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JAL-2049 set Ensembl variant source to ENSEMBL if '.' (not provided) and
2016-08-02 Jim ProcterJAL-2046 additional logic to suppress spurious implementatio...
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2016-08-02 Jim ProcterMerge branch 'efficiency/JAL-2034_JAL-1421' into develop
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2016-08-02 Jim ProcterJAL-2034 show greyed out image during overview update
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2016-08-02 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
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2016-08-02 Jim ProcterJAL-2068 reinstated false return value for notifyWorking
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2016-08-02 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
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2016-08-01 Jim ProcterJAL-2164 TODO: make test pass for JMOL_PARSER
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2016-08-01 Jim ProcterJAL-2164 JAL-1919 JAL-1270 use structure import settings...
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2016-08-01 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-08-01 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into develop
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2016-08-01 Jim ProcterMerge branch 'task/JAL-2164_mcviewforoldjalviewprojects...
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2016-08-01 Jim ProcterJAL-2164 prevent jalview news from opening
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2016-08-01 Jim ProcterJAL-2164 clear the desktop before testStoreAndRecoverExpande...
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2016-08-01 Jim ProcterMerge branch 'task/JAL-2164_mcviewforoldjalviewprojects...
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2016-08-01 Jim ProcterJAL-1772 make sure we actually return reference to...
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2016-07-29 Jim ProcterJAL-1772 JAL-2164 make expanded view save/restore test...
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2016-07-29 Jim ProcterJAL-2164 JAL-1772 explodeViews can be static, so make...
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2016-07-29 Jim ProcterJAL-2164 revert tests depending on import of legacy...
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2016-07-29 Jim ProcterJAL-2154 disable visual delay only after completed...
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2016-07-29 Jim ProcterJAL-2154 register any new dataset codon frames only...
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2016-07-29 Jim ProcterJAL-2154 only include mappings in dbref/alcodon in...
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2016-07-27 Jim ProcterJAL-2154 toString for forward references
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2016-07-27 Jim ProcterMerge branch 'patch/JAL-2156_JAL-2163_saveSplitFrameFromSave...
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2016-07-27 Jim ProcterJAL-2163 set title for the alignframe from restored...
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2016-07-27 Jim ProcterJAL-2156 resolve and add complementary views for saveAlignment
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2016-07-27 Jim ProcterJAL-2156 refactor saveState & saveAlignment to common...
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2016-07-27 Jim ProcterJAL-2156 getter for AlignFrame(s) held in a splitframe
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2016-07-26 Jim ProcterJAL-2157 todo: verify parser/file format enums and...
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2016-07-24 Jim ProcterJAL-2154 formatting
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2016-07-24 Jim ProcterJAL-2154 keep track of incomplete sequences and report...
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2016-07-24 Jim ProcterJAL-2154 systematic pattern for defining/resolving...
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2016-07-23 Jim ProcterJAL-2154 patch the hack (Jalview2XML tests pass)
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2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop
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2016-07-20 Jim ProcterJAL-1926 JAL-2106 fix name for flag controlling addition...
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2016-07-20 Jim ProcterJAL-1926 JAL-2106 don’t use PDB database constant as...
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2016-07-20 Jim ProcterJAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMAT...
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2016-07-20 Jim ProcterJAL-1926 JAL-2106 remove startRes/endRes fields - not...
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2016-07-19 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
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2016-07-18 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-07-18 Jim ProcterJAL-666 patch JAL-1947 in applet where overview is...
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2016-07-18 Jim ProcterJAL-2068 clearer instructions on how to use script...
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2016-07-18 Jim ProcterJAL-2068 clarify comments
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2016-07-18 Jim ProcterJAL-2068 scale annotation display character to width...
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2016-07-18 Jim ProcterJAL-2121 cleanup TODO
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2016-07-18 Jim ProcterJAL-2110 JAL-2145 fix out of date test for 2baee069f9edaef28...
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2016-07-18 Jim ProcterMerge branch 'features/JAL-2068groovyAnnotationWorker...
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2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation...
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2016-07-18 Jim ProcterJAL-2145 documentation of getWidth()
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2016-07-18 Jim ProcterJAL-2145 JAL-1551 formatting
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2016-07-18 Jim ProcterJAL-2145 fix: build alignments before building AlignFrame...
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2016-07-14 Jim Procterfix for JAL-2147
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2016-07-14 Jim ProcterJAL-2147 findMappingsBetweenSequenceAndOthers for scoping...
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2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility...
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2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI)
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2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstructed...
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2016-07-13 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
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2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefDuplic...
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2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and...
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2016-07-12 Jim ProcterJAL-2110 avoid potential race condition where user...
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2016-07-12 Jim ProcterJAL-2110 TODO for JAL-2131
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2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequences...
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2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current implementa...
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2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation
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2016-07-12 Jim ProcterJAL-2110 javadoc
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2016-07-12 Jim ProcterJAL-2110 scalability todo
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2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO
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2016-07-12 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-07-12 Jim ProcterJAL-1369 release notes for patch of save/restore representat...
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2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110
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2016-06-23 Jim ProcterJAL-1270 test group fix
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2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filtering...
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2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds...
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2016-06-23 Jim ProcterJAL-2110 clarify javadoc
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2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref...
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2016-06-23 Jim ProcterJAL-2110 JAL-1551 formatting
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2016-06-23 Jim ProcterJAL-2110 enable and fix failing tests
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2016-06-23 Jim ProcterJAL-2110 enable and fix test
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2016-06-23 Jim ProcterJAL-2110 refactor sequenceFetcherTest to allow verifying...
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2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein()
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2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method
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2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context...
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2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
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2016-06-21 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
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2016-06-21 Jim ProcterJAL-1270 ensure before/after clauses have at least...
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2016-06-21 Jim ProcterJAL-2089 cleared out old ‘What’s new’
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2016-06-21 Jim ProcterJAL-192 JAL-1369 release notes
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2016-06-21 Jim ProcterMerge branch 'features/JAL-1369_refseqproject' into...
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2016-06-21 Jim ProcterJAL-1369 make sure desktop is cleared before test starts
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2016-06-21 Jim ProcterJAL-1369 jalview2xml tests need to be run sequentially
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2016-06-21 Jim ProcterJAL-1369 mark reference sequence & view state and restore it
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2016-06-21 Jim ProcterJAL-1369 project XML efficiency TODO
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2016-06-21 Jim ProcterJAL-1369 dead code TODO?
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2016-06-21 Jim ProcterJAL-1369 ensure *real* alignment’s metadata written...
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2016-06-21 Jim ProcterJAL-1369 fix the test
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2016-06-21 Jim ProcterJAL-1369 make sure the fake AlignmentI produced by...
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2016-06-21 Jim ProcterJAL-1369 HUGE WARNING: datamodel.HiddenSequences is...
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2016-06-20 Jim ProcterJAL-1369 updated project schema - flag on JSeq to mark...
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2016-06-20 Jim ProcterJAL-1369 failing test
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2016-06-20 Jim ProcterJAL-1989 JAL-1011 release notes
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