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Merge branch 'patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles' into...
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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2016-07-24 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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2016-07-18 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2016-07-18 Jim ProcterJAL-2110 JAL-2145 fix out of date test for 2baee069f9edaef28...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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2016-06-20 Jim ProcterJAL-2086 JAL-2085 release notes
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2016-06-20 Jim ProcterMerge branch 'develop' of http://source.jalview.org...
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2016-06-20 Jim ProcterJAL-2065 release notes
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2016-06-20 Jim ProcterMerge branch 'bugs/JAL-2065' into develop
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2016-06-20 Jim ProcterJAL-2065 port patch to applet
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2016-06-20 Jim ProcterJAL-1551 tidy
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2016-06-20 Jim ProcterJAL-1551 tidy
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2016-06-20 Jim ProcterJAL-2065 don’t pass stale group reference
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2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus...
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2016-06-20 Jim ProcterJAL-2065 check position lies within group before getting...
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2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-2068groovyAnnotatio...
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2016-06-20 Jim ProcterMerge branch 'r291_docs' into develop
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2016-06-20 Jim ProcterJAL-1812 groovy always present
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2016-06-20 Jim ProcterJAL-1812 release notes
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2016-06-20 Jim ProcterJAL-1812 documentation TBC for AlignFrame->Calculate...
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2016-06-20 Jim ProcterJAL-2089 typo
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2016-06-20 Jim ProcterJAL-1868 fix typo in test data.
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2016-06-20 Jim ProcterMerge branch 'features/JAL-1812_JAL-2083_groovyBinding...
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2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-1812_JAL-2083_groov...
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2016-06-20 Jim ProcterJAL-2110 pass dataset to makeCDSalignment
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2016-06-20 Jim ProcterJAL-2110 catch case when updateDBRef argument has null...
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2016-06-20 Jim ProcterJAL-2110 List now used for AlignCodonFrame references
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2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor...
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2016-06-19 Jim ProcterJAL-2110 distinct alignedcodonframe entries for tests
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2016-06-19 Jim ProcterJAL-2110 test alcodonframes must be distinct
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2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
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2016-06-16 Jim Proctertests for validating start-end number/sequence length...
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2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences...
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2016-06-16 Jim ProcterJAL-2110 change test for desired behaviour of getCodonFrame()
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