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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.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
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff
2020-03-30 gmungocJAL-3210 debug logging commented out commit | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... commit | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... commit | commitdiff
2019-01-29 hansonrtime check, iterators commit | commitdiff
2019-01-29 hansonrmore iterators out; some time checks commit | commitdiff
2019-01-26 hansonrPlatform.timecheck calls removed or commented out. commit | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... commit | commitdiff
2019-01-25 hansonrJSON refactoring commit | commitdiff
2019-01-25 gmungocJAL-3187 don't compute variant features on peptide... commit | commitdiff
2018-11-12 gmungocJAL-3076 JalviewJS requires lower case content-type... commit | commitdiff
2018-10-25 gmungocJAL-3143 comma-delimited feature attributes for alleles, commit | commitdiff
2018-10-25 gmungocJAL-3143 fetch Ensembl(Genomes) features as JSON not GFF commit | commitdiff
2018-09-03 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... commit | commitdiff
2018-09-03 Jim ProcterJAL-3076 clarify javadoc handling single sequence respo... bug/JAL-3076ensemblGeneId commit | commitdiff
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene... commit | commitdiff
2018-08-10 gmungocJAL-3076 fetch Ensembl sequence as JSON instead of... commit | commitdiff
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... commit | commitdiff
2018-01-26 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff
2018-01-17 gmungocJAL-2679 case-insensitive comparison of query and retri... commit | commitdiff
2018-01-16 gmungocJAL-2679 use object_type=Transcript for lookup of Paren... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu... commit | commitdiff
2017-08-25 gmungocJAL-2480 suppress debug timing output that got left in 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
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... commit | commitdiff
2017-05-24 gmungocJAL-2529 add object_type=cdna to EnsemblCdna parameters commit | commitdiff
2017-05-12 gmungocJAL-2480 renamed java.util.RangeComparator to IntRangeC... commit | commitdiff
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final... commit | commitdiff
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera... commit | commitdiff
2016-12-07 gmungocJAL-2354 handle error response when fetching features commit | commitdiff
2016-11-08 gmungocJAL-2295 make RangeComparator a top level class for... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 apply license commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-10-03 gmungocJAL-2110 JAL-1705 handle not found (400) better commit | commitdiff
2016-09-30 Jim ProcterJAL-2210 add uniprot+mapping between ENST and ENSP... commit | commitdiff
2016-09-27 Jim ProcterJAL-2210 report stack trace for unexpected exceptions commit | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... commit | commitdiff
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... commit | commitdiff
2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify... commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... commit | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi... commit | commitdiff
2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g.... commit | commitdiff
2016-04-11 gmungocJAL-1705 code/comment tidy only commit | commitdiff
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms) commit | commitdiff
2016-03-23 gmungocJAL-1705 add DBRefEntry for 'self' to retrieved transcr... commit | commitdiff
2016-03-16 gmungocJAL-1705 xref ENST to correct (ENSP) accession id commit | commitdiff
2016-03-15 gmungocJAL-1705 compute reverse complement of variants on... commit | commitdiff
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot commit | commitdiff
2016-03-04 gmungocJAL-1705 parse 'description' from GFF as sequence descr... commit | commitdiff
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support... commit | commitdiff
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts commit | commitdiff
2016-02-19 gmungocJAL-1705 regular expression updates, tests, other refac... commit | commitdiff
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl... commit | commitdiff
2016-02-04 gmungocJAL-1705 additional tests, validation regexp tweaks... commit | commitdiff
2016-02-01 gmungocJAL-1705 further unit tests commit | commitdiff
2016-02-01 gmungocJAL-1705 set Uniprot xref as 'source dbref' (for SIFTS... commit | commitdiff
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard... commit | commitdiff
2016-01-30 gmungocJAL-1705 refactored cross-reference fetching (CCDS... commit | commitdiff
2016-01-29 gmungocJAL-1705 fetch Uniprot and PDB xrefs for Ensembl protei... commit | commitdiff
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... commit | commitdiff
2016-01-28 gmungocJAL-1705 tests added, minor bugfix and refactoring commit | commitdiff
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid... commit | commitdiff
2016-01-27 gmungocJAL-1705 use GET for single queries; set gene name... commit | commitdiff
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence... commit | commitdiff
2016-01-25 gmungocJAL-1705 EnsemblGene added, and related refactoring commit | commitdiff
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... commit | commitdiff
2016-01-21 gmungocJAL-1705 reworked Ensembl clients now fetching and... commit | commitdiff
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods... commit | commitdiff
2015-06-28 Jim ProcterJAL-1705 renamed SeqFetcherTest to EnsemblSeqProxyTest commit | commitdiff