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2011-10-28	jprocter	JAL-969 - refactor initialisation of automatic annotation...	commit \| commitdiff \| tree
2011-10-28	jprocter	JAL-885 more efficient calculation and robust for mismatch...	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-885 JAL-580) ignore invalid RNA structure lines	commit \| commitdiff \| tree
2011-10-28	jprocter	JAL-902 structure conservation row for applet	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-970) interactive editing of RNA helix annotation...	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-966) efficiency	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-889) ensure annotation row is revalidated after...	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-885,JAL-580) structure consensus should only be...	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-889) ensure latest version of RNA pairlist is...	commit \| commitdiff \| tree
2011-10-28	jprocter	JAL-580 - display position where wuss parsing error...	commit \| commitdiff \| tree
2011-10-28	jprocter	JAL-580 ensure WUSS annotation string is up to date...	commit \| commitdiff \| tree
2011-10-28	jprocter	use stack rather than vector and throw parse exceptions	commit \| commitdiff \| tree
2011-10-28	jprocter	JAL-580 ensure WUSS annotation is reparsed if necessary...	commit \| commitdiff \| tree
2011-10-28	jprocter	NPE exception if annotation manually edited	commit \| commitdiff \| tree
2011-10-28	jprocter	extend API	commit \| commitdiff \| tree
2011-10-28	jprocter	refactor to use model API	commit \| commitdiff \| tree
2011-10-28	jprocter	(JAL-963) refactor RNA helix helper class to schemes	commit \| commitdiff \| tree
2011-10-27	jprocter	Merge branch 'refactor_aligcalcs' into develop	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-969) efficiency	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-969) fix logic bug introduced during refactoring	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-969) removed TODOs	commit \| commitdiff \| tree
2011-10-27	jprocter	renamed menu entry to avoid field name clash	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-969) todo test re refactoring and possible change...	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-969) refactored alignmentViewport base class to...	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-961) refactored consensus and rna structure consensus...	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-961) use simplified notification logic to test...	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-961) methods for checking calculation status	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-961) more calculation annotation and result object...	commit \| commitdiff \| tree
2011-10-27	jprocter	(JAL-967) ensure annotation panel is rendered with...	commit \| commitdiff \| tree
2011-10-21	jprocter	Refactored alignment viewport to use common base, extended...	commit \| commitdiff \| tree
2011-10-21	jprocter	new base class to hold core visualization settings...	commit \| commitdiff \| tree
2011-10-21	jprocter	todo	commit \| commitdiff \| tree
2011-10-21	jprocter	static convenience methods for constructing and calculating...	commit \| commitdiff \| tree
2011-10-21	jprocter	use List rather than Vector	commit \| commitdiff \| tree
2011-10-21	jprocter	extend alignPanel api with OOMHandler call to raise...	commit \| commitdiff \| tree
2011-10-21	jprocter	remove unnecessary import	commit \| commitdiff \| tree
2011-10-21	jprocter	Introduced new AlignCalcWorker/manager interface.	commit \| commitdiff \| tree
2011-10-21	jprocter	Merge branch 'Release_2_7_Branch_hotfix_JAL-962' into...	commit \| commitdiff \| tree
2011-10-21	jprocter	(JAL-965) new api methods to allow features to be loaded...	commit \| commitdiff \| tree
2011-10-21	jprocter	(JAL-962) rejig parameter processing order so groups...	commit \| commitdiff \| tree
2011-10-21	jprocter	(JAL-962) allow group visibility to be specified before...	commit \| commitdiff \| tree
2011-10-20	jprocter	(JAL-963) jalviewLite RNA alignment example (reusing...	commit \| commitdiff \| tree
2011-10-18	jprocter	Merge branch 'logo_feature_JAL-958' into develop	commit \| commitdiff \| tree
2011-10-18	jprocter	backout parts of the interface from another development...	commit \| commitdiff \| tree
2011-10-18	jprocter	Merge branch 'logo_feature_JAL-958' into develop	commit \| commitdiff \| tree
2011-10-18	jprocter	(Jalview 3) refactored Graphics2D annotation rendering...	commit \| commitdiff \| tree
2011-10-17	jprocter	Merge branch 'logo_feature_JAL-958' into develop	commit \| commitdiff \| tree
2011-10-17	jprocter	(ahem) new renderer package containing api and rendering...	commit \| commitdiff \| tree
2011-10-14	jprocter	Merge branch 'logo_feature_JAL-958' into develop	commit \| commitdiff \| tree
2011-10-14	jprocter	(JAL-958) documented normalised sequence logo parameter	commit \| commitdiff \| tree
2011-10-14	jprocter	(JAL-958) - normalised sequence logo for applet	commit \| commitdiff \| tree
2011-10-11	jprocter	normalised logo rendering (JAL-958)	commit \| commitdiff \| tree
2011-10-10	jprocter	(JAL-957) change splash screen and about to HTML text...	commit \| commitdiff \| tree
2011-10-10	jprocter	update author list in license for (JAL-826)	commit \| commitdiff \| tree
2011-10-07	jprocter	merge Jan and Lauren's RNA GUI changes into develop...	commit \| commitdiff \| tree
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_merge...	commit \| commitdiff \| tree
2011-10-03	jprocter	Merge branch 'Release_2_7_Branch'	commit \| commitdiff \| tree
2011-10-03	jprocter	redact previous commit - fileassociation tag not allowed...	commit \| commitdiff \| tree
2011-10-03	jprocter	removed unnecessary parameters and changed alignment...	commit \| commitdiff \| tree
2011-10-03	jprocter	compile swingreader component for java 1.5 (JAL-948)	commit \| commitdiff \| tree
2011-09-28	jprocter	Merge branch 'Release_2_7_Branch'	commit \| commitdiff \| tree
2011-09-28	jprocter	jnlps with and without file associations for default...	commit \| commitdiff \| tree
2011-09-28	jprocter	broken link. rearranged opening pg	commit \| commitdiff \| tree
2011-09-27	jprocter	typo	commit \| commitdiff \| tree
2011-09-27	jprocter	switch to git release building	commit \| commitdiff \| tree
2011-09-27	jprocter	patch name, reference and URL for Multi-Harmony : JAL-724	commit \| commitdiff \| tree
2011-09-27	jprocter	ensure server errors return a URL and response document...	commit \| commitdiff \| tree
2011-09-27	jprocter	use jalview properties preference to enable RSBS editor...	commit \| commitdiff \| tree
2011-09-27	jprocter	same overzeaolous logic (JAL-915)	commit \| commitdiff \| tree
2011-09-27	jprocter	start of Release 2.7	commit \| commitdiff \| tree
2011-09-27	jprocter	JAL-944 - replaced stale PFAM links for 2.7 release...	commit \| commitdiff \| tree
2011-09-27	jprocter	backout overzealous logic disabling feature links in...	commit \| commitdiff \| tree
2011-09-27	jprocter	NPE fix	commit \| commitdiff \| tree
2011-09-27	jprocter	apply version 2.7 copyright	commit \| commitdiff \| tree
2011-09-26	jprocter	exclude build artefacts from repository	commit \| commitdiff \| tree
2011-09-26	jprocter	updated documentation table of contents, menus and...	commit \| commitdiff \| tree
2011-09-26	jprocter	documentation for news reader (JAL-943)	commit \| commitdiff \| tree
2011-09-26	jprocter	tweak installer with IA2010 - fixes installerObjects...	commit \| commitdiff \| tree
2011-09-26	jprocter	fix jar dependency in InstallAnywhere	commit \| commitdiff \| tree
2011-09-26	jprocter	tidying classpath and fixing InstallAnywhere build	commit \| commitdiff \| tree
2011-09-26	jprocter	tweaked dialog layout. should consider refactoring	commit \| commitdiff \| tree
2011-09-26	jprocter	add new dependencies for 2.7 release	commit \| commitdiff \| tree
2011-09-26	jprocter	make news window a modal dialog on the jalview desktop...	commit \| commitdiff \| tree
2011-09-26	jprocter	avoid deprecation and ensure dialog close event is...	commit \| commitdiff \| tree
2011-09-25	jprocter	organise imports	commit \| commitdiff \| tree
2011-09-25	jprocter	more focus fixing (JAL-943)	commit \| commitdiff \| tree
2011-09-25	jprocter	fix logic to ensure first check for news is correct...	commit \| commitdiff \| tree
2011-09-23	jprocter	try even harder to get focus - for benefit of windows...	commit \| commitdiff \| tree
2011-09-23	jprocter	ensure blog window gets put to front after dialogs...	commit \| commitdiff \| tree
2011-09-23	jprocter	debugged example file again - old version had view...	commit \| commitdiff \| tree
2011-09-22	jprocter	refactor and remove excess imports (JAL-943)	commit \| commitdiff \| tree
2011-09-22	jprocter	jalview rss reader based on jswingreader (JAL-943)	commit \| commitdiff \| tree
2011-09-20	jprocter	help documentation for Jalview 2.7	commit \| commitdiff \| tree
2011-09-16	jprocter	JAL-747 - made warning message friendlier and more...	commit \| commitdiff \| tree
2011-09-16	jprocter	fix for JAL-895 - new exampleFile_2_7.jar and logic...	commit \| commitdiff \| tree
2011-09-16	jprocter	numerically ataxic comments.	commit \| commitdiff \| tree
2011-09-16	jprocter	JAL-574 added option to enable/disable 'follow selection...	commit \| commitdiff \| tree
2011-09-16	jprocter	JAL-940 - removed legacy service options from preferences...	commit \| commitdiff \| tree
2011-09-16	jprocter	JAL-468 typo and label length in dialog	commit \| commitdiff \| tree
2011-09-16	jprocter	patch for JAL-935 - warning messages raised when alignment...	commit \| commitdiff \| tree
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