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2016-08-31	Jim Procter	JAL-2034 fix logic so recalcConservation(true) returns...	commit \| commitdiff \| tree
2016-08-31	Jim Procter	JAL-2034 moved ‘isDefinedGroup’ flag to a test method...	commit \| commitdiff \| tree
2016-08-31	Jim Procter	JAL-2034 remove todo - answer is yes!	commit \| commitdiff \| tree
2016-08-02	Jim Procter	JAL-2046 additional logic to suppress spurious implementatio...	commit \| commitdiff \| tree
2016-08-02	Jim Procter	Merge branch 'efficiency/JAL-2034_JAL-1421' into develop	commit \| commitdiff \| tree
2016-08-02	Jim Procter	JAL-2034 show greyed out image during overview update	commit \| commitdiff \| tree
2016-08-02	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	commit \| commitdiff \| tree
2016-08-02	Jim Procter	JAL-2068 reinstated false return value for notifyWorking	commit \| commitdiff \| tree
2016-08-02	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	commit \| commitdiff \| tree
2016-08-01	Jim Procter	JAL-2164 TODO: make test pass for JMOL_PARSER	commit \| commitdiff \| tree
2016-08-01	Jim Procter	JAL-2164 JAL-1919 JAL-1270 use structure import settings...	commit \| commitdiff \| tree
2016-08-01	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-08-01	Jim Procter	Merge branch 'bug/JAL-2154projectMappings' into develop	commit \| commitdiff \| tree
2016-08-01	Jim Procter	Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects...	commit \| commitdiff \| tree
2016-08-01	Jim Procter	JAL-2164 prevent jalview news from opening	commit \| commitdiff \| tree
2016-08-01	Jim Procter	JAL-2164 clear the desktop before testStoreAndRecoverExpande...	commit \| commitdiff \| tree
2016-08-01	Jim Procter	Merge branch 'task/JAL-2164_mcviewforoldjalviewprojects...	commit \| commitdiff \| tree
2016-08-01	Jim Procter	JAL-1772 make sure we actually return reference to...	commit \| commitdiff \| tree
2016-07-29	Jim Procter	JAL-1772 JAL-2164 make expanded view save/restore test...	commit \| commitdiff \| tree
2016-07-29	Jim Procter	JAL-2164 JAL-1772 explodeViews can be static, so make...	commit \| commitdiff \| tree
2016-07-29	Jim Procter	JAL-2164 revert tests depending on import of legacy...	commit \| commitdiff \| tree
2016-07-29	Jim Procter	JAL-2154 disable visual delay only after completed...	commit \| commitdiff \| tree
2016-07-29	Jim Procter	JAL-2154 register any new dataset codon frames only...	commit \| commitdiff \| tree
2016-07-29	Jim Procter	JAL-2154 only include mappings in dbref/alcodon in...	commit \| commitdiff \| tree
2016-07-27	Jim Procter	JAL-2154 toString for forward references	commit \| commitdiff \| tree
2016-07-27	Jim Procter	Merge branch 'patch/JAL-2156_JAL-2163_saveSplitFrameFromSave...	commit \| commitdiff \| tree
2016-07-27	Jim Procter	JAL-2163 set title for the alignframe from restored...	commit \| commitdiff \| tree
2016-07-27	Jim Procter	JAL-2156 resolve and add complementary views for saveAlignment	commit \| commitdiff \| tree
2016-07-27	Jim Procter	JAL-2156 refactor saveState & saveAlignment to common...	commit \| commitdiff \| tree
2016-07-27	Jim Procter	JAL-2156 getter for AlignFrame(s) held in a splitframe	commit \| commitdiff \| tree
2016-07-26	Jim Procter	JAL-2157 todo: verify parser/file format enums and...	commit \| commitdiff \| tree
2016-07-24	Jim Procter	JAL-2154 formatting	commit \| commitdiff \| tree
2016-07-24	Jim Procter	JAL-2154 keep track of incomplete sequences and report...	commit \| commitdiff \| tree
2016-07-24	Jim Procter	JAL-2154 systematic pattern for defining/resolving...	commit \| commitdiff \| tree
2016-07-23	Jim Procter	JAL-2154 patch the hack (Jalview2XML tests pass)	commit \| commitdiff \| tree
2016-07-21	Jim Procter	Merge branch 'apifix/JAL-1926_JAL-2106' into develop	commit \| commitdiff \| tree
2016-07-20	Jim Procter	JAL-1926 JAL-2106 fix name for flag controlling addition...	commit \| commitdiff \| tree
2016-07-20	Jim Procter	JAL-1926 JAL-2106 don’t use PDB database constant as...	commit \| commitdiff \| tree
2016-07-20	Jim Procter	JAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMAT...	commit \| commitdiff \| tree
2016-07-20	Jim Procter	JAL-1926 JAL-2106 remove startRes/endRes fields - not...	commit \| commitdiff \| tree
2016-07-19	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-666 patch JAL-1947 in applet where overview is...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2068 clearer instructions on how to use script...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2068 clarify comments	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2068 scale annotation display character to width...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2121 cleanup TODO	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2110 JAL-2145 fix out of date test for 2baee069f9edaef28...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	Merge branch 'features/JAL-2068groovyAnnotationWorker...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2145 improvement: ensure conservation calculation...	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2145 documentation of getWidth()	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2145 JAL-1551 formatting	commit \| commitdiff \| tree
2016-07-18	Jim Procter	JAL-2145 fix: build alignments before building AlignFrame...	commit \| commitdiff \| tree
2016-07-14	Jim Procter	fix for JAL-2147	commit \| commitdiff \| tree
2016-07-14	Jim Procter	JAL-2147 findMappingsBetweenSequenceAndOthers for scoping...	commit \| commitdiff \| tree
2016-07-14	Jim Procter	JAL-1115 change implementation to avoid possibility...	commit \| commitdiff \| tree
2016-07-14	Jim Procter	JAL-1270 test coverage TODO Alignment.append(AlignmentI)	commit \| commitdiff \| tree
2016-07-14	Jim Procter	JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstructed...	commit \| commitdiff \| tree
2016-07-13	Jim Procter	Merge branch 'features/JAL-2110_crossRefDuplications...	commit \| commitdiff \| tree
2016-07-13	Jim Procter	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2144 TODO - new methods for canonicalisation and...	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 avoid potential race condition where user...	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 TODO for JAL-2131	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 note about use case for when alignAsSameSequences...	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 test demonstrating limitation of current implementa...	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 javadoc and TODO re shortcomings of implementation	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 javadoc	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-2110 scalability todo	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-1381 JAL-2110 efficiency TODO	commit \| commitdiff \| tree
2016-07-12	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-07-12	Jim Procter	JAL-1369 release notes for patch of save/restore representat...	commit \| commitdiff \| tree
2016-06-23	Jim Procter	Merge branch 'develop' into merge_JAL-2110	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-1270 test group fix	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 make indirect xref searches work by not filtering...	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 warning message when routine finds non-ds...	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 clarify javadoc	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 refactor to split SequenceFetcher from x-ref...	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 JAL-1551 formatting	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 enable and fix failing tests	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 enable and fix test	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 refactor sequenceFetcherTest to allow verifying...	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 use SequenceI.isProtein()	commit \| commitdiff \| tree
2016-06-23	Jim Procter	JAL-2110 SequenceI.isProtein method	commit \| commitdiff \| tree
2016-06-22	Jim Procter	JAL-2110 remove hardwired detection of search context...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	Merge branch 'features/JAL-2110_crossRefDuplications...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	Merge branch 'features/JAL-1956_featureStyles' into...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1270 ensure before/after clauses have at least...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-2089 cleared out old ‘What’s new’	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-192 JAL-1369 release notes	commit \| commitdiff \| tree
2016-06-21	Jim Procter	Merge branch 'features/JAL-1369_refseqproject' into...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 make sure desktop is cleared before test starts	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 jalview2xml tests need to be run sequentially	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 mark reference sequence & view state and restore it	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 project XML efficiency TODO	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 dead code TODO?	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 ensure real alignment’s metadata written...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 fix the test	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 make sure the fake AlignmentI produced by...	commit \| commitdiff \| tree
2016-06-21	Jim Procter	JAL-1369 HUGE WARNING: datamodel.HiddenSequences is...	commit \| commitdiff \| tree
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