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JAL-2232 some fix / partial fix of failing tests
[jalview.git] / src /
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase... tree | commitdiff
2016-10-03 gmungocJAL-2110 javadoc formatting only tree | commitdiff
2016-10-03 gmungocJAL-2110 JAL-1705 handle not found (400) better tree | commitdiff
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad... 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
2016-10-03 Jim ProcterJAL-2210 hack to remove EMBL from Protein crossrefs... tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 explicit ‘doNotAdd’ list to prevent sequences... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list: tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 two pass attempt to import retrieved sequences... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 try to merge all sequences referenced by a... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 comments tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 discover candidate dataset sequences for an... tree | commitdiff
2016-10-02 Jim ProcterJAL-2079 pass server name when reporting FTS ‘warning... tree | commitdiff
2016-10-01 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro... tree | commitdiff
2016-10-01 Jim ProcterJAL-2210 factored out code for processing cross-referen... tree | commitdiff
2016-10-01 Jim ProcterJAL-2210 refactor code to remove from a list of dbrefs... tree | commitdiff
2016-09-30 Jim ProcterJAL-2210 some DBRef xref/ref correspondences may add... tree | commitdiff
2016-09-30 Jim ProcterJAL-2210 CrossRef.findInDataset should search for prese... tree | commitdiff
2016-09-30 Jim ProcterJAL-2210 add uniprot+mapping between ENST and ENSP... tree | commitdiff
2016-09-30 gmungocJAL-2236 code restored (and some compiler warnings... tree | commitdiff
2016-09-30 gmungocMerge branch 'develop' into features/JAL-1856dbRefFetch... tree | commitdiff
2016-09-30 gmungocJAL-2236 fixes for desktop and applet implementation... tree | commitdiff
2016-09-29 gmungocJAL-1856 better warning messages for sequence matching... features/JAL-1856dbRefFetcherMessages tree | commitdiff
2016-09-29 gmungocJAL-2213 code warnings addressed (typed collections... tree | commitdiff
2016-09-29 gmungocJAL-2213 removed PDB from db sources list; also code... tree | commitdiff
2016-09-29 gmungocJAL-2213 made RESNUM constant private (not used elsewhe... tree | commitdiff
2016-09-29 gmungocJAL-2213 corrected wait for files to load in Jmol;... tree | commitdiff
2016-09-29 gmungocJAL-2237 apply default filter as sort in initial search tree | commitdiff
2016-09-29 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-09-29 Jim ProcterJAL-2236 include associated sequence id for annotation... tree | commitdiff
2016-09-29 Jim ProcterMerge branch 'patch/JAL-2238_tcoffee_subgroups' into... tree | commitdiff
2016-09-29 Jim ProcterJAL-2236 fix: bail if no context available for subgroup tree | commitdiff
2016-09-29 gmungocJAL-1903 increase REST reply timeout from 5 to 15 seconds tree | commitdiff
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc... tree | commitdiff
2016-09-28 Jim ProcterJAL-2210 patch for when no DBRefs on sequence tree | commitdiff
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries tree | commitdiff
2016-09-28 Jim ProcterJAL-2210 JAL-2232 check response code before attempting... tree | commitdiff
2016-09-28 Jim ProcterJAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot... tree | commitdiff
2016-09-27 gmungocJAL-2233 less verbose logging for Jmol tree | commitdiff
2016-09-27 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro... tree | commitdiff
2016-09-27 Jim ProcterJAL-2210 formatting tree | commitdiff
2016-09-27 Jim ProcterJAL-2210 report stack trace for unexpected exceptions tree | commitdiff
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources... tree | commitdiff
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen... tree | commitdiff
2016-09-27 gmungocJAL-2231 save preferred scroll height _without_ progres... tree | commitdiff
2016-09-27 gmungocJAL-2230 use correct mapping to transfer features to... tree | commitdiff
2016-09-24 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop tree | commitdiff
2016-09-23 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-09-23 tcofoegbuJAL-2164 JAL-1919 fixed failed revert commit tree | commitdiff
2016-09-23 Jim ProcterJAL-2214 fix docs (consistent and correct base pair... tree | commitdiff
2016-09-23 gmungocJAL-2214 Javadoc tree | commitdiff
2016-09-22 gmungocJAL-1421 use declared type of ResidueProperties.propHash tree | commitdiff
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... tree | commitdiff
2016-09-22 gmungocJAL-2216 null currentAlignFrame on close all windows... tree | commitdiff
2016-09-22 gmungocJAL-2216 finalize call super.finalize() tree | commitdiff
2016-09-22 gmungocJAL-2216 finalise corrected to finalize tree | commitdiff
2016-09-22 gmungocJAL-2216 explicitly null AnnotationPanel and Annotation... tree | commitdiff
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat... tree | commitdiff
2016-09-22 gmungocJAL-2216 new dispose() method to null references tree | commitdiff
2016-09-22 gmungocJAL-2216 finalize call super.finalize() tree | commitdiff
2016-09-21 Jim ProcterJAL-2214 JAL-1841 compute canonical, canonicalAndWobble... tree | commitdiff
2016-09-21 Jim ProcterJAL-1841 JAL-2215 add the ‘ignore gaps’ structure conse... tree | commitdiff
2016-09-21 Jim ProcterJAL-2214 test for strict Watson-Crick pairing tree | commitdiff
2016-09-21 Jim ProcterJAL-2215 fix - trigger alignment update when ‘ignore... tree | commitdiff
2016-09-20 gmungocJAL-1306 calculate Quality also when Conservation not... tree | commitdiff
2016-09-19 gmungocJAL-2118 reorder annotations after add/delete/hide... tree | commitdiff
2016-09-19 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... tree | commitdiff
2016-09-19 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-09-19 gmungocJAL-2172 test and code updates for readonly selection... tree | commitdiff
2016-09-19 tcofoegbumerge tree | commitdiff
2016-09-18 Jim ProcterJAL-1795 JAL-2206 prevent NPE when no data returned... tree | commitdiff
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds... tree | commitdiff
2016-09-16 gmungocJAL-2183 don't open two free text panels; give input... tree | commitdiff
2016-09-16 gmungocJAL-2183 avoid duplicate closeDialog() tree | commitdiff
2016-09-16 gmungocJAL-2164 removed unused parameters from JmolParser... tree | commitdiff
2016-09-14 Jim ProcterJAL-2164 create RESNUM features with padding the same... tree | commitdiff
2016-09-13 tcofoegbuJAL-2164 JAL-1919 disabled PDB file parser configuratio... tree | commitdiff
2016-09-13 tcofoegbuRevert "JAL-2164 JAL-1919 disabled and removed PDB... tree | commitdiff
2016-09-13 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-09-13 tcofoegbuJAL-2164 JAL-1919 disabled and removed PDB file parser... tree | commitdiff
2016-09-13 gmungocJAL-1803 extracted class ChainId to jalview.util.CaseIn... tree | commitdiff
2016-09-13 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-09-13 tcofoegbuJAL-2195 bug fix to enable restoring jmol session save... tree | commitdiff
2016-09-12 Jim ProcterMerge branch 'patch/JAL-2068_JAL-2169_multiviewannotwor... tree | commitdiff
2016-09-09 tcofoegbumerge tree | commitdiff
2016-09-08 tcofoegbuJAL-2164 renamed 'DEFAULT_STRUCTURE_FORMAT' property... tree | commitdiff
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157 tree | commitdiff
2016-09-07 Jim ProcterJAL-2191 comments re chimera view code redundancy and... tree | commitdiff
2016-09-07 Jim ProcterJAL-282 TODO - Sequence name from PDB had redundant... tree | commitdiff
2016-09-07 Jim ProcterJAL-1803 transfer mapped chain’s PDBEntry to the *datas... tree | commitdiff
2016-09-07 Jim ProcterJAL-1803 JAL-1919 set type when structure file is parsed tree | commitdiff
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry tree | commitdiff
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid... tree | commitdiff
2016-09-06 gmungocJAL-2147 additional test coverage for findMappingsForSe... tree | commitdiff
2016-09-05 gmungocJAL-2154 made Java 7 compatible tree | commitdiff
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs tree | commitdiff
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and... tree | commitdiff
2016-09-04 Jim ProcterJAL-1919 preserve filename on restore of project so... tree | commitdiff
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