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Merge branch 'bug/JAL-1841rnaSecStr' into develop
2016-08-29 gmungocMerge branch 'bug/JAL-1841rnaSecStr' into develop
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2016-08-29 gmungocJAL-1448 updated unit test for last change
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2016-08-29 gmungocJAL-1841 robustness fix
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2016-08-29 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
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2016-08-26 gmungocJAL-1854 two more rules, readme notes
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2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
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2016-08-26 gmungocJAL-1854 commented FallThrough rule
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2016-08-26 gmungocJAL-1854 corrected nested package rule
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2016-08-26 gmungocJAL-2049 set Ensembl variant source to ENSEMBL if ...
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2016-08-26 gmungocJAL-1854 comment switch case fallthrough
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2016-08-25 gmungocJAL-1854 missing case break statements added
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2016-08-25 gmungocJAL-1854 initial checkstyle config
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2016-08-25 gmungocJAL-2178 remove duplicate Uniprot db source
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2016-08-25 gmungocJAL-1424 duplicate key removed
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2016-08-24 gmungocJAL-1355 correct 'thereshold' to 'threshold' in message...
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2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys
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2016-08-24 gmungocJAL-1424 tidy / recode MessageManager calls to support...
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2016-08-24 gmungocJAL-1854 removed pointless method override
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2016-08-24 gmungocJAL-1424 removed two redundant (overwritten) setText...
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2016-08-24 gmungocJAL-1424 corrected Message bundle lookup key
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2016-08-24 gmungocJAL-1424 undo i18n of exception message
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2016-08-24 gmungocJAL-1854 declare immutable class as final
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2016-08-24 gmungocJAL-1424 recode calls to MessageManager to allow code...
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2016-08-24 gmungocJAL-2151 port fix to applet
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2016-08-24 gmungocJAL-1424 enhanced for cleaner reporting, checks calls...
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2016-08-24 gmungocJAL-1424 also report (obsolete) keys in translated...
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2016-08-23 gmungocJAL-2176 unused field / methods removed
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2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection
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2016-08-22 gmungocJAL-1448 corrected for backwards compatibility for...
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2016-08-22 gmungocJAL-2175 code tidying
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2016-08-22 gmungocJAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip
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2016-08-22 gmungocJAL-2011 adjust method to fix failing unit test
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2016-08-19 gmungocJAL-2174 bug fixes + refactoring to allow + unit tests
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2016-08-18 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
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2016-08-18 gmungocJAL-2077 using Platform method to check for Ctrl-down
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2016-08-18 gmungocJAL-1445 status message '...not containing...' for...
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2016-08-18 gmungocJAL-1693 show warning dialog if unable to make CDS...
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2016-08-18 gmungocJAL-1855 fail gracefully if XML has no <sequence> element
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2016-08-18 gmungocJAL-2077 handling Cmd-click in scale panel for Mac...
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2016-08-18 gmungocJAL-2001 return copy of selection in getSelected()
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2016-08-17 gmungocJAL-2146 status message now with formatted residue...
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2016-08-17 gmungocJAL-2173 don't remove annotation from hidden columns
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2016-08-17 gmungocJAL-2172 reverted to not sorting column selection
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2016-08-17 gmungocJAL-2105 rest versions updated to 4.6, change log link...
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2016-08-17 gmungocJAL-2172 handle case where column selection is not...
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2016-08-16 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
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2016-08-16 gmungocJAL-2172 unit test added
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2016-08-16 gmungocJAL-2171 matching bracket default character for rna...
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2016-08-16 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
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2016-08-15 gmungocJAL-1841 better i18n text
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2016-08-12 gmungocJAL-1841 count (logo height) is valid pairs only; detect...
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2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
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2016-08-12 gmungocJAL-1841, bug fix in rna SS consensus, additions to...
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2016-08-12 gmungocJAL-2171 default SS symbol to existing (if present)
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2016-08-10 gmungocJAL-2124 i18n of 'All' menu item
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2016-08-10 gmungocJAL-2124 i18n of "All" menu item
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2016-08-10 gmungocJAL-2146 small optimisation (avoid String creation)
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2016-08-10 gmungocJAL-2146 show Column no [Sequence no [Residue / pos...
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2016-08-08 gmungocJAL-1577 rebuild menus when secondary structure manually...
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2016-08-08 gmungocJAL-2119 replaced link with a non-404 alternative
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2016-08-08 gmungocJAL-2168 -nonews option also mentioned here
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2016-08-08 gmungocJAL-2119 updates to invalid / obsolete help links
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2016-08-08 gmungocJAL-2168 document '-nonews' parameter
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2016-08-05 gmungocJAL-2168 skip news feed if parameter "-nonews" is supplied
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2016-08-05 gmungocJAL-1448 always use UK locale for formatted date properties
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2016-08-05 gmungocJAL-2164 add transferred annotation to sequence
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2016-08-04 gmungocJAL-2164 changed to be Java 1.7 compliant
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2016-08-04 gmungocJAL-2008 handle fast mouse drag of feature ordering...
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2016-08-04 gmungocJAL-2015 convert Color from colour picker to FeatureColour
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2016-07-20 gmungocJAL-2154 poke JSeq start/end into Vamsas sequence
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2016-07-20 gmungocJAL-2023 stronger check for whether to start cdna consensus
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2016-07-20 gmungocJAL-2023 avoid writing / loading empty mappings
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2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co...
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2016-07-20 gmungocJAL-2068 AnnotationWorker create/update annotation...
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2016-07-19 gmungocJAL-2068 small refactor to reuse shared method
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2016-07-19 gmungocJAL-2068 update rather than recreate AlignmentAnnotation...
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2016-07-19 gmungocJAL-391 corrected handling of gapped sequences
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2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response
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2016-07-18 gmungocJAL-2099 ensure initial setting of scaleAbove reaches...
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2016-07-18 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-07-18 gmungocJAL-2099 JAL-2100 port scale number / hidden column...
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2016-07-18 gmungocJAL-1976 Spanish version of new message
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2016-07-18 gmungocJAL-2015 restore check for null colour in paint()
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2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
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2016-07-07 gmungocJAL-2110 field 'cf' moved to stack
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2016-07-06 gmungocJAL-2110 generic rather than specific check for gap...
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2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented
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2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
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2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...
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2016-07-06 gmungocJAL-2110 cross-refs from protein to show cds not non...
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2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL...
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2016-07-04 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment...
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2016-07-04 gmungocJAL-2110 added another test case (should fail but doesn't)
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2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
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2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
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2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings...
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2016-07-04 gmungocJAL-2110 unused method removed
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2016-07-04 gmungocJAL-2110 defensive check in code
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