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JAL-3675 release notes for JAL-3750 JAL-3751
[jalview.git] / src / jalview / ws / dbsources /
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-27 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-27 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-01-17 Jim ProcterJAL-3116 clear out whitespace when materialising Sequen... tree | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... tree | commitdiff
2018-09-17 gmungocJAL-3116 unit tests adapted to EMBL over JAXB tree | commitdiff
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit... tree | commitdiff
2018-09-13 gmungocJAL-3116 Uniprot XML unmarshalled using JAXB not Castor tree | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch tree | commitdiff
2018-06-26 Jim ProcterJAL-3035 - jalview-das is no more ! tree | commitdiff
2018-06-07 gmungocJAL-2920 wrap description in <html/> if it includes... tree | commitdiff
2018-06-06 Jim ProcterJAL-2920 revised TODO for JAL-3025 bug/JAL-2920_uniprotvariantfeature tree | commitdiff
2018-06-06 Jim ProcterJAL-2920 don’t output variant/original sequence as... tree | commitdiff
2018-06-06 Jim ProcterJAL-1920 JAL-3017 use newline not <br/> in description... tree | commitdiff
2018-06-04 Jim ProcterJAL-3017 parse multiple variant elements for uniprot... tree | commitdiff
2018-05-21 gmungocJAL-2920 use HGVS notation for protein variant feature tree | commitdiff
2018-03-08 gmungocJAL-2885 tests updated for code changes tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain.. tree | commitdiff
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam... tree | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) tree | commitdiff
2017-11-13 Jim ProcterJAL-2758 remove configurable behaviour - Uniprot sequen... tree | commitdiff
2017-11-13 Jim ProcterJAL-2758 typo tree | commitdiff
2017-10-06 Jim ProcterJAL-2758 flag and tests for omitting uniprot accession... features/JAL-2758_shorteruniprot tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-09-29 Jim ProcterJAL-2748 formatting tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org tree | commitdiff
2017-09-29 Jim ProcterJAL-2748 formatting tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1... tree | commitdiff
2017-08-22 Jim ProcterJAL-1551 formatting 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
2017-08-10 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-08-09 Jim ProcterJAL-2426 Rfam download suffix tree | commitdiff
2017-08-09 Jim ProcterJAL-2426 JAL-1270 report Xfam download URL used if... tree | commitdiff
2017-08-09 Jim ProcterJAL-2425 raw stockholm download URLs tree | commitdiff
2017-08-09 Jim ProcterJAL-2425 remove overloaded getSequenceRecords method... tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... tree | commitdiff
2017-05-24 gmungocJAL-2506 relocate Uniprot binding classes, bind to... tree | commitdiff
2017-05-16 gmungocJAL-2505 set SequenceFeature group in constructor tree | commitdiff
2017-03-22 kiramtJAL-2461 Removed DAS error stack trace, updated message tree | commitdiff
2016-11-30 gmungocJAL-2344 use ".cif" for saved mmCIF file (and refactor... tree | commitdiff
2016-11-29 gmungocJAL-2344 corrected conversion of Type enum to FileFormat features/JAL-2344FileFormatI tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch tree | commitdiff
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch' tree | commitdiff
2016-10-14 gmungocMerge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties tree | commitdiff
2016-10-06 gmungocJAL-2254 map error text in root node of EMBL XML response tree | commitdiff
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties tree | commitdiff
2016-10-06 gmungocJAL-2245 checks for null added (in case EMBL fetch... tree | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting tree | commitdiff
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties tree | commitdiff
2016-10-05 Jim ProcterRevert "JAL-2245 Castor mapping and code changes for... tree | commitdiff
2016-10-04 gmungocMerge branch 'bug/JAL-2245enaXmlChange' into develop tree | commitdiff
2016-10-04 gmungocJAL-2245 Castor mapping and code changes for change... bug/JAL-2245enaXmlChange tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 use addDBRef to ensure normalisation (just... tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 need to add both transcript and product, and... tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 JAL-2232 remove version number from ENACDS... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list: tree | commitdiff
2016-10-01 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro... tree | commitdiff
2016-09-29 gmungocJAL-2213 code warnings addressed (typed collections... tree | commitdiff
2016-09-28 Jim ProcterJAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot... tree | commitdiff
2016-09-07 Jim ProcterJAL-282 TODO - Sequence name from PDB had redundant... tree | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... tree | commitdiff
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring tree | commitdiff
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop tree | commitdiff
2016-07-20 Jim ProcterJAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMA... tree | commitdiff
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... tree | commitdiff
2016-07-12 gmungocFileFormat enum wip changes tree | commitdiff
2016-07-11 gmungocfile format enum wip changes tree | commitdiff
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... tree | commitdiff
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser... tree | commitdiff
2016-06-20 gmungocJAL-1667 updated PDB example query to a valid id (witho... tree | commitdiff
2016-05-31 Jim ProcterMerge branch 'develop' into features/JAL-2113_emblXml1.2 tree | commitdiff
2016-05-27 gmungocJAL-1911 correct typo in field name tree | commitdiff
2016-05-26 tcofoegbuJAL-1911 bugfix - do not save i18n text in preference... tree | commitdiff
2016-05-23 gmungocJAL-2113 EBIFetchClient refactor / unit tests / remove... tree | commitdiff
2016-05-20 gmungocJAL-2113 embl_mapping.xml and code updated for EMBL... tree | commitdiff
2016-04-26 Jim ProcterJAL-2079 fix broken cherry-pick conflict merge tree | commitdiff
2016-04-26 Jim ProcterJAL-2079 use new service to retrieve Rfam Seed alignment tree | commitdiff
2016-04-26 Jim ProcterJAL-2079 update URL for RFAM and PFAM sources tree | commitdiff
2016-04-26 Jim ProcterJAL-2079 allow prefix+<XFAMID>+suffix type URL signature tree | commitdiff
2016-04-19 tcofoegbuJAL-2071 architectural improvement for Plugable Free... tree | commitdiff
2016-03-24 tcofoegbuJAL-1919 set DEFUALT_STRUCTURE_FORMAT to PDB tree | commitdiff
2016-03-23 tcofoegbuJAL-2009 added programmatic custom feature setting... tree | commitdiff
2016-03-22 tcofoegburesolve conflict with Mungo's merge tree | commitdiff
2016-03-22 tcofoegbuJAL-1919 code improvement to make PDB sequence fetcher... tree | commitdiff
2016-03-21 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-21 tcofoegbudevelop merge features/JAL-1919_mmCIF-Support tree | commitdiff
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings tree | commitdiff
2016-03-21 tcofoegbuJAL-2028 added improvement for preconfigured ordering... tree | commitdiff
2016-03-21 tcofoegbudevelop merge tree | commitdiff
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