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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
2016-06-20	Jim Procter	JAL-1369 updated project schema - flag on JSeq to mark...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1369 failing test	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1989 JAL-1011 release notes	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2086 JAL-2085 release notes	commit \| commitdiff \| tree
2016-06-20	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2065 release notes	commit \| commitdiff \| tree
2016-06-20	Jim Procter	Merge branch 'bugs/JAL-2065' into develop	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2065 port patch to applet	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1551 tidy	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1551 tidy	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2065 don’t pass stale group reference	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2068 avoid ArrayIndexOutOfBounds when consensus...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2065 check position lies within group before getting...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	Merge branch 'r291_docs' into develop	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1812 groovy always present	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1812 release notes	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1812 documentation TBC for AlignFrame->Calculate...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2089 typo	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-1868 fix typo in test data.	commit \| commitdiff \| tree
2016-06-20	Jim Procter	Merge branch 'features/JAL-1812_JAL-2083_groovyBinding...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	Merge branch 'develop' into features/JAL-1812_JAL-2083_groov...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2110 pass dataset to makeCDSalignment	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2110 catch case when updateDBRef argument has null...	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2110 List now used for AlignCodonFrame references	commit \| commitdiff \| tree
2016-06-20	Jim Procter	JAL-2110 copy alcodonframes only if copy constructor...	commit \| commitdiff \| tree
2016-06-19	Jim Procter	JAL-2110 distinct alignedcodonframe entries for tests	commit \| commitdiff \| tree
2016-06-19	Jim Procter	JAL-2110 test alcodonframes must be distinct	commit \| commitdiff \| tree
2016-06-19	Jim Procter	JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...	commit \| commitdiff \| tree
2016-06-16	Jim Procter	tests for validating start-end number/sequence length...	commit \| commitdiff \| tree
2016-06-16	Jim Procter	JAL-2110 todo - select mappings involving sequences...	commit \| commitdiff \| tree
2016-06-16	Jim Procter	JAL-2110 change test for desired behaviour of getCodonFrame()	commit \| commitdiff \| tree
2016-06-16	Jim Procter	JAL-2110 equals and hashcode should check fromSeq	commit \| commitdiff \| tree
2016-06-16	Jim Procter	JAL-2110 throw implementation error if not given a...	commit \| commitdiff \| tree
2016-06-16	Jim Procter	JAL-2110 typo caused infinite loop	commit \| commitdiff \| tree
2016-06-15	Jim Procter	Merge branch 'develop' into features/JAL-2110_crossRefDuplic...	commit \| commitdiff \| tree
2016-06-10	Jim Procter	Merge branch 'r291_docs' into develop	commit \| commitdiff \| tree
2016-06-10	Jim Procter	JAL-2089 docs for June 10th	commit \| commitdiff \| tree
2016-06-10	Jim Procter	JAL-2089 signed off bug release notes	commit \| commitdiff \| tree
2016-06-10	Jim Procter	JAL-1941 remove improper test tag from Annotate3D test...	commit \| commitdiff \| tree
2016-06-10	Jim Procter	JAL-2089 documenting for 8th june RC1	commit \| commitdiff \| tree
2016-06-10	Jim Procter	JAL-1941 added test URL and notes about PyRNA restclient	commit \| commitdiff \| tree
2016-06-10	Jim Procter	JAL-1941 Annotate3d tests should be in network group	commit \| commitdiff \| tree
2016-06-02	Jim Procter	JAL-2125 remove SHA256 digest manifest and signatures...	commit \| commitdiff \| tree
2016-06-02	Jim Procter	JAL-2125 remove SHA256 digest manifest and signatures...	commit \| commitdiff \| tree
2016-06-01	Jim Procter	Merge branch 'testfix/JAL-2038' into develop	commit \| commitdiff \| tree
2016-06-01	Jim Procter	JAL-2038 fix tests for case insensitive eSequenceIdMatcher	commit \| commitdiff \| tree
2016-06-01	Jim Procter	JAL-2038 ensure bare Strings are lowercased before...	commit \| commitdiff \| tree
2016-06-01	Jim Procter	Merge branch 'apifix/JAL-1926_JAL-2106' into develop	commit \| commitdiff \| tree
2016-06-01	Jim Procter	fix build	commit \| commitdiff \| tree
2016-05-31	Jim Procter	Merge branch 'apifix/JAL-1926_JAL-2106' into develop	commit \| commitdiff \| tree
2016-05-31	Jim Procter	JAL-1551 JAL-2106 javadoc	commit \| commitdiff \| tree
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