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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
2016-06-21 Jim ProcterJAL-2089 cleared out old ‘What’s new’ commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-192 JAL-1369 release notes commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterMerge branch 'features/JAL-1369_refseqproject' into... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 make sure desktop is cleared before test starts commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 jalview2xml tests need to be run sequentially commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-2110 updated unit test to match code changes commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 mark reference sequence & view state and resto... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 project XML efficiency TODO commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 dead code TODO? commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 ensure *real* alignment’s metadata written... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 fix the test commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 make sure the fake AlignmentI produced by... commit | commitdiff | tree | snapshot
2016-06-21 Jim ProcterJAL-1369 HUGE WARNING: datamodel.HiddenSequences is... commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs... commit | commitdiff | tree | snapshot
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs... commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-1369 updated project schema - flag on JSeq to mark... commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-1369 failing test commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-1989 JAL-1011 release notes commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-2086 JAL-2085 release notes commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-2065 release notes commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterMerge branch 'bugs/JAL-2065' into develop commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-2065 port patch to applet commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-1551 tidy commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-1551 tidy commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-2065 don’t pass stale group reference commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus... commit | commitdiff | tree | snapshot
2016-06-20 Jim ProcterJAL-2065 check position lies within group before gettin... commit | commitdiff | tree | snapshot
2016-06-20 tcofoegbuJAL-1996 added JalviewApplet to download list in applet... commit | commitdiff | tree | snapshot
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