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2016-08-22	gmungoc	JAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip	commit \| commitdiff \| tree
2016-08-22	gmungoc	JAL-2011 adjust method to fix failing unit test	commit \| commitdiff \| tree
2016-08-19	gmungoc	JAL-2174 bug fixes + refactoring to allow + unit tests	commit \| commitdiff \| tree
2016-08-18	gmungoc	JAL-2077 using Platform method to check for Ctrl-down	commit \| commitdiff \| tree
2016-08-18	gmungoc	JAL-1445 status message '...not containing...' for...	commit \| commitdiff \| tree
2016-08-18	gmungoc	JAL-1693 show warning dialog if unable to make CDS...	commit \| commitdiff \| tree
2016-08-18	gmungoc	JAL-1855 fail gracefully if XML has no <sequence> element	commit \| commitdiff \| tree
2016-08-18	gmungoc	JAL-2077 handling Cmd-click in scale panel for Mac...	commit \| commitdiff \| tree
2016-08-18	gmungoc	JAL-2001 return copy of selection in getSelected()	commit \| commitdiff \| tree
2016-08-17	gmungoc	JAL-2146 status message now with formatted residue...	commit \| commitdiff \| tree
2016-08-17	gmungoc	JAL-2173 don't remove annotation from hidden columns	commit \| commitdiff \| tree
2016-08-17	gmungoc	JAL-2172 reverted to not sorting column selection	commit \| commitdiff \| tree
2016-08-17	gmungoc	JAL-2105 rest versions updated to 4.6, change log link...	commit \| commitdiff \| tree
2016-08-17	gmungoc	JAL-2172 handle case where column selection is not...	commit \| commitdiff \| tree
2016-08-16	gmungoc	JAL-2172 unit test added	commit \| commitdiff \| tree
2016-08-10	gmungoc	JAL-2124 i18n of 'All' menu item	commit \| commitdiff \| tree
2016-08-10	gmungoc	JAL-2124 i18n of "All" menu item	commit \| commitdiff \| tree
2016-08-10	gmungoc	JAL-2146 small optimisation (avoid String creation)	commit \| commitdiff \| tree
2016-08-10	gmungoc	JAL-2146 show Column no [Sequence no [Residue / pos...	commit \| commitdiff \| tree
2016-08-08	gmungoc	JAL-1577 rebuild menus when secondary structure manually...	commit \| commitdiff \| tree
2016-08-08	gmungoc	JAL-2119 replaced link with a non-404 alternative	commit \| commitdiff \| tree
2016-08-08	gmungoc	JAL-2168 -nonews option also mentioned here	commit \| commitdiff \| tree
2016-08-08	gmungoc	JAL-2119 updates to invalid / obsolete help links	commit \| commitdiff \| tree
2016-08-08	gmungoc	JAL-2168 document '-nonews' parameter	commit \| commitdiff \| tree
2016-08-05	gmungoc	JAL-2168 skip news feed if parameter "-nonews" is supplied	commit \| commitdiff \| tree
2016-08-05	gmungoc	JAL-1448 always use UK locale for formatted date properties	commit \| commitdiff \| tree
2016-08-05	gmungoc	JAL-2164 add transferred annotation to sequence	commit \| commitdiff \| tree
2016-08-04	gmungoc	JAL-2164 changed to be Java 1.7 compliant	commit \| commitdiff \| tree
2016-08-04	gmungoc	JAL-2008 handle fast mouse drag of feature ordering...	commit \| commitdiff \| tree
2016-08-04	gmungoc	JAL-2015 convert Color from colour picker to FeatureColour	commit \| commitdiff \| tree
2016-07-20	gmungoc	JAL-2154 poke JSeq start/end into Vamsas sequence	commit \| commitdiff \| tree
2016-07-20	gmungoc	JAL-2023 stronger check for whether to start cdna consensus	commit \| commitdiff \| tree
2016-07-20	gmungoc	JAL-2023 avoid writing / loading empty mappings	commit \| commitdiff \| tree
2016-07-20	gmungoc	JAL-2023 JAL-1681 fixed bug in computing '+' for co...	commit \| commitdiff \| tree
2016-07-20	gmungoc	JAL-2068 AnnotationWorker create/update annotation...	commit \| commitdiff \| tree
2016-07-19	gmungoc	JAL-2068 small refactor to reuse shared method	commit \| commitdiff \| tree
2016-07-19	gmungoc	JAL-2068 update rather than recreate AlignmentAnnotation...	commit \| commitdiff \| tree
2016-07-19	gmungoc	JAL-391 corrected handling of gapped sequences	commit \| commitdiff \| tree
2016-07-18	gmungoc	JAL-2105 check content of Ensembl REST ping response	commit \| commitdiff \| tree
2016-07-18	gmungoc	JAL-2099 ensure initial setting of scaleAbove reaches...	commit \| commitdiff \| tree
2016-07-18	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-07-18	gmungoc	JAL-2099 JAL-2100 port scale number / hidden column...	commit \| commitdiff \| tree
2016-07-18	gmungoc	JAL-1976 Spanish version of new message	commit \| commitdiff \| tree
2016-07-18	gmungoc	JAL-2015 restore check for null colour in paint()	commit \| commitdiff \| tree
2016-07-09	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-07-07	gmungoc	JAL-2110 added alignAsSameSequences to handle 'direct...	commit \| commitdiff \| tree
2016-07-07	gmungoc	JAL-2110 field 'cf' moved to stack	commit \| commitdiff \| tree
2016-07-06	gmungoc	JAL-2110 generic rather than specific check for gap...	commit \| commitdiff \| tree
2016-07-06	gmungoc	JAL-2110 AlignmentUtils.alignCdsAsProtein implemented	commit \| commitdiff \| tree
2016-07-06	gmungoc	JAL-2110 ensuring mapped dbrefs between protein and cds	commit \| commitdiff \| tree
2016-07-06	gmungoc	JAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...	commit \| commitdiff \| tree
2016-07-06	gmungoc	JAL-2110 cross-refs from protein to show cds not non...	commit \| commitdiff \| tree
2016-07-06	gmungoc	JAL-2110 fixes and tests for adding dbrefs to EMBL...	commit \| commitdiff \| tree
2016-07-04	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-07-04	gmungoc	JAL-2110 use shared dataset when copying alignment...	commit \| commitdiff \| tree
2016-07-04	gmungoc	JAL-2110 added another test case (should fail but doesn't)	commit \| commitdiff \| tree
2016-07-04	gmungoc	Revert "JAL-2110 use shared alignment dataset when...	commit \| commitdiff \| tree
2016-07-04	gmungoc	JAL-2110 use shared alignment dataset when copying...	commit \| commitdiff \| tree
2016-07-04	gmungoc	JAL-2110 bug fix / test for searchDataset mappings...	commit \| commitdiff \| tree
2016-07-04	gmungoc	JAL-2110 unused method removed	commit \| commitdiff \| tree
2016-07-04	gmungoc	JAL-2110 defensive check in code	commit \| commitdiff \| tree
2016-07-01	gmungoc	JAL-2110 bug fixing and tidying for get cross-refs	commit \| commitdiff \| tree
2016-07-01	gmungoc	JAL-2110 set reasonable bounds to initial split of...	commit \| commitdiff \| tree
2016-07-01	gmungoc	JAL-2110 add 'products' parameter to filter results...	commit \| commitdiff \| tree
2016-07-01	gmungoc	JAL-2110 code/comment tidy	commit \| commitdiff \| tree
2016-06-30	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-06-30	gmungoc	JAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...	commit \| commitdiff \| tree
2016-06-30	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-06-29	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-06-29	gmungoc	JAL-1270 avoid overwriting .jalview_properties with...	commit \| commitdiff \| tree
2016-06-29	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-06-29	gmungoc	JAL-1369 fix bug reloading a project with group sequence...	commit \| commitdiff \| tree
2016-06-27	gmungoc	tidied loop with generic iteration / loop variable	commit \| commitdiff \| tree
2016-06-27	gmungoc	JAL-2133 refactored duplicated code to AlignmentViewport	commit \| commitdiff \| tree
2016-06-27	gmungoc	JAL-1369 additional asserts in testStoreAndRecoverReferenceS...	commit \| commitdiff \| tree
2016-06-27	gmungoc	JAL-1270 unit tests for HiddenSequences	commit \| commitdiff \| tree
2016-06-23	gmungoc	JAL-2130 now simply viewer.dispose() to close down...	commit \| commitdiff \| tree
2016-06-22	gmungoc	JAL-2015 fixed bug in copy constructor and added tests	commit \| commitdiff \| tree
2016-06-22	gmungoc	JAL-1982 defensive checks for null annotations array	commit \| commitdiff \| tree
2016-06-22	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-06-22	gmungoc	JAL-1982 defensive test for null array of annotations	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2074 suppress prompt to save closed Groovy script...	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-1270 remove test artefact file after test	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-1270 added runAlways=true to setUp method	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2074 reuse Groovy window when reopening; rebind...	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2110 updated unit test to match code changes	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2113 tidy up canonicalisation of Uniprot xrefs...	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2113 tidy up canonicalisation of Uniprot xrefs...	commit \| commitdiff \| tree
2016-06-20	gmungoc	JAL-2130 call viewer.dispose() on closing Jmol	commit \| commitdiff \| tree
2016-06-20	gmungoc	JAL-1667 updated PDB example query to a valid id (without...	commit \| commitdiff \| tree
2016-06-17	gmungoc	JAL-1557 selection from annotation (and group annotation...	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-1993 close sequence fetcher when opening database...	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-2124 JAL-1990 additional translations	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-2112 optimisation of EMBL CDS parsing	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-1993 hide sequence fetcher dialogue until database...	commit \| commitdiff \| tree
2016-06-15	gmungoc	JAL-2025 unit tests added	commit \| commitdiff \| tree
2016-06-15	gmungoc	JAL-2101 unit test updated to match config file	commit \| commitdiff \| tree
2016-06-14	gmungoc	JAL-2114 more helpful reporting of parse failures	commit \| commitdiff \| tree
2016-06-14	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-06-14	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
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