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2016-08-23	Jim Procter	JAL-2154 should only add mappings between dataset sequences	commit \| commitdiff \| tree
2016-08-23	Jim Procter	JAL-2154 - only copy DBRef from contig to new CDS sequence...	commit \| commitdiff \| tree
2016-08-23	Jim Procter	Merge branch 'develop' into bug/JAL-2154projectMappings	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 - rejig test pass code for breadth-first ...	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 verify recovered xref sequence not already...	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 regression warning - should never recover...	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 always check dataset sequence for sequence...	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 patch verifyAlignment so it fails for duplicate...	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 tidy assert messages and fix test to verify...	commit \| commitdiff \| tree
2016-08-22	Jim Procter	JAL-2154 test that verifyAlignment fails for duplicate...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 - possible patch .. but leads to new stringify...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 major rejigging of test looping again	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 disable DAS sources for Jalview2XML tests	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 fix looping structure so for a particular...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 drop unused hashes	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 testNG like assertAlignmentDatasetRefs static...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 reorder the dataset sequences according to...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 belt-and-braces patch:	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 verify mapping’s sequenceI ref has been resolved...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 use right reference string for recovering...	commit \| commitdiff \| tree
2016-08-19	Jim Procter	JAL-2154 refactor setSequenceAt to replaceSequenceAt...	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 verify sequenceI/dataset refs for codonmappings	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 make sure any new sequences via DBRefEntry...	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 check alignment isn’t null before validating	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 always resolve dataset sequences when creating...	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 [test] verify reference integrity for alignment...	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 formatting	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 new assert to check reference integrity for...	commit \| commitdiff \| tree
2016-08-16	Jim Procter	JAL-2154 xref test harness - test fails if there are...	commit \| commitdiff \| tree
2016-08-13	Jim Procter	JAL-2154 refactor CrossRef UI code to its own class	commit \| commitdiff \| tree
2016-08-13	Jim Procter	JAL-2154 check if the desktop is constructed before...	commit \| commitdiff \| tree
2016-08-13	Jim Procter	JAL-2154 ignore all but the primary source resolved...	commit \| commitdiff \| tree
2016-08-13	Jim Procter	JAL-2154 make sure we wait for constructor thread to...	commit \| commitdiff \| tree
2016-08-11	Jim Procter	JAL-2154 clear the desktop before every 2xml test	commit \| commitdiff \| tree
2016-08-11	Jim Procter	JAL-2154 jalview.gui.SequenceFetcher.fetchAndShow(db...	commit \| commitdiff \| tree
2016-08-11	Jim Procter	JAL-2154 JAL-1993 relocate show dbchooser action out...	commit \| commitdiff \| tree
2016-08-11	Jim Procter	JAL-2154 refactor setup/teardown from Jalview2xml for...	commit \| commitdiff \| tree
2016-08-07	Jim Procter	JAL-2154 add in missing class for createDatasetAlignment...	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2154 make sure codon mappings between sequences...	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2154 todo	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2154 use convenience method	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2154 make sure all sequences referenced via DBRefEntry...	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2110 comment on failing test (consider skipping...	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2154 test for CDS->protein map	commit \| commitdiff \| tree
2016-08-04	Jim Procter	JAL-2046 stack trace for implementation warning	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
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