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Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings
[jalview.git] / src /
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
2016-08-24 gmungocJAL-1355 correct 'thereshold' to 'threshold' in message... tree | commitdiff
2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys tree | commitdiff
2016-08-24 gmungocJAL-1424 tidy / recode MessageManager calls to support... tree | commitdiff
2016-08-24 gmungocJAL-1854 removed pointless method override tree | commitdiff
2016-08-24 gmungocJAL-1424 removed two redundant (overwritten) setText... tree | commitdiff
2016-08-24 gmungocJAL-1424 corrected Message bundle lookup key tree | commitdiff
2016-08-24 gmungocJAL-1424 undo i18n of exception message tree | commitdiff
2016-08-24 gmungocJAL-1854 declare immutable class as final tree | commitdiff
2016-08-24 gmungocJAL-1424 recode calls to MessageManager to allow code... tree | commitdiff
2016-08-24 gmungocJAL-2151 port fix to applet tree | commitdiff
2016-08-23 Jim ProcterJAL-2154 propagate from contig to CDS after constructin... tree | commitdiff
2016-08-23 Jim ProcterJAL-2154 should only add mappings between dataset sequences tree | commitdiff
2016-08-23 Jim ProcterJAL-2154 - only copy DBRef from contig to new CDS seque... tree | commitdiff
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings tree | commitdiff
2016-08-23 gmungocJAL-2176 unused field / methods removed tree | commitdiff
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection tree | commitdiff
2016-08-22 gmungocJAL-1448 corrected for backwards compatibility for... tree | commitdiff
2016-08-22 gmungocJAL-2175 code tidying tree | commitdiff
2016-08-22 gmungocJAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip tree | commitdiff
2016-08-22 Jim ProcterJAL-2154 verify recovered xref sequence not already... tree | commitdiff
2016-08-22 Jim ProcterJAL-2154 regression warning - should never recover... tree | commitdiff
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence... tree | commitdiff
2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test tree | commitdiff
2016-08-19 gmungocJAL-2174 bug fixes + refactoring to allow + unit tests tree | commitdiff
2016-08-19 Jim ProcterJAL-2154 - possible patch .. but leads to new stringify... tree | commitdiff
2016-08-19 Jim ProcterJAL-2154 reorder the dataset sequences according to... tree | commitdiff
2016-08-19 Jim ProcterJAL-2154 belt-and-braces patch: tree | commitdiff
2016-08-19 Jim ProcterJAL-2154 verify mapping’s sequenceI ref has been resolv... tree | commitdiff
2016-08-19 Jim ProcterJAL-2154 refactor setSequenceAt to replaceSequenceAt... tree | commitdiff
2016-08-18 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-18 gmungocJAL-2077 using Platform method to check for Ctrl-down tree | commitdiff
2016-08-18 gmungocJAL-1445 status message '...not containing...' for... tree | commitdiff
2016-08-18 gmungocJAL-1693 show warning dialog if unable to make CDS... tree | commitdiff
2016-08-18 gmungocJAL-1855 fail gracefully if XML has no <sequence> element tree | commitdiff
2016-08-18 gmungocJAL-2077 handling Cmd-click in scale panel for Mac... tree | commitdiff
2016-08-18 gmungocJAL-2001 return copy of selection in getSelected() tree | commitdiff
2016-08-17 gmungocJAL-2146 status message now with formatted residue... tree | commitdiff
2016-08-17 gmungocJAL-2173 don't remove annotation from hidden columns tree | commitdiff
2016-08-17 gmungocJAL-2172 reverted to not sorting column selection tree | commitdiff
2016-08-17 gmungocJAL-2105 rest versions updated to 4.6, change log link... tree | commitdiff
2016-08-17 gmungocJAL-2172 handle case where column selection is not... tree | commitdiff
2016-08-16 Jim ProcterJAL-2154 make sure any new sequences via DBRefEntry... tree | commitdiff
2016-08-16 Jim ProcterJAL-2154 always resolve dataset sequences when creating... tree | commitdiff
2016-08-16 gmungocJAL-2171 matching bracket default character for rna... tree | commitdiff
2016-08-16 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-15 tcofoegbuJAL-1128 fix for truncated bottom boarder pixels in... tree | commitdiff
2016-08-15 tcofoegbuJAL-1128 fix for truncated bottom boarder pixels in... tree | commitdiff
2016-08-15 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-08-15 tcofoegbuJAL-1919 Added improvement to ensure consistence of... tree | commitdiff
2016-08-13 Jim ProcterJAL-2154 refactor CrossRef UI code to its own class tree | commitdiff
2016-08-13 Jim ProcterJAL-2154 ignore all but the primary source resolved... tree | commitdiff
2016-08-13 Jim ProcterJAL-2154 make sure we wait for constructor thread to... tree | commitdiff
2016-08-12 gmungocJAL-1841 count (logo height) is valid pairs only; detec... tree | commitdiff
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering... tree | commitdiff
2016-08-12 gmungocJAL-1841, bug fix in rna SS consensus, additions to... tree | commitdiff
2016-08-12 gmungocJAL-2171 default SS symbol to existing (if present) tree | commitdiff
2016-08-11 Jim ProcterJAL-2154 jalview.gui.SequenceFetcher.fetchAndShow(db... tree | commitdiff
2016-08-11 Jim ProcterJAL-2154 JAL-1993 relocate show dbchooser action out... tree | commitdiff
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