JAL-2994 put ‘\’ first in character class clause of regex - otherwise doesn’t compile...
[jalview.git] / src / jalview / ext /
2018-06-07 gmungocJAL-2755 correct Javadoc and error handling
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-05-07 Jim ProcterJAL-2321 use StructureImportSettings singleton settings...
2018-05-07 Jim ProcterJAL-2321 allow JmolParser to be configured before parsi...
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
2018-05-04 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_...
2018-05-01 Jim ProcterJAL-2899 colouring moved from SwingWorker to a backgrou...
2018-04-30 Jim ProcterMerge branch 'bug/JAL-2899' into releases/Release_2_10_...
2018-04-05 Jim ProcterJAL-2945 resolve model as PDB file. Need to verify...
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe...
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea...
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-12 Jim ProcterJAL-2780 JAL-2781 ahem - add a semicolon if there isn...
2018-02-07 Jim ProcterJAL-2780 JAL-2781 don’t assume contiguous mapping to...
2018-02-02 gmungocJAL-2899 asynchronous Jmol colour updates bug/JAL-2899
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressio...
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved...
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri...
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren...
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere...
2017-12-01 gmungocJAL-2835 spike updated to latest (use specific SO term...
2017-11-30 gmungocJAL-1766 additional tests for stub htsjdk wrapper
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-13 gmungocJAL-2679 example accession changed to CAD01290
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome...
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging
2017-10-24 gmungocJAL-2743 look up species and gene loci for Ensembl...
2017-10-24 gmungocJAL-1739 Javadoc updated for Lambda expression parser...
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd...
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2253' into develop
2017-10-23 gmungocJAL-1854 keep fallthrough but with comment to suppress...
2017-10-23 gmungocJAL-1854 remove fallthrough of switch case (Checkstyle...
2017-10-20 gmungocPush 1793 latest to spike branch
2017-10-20 gmungocJAL-2253 pull up constant, additional unit test bug/JAL-2253
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci
2017-10-19 gmungocJAL-2755 add species lookup
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
2017-10-17 Jim ProcterJAL-2777 patch for whitespace chain bugs/JAL-2777_whitespaceChain
2017-10-10 Jim ProcterMerge branch 'codereviews/JAL-1990_IProgressIndicator_j...
2017-10-09 gmungocJAL-2523 basic sleep and retry (3 times) on 429 respons... features/JAL-2523httpRetries
2017-10-09 gmungocJAL-2523 convenience method to get model organisms
2017-10-04 gmungocJAL-2523 start of refactoring...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-10-02 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-02 gmungocJAL-2525 lookup transcript features by Ontology
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever...
2017-09-25 gmungocJAL-2738 query unindexed file, unit test for VCFLoader
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu...
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping
2017-09-21 gmungocJAL-2738 add chromosome coordinate mappings to transcripts
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence
2017-09-19 gmungocJAL-1793 wrapper for plain or indexed VCF + simple...
2017-08-31 gmungocJAL-2105 REST versions updated to 6.1 (Ensembl) 6.0...
2017-08-31 gmungocJAL-2253 safer simpler resolution of identifiers using...
2017-08-25 gmungocJAL-2480 suppress debug timing output that got left in
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources
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
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2582 comment about IDs being lost if they resembl...
2017-06-04 Jim ProcterJAL-2582 recognise ENS…P peptide IDs and make two getPa...
2017-05-30 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu...
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-24 gmungocJAL-2529 add object_type=cdna to EnsemblCdna parameters
2017-05-18 gmungocJAL-2490 retrieve visible features only
2017-05-16 gmungocJAL-2525 put in missing "transcript" feature type
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s...
2017-05-12 gmungocJAL-2480 renamed java.util.RangeComparator to IntRangeC...
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final...
2017-05-08 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into
2017-05-03 gmungocJAL-2105 Ensembl REST now at 5.0
2017-05-01 tcofoegbuJAL-2465 bugfix and rerefactor renamed getPdbFile(...
2017-04-26 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-04-26 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-04-24 gmungocJAL-2487 remove redundant refreshGUI to minimise thread...
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
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