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JAL-3725 helper methods for computing mapped feature range overlap
[jalview.git] / src / jalview / ext / ensembl /
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-02-06 gmungocJAL-1842 adjust code to match changed semantics of... tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-06-11 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-11 gmungocJAL-3143 also parse "phase" from JSON response if present tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-04-26 gmungocJAL-2743 class Javadoc tree | commitdiff
2019-04-18 gmungocJAL-3193 dbSource always "ENSEMBL" tree | commitdiff
2019-04-10 gmungocJAL-3193 rest.ensemblgenomes.org merged to rest.ensembl.org tree | commitdiff
2019-04-10 gmungocJAL-3018 REST version updated to 10.0 tree | commitdiff
2019-03-08 gmungocJAL-3193 defensive trim of URL read from properties... tree | commitdiff
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge... tree | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... tree | commitdiff
2019-01-29 gmungocJAL-3143 format alleles array for feature description tree | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... tree | commitdiff
2019-01-24 gmungocJAL-3018 Ensembl version updated to 9.0 tree | commitdiff
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... tree | commitdiff
2018-10-25 gmungocJAL-3143 comma-delimited feature attributes for alleles, tree | commitdiff
2018-10-25 gmungocJAL-3143 fetch Ensembl(Genomes) features as JSON not GFF tree | commitdiff
2018-09-03 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... tree | commitdiff
2018-09-03 Jim ProcterJAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId tree | commitdiff
2018-08-10 gmungocJAL-3018 updated to Ensembl REST 7.0 tree | commitdiff
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene... tree | commitdiff
2018-08-10 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... tree | commitdiff
2018-06-07 gmungocJAL-2755 correct Javadoc and error handling tree | commitdiff
2018-06-04 gmungocJAL-3018 updated REST versions to 6.3 tree | commitdiff
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... tree | commitdiff
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL tree | commitdiff
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... tree | commitdiff
2018-01-29 gmungocJAL-2743 recoded EnsemblLookup without lambda expressio... tree | commitdiff
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2018-01-18 gmungocJAL-2679 update query id to actual case of retrieved... tree | commitdiff
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri... tree | commitdiff
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren... tree | commitdiff
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam... tree | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest tree | commitdiff
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-11-13 gmungocJAL-2679 example accession changed to CAD01290 tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
2017-10-25 gmungocJAL-2743 fall back to parsing description if chromosome... tree | commitdiff
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging tree | commitdiff
2017-10-24 gmungocJAL-2743 look up species and gene loci for Ensembl... tree | commitdiff
2017-10-24 gmungocJAL-1739 Javadoc updated for Lambda expression parser... tree | commitdiff
2017-10-24 gmungocJAL-2738 update spike branch with latest tree | commitdiff
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... tree | commitdiff
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2253' into develop tree | commitdiff
2017-10-20 gmungocPush 1793 latest to spike branch tree | commitdiff
2017-10-20 gmungocJAL-2253 pull up constant, additional unit test bug/JAL-2253 tree | commitdiff
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci tree | commitdiff
2017-10-19 gmungocJAL-2755 add species lookup tree | commitdiff
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true... tree | commitdiff
2017-10-09 gmungocJAL-2523 basic sleep and retry (3 times) on 429 respons... features/JAL-2523httpRetries tree | commitdiff
2017-10-09 gmungocJAL-2523 convenience method to get model organisms tree | commitdiff
2017-10-04 gmungocJAL-2523 start of refactoring... tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-10-02 gmungocMerge branch 'develop' into features/JAL-1793VCF tree | commitdiff
2017-10-02 gmungocJAL-2525 lookup transcript features by Ontology tree | commitdiff
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry tree | commitdiff
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene tree | commitdiff
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever... tree | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... tree | commitdiff
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes tree | commitdiff
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping tree | commitdiff
2017-09-21 gmungocJAL-2738 add chromosome coordinate mappings to transcripts tree | commitdiff
2017-08-31 gmungocJAL-2105 REST versions updated to 6.1 (Ensembl) 6.0... tree | commitdiff
2017-08-31 gmungocJAL-2253 safer simpler resolution of identifiers using... tree | commitdiff
2017-08-25 gmungocJAL-2480 suppress debug timing output that got left in tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-06-04 Jim ProcterJAL-2582 comment about IDs being lost if they resembl... tree | commitdiff
2017-06-04 Jim ProcterJAL-2582 recognise ENS…P peptide IDs and make two getPa... tree | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... tree | commitdiff
2017-05-24 gmungocJAL-2529 add object_type=cdna to EnsemblCdna parameters tree | commitdiff
2017-05-16 gmungocJAL-2525 put in missing "transcript" feature type tree | commitdiff
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s... tree | commitdiff
2017-05-12 gmungocJAL-2480 renamed java.util.RangeComparator to IntRangeC... tree | commitdiff
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final... tree | commitdiff
2017-05-03 gmungocJAL-2105 Ensembl REST now at 5.0 tree | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-12-09 gmungocJAL-2105 updated for reviewed REST version 4.8 tree | commitdiff
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-12-07 gmungocJAL-2354 handle error response when fetching features tree | commitdiff
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for... tree | commitdiff
2016-10-13 gmungocJAL-2253 2 second timeout on ping URL, default 5 minute... feature/JAL-2553ensemblGenomes tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 apply license tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting tree | commitdiff
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