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Merge branch 'efficiency/JAL-2034_JAL-1421' into develop
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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2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
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2016-07-01 gmungocJAL-2110 set reasonable bounds to initial split of...
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2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
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2016-07-01 gmungocJAL-2110 code/comment tidy
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2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...
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2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-06-29 gmungocJAL-1270 avoid overwriting .jalview_properties with...
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2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-06-29 gmungocJAL-1369 fix bug reloading a project with group sequence...
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2016-06-27 gmungoctidied loop with generic iteration / loop variable
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2016-06-27 gmungocJAL-2133 refactored duplicated code to AlignmentViewport
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2016-06-27 gmungocJAL-1369 additional asserts in testStoreAndRecoverReferenceS...
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2016-06-27 gmungocJAL-1270 unit tests for HiddenSequences
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2016-06-23 gmungocJAL-2130 now simply viewer.dispose() to close down...
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2016-06-22 gmungocJAL-2015 fixed bug in copy constructor and added tests
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2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
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2016-06-22 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-06-22 gmungocJAL-1982 defensive test for null array of annotations
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2016-06-21 gmungocJAL-2074 suppress prompt to save closed Groovy script...
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2016-06-21 gmungocJAL-1270 remove test artefact file after test
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2016-06-21 gmungocJAL-1270 added runAlways=true to setUp method
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2016-06-21 gmungocJAL-2074 reuse Groovy window when reopening; rebind...
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2016-06-21 gmungocJAL-2110 updated unit test to match code changes
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2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs...
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2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs...
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2016-06-20 gmungocJAL-2130 call viewer.dispose() on closing Jmol
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2016-06-20 gmungocJAL-1667 updated PDB example query to a valid id (without...
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2016-06-17 gmungocJAL-1557 selection from annotation (and group annotation...
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2016-06-16 gmungocJAL-1993 close sequence fetcher when opening database...
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2016-06-16 gmungocJAL-2124 JAL-1990 additional translations
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2016-06-16 gmungocJAL-2112 optimisation of EMBL CDS parsing
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2016-06-16 gmungocJAL-1993 hide sequence fetcher dialogue until database...
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2016-06-15 gmungocJAL-2025 unit tests added
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2016-06-15 gmungocJAL-2101 unit test updated to match config file
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2016-06-14 gmungocJAL-2114 more helpful reporting of parse failures
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2016-06-14 gmungocMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-06-14 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-06-14 gmungocJAL-2110 fixes to dbref resolution and mappings, use...
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2016-06-14 gmungocJAL-2110 ensure "UniProtKB/Swiss-Prot" dbrefs canonicalised...
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2016-06-14 gmungocJAL-1686 JAL-2110 equals and/or hashCode method added
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2016-06-09 gmungocJAL-2110 work in progress
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2016-06-09 gmungocMerge branch 'develop' into features/JAL-2110_makeSenseOfCro...
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2016-06-09 gmungocJAL-2114 corrected Javadoc
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2016-06-03 gmungocJAL-2110 random stuff
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2016-06-02 gmungocMerge branch 'develop' into features/JAL-2110_makeSenseOfCro...
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2016-06-02 gmungocJAL-2124 additional Spanish text strings
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2016-06-02 gmungocMerge branch 'develop' into features/JAL-2110_makeSenseOfCro...
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2016-06-02 gmungocJAL-1424 corrected typos in message text keys
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2016-06-02 gmungocJAL-1424 removed duplicate entry and unneeded full...
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2016-06-01 gmungocJAL-1424 clearer messaging
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2016-06-01 gmungocJAL-1424 utility to check resource bundle labels used...
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2016-05-31 gmungocJAL-2023 adjustments to mappings added for split frame...
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2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version...
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2016-05-31 gmungocJAL-1011 JAL-1989 don't mirror column-only selections...
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2016-05-31 gmungocJAL-2123 use "rlabel" command to highlight with label...
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2016-05-30 gmungocJAL-1670 JAL-2018 updated unit test for added example...
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2016-05-30 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-05-30 gmungocJAL-1989 equals method strengthened to fully match...
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2016-05-30 gmungocJAL-2119 help links checker added to /utils
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2016-05-30 gmungocJAL-2119 updated Valdar group link
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2016-05-29 gmungocJAL-2119 fixes for broken links in help files
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2016-05-27 gmungocJAL-1989 tightened up use of flag for 'column selection...
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2016-05-27 gmungocJAL-1989 added hashCode and equals, renamed field to...
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2016-05-27 gmungocJAL-1911 use existing object when setting 'Prompt each...
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2016-05-27 gmungocJAL-1942 small tidy (formatting, explict imports, typed...
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2016-05-27 gmungocJAL-1911 correct typo in field name
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2016-05-26 gmungocJAL-391 add reverse / complement to command history...
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