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2009-08-21	jprocter	viewport setting for displaying sequence logos	commit \| commitdiff \| tree
2009-08-21	jprocter	reversed order of addition of group consensus and conservation	commit \| commitdiff \| tree
2009-08-21	jprocter	prototype make groups from selection function and shift...	commit \| commitdiff \| tree
2009-08-21	jprocter	prototype make groups from selection function	commit \| commitdiff \| tree
2009-08-21	jprocter	new sortbyPID for specific start/end region	commit \| commitdiff \| tree
2009-08-21	jprocter	race condition null pointer bugfix	commit \| commitdiff \| tree
2009-08-21	jprocter	bugfix	commit \| commitdiff \| tree
2009-08-21	jprocter	todo for 2.5	commit \| commitdiff \| tree
2009-08-21	jprocter	null pointer exception bug fix	commit \| commitdiff \| tree
2009-08-21	jprocter	commented debug lines indicating calculation progress	commit \| commitdiff \| tree
2009-08-21	jprocter	start/stop for per-group consensus calculation	commit \| commitdiff \| tree
2009-08-21	jprocter	store symbol profile and extract it for display	commit \| commitdiff \| tree
2009-08-21	jprocter	pir format ambiguity and todo regarding 'format override...	commit \| commitdiff \| tree
2009-08-21	jprocter	basic implementation of profile display and todos	commit \| commitdiff \| tree
2009-08-21	jprocter	todo	commit \| commitdiff \| tree
2009-08-21	jprocter	routines for creating groups over an alignment	commit \| commitdiff \| tree
2009-08-21	jprocter	asparagine is polar but not charged	commit \| commitdiff \| tree
2009-08-03	jprocter	fix feature creation for selected region beyond end...	commit \| commitdiff \| tree
2009-07-24	jprocter	explicitly grab all permissions for application execution...	commit \| commitdiff \| tree
2009-07-24	jprocter	update annotation when group state is changed	commit \| commitdiff \| tree
2009-07-24	jprocter	show group annotation menu entries	commit \| commitdiff \| tree
2009-07-24	jprocter	colour by label prototype flag	commit \| commitdiff \| tree
2009-07-24	jprocter	catch null pointer exception in headless context	commit \| commitdiff \| tree
2009-07-24	jprocter	get consensus sequence and set ignore gaps flag for...	commit \| commitdiff \| tree
2009-07-24	jprocter	annotation update method synchronises group annotation	commit \| commitdiff \| tree
2009-07-24	jprocter	headless warning messages, prototype group annotation...	commit \| commitdiff \| tree
2009-07-24	jprocter	refactored conservation thread, added showgroupannotation...	commit \| commitdiff \| tree
2009-07-24	jprocter	conservation thread refactored from AlignViewport	commit \| commitdiff \| tree
2009-07-24	jprocter	feature colour by label flag/style	commit \| commitdiff \| tree
2009-07-24	jprocter	headless test	commit \| commitdiff \| tree
2009-07-24	jprocter	todo	commit \| commitdiff \| tree
2009-07-24	jprocter	implement new insert annotation row method and ensure...	commit \| commitdiff \| tree
2009-07-24	jprocter	insert annotation at specific position	commit \| commitdiff \| tree
2009-07-24	jprocter	optional sequencegroup ref for annotation row	commit \| commitdiff \| tree
2009-07-24	jprocter	sequence groups carry their own conservation and consensus...	commit \| commitdiff \| tree
2009-07-24	jprocter	complete alignment annotation row procedure	commit \| commitdiff \| tree
2009-06-24	jprocter	ensure annotation row height is honoured for new VAMSAS...	commit \| commitdiff \| tree
2009-06-24	jprocter	all alignment sequences associated with a dataset sequence...	commit \| commitdiff \| tree
2009-06-24	jprocter	can use whitespace, comma or semicolon to separate IDs	commit \| commitdiff \| tree
2009-06-24	jprocter	fix to cope with EMBL records containing a CDS fragment...	commit \| commitdiff \| tree
2009-06-24	jprocter	take the average of the three consecutive codon sites...	commit \| commitdiff \| tree
2009-06-19	jprocter	implementation error warning todo	commit \| commitdiff \| tree
2009-06-19	jprocter	debug and cyclefix for dbrefs with embedded sequences	commit \| commitdiff \| tree
2009-06-19	jprocter	javadoc and datastoreitem registry support for binding...	commit \| commitdiff \| tree
2009-06-19	jprocter	more efficient synchronized methods	commit \| commitdiff \| tree
2009-06-19	jprocter	bugfix mapped reference transfer and made picr ID retrieval...	commit \| commitdiff \| tree
2009-06-19	jprocter	selection handler and sender bugfix	commit \| commitdiff \| tree
2009-06-19	jprocter	todo	commit \| commitdiff \| tree
2009-06-19	jprocter	selections sent when mouse is released (drags on ID...	commit \| commitdiff \| tree
2009-06-19	jprocter	progress bars (still need to be threaded properly)...	commit \| commitdiff \| tree
2009-06-19	jprocter	smoother scroll-to-position action	commit \| commitdiff \| tree
2009-06-19	jprocter	drag'n'drop a URL on to an alignment	commit \| commitdiff \| tree
2009-06-19	jprocter	parent db references and mappings added to retrieved...	commit \| commitdiff \| tree
2009-06-19	jprocter	intersect did not intersect (used in selection listener)	commit \| commitdiff \| tree
2009-06-19	jprocter	regex validator for uniprot	commit \| commitdiff \| tree
2009-06-19	jprocter	usepicr config property	commit \| commitdiff \| tree
2009-06-19	jprocter	debug	commit \| commitdiff \| tree
2009-06-19	jprocter	debug comments	commit \| commitdiff \| tree
2009-06-19	jprocter	new coverage comparison - no test case in main method yet	commit \| commitdiff \| tree
2009-06-12	jprocter	updated Iclientfactory interface, XMl viewer tests...	commit \| commitdiff \| tree
2009-06-12	jprocter	synching of all db references and sequence features	commit \| commitdiff \| tree
2009-06-12	jprocter	prevent dbref->map->to->datasetsequence->dbref-> type...	commit \| commitdiff \| tree
2009-06-12	jprocter	reinstate links on features	commit \| commitdiff \| tree
2009-06-12	jprocter	datastore registration and class cast exception fix	commit \| commitdiff \| tree
2009-06-12	jprocter	prevent and keep track of which objects handling element...	commit \| commitdiff \| tree
2009-06-12	jprocter	numerous bugfixs (tree panel synchs) and DatastoreRegistry...	commit \| commitdiff \| tree
2009-06-12	jprocter	methods for importing anonymous vamsas documents into...	commit \| commitdiff \| tree
2009-06-12	jprocter	nullpointer bugfix (possibly not needed - was an error...	commit \| commitdiff \| tree
2009-06-12	jprocter	recover pdb from jalview-xml in vamsas doc	commit \| commitdiff \| tree
2009-06-12	jprocter	send selection on drag over sequence ids	commit \| commitdiff \| tree
2009-06-12	jprocter	retrieve and init vamsas session from vdoc at URL	commit \| commitdiff \| tree
2009-06-12	jprocter	reinstated blind querying of datasources. Transfer...	commit \| commitdiff \| tree
2009-06-12	jprocter	more ID validation	commit \| commitdiff \| tree
2009-06-12	jprocter	javadoc	commit \| commitdiff \| tree
2009-06-10	jprocter	com.boxysystems.jgogleanalytics is now an optional...	commit \| commitdiff \| tree
2009-06-09	jprocter	fix null pointer when new view is created then closed...	commit \| commitdiff \| tree
2009-06-09	jprocter	fix null pointer when new view created on alignment...	commit \| commitdiff \| tree
2009-06-08	jprocter	use structured UA naming for googleanalytics client	commit \| commitdiff \| tree
2009-06-08	jprocter	upgrade to simple vamsas client version 0.2 (not runtime...	commit \| commitdiff \| tree
2009-06-08	jprocter	trial of jGA with proper useragent info	commit \| commitdiff \| tree
2009-06-08	jprocter	experimental use of picr apply gpl development license	commit \| commitdiff \| tree
2009-06-08	jprocter	clargs documentation, new vamsas session import and...	commit \| commitdiff \| tree
2009-06-08	jprocter	refactored public methods for non-interactive import...	commit \| commitdiff \| tree
2009-06-08	jprocter	refactored for non-interactive import and initiation...	commit \| commitdiff \| tree
2009-06-08	jprocter	sequence scores only shown if they vary. shift stops...	commit \| commitdiff \| tree
2009-06-08	jprocter	debug messages and graceful recovery when structure...	commit \| commitdiff \| tree
2009-06-08	jprocter	better thread safety for tooltip. apply gpl development...	commit \| commitdiff \| tree
2009-06-08	jprocter	ensure listeners are deregistered when panel is closed...	commit \| commitdiff \| tree
2009-06-08	jprocter	ensure listeners are deregistered when panel is closed...	commit \| commitdiff \| tree
2009-06-08	jprocter	ga tracker option and apply gpl development license	commit \| commitdiff \| tree
2009-06-08	jprocter	apply gpl development license	commit \| commitdiff \| tree
2009-06-08	jprocter	minor optimization. apply gpl development license	commit \| commitdiff \| tree
2009-06-08	jprocter	patch for wierd format header lines and apply gpl developmen...	commit \| commitdiff \| tree
2009-06-08	jprocter	ga in 2.4.0b2 release	commit \| commitdiff \| tree
2009-06-08	jprocter	nousagestats cli	commit \| commitdiff \| tree
2009-06-08	jprocter	apply gpl development license and new donotobfuscate...	commit \| commitdiff \| tree
2009-06-04	jprocter	full reference added.	commit \| commitdiff \| tree
2009-06-04	jprocter	spelling	commit \| commitdiff \| tree
2009-06-04	jprocter	script goes at beginning of body to allow linkthrus...	commit \| commitdiff \| tree
2009-06-02	jprocter	update minor version of release branch	commit \| commitdiff \| tree
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