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2016-05-13	Jim Procter	JAL-2103 propagate inserts only used for reconstructing...	commit \| commitdiff \| tree
2016-05-13	Jim Procter	JAL-2103 always remove gaps from input sequence, then...	commit \| commitdiff \| tree
2016-05-12	Jim Procter	JAL-2103 patch routine for inserting gaps for hidden...	commit \| commitdiff \| tree
2016-05-12	Jim Procter	JAL-2103 typo and more explicit javadoc	commit \| commitdiff \| tree
2016-05-12	Jim Procter	JAL-2103 fix test	commit \| commitdiff \| tree
2016-05-12	Jim Procter	JAL-2103 fallback to returning trimmed profile if full...	commit \| commitdiff \| tree
2016-05-12	Jim Procter	JAL-2103 - refactored msa transformation routines and...	commit \| commitdiff \| tree
2016-05-10	Jim Procter	JAL-2103 don’t get full-width alignment if MSA based...	commit \| commitdiff \| tree
2016-05-10	Jim Procter	JAL-2103 extracted result processing code to allow...	commit \| commitdiff \| tree
2016-05-10	Jim Procter	JAL-2103 reinstate legacy behaviour (when full_MSA...	commit \| commitdiff \| tree
2016-05-10	Jim Procter	JAL-2103 proof of concept - patch to retrieve full...	commit \| commitdiff \| tree
2016-05-10	Jim Procter	JAL-1551 formatting	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	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
2016-04-25	Jim Procter	JAL-2074 switch to non-indy groovy to see if class...	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-1551 JAL-2077 formatting	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2077 - reinstate popups on osx	commit \| commitdiff \| tree
2016-04-24	Jim Procter	Merge branch 'JAL-2075_features_hiddeng' into develop	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2075 test showing hidden columns bug in feature...	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2075 refactor FeatureScoreModel to native testNG...	commit \| commitdiff \| tree
2016-04-24	Jim Procter	JAL-2075 make GroovyConsole a singleton so tests requiring...	commit \| commitdiff \| tree
2016-04-23	Jim Procter	JAL-2075 fix: use AlignmentView.getVisibleContigs and...	commit \| commitdiff \| tree
2016-04-23	Jim Procter	JAL-2075 findPosition for SeqCigar (with test)	commit \| commitdiff \| tree
2016-04-23	Jim Procter	JAL-2075 formatting	commit \| commitdiff \| tree
2016-04-20	Jim Procter	Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into...	commit \| commitdiff \| tree
2016-04-20	Jim Procter	JAL-2074 updated URLs and removed 'how to get groovy...	commit \| commitdiff \| tree
2016-04-20	Jim Procter	JAL-2074 updated groovy-all to 2.4.6-indy	commit \| commitdiff \| tree
2016-04-20	Jim Procter	fix for JAL-2072	commit \| commitdiff \| tree
2016-04-13	Jim Procter	JAL-2046 fix: patched SeqsetUtils so sequence features...	commit \| commitdiff \| tree
2016-04-13	Jim Procter	JAL-2046 test to demonstrate feature duplication bug	commit \| commitdiff \| tree
2016-04-13	Jim Procter	Merge branch 'bug/JAL-2046_ds_sharing_features_broken...	commit \| commitdiff \| tree
2016-04-08	Jim Procter	Merge branch 'feature/JAL-2050_intronhidden' into develop	commit \| commitdiff \| tree
2016-04-08	Jim Procter	JAL-2050 JAL-1722 new getSelectedRange() method to...	commit \| commitdiff \| tree
2016-04-08	Jim Procter	JAL-2053 fix erratic hidden column marker display	commit \| commitdiff \| tree
2016-04-08	Jim Procter	JAL-2053 JAL-1551 javadoc and simpler code	commit \| commitdiff \| tree
2016-04-07	Jim Procter	JAL-1722 fix: don’t draw visible regions outside viewport...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 RFC about cyclic dataset sequence references...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 revise test for ambiguous case	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 ambiguous test for addSequenceFeature when...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 RFC on addSequenceFeature behaviour after...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 test behaviour of copy constructor in different...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 add/delete SequenceFeature operate on dataset...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 setSequenceFeature contract implementation...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 explicit contract for get/set SequenceFeatures...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 remove javadoc	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 simpler deriveSequence - promote to dataset...	commit \| commitdiff \| tree
2016-04-05	Jim Procter	JAL-2046 clarify contract for copy constructor and...	commit \| commitdiff \| tree
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