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2016-06-19	Jim Procter	JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...	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
2016-05-31	Jim Procter	JAL-2110 abstract methods should never reference their...	commit \| commitdiff \| tree
2016-05-31	Jim Procter	Merge branch 'features/JAL-2113_emblXml1.2' into develop	commit \| commitdiff \| tree
2016-05-31	Jim Procter	Merge branch 'develop' into features/JAL-2113_emblXml1.2	commit \| commitdiff \| tree
2016-05-31	Jim Procter	Merge branch 'jims/291patches' into develop	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-553 JAL-1557 always send selections after triggering...	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-1557 allow group associated rows to be used to...	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-2077 release notes	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-2077 fix: convenience method and checks for CMD...	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-2089 update release date for 2.9.1	commit \| commitdiff \| tree
2016-05-30	Jim Procter	JAL-1552 fix JAL-2122 resolve File->string before adding...	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-2030 - add servlet-api-3.1.jar to installAnywhere...	commit \| commitdiff \| tree
2016-05-26	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-2121 refactor todo	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-2089 update developer doc	commit \| commitdiff \| tree
2016-05-26	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-1400 JAL-2089 allow configurable signature algorithms	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-1552 refactor shared dataflavor hander	commit \| commitdiff \| tree
2016-05-26	Jim Procter	JAL-1552 extra debug logging for dataflavor if drop...	commit \| commitdiff \| tree
2016-05-25	Jim Procter	JAL-1522 patch - try to pick best text dataflavor	commit \| commitdiff \| tree
2016-05-06	Jim Procter	Merge branch 'features/JAL-192_scalerelativetoseq'...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 fix javadoc	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 JAL-2099 unused variables	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 JAL-2099 reuse refactored scale code for wrapped...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 JAL-2099 factored out calculation from rendering...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 JAL-2099 factored out calculation from rendering...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 JAL-2099 factored out calculation from rendering...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-2100 centre triangles on hidden column vertical...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-2100 optimisation	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-2100 triangles shown below in jvdesktop unwrapped...	commit \| commitdiff \| tree
2016-05-06	Jim Procter	JAL-192 patch off-by-one for pathological gap case	commit \| commitdiff \| tree
2016-05-05	Jim Procter	JAL-192 patch for off-by one and pathological case...	commit \| commitdiff \| tree
2016-05-04	Jim Procter	Revert "JAL-2074 removed xerces to explore wierdness"	commit \| commitdiff \| tree
2016-05-03	Jim Procter	Merge branch 'r291_docs' into develop	commit \| commitdiff \| tree
2016-05-02	Jim Procter	JAL-1270 move some Network tests to External (require...	commit \| commitdiff \| tree
2016-05-02	Jim Procter	JAL-1270 capitalise test groups	commit \| commitdiff \| tree
2016-05-02	Jim Procter	JAL-2089 JAL-1551 formatting	commit \| commitdiff \| tree
2016-05-02	Jim Procter	JAL-2089 release 2.9.1 entry in release notes	commit \| commitdiff \| tree
2016-04-29	Jim Procter	Merge branch 'features/JAL-192_scalerelativetoseq'...	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-192 need visible and actual sequence limits for...	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-192 fix bounds when no hidden regions, and when...	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-192 scale origin relative to start of reference...	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-966 JAL-1553  todo: remove UI components from Column...	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-192 ‘efficiently’ locate visible bounds for a sequence...	commit \| commitdiff \| tree
2016-04-29	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2016-04-27	Jim Procter	Merge branch 'features/JAL-192_scalerelativetoseq'...	commit \| commitdiff \| tree
2016-04-27	Jim Procter	JAL-192 fix off-by-one for alignment ruler with no...	commit \| commitdiff \| tree
2016-04-27	Jim Procter	Merge branch 'features/JAL-192_scalerelativetoseq'...	commit \| commitdiff \| tree
2016-04-27	Jim Procter	JAL-192 show reference sequence position and residue...	commit \| commitdiff \| tree
2016-04-27	Jim Procter	JAL-1366 JAL-2086 reinstate bolding of reference sequence	commit \| commitdiff \| tree
2016-04-27	Jim Procter	JAL-2085 JAL-2086 fix hiddenRepSequence and new referenceSeq...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2079 fix broken cherry-pick conflict merge	commit \| commitdiff \| tree
2016-04-26	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2079 update GPL header for new Xfam tests	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2079 use new service to retrieve Rfam Seed alignment	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2084 JAL-2079 removed RFAM(Full) from Xfam Network...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2079 disable RFAM(Full) source until we can retrieve...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2079 update URL for RFAM and PFAM sources	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2079 allow prefix+<XFAMID>+suffix type URL signature	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2077 reinstate JAL-1554 fix for left-then-right...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2077 reinstate annotation label popup by handling...	commit \| commitdiff \| tree
2016-04-26	gmungoc	JAL-1981 catch any exception when setting QuaQua look...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	Merge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4	commit \| commitdiff \| tree
2016-04-26	Jim Procter	Merge branch 'bug/JAL-2080_javaws_slow_291' into develop	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2080 removed all 'Class-Path' references in libs	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2080 removed classpath references to Xerces and...	commit \| commitdiff \| tree
2016-04-26	Jim Procter	JAL-2080 mark jalview.jar as main jar resource	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 disable security manager at start up re: http...	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 removed xerces to explore wierdness	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 reinstate upgrade to groovy 2.8.4-indy	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 reinstate upgrade to groovy 2.8.4-indy	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 add the groovy 1.8.2 library back to classpath	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 backed out groovy upgrade - back to 1.8.2	commit \| commitdiff \| tree
2016-04-25	Jim Procter	JAL-2074 groovy-all didn’t get added :q	commit \| commitdiff \| tree
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