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JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API
[jalview.git] / src / jalview / ws / dbsources /
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-02-17 Jim ProcterJAL-3959 add key retrieval urls that support CORS neede... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-26 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2021-12-13 Jim ProcterJAL-3855 JAL-3829 don’t need to make up alphafold model... tree | commitdiff
2021-12-08 Jim ProcterJAL-3929 URLencode pdbid to remove problematic characte... tree | commitdiff
2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2021-09-29 Jim ProcterJAL-3884 squish alarming but harmless errors when unipr... tree | commitdiff
2021-09-23 Jim ProcterJAL-3692 JAL-3861 remove extra call to .parse() so... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 JAL-3855 ignore case when detecting alphafold ID tree | commitdiff
2021-08-30 Jim ProcterJAL-3829 generalised Alphafold retrieval mechanism... tree | commitdiff
2021-08-30 Jim ProcterJAL-3863 mark first accession retrieved from Uniprot... tree | commitdiff
2021-08-30 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import... tree | commitdiff
2021-08-30 arngucciJAL-3829_spike minor changes tree | commitdiff
2021-08-30 Jim ProcterJAL-3829 forgot to add in the dummy 3d-beacons db proxy tree | commitdiff
2021-07-27 Jim ProcterJAL-3855 ALPHAFOLD database source based on the PDB... tree | commitdiff
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch... tree | commitdiff
2020-10-28 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
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
2020-07-27 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-07-21 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-02 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-02 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge 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
2018-11-08 gmungocJAL-3116 better unmarshalling of EMBL/Uniprot XML tree | commitdiff
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH... 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
2018-08-24 hansonrJAL-3026 GD#107,128,130,139 build-site.xml tree | commitdiff
2018-06-27 hansonrJAL-3032 just the changes pulled already 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
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