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Merge branch 'develop' into features/JAL-2094_colourInterface
[jalview.git] / src /
2016-09-19 gmungocMerge branch 'develop' into features/JAL-2094_colourInt... features/JAL-2094_colourInterface 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
2016-09-04 Jim ProcterJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loade... tree | commitdiff
2016-09-04 Jim ProcterJAL-1803 recover type field faithfully for mmCIF/PDB... tree | commitdiff
2016-09-04 Jim ProcterJAL-1803 restore property array for a sequence’s associ... tree | commitdiff
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as... tree | commitdiff
2016-09-01 Jim ProcterMerge branch 'bug/JAL-2034_fix' into develop tree | commitdiff
2016-09-01 Jim ProcterJAL-2034 - remember to reset needsOverviewUpdate at... tree | commitdiff
2016-09-01 gmungocJAL-2077 check isPopupTrigger in mouseReleased not... tree | commitdiff
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive... tree | commitdiff
2016-09-01 Jim ProcterJAL-2034 check context of selection group to catch... tree | commitdiff
2016-09-01 gmungocJAL-2077 do nothing in mousePressed if right button... tree | commitdiff
2016-09-01 gmungocJAL-2077 force defer right-click handling to mouseRelea... tree | commitdiff
2016-09-01 Jim ProcterJAL-1803 JAL-2188 experimental: tree | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 source DB refs come from SequenceI... tree | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 resolve source DB refs using canonica... tree | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:... tree | commitdiff
2016-08-31 gmungocJAL-2077 test isPopupTrigger in mouseReleased or mouseC... tree | commitdiff
2016-08-31 gmungocJAL-2077 more javadoc tree | commitdiff
2016-08-31 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-08-31 Jim ProcterJAL-2157 JAL-2154 simplify CanshowProducts code to... tree | commitdiff
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns... tree | commitdiff
2016-08-31 Jim ProcterJAL-2034 moved ‘isDefinedGroup’ flag to a test method... tree | commitdiff
2016-08-31 Jim ProcterJAL-2034 remove todo - answer is yes! tree | commitdiff
2016-08-31 gmungocJAL-2077 check for isPopupTrigger() in mousePressed... tree | commitdiff
2016-08-31 tcofoegbuJAL-2148 further enhancment to CA HETATM processing tree | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... merge/develop_bug/JAL-2154projectMappings tree | commitdiff
2016-08-30 Jim ProcterJAL-2154 always compare canonicalised DBRefEntry source... tree | commitdiff
2016-08-30 Jim ProcterJAL-2154 simplify expression tree | commitdiff
2016-08-30 gmungocJAL-2183 defensive check for openFrameCount < 0 (should... tree | commitdiff
2016-08-30 gmungocJAL-2183 simplified database tree actionPerformed,... tree | commitdiff
2016-08-30 gmungocJAL-2183 revised change (= no change) tree | commitdiff
2016-08-30 gmungocJAL-2183 formatter added @Override (only) tree | commitdiff
2016-08-30 gmungocJAL-2183 removed redundant (overriden) add panel to... tree | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 don’t synthesise multiple CDS|<Acc> sequences... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 filter out dbrefs that already match primary... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 refactor if (for easier breakpoint) and formatting tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 canonical dbsources are lowercased before... tree | commitdiff
2016-08-29 Jim ProcterJAL-2154 ENA specific Ensembl canonical db prefixes tree | commitdiff
2016-08-29 gmungocJAL-1841 robustness fix bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB... tree | commitdiff
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 check that xref is a coding xref before adding... tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 don’t add any remaining xrefed sequences of... tree | commitdiff
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ... tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from... tree | commitdiff
2016-08-26 gmungocJAL-1854 comment switch case fallthrough tree | commitdiff
2016-08-25 Jim ProcterJAL-2106 JAL-2154 cross-refs from Ensembl should verify... tree | commitdiff
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB tree | commitdiff
2016-08-25 Jim ProcterJAL-2154 JAL-2106 transfer primary refs to CDS for... tree | commitdiff
2016-08-25 Jim ProcterJAL-2154 copy and paste error tree | commitdiff
2016-08-25 gmungocJAL-1854 missing case break statements added tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'trailm' into trial_fixMakeCDSDBRefPropagation tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... tree | commitdiff
2016-08-25 gmungocJAL-2178 remove duplicate Uniprot db source tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 tidy up and comments for DBRefFetcher tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 javadoc for sifts mapping method tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 prevent SIFTS mappings for sequences that... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 formatting tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implemen... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names... tree | commitdiff
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