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2016-09-08 Jim ProcterJAL-2089 JAL-2119 help link fixups commit | commitdiff | tree | snapshot
2016-09-08 Jim ProcterJAL-2119 linkcheck target. runs before build indices commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterMerge branch 'bug/JAL-1803_JAL-2157' into develop commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-1670 groundhog day: fix FeaturesFileTest by redacti... bug/JAL-1803_JAL-2157 commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterMerge branch 'bug/JAL-1803_JAL-2157' into develop commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157 commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-2192 TODO commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-2191 comments re chimera view code redundancy and... commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-282 TODO - Sequence name from PDB had redundant... commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-1803 transfer mapped chain’s PDBEntry to the *datas... commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-1803 JAL-1919 set type when structure file is parsed commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry commit | commitdiff | tree | snapshot
2016-09-07 Jim ProcterJAL-1803 switched so ‘expected’ is constant in assert commit | commitdiff | tree | snapshot
2016-09-07 gmungocJAL-2164 fix failing test commit | commitdiff | tree | snapshot
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid... commit | commitdiff | tree | snapshot
2016-09-06 gmungocJAL-2147 additional test coverage for findMappingsForSe... commit | commitdiff | tree | snapshot
2016-09-06 Jim ProcterMerge branch 'releases/Release_2_10_Branch' into develop commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-1563 UniProt FTS doc revisions commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-2089 reworked and formatted doc for commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-2089 reworked and formatted doc for commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-2089 update Uniprot to UniProt in help docs. commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-2089 drop MCView documentation from contents. commit | commitdiff | tree | snapshot
2016-09-05 gmungocJAL-2154 made Java 7 compatible commit | commitdiff | tree | snapshot
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-1919 revised mmCIF documentation commit | commitdiff | tree | snapshot
2016-09-05 Jim ProcterJAL-2089 bump release date for 2.10 commit | commitdiff | tree | snapshot
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-1919 preserve filename on restore of project so... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-1803 JAL-2106 patch tests for tighter PDB Primary... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loade... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-1803 recover type field faithfully for mmCIF/PDB... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-1803 restore property array for a sequence’s associ... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as... commit | commitdiff | tree | snapshot
2016-09-04 Jim ProcterJAL-1803 patch test: PDBEntry.getFile() will always... commit | commitdiff | tree | snapshot
2016-09-01 Jim ProcterMerge branch 'bug/JAL-2034_fix' into develop commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-2077 don't mess with the look and feel commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-2077 less drastic exit on close commit | commitdiff | tree | snapshot
2016-09-01 Jim ProcterJAL-2034 - remember to reset needsOverviewUpdate at... commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-2077 test harness for inspecting mouse events commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-2077 check isPopupTrigger in mouseReleased not... commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive... commit | commitdiff | tree | snapshot
2016-09-01 Jim ProcterJAL-2034 check context of selection group to catch... commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-1854 rule to disallow import of swing in appletgui commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-2077 do nothing in mousePressed if right button... commit | commitdiff | tree | snapshot
2016-09-01 gmungocJAL-2077 force defer right-click handling to mouseRelea... commit | commitdiff | tree | snapshot
2016-09-01 Jim ProcterJAL-1803 JAL-2188 experimental: commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-1926 JAL-2106 source DB refs come from SequenceI... commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-1926 JAL-2106 resolve source DB refs using canonica... commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:... commit | commitdiff | tree | snapshot
2016-08-31 gmungocJAL-2077 test isPopupTrigger in mouseReleased or mouseC... commit | commitdiff | tree | snapshot
2016-08-31 gmungocJAL-2077 more javadoc commit | commitdiff | tree | snapshot
2016-08-31 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-2157 JAL-2154 simplify CanshowProducts code to... commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns... commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-2034 moved ‘isDefinedGroup’ flag to a test method... commit | commitdiff | tree | snapshot
2016-08-31 Jim ProcterJAL-2034 remove todo - answer is yes! commit | commitdiff | tree | snapshot
2016-08-31 gmungocJAL-2077 check for isPopupTrigger() in mousePressed... commit | commitdiff | tree | snapshot
2016-08-31 tcofoegbuJAL-2148 further enhancment to CA HETATM processing commit | commitdiff | tree | snapshot
2016-08-31 gmungocJAL-1670 repositioned feature for backwards compatibili... commit | commitdiff | tree | snapshot
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... merge/develop_bug/JAL-2154projectMappings commit | commitdiff | tree | snapshot
2016-08-30 Jim ProcterJAL-2154 doc & AssertError trap for known failure case... commit | commitdiff | tree | snapshot
2016-08-30 Jim ProcterJAL-2154 always compare canonicalised DBRefEntry source... commit | commitdiff | tree | snapshot
2016-08-30 Jim ProcterJAL-2154 simplify expression commit | commitdiff | tree | snapshot
2016-08-30 gmungocJAL-2183 defensive check for openFrameCount < 0 (should... commit | commitdiff | tree | snapshot
2016-08-30 gmungocJAL-2183 simplified database tree actionPerformed,... commit | commitdiff | tree | snapshot
2016-08-30 gmungocJAL-2183 revised change (= no change) commit | commitdiff | tree | snapshot
2016-08-30 gmungocJAL-2183 formatter added @Override (only) commit | commitdiff | tree | snapshot
2016-08-30 gmungocJAL-2183 removed redundant (overriden) add panel to... commit | commitdiff | tree | snapshot
2016-08-30 Jim ProcterJAL-2154 javadoc, fix underloaded version of assertData... commit | commitdiff | tree | snapshot
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 canonical dbsources are lowercased before... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 ENA specific Ensembl canonical db prefixes commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 endless loop fixed (hopefully :) ) commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1854 tweaks to rules and README commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 catch insertion of duplicate CDS after retriev... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 Optional message parameter for assertDatasetNo... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 new assertDatasetIsNormalised to trivially... commit | commitdiff | tree | snapshot
2016-08-29 Jim ProcterJAL-2154 additional test that removing a duplicate... commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1854 checkstyle relocated to /utils, newlines to... commit | commitdiff | tree | snapshot
2016-08-29 gmungocMerge branch 'bug/JAL-1841rnaSecStr' into develop commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1448 updated unit test for last change commit | commitdiff | tree | snapshot
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr commit | commitdiff | tree | snapshot
2016-08-29 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 two more rules, readme notes commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into merge... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 ENSEMBL and Uniprot tests commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 report any db fetch failures as a fail at end commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 ensure pass increments actually result in... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 catch and report a failures when xrefed projec... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding... commit | commitdiff | tree | snapshot
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of... commit | commitdiff | tree | snapshot
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 commented FallThrough rule commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-1854 corrected nested package rule commit | commitdiff | tree | snapshot
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... commit | commitdiff | tree | snapshot
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