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jalview.git
2016-10-05 Jim ProcterJAL-2189 release notes commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 tidy up release notes commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 tweak ensembl release notes commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterMerge branch 'develop' into releases/Release_2_10_Branch commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 formatting and release notes commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 license header commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 apply license commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 format help commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 format tests commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 formatting and GPL commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff | tree | snapshot
2016-10-05 tcofoegbuQQMerge branch 'develop' of https://source.jalview... commit | commitdiff | tree | snapshot
2016-10-05 tcofoegbuJAL-1563 JAL-1479 minor house-keeping for Uniprot FTS... commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterRevert "JAL-2245 Castor mapping and code changes for... commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 release notes/whats new commit | commitdiff | tree | snapshot
2016-10-05 Jim ProcterJAL-2189 JAL-2152 Chimera 1.11.1 minimum version requir... commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-1191 revert to using SequenceOntologyLite due to... commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-1191 configure full SO for desktop, SOLite for... commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-2245 defence against NullPointer if no EMBL data... commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-1191 use full SO in desktop application commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-2105 update Ensembl REST version to 4.7 commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-1191 refined warning message commit | commitdiff | tree | snapshot
2016-10-05 gmungocJAL-1191 added mRNA isA transcript to SequenceOntologyL... commit | commitdiff | tree | snapshot
2016-10-04 gmungocMerge branch 'bug/JAL-2245enaXmlChange' into develop commit | commitdiff | tree | snapshot
2016-10-04 gmungocMerge branch 'bug/JAL-2210_hack_for_Release_2_10' into... commit | commitdiff | tree | snapshot
2016-10-04 gmungocJAL-2245 Castor mapping and code changes for change... bug/JAL-2245enaXmlChange commit | commitdiff | tree | snapshot
2016-10-04 gmungocJAL-2232 some fix / partial fix of failing tests bug/JAL-2210_hack_for_Release_2_10 commit | commitdiff | tree | snapshot
2016-10-04 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop commit | commitdiff | tree | snapshot
2016-10-04 Jim ProcterJAL-2189 release notes commit | commitdiff | tree | snapshot
2016-10-04 gmungocJAL-2232 added test that failed before last fix, passes... commit | commitdiff | tree | snapshot
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase... commit | commitdiff | tree | snapshot
2016-10-04 Jim ProcterJAL-2189 link to feature sorting documentation commit | commitdiff | tree | snapshot
2016-10-04 Jim ProcterJAL-2189 JAL-2005 mention alignment order preservation... commit | commitdiff | tree | snapshot
2016-10-04 Jim ProcterJAL-2189 release notes commit | commitdiff | tree | snapshot
2016-10-04 Jim ProcterJAL-2005 JAL-599 test alignment and features for checki... commit | commitdiff | tree | snapshot
2016-10-03 gmungocJAL-2110 javadoc formatting only commit | commitdiff | tree | snapshot
2016-10-03 gmungocJAL-2110 JAL-1705 handle not found (400) better commit | commitdiff | tree | snapshot
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad... commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2189 update RELEASE file commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2189 more release notes commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2189 ensembl sequence fetching, locus view and... commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2189 release notes commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2210 use addDBRef to ensure normalisation (just... commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2210 need to add both transcript and product, and... commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2210 JAL-2232 remove version number from ENACDS... commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2210 hack to remove EMBL from Protein crossrefs... commit | commitdiff | tree | snapshot
2016-10-03 Jim ProcterJAL-2210 explicit ‘doNotAdd’ list to prevent sequences... commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2210 first pass at attempting to fix CrossRef tests... commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list: commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences... commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a... commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2210 comments commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an... commit | commitdiff | tree | snapshot
2016-10-02 Jim ProcterJAL-2079 pass server name when reporting FTS ‘warning... commit | commitdiff | tree | snapshot
2016-10-01 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro... commit | commitdiff | tree | snapshot
2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referen... commit | commitdiff | tree | snapshot
2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs... commit | commitdiff | tree | snapshot
2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add... commit | commitdiff | tree | snapshot
2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for prese... commit | commitdiff | tree | snapshot
2016-09-30 Jim ProcterJAL-2210 add uniprot+mapping between ENST and ENSP... commit | commitdiff | tree | snapshot
2016-09-30 Jim ProcterJAL-2238 release notes commit | commitdiff | tree | snapshot
2016-09-30 Jim ProcterJAL-2236 release notes and additional docs commit | commitdiff | tree | snapshot
2016-09-30 Jim ProcterMerge branch 'develop' into releases/Release_2_10_Branch commit | commitdiff | tree | snapshot
2016-09-30 gmungocJAL-2236 code restored (and some compiler warnings... commit | commitdiff | tree | snapshot
2016-09-30 gmungocMerge branch 'develop' into features/JAL-1856dbRefFetch... commit | commitdiff | tree | snapshot
2016-09-30 gmungocJAL-2234 FER1_ARATH renamed FER2_ARATH and vice versa commit | commitdiff | tree | snapshot
2016-09-30 gmungocJAL-2236 fixes for desktop and applet implementation... commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-1856 better warning messages for sequence matching... features/JAL-1856dbRefFetcherMessages commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-2213 code warnings addressed (typed collections... commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-2213 removed PDB from db sources list; also code... commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-2213 made RESNUM constant private (not used elsewhe... commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-2213 corrected wait for files to load in Jmol;... commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-2237 apply default filter as sort in initial search commit | commitdiff | tree | snapshot
2016-09-29 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-09-29 Jim ProcterJAL-2089 fix broken help link commit | commitdiff | tree | snapshot
2016-09-29 Jim ProcterMerge branch 'patch/JAL-2236_filtercolumns_seqassoc... commit | commitdiff | tree | snapshot
2016-09-29 Jim ProcterJAL-2236 include associated sequence id for annotation... commit | commitdiff | tree | snapshot
2016-09-29 Jim ProcterMerge branch 'patch/JAL-2238_tcoffee_subgroups' into... commit | commitdiff | tree | snapshot
2016-09-29 Jim ProcterJAL-2236 fix: bail if no context available for subgroup commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-2047 allow title to be shrunk; spelling fix commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-1544 typo commit | commitdiff | tree | snapshot
2016-09-29 gmungocJAL-1903 increase REST reply timeout from 5 to 15 seconds commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2210 patch network test for additional refs commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2210 JAL-2235 fix deriveSequence test for tightened... commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-1270 read test props before manipulating config... commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2235 patch tests where self-reference was used... commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2235 implicit test to check that exception is raise... commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc... commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2210 patch for when no DBRefs on sequence commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2210 JAL-2232 check response code before attempting... commit | commitdiff | tree | snapshot
2016-09-28 Jim ProcterJAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot... commit | commitdiff | tree | snapshot
2016-09-27 gmungocJAL-2233 less verbose logging for Jmol commit | commitdiff | tree | snapshot
2016-09-27 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro... commit | commitdiff | tree | snapshot
2016-09-27 Jim ProcterJAL-2210 formatting commit | commitdiff | tree | snapshot
2016-09-27 Jim ProcterJAL-2210 report stack trace for unexpected exceptions commit | commitdiff | tree | snapshot
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources... commit | commitdiff | tree | snapshot
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen... commit | commitdiff | tree | snapshot
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