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jalview.git
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 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
2016-10-03 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-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 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
2016-09-27 gmungocJAL-2231 save preferred scroll height _without_ progres... commit | commitdiff | tree | snapshot
2016-09-27 gmungocJAL-2230 JAL-2049 added sequence feature transfer to commit | commitdiff | tree | snapshot
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to... commit | commitdiff | tree | snapshot
2016-09-24 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop commit | commitdiff | tree | snapshot
2016-09-24 Jim ProcterJAL-1919 whats new link commit | commitdiff | tree | snapshot
2016-09-23 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-09-23 tcofoegbuJAL-2164 JAL-1919 fixed failed revert commit commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterJAL-1957 JAL-1479 tweak SIFTS mappings documentation... commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterJAL-1957 JAL-1479 mention SIFTS mappings in PDB Structu... commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterJAL-1957 release notes commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterJAL-1962 release notes commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterJAL-2214 fix docs (consistent and correct base pair... commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterMerge branch 'develop' into releases/Release_2_10_Branch commit | commitdiff | tree | snapshot
2016-09-23 Jim ProcterJAL-2189 JAL-1479 JAL-1491 JAL-1827 release notes commit | commitdiff | tree | snapshot
2016-09-23 gmungocJAL-2214 Javadoc commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2275 release notes commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2151 release notes commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-1421 use declared type of ResidueProperties.propHash commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2168 -news release notes commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-1557 release notes commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2189 bumped date to 27th September \o/ commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 null currentAlignFrame on close all windows... commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2189 JAL-1812 JAL-2068 new groovy docs (new files... commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2189 JAL-2092 popup show/hide cols with feature... commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 finalize call super.finalize() commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 finalise corrected to finalize commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 explicitly null AnnotationPanel and Annotation... commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2189 JAL-2077 note about CTRL-Click to right click... commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2189 tidy up docs commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat... commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-1812 JAL-1868 release notes commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 new dispose() method to null references commit | commitdiff | tree | snapshot
2016-09-22 Jim ProcterJAL-2189 JAL-1812 JAL-2068 new groovy doc section and... commit | commitdiff | tree | snapshot
2016-09-22 gmungocJAL-2216 finalize call super.finalize() commit | commitdiff | tree | snapshot
2016-09-21 Jim ProcterJAL-2189 JAL-2171 JAL-2214 JAL-1841 JAL-2215 release... commit | commitdiff | tree | snapshot
2016-09-21 Jim ProcterJAL-1841 JAL-2214 updated RNA Structure Consensus docum... commit | commitdiff | tree | snapshot
2016-09-21 Jim ProcterJAL-2214 JAL-1841 compute canonical, canonicalAndWobble... commit | commitdiff | tree | snapshot
2016-09-21 Jim ProcterJAL-1841 JAL-2215 add the ‘ignore gaps’ structure conse... commit | commitdiff | tree | snapshot
2016-09-21 Jim ProcterJAL-2214 test for strict Watson-Crick pairing commit | commitdiff | tree | snapshot
2016-09-21 Jim ProcterJAL-2215 fix - trigger alignment update when ‘ignore... commit | commitdiff | tree | snapshot
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