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2016-07-18 Jim ProcterJAL-2145 fix: build alignments before building AlignFra... commit | commitdiff | tree | snapshot
2016-07-14 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-14 tcofoegbuJAL-1919 house-keeping commit | commitdiff | tree | snapshot
2016-07-14 Jim Procterfix for JAL-2147 commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-2147 findMappingsBetweenSequenceAndOthers for scopi... commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility... commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI) commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... commit | commitdiff | tree | snapshot
2016-07-13 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications... commit | commitdiff | tree | snapshot
2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-07-13 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-13 tcofoegbuJAL-2135 minor house-keeping commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 avoid potential race condition where user... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 TODO for JAL-2131 commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequen... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 javadoc commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 scalability todo commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-1369 release notes for patch of save/restore repres... commit | commitdiff | tree | snapshot
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with... commit | commitdiff | tree | snapshot
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications commit | commitdiff | tree | snapshot
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... commit | commitdiff | tree | snapshot
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... commit | commitdiff | tree | snapshot
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap... commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL... commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 cross-refs from protein to show cds not non... commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL... commit | commitdiff | tree | snapshot
2016-07-04 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment... commit | commitdiff | tree | snapshot
2016-07-04 gmungocJAL-2110 added another test case (should fail but doesn't) commit | commitdiff | tree | snapshot
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when... commit | commitdiff | tree | snapshot
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying... commit | commitdiff | tree | snapshot
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings... commit | commitdiff | tree | snapshot
2016-07-04 gmungocJAL-2110 unused method removed commit | commitdiff | tree | snapshot
2016-07-04 gmungocJAL-2110 defensive check in code commit | commitdiff | tree | snapshot
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs commit | commitdiff | tree | snapshot
2016-07-01 gmungocJAL-2110 set reasonable bounds to initial split of... commit | commitdiff | tree | snapshot
2016-07-01 tcofoegbuJAL-2135 bugfix for error preventing processing of... commit | commitdiff | tree | snapshot
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results... commit | commitdiff | tree | snapshot
2016-07-01 gmungocJAL-2110 code/comment tidy commit | commitdiff | tree | snapshot
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-06-30 tcofoegbuJAL-2074 Improvement to StructureChooser and FTS interf... commit | commitdiff | tree | snapshot
2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN... commit | commitdiff | tree | snapshot
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser... commit | commitdiff | tree | snapshot
2016-06-29 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-29 tcofoegbuJAL-1479 added test case to elaborate getEntityByMostOp... commit | commitdiff | tree | snapshot
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-06-29 gmungocJAL-1270 avoid overwriting .jalview_properties with... commit | commitdiff | tree | snapshot
2016-06-29 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-29 tcofoegbuJAL-1479 improved Sifts PID calculation for determining... commit | commitdiff | tree | snapshot
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-06-29 gmungocJAL-1369 fix bug reloading a project with group sequenc... commit | commitdiff | tree | snapshot
2016-06-28 tcofoegbuJAL-1479 minor refactor and housekeeping commit | commitdiff | tree | snapshot
2016-06-28 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-28 tcofoegbuJAL-1479 improved SiftsClient test coverage and impleme... commit | commitdiff | tree | snapshot
2016-06-27 gmungoctidied loop with generic iteration / loop variable commit | commitdiff | tree | snapshot
2016-06-27 gmungocJAL-2133 refactored duplicated code to AlignmentViewport commit | commitdiff | tree | snapshot
2016-06-27 gmungocJAL-1369 additional asserts in testStoreAndRecoverRefer... commit | commitdiff | tree | snapshot
2016-06-27 gmungocJAL-1270 unit tests for HiddenSequences commit | commitdiff | tree | snapshot
2016-06-24 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-24 tcofoegbuJAL-1960 updated unit test to include the test case... commit | commitdiff | tree | snapshot
2016-06-23 gmungocJAL-2130 now simply viewer.dispose() to close down... commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110 commit | commitdiff | tree | snapshot
2016-06-23 tcofoegbuJAL-1996 added notes for an alternative way to view... commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-1270 test group fix commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter... commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds... commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 clarify javadoc commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref... commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 JAL-1551 formatting commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 enable and fix failing tests commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 enable and fix test commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 refactor sequenceFetcherTest to allow verifyin... commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein() commit | commitdiff | tree | snapshot
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method commit | commitdiff | tree | snapshot
2016-06-22 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-22 tcofoegbuJAL-1996 added link for viewing example source codes... commit | commitdiff | tree | snapshot
2016-06-22 gmungocJAL-2015 fixed bug in copy constructor and added tests commit | commitdiff | tree | snapshot
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array commit | commitdiff | tree | snapshot
2016-06-22 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-22 gmungocJAL-1982 defensive test for null array of annotations commit | commitdiff | tree | snapshot
2016-06-22 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-06-22 tcofoegbuJAL-1996 removed quick links in example pages, added... commit | commitdiff | tree | snapshot
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-2074 suppress prompt to save closed Groovy script... commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-1270 remove test artefact file after test commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1270 ensure before/after clauses have at least... commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-1270 added runAlways=true to setUp method commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-2074 reuse Groovy window when reopening; rebind... commit | commitdiff | tree | snapshot
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