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JAL-3855 try harder to ignore DNA/RNA only structures when deciding whether to downlo...
[jalview.git] / src / jalview / ws /
2021-09-29 Jim ProcterJAL-3884 squish alarming but harmless errors when unipr... tree | commitdiff
2021-09-29 Jim ProcterJAL-3881 split on any nonalphanumeric symbol (plus... 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
2021-09-16 Ben SoaresJAL-3739 (combined) commits from feature/JAL-3739_useFo... 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
2021-09-14 Jim ProcterJAL-3829 3d-beacons doesn’t work as a sequence source... 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
2021-04-06 Jim ProcterJAL-3832 dummy 3d-beacons database client and code... tree | commitdiff
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch... tree | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... 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
2020-05-29 gmungocMerge branch 'feature/JAL-3551Pymol' into develop tree | commitdiff
2020-05-19 gmungocMerge branch 'develop' into feature/JAL-3551Pymol tree | commitdiff
2020-05-19 gmungocJAL-3624 use temp file for SIFT download in JS, correct... feature/JAL-3624siftsInJS tree | commitdiff
2020-05-18 gmungocJAL-3463 avoid Thread.sleep() as not supported in SwingJS tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2020-03-09 gmungocMerge branch 'develop' into feature/JAL-2422ChimeraX tree | commitdiff
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into... tree | commitdiff
2019-12-13 gmungocJAL-2422 basic proof of concept of ChimeraX opened... tree | commitdiff
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-06-26 Jim ProcterJAL-3332 test to check for duplicate db sources and... tree | commitdiff
2019-06-24 Jim ProcterJAL-3330 dbreffetcher: record any feature display model... tree | commitdiff
2019-04-23 Jim ProcterMerge branch 'develop' into bug/JAL-3224_getdown_change... tree | commitdiff
2019-04-17 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-04-15 gmungocJAL-3193 no separatge EnsemblGenomes source in Sequence... tree | commitdiff
2019-04-04 gmungocJAL-3220 j2sIgnore on main methods on test / utility... tree | commitdiff
2019-04-04 gmungocJAL-3220 unneeded main methods removed tree | commitdiff
2019-04-03 hansonrj2sNative clean-up. Fixes problem with second try of... tree | commitdiff
2019-03-31 hansonrclean up implicit object refs tree | commitdiff
2019-03-27 hansonrconsolidation of Platform isJS calls tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-13 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-03-06 gmungocMerge branch 'tasks/JAL-3035_remove_dasobert_dependency... tree | commitdiff
2019-03-06 gmungocJAL-3035 more das bits removed tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3120restoreFeatureColour' into... tree | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... tree | commitdiff
2019-01-17 gmungocMerge branch 'develop' into Jalview-BH/JAL-3026-JAL... tree | commitdiff
2019-01-17 Jim ProcterJAL-3116 clear out whitespace when materialising Sequen... tree | commitdiff
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA... tree | commitdiff
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures 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
2018-10-31 gmungocMerge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into... feature/JAL-3144noJTree tree | commitdiff
2018-10-29 gmungocJAL-3144 SequenceFetcher without JDatabaseTree tree | commitdiff
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH... tree | commitdiff
2018-09-21 gmungocJAL-3120 preserve feature colour/mincolour/maxcolour... bug/JAL-3120restoreFeatureColour 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
2018-08-21 hansonrmc_view references were MCview tree | commitdiff
2018-07-10 gmungocJAL-3048 code reordered for JalviewJS compliance tree | commitdiff
2018-06-27 hansonrJAL-3032 just the changes pulled already tree | commitdiff
2018-06-26 Jim ProcterMerge branch 'tasks/JAL-3035_remove_dasobert_dependency... tree | commitdiff
2018-06-26 Jim ProcterJAL-3035 - jalview-das is no more ! tree | commitdiff
2018-06-22 gmungocJAL-3032 avoid assignments on the same line as synchronized 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
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... 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
2018-02-13 Jim ProcterJAL-2780 JAL-2781 don’t create a mapping if sequence... tree | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 only create a mapping entry or write... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 JAL-2780 include sequence start number when... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor ‘trim retrieved sequence’ preference... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 use PDBe numbering to map between... tree | commitdiff
2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 include a Mapping object in Structure... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Intege... tree | commitdiff
2018-02-09 Jim ProcterUse the “PDBe” or “PDB” numbering (starts from 1, corre... tree | commitdiff
2018-02-09 Jim ProcterJAL-2780 JAL-2781 should always ensure SIFTS mappings... tree | commitdiff
2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns 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
2017-11-16 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures tree | commitdiff
2017-11-13 Jim ProcterMerge branch 'features/JAL-2758_shorteruniprot' into... tree | commitdiff
2017-11-13 Jim ProcterJAL-2758 remove configurable behaviour - Uniprot sequen... tree | commitdiff
2017-11-13 Jim ProcterJAL-2758 typo tree | commitdiff
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