jprocterrefactor abstract sequence fetching and DBSource machin... commit | commitdiff
2007-11-12 jproctercrossrefs have properly updated pdbId lists commit | commitdiff
2007-09-07 jprocterformatting and ensure that dataset is actually searched... commit | commitdiff
2007-08-01 jprocternull pointer exception bug fix commit | commitdiff
next