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2011-07-28	jprocter	refer to local default setting for proxy when connecting to	commit \| commitdiff \| tree
2011-07-28	jprocter	added 'since 2.x notes to parameters'. User configurable...	commit \| commitdiff \| tree
2011-07-26	jprocter	example alignment for JAL-862 - removed signal peptides	commit \| commitdiff \| tree
2011-07-25	jprocter	use proper encoding for storing colour as user preference...	commit \| commitdiff \| tree
2011-07-22	jprocter	todo for JAL-860 - associate multiple sequences with...	commit \| commitdiff \| tree
2011-07-22	jprocter	applet min/max annotation shading parameter documentation...	commit \| commitdiff \| tree
2011-07-22	jprocter	ensure propagation of colour change on annotation update...	commit \| commitdiff \| tree
2011-07-22	jprocter	fix NPE when annotation colourgradient is applied	commit \| commitdiff \| tree
2011-07-22	jprocter	code style	commit \| commitdiff \| tree
2011-07-22	jprocter	default parameter for colours in annotation shading...	commit \| commitdiff \| tree
2011-07-22	jprocter	method to get a user default colour (JAL-234)	commit \| commitdiff \| tree
2011-07-21	jprocter	retrieve all sequences matching a particular name ...	commit \| commitdiff \| tree
2011-07-21	jprocter	local instance of deployJava script from Sun/Oracle	commit \| commitdiff \| tree
2011-07-21	jprocter	refined applet example on examples page	commit \| commitdiff \| tree
2011-07-21	jprocter	better layout and structure display on startup	commit \| commitdiff \| tree
2011-07-21	jprocter	ensure contents of hash is extended JAL-876	commit \| commitdiff \| tree
2011-07-18	jprocter	fixed mouseover problem - still need to deal with flickering...	commit \| commitdiff \| tree
2011-07-10	jprocter	progress when saving state (JAL-870) and hack to trap...	commit \| commitdiff \| tree
2011-07-09	jprocter	documentation for menu item JAL-860	commit \| commitdiff \| tree
2011-07-09	jprocter	menu item and constructor to open a bunch of structures...	commit \| commitdiff \| tree
2011-07-09	jprocter	refactored from PopupMenu (for JAL-860)	commit \| commitdiff \| tree
2011-07-09	jprocter	todo re JAL-732	commit \| commitdiff \| tree
2011-07-09	jprocter	JAL-868 todo	commit \| commitdiff \| tree
2011-07-08	jprocter	open each query result from an alignment datasource...	commit \| commitdiff \| tree
2011-07-07	jprocter	comment re JAL-153	commit \| commitdiff \| tree
2011-07-07	jprocter	Set job title correctly and pass reason why	commit \| commitdiff \| tree
2011-07-07	jprocter	extract sequence from DNA bases like 'DG' (JAL-866)	commit \| commitdiff \| tree
2011-07-06	jprocter	ensure selseq is trimmed to just sequences included...	commit \| commitdiff \| tree
2011-07-05	jprocter	Revert "partial patch for JAL-411 - text rendered above...	commit \| commitdiff \| tree
2011-07-05	jprocter	partial patch for JAL-411 - text rendered above features	commit \| commitdiff \| tree
2011-07-05	jprocter	ensure javascript and jmol example directories are...	commit \| commitdiff \| tree
2011-07-05	jprocter	Merge branch 'master' of https://source.jalview.org...	commit \| commitdiff \| tree
2011-07-05	jprocter	Revert "Revert "needed for linkedapplets_ng.html (JAL...	commit \| commitdiff \| tree
2011-07-05	jprocter	Revert "needed for linkedapplets_ng.html (JAL-859,JAL...	commit \| commitdiff \| tree
2011-07-05	jprocter	needed for linkedapplets_ng.html (JAL-859,JAL-469)	commit \| commitdiff \| tree
2011-07-05	jprocter	whole frame should be validated.	commit \| commitdiff \| tree
2011-07-05	jprocter	ignore any events after manager has already been finalized.	commit \| commitdiff \| tree
2011-07-05	jprocter	refactor to send list of model filenames involved in...	commit \| commitdiff \| tree
2011-07-05	jprocter	(JAL-856,JAL-621)	commit \| commitdiff \| tree
2011-07-05	jprocter	new and restructured javascript examples and documentation...	commit \| commitdiff \| tree
2011-07-04	jprocter	jmb isn't created yet, so use another SSM provider	commit \| commitdiff \| tree
2011-07-03	jprocter	TODO re JAL-433 - filter events if alignFrame is specified...	commit \| commitdiff \| tree
2011-07-03	jprocter	documentation (JAL-859, JAL-816, JAL-621)	commit \| commitdiff \| tree
2011-07-03	jprocter	extracted jalviewlite API calls as separate interface...	commit \| commitdiff \| tree
2011-07-03	jprocter	groovy scripting examples (JAL-???)	commit \| commitdiff \| tree
2011-07-03	jprocter	javadoc built under dist directory for all Jalview...	commit \| commitdiff \| tree
2011-06-30	jprocter	set initial annotation panel height appropriately ...	commit \| commitdiff \| tree
2011-06-29	jprocter	standard embedded jalviewLite example (JAL-815)	commit \| commitdiff \| tree
2011-06-29	jprocter	documentation and targets for building a working applet...	commit \| commitdiff \| tree
2011-06-29	jprocter	repaint image buffer height change (JAL-564) and ensure...	commit \| commitdiff \| tree
2011-06-29	jprocter	repaint image buffer resize when panel height changes...	commit \| commitdiff \| tree
2011-06-29	jprocter	preliminary patch to reduce problem observed in JAL-546	commit \| commitdiff \| tree
2011-06-29	jprocter	ensure annotation height adjuster doesn't disappear...	commit \| commitdiff \| tree
2011-06-28	jprocter	fixes JAL-849 - double check after waiting a bit that...	commit \| commitdiff \| tree
2011-06-26	jprocter	reinstated valid XML content : additional for JAL-775	commit \| commitdiff \| tree
2011-06-26	jprocter	basic Netbeans project files and enriched build documentatio...	commit \| commitdiff \| tree
2011-06-24	jprocter	fix to preserve sequence numbering in MSF (JAL-847)	commit \| commitdiff \| tree
2011-06-23	jprocter	jmb isn't created yet, so use another SSM provider	commit \| commitdiff \| tree
2011-06-23	jprocter	patch for JAL-846 made targetChain mapping constraint...	commit \| commitdiff \| tree
2011-05-30	jprocter	bug for clients using NJTree directly - pwtype should...	commit \| commitdiff \| tree
2011-05-30	jprocter	first patch for JAL-838 - allow new typed of PID calcs	commit \| commitdiff \| tree
2011-05-19	jprocter	example applet and desktop application files that should...	commit \| commitdiff \| tree
2011-05-19	jprocter	example applet and desktop application files that should...	commit \| commitdiff \| tree
2011-05-19	jprocter	Revert "just a test"	commit \| commitdiff \| tree
2011-05-18	jprocter	just a test	commit \| commitdiff \| tree
2011-05-17	jprocter	refactor to allow distinct StructureSelectionManager...	commit \| commitdiff \| tree
2011-05-17	jprocter	interface for objects at root of a jalview session's	commit \| commitdiff \| tree
2011-05-17	jprocter	interface for handlers of alignmentViewPanel events	commit \| commitdiff \| tree
2011-05-17	jprocter	cruisecontrol again	commit \| commitdiff \| tree
2011-05-17	jprocter	another cc test	commit \| commitdiff \| tree
2011-05-17	jprocter	Merge branch 'master' of https://source.jalview.org...	commit \| commitdiff \| tree
2011-05-17	jprocter	test cruisecontrol	commit \| commitdiff \| tree
2011-05-17	jprocter	test cruisecontrol	commit \| commitdiff \| tree
2011-05-17	jprocter	ensure all colour statements added to string set	commit \| commitdiff \| tree
2011-05-05	jprocter	uncommentable debug message for JAL-771	commit \| commitdiff \| tree
2011-05-05	jprocter	html tags	commit \| commitdiff \| tree
2011-05-05	jprocter	improved javascript callback execution thread and provided...	commit \| commitdiff \| tree
2011-05-05	jprocter	separation of jmol script command generation from jmol...	commit \| commitdiff \| tree
2011-05-05	jprocter	javadoc and informative error message when external...	commit \| commitdiff \| tree
2011-05-05	jprocter	ensure feature renderer settings come from the given...	commit \| commitdiff \| tree
2011-05-05	jprocter	added simple stdout debug function	commit \| commitdiff \| tree
2011-04-25	jprocter	JAL-824 - additional methods to allow jmol colouring...	commit \| commitdiff \| tree
2011-04-25	jprocter	JAL-824 - patch to schema to allow jmol colouring state...	commit \| commitdiff \| tree
2011-04-25	jprocter	toggle of inclusion/exclusion of views for colouring...	commit \| commitdiff \| tree
2011-04-25	jprocter	JAL-824 - ensure Jmol colouring is a radio button	commit \| commitdiff \| tree
2011-04-25	jprocter	documentation for JAL-824 and JAL-621	commit \| commitdiff \| tree
2011-04-25	jprocter	documentation for JAL-732	commit \| commitdiff \| tree
2011-04-25	jprocter	htmlfix	commit \| commitdiff \| tree
2011-04-22	jprocter	formatting	commit \| commitdiff \| tree
2011-04-22	jprocter	removed useless flag (was always null for button press...	commit \| commitdiff \| tree
2011-04-22	jprocter	JAL-823 and JAL-824 - seqColour no longer the default...	commit \| commitdiff \| tree
2011-04-22	jprocter	comments re JAL-823 legacy issue	commit \| commitdiff \| tree
2011-04-22	jprocter	clarify tooltip	commit \| commitdiff \| tree
2011-04-22	jprocter	moved loadingFromArchive flag modification to after...	commit \| commitdiff \| tree
2011-04-22	jprocter	option for enabling Jmol colouring mode JAL-824	commit \| commitdiff \| tree
2011-04-21	jprocter	JAL-641 patch	commit \| commitdiff \| tree
2011-04-21	jprocter	patch for JAL-733	commit \| commitdiff \| tree
2011-04-21	jprocter	patch for JAL-820 and JAL-821	commit \| commitdiff \| tree
2011-04-21	jprocter	separated alignment annotation height calculation from...	commit \| commitdiff \| tree
2011-04-21	jprocter	moved to same place as in jalview.gui	commit \| commitdiff \| tree
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