jalview.git
2016-07-29 Jim ProcterJAL-2154 disable visual delay only after completed...
2016-07-29 Jim ProcterJAL-2154 register any new dataset codon frames only...
2016-07-29 Jim ProcterJAL-2154 only include mappings in dbref/alcodon in...
2016-07-27 Jim ProcterJAL-2154 toString for forward references
2016-07-27 Jim ProcterMerge branch 'patch/JAL-2156_JAL-2163_saveSplitFrameFro...
2016-07-27 Jim ProcterJAL-2163 set title for the alignframe from restored... patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles
2016-07-27 Jim ProcterJAL-2156 resolve and add complementary views for saveAl...
2016-07-27 Jim ProcterJAL-2156 refactor saveState & saveAlignment to common...
2016-07-27 Jim ProcterJAL-2156 getter for AlignFrame(s) held in a splitframe
2016-07-24 Jim ProcterJAL-2154 formatting
2016-07-24 Jim ProcterJAL-2154 keep track of incomplete sequences and report...
2016-07-24 Jim ProcterJAL-2154 systematic pattern for defining/resolving...
2016-07-23 Jim ProcterJAL-2154 patch the hack (Jalview2XML tests pass)
2016-07-20 gmungocJAL-2154 poke JSeq start/end into Vamsas sequence
2016-07-20 gmungocJAL-2023 stronger check for whether to start cdna consensus
2016-07-20 gmungocJAL-2023 avoid writing / loading empty mappings
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co...
2016-07-20 gmungocJAL-2068 AnnotationWorker create/update annotation...
2016-07-19 gmungocJAL-2068 small refactor to reuse shared method
2016-07-19 gmungocJAL-2068 update rather than recreate AlignmentAnnotatio...
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF...
2016-07-18 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie...
2016-07-18 Jim ProcterJAL-666 patch JAL-1947 in applet where overview is...
2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response
2016-07-18 gmungocJAL-2099 ensure initial setting of scaleAbove reaches...
2016-07-18 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-07-18 gmungocJAL-2099 JAL-2100 port scale number / hidden column...
2016-07-18 Jim ProcterJAL-2068 clearer instructions on how to use script...
2016-07-18 Jim ProcterJAL-2068 clarify comments
2016-07-18 Jim ProcterJAL-2068 scale annotation display character to width...
2016-07-18 Jim ProcterJAL-2121 cleanup TODO
2016-07-18 Jim ProcterJAL-2110 JAL-2145 fix out of date test for 2baee069f9ed...
2016-07-18 gmungocJAL-1976 Spanish version of new message
2016-07-18 gmungocJAL-2015 restore check for null colour in paint()
2016-07-18 Jim ProcterMerge branch 'features/JAL-2068groovyAnnotationWorker...
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation...
2016-07-18 Jim ProcterJAL-2145 documentation of getWidth()
2016-07-18 Jim ProcterJAL-2145 JAL-1551 formatting
2016-07-18 Jim ProcterJAL-2145 fix: build alignments before building AlignFra...
2016-07-14 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-07-14 tcofoegbuJAL-1919 house-keeping
2016-07-14 Jim Procterfix for JAL-2147
2016-07-14 Jim ProcterJAL-2147 findMappingsBetweenSequenceAndOthers for scopi...
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility...
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI)
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
2016-07-13 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-07-13 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-07-13 tcofoegbuJAL-2135 minor house-keeping
2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and...
2016-07-12 Jim ProcterJAL-2110 avoid potential race condition where user...
2016-07-12 Jim ProcterJAL-2110 TODO for JAL-2131
2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequen...
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple...
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation
2016-07-12 Jim ProcterJAL-2110 javadoc
2016-07-12 Jim ProcterJAL-2110 scalability todo
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO
2016-07-12 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie...
2016-07-12 Jim ProcterJAL-1369 release notes for patch of save/restore repres...
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with...
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing...
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap...
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...
2016-07-06 gmungocJAL-2110 cross-refs from protein to show cds not non...
2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL...
2016-07-04 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment...
2016-07-04 gmungocJAL-2110 added another test case (should fail but doesn't)
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings...
2016-07-04 gmungocJAL-2110 unused method removed
2016-07-04 gmungocJAL-2110 defensive check in code
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-07-01 gmungocJAL-2110 set reasonable bounds to initial split of...
2016-07-01 tcofoegbuJAL-2135 bugfix for error preventing processing of...
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
2016-07-01 gmungocJAL-2110 code/comment tidy
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-30 tcofoegbuJAL-2074 Improvement to StructureChooser and FTS interf...
2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser...
2016-06-29 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-29 tcofoegbuJAL-1479 added test case to elaborate getEntityByMostOp...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-29 gmungocJAL-1270 avoid overwriting .jalview_properties with...
2016-06-29 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-29 tcofoegbuJAL-1479 improved Sifts PID calculation for determining...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-29 gmungocJAL-1369 fix bug reloading a project with group sequenc...
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