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2008-12-15	jprocter	added (and enabled) switch to store gff source string...	commit \| commitdiff \| tree
2008-12-15	jprocter	temporary fix and note about null feature group mucking...	commit \| commitdiff \| tree
2008-12-15	jprocter	warning for failed parsing of newick strings	commit \| commitdiff \| tree
2008-12-15	jprocter	new callback handler allowing threads that request...	commit \| commitdiff \| tree
2008-12-15	jprocter	structureState element to structure view Id is a many...	commit \| commitdiff \| tree
2008-12-08	jprocter	DAS feature scores are parsed into floats on sequence...	commit \| commitdiff \| tree
2008-12-08	jprocter	output average score to stdout	commit \| commitdiff \| tree
2008-12-08	jprocter	display feature score in tooltip	commit \| commitdiff \| tree
2008-12-08	jprocter	order by feature documentation	commit \| commitdiff \| tree
2008-12-08	jprocter	experimental buttons for sort on score/density and...	commit \| commitdiff \| tree
2008-12-08	jprocter	new sort functions for ordering sequence by annotated...	commit \| commitdiff \| tree
2008-12-05	jprocter	added location of menu option and keystroke	commit \| commitdiff \| tree
2008-12-05	jprocter	support for multiple accession retrieval from a database...	commit \| commitdiff \| tree
2008-12-04	jprocter	added local das sequence source CLI and documentation	commit \| commitdiff \| tree
2008-12-04	jprocter	fetch database references for all EBI db + selected...	commit \| commitdiff \| tree
2008-12-04	jprocter	sequence fetchers generated for local das sequence...	commit \| commitdiff \| tree
2008-12-04	jprocter	das source browser uses local source method from jalview...	commit \| commitdiff \| tree
2008-12-04	jprocter	allow sequence source to be specified as sequence:http...	commit \| commitdiff \| tree
2008-12-04	jprocter	local das source properties string constants and routine...	commit \| commitdiff \| tree
2008-12-04	jprocter	properly catch exceptions from querying server with...	commit \| commitdiff \| tree
2008-12-04	jprocter	minimise exceptions for bad uniprot ids	commit \| commitdiff \| tree
2008-12-04	jprocter	select source by implementation class	commit \| commitdiff \| tree
2008-12-04	jprocter	fix null pointer exception for sources which don't...	commit \| commitdiff \| tree
2008-12-04	jprocter	clarity of tree menu calculation widget name	commit \| commitdiff \| tree
2008-12-01	jprocter	match case switch should work for both sequence ID...	commit \| commitdiff \| tree
2008-11-12	jprocter	beginning documentation for new hidecol/hiderep and...	commit \| commitdiff \| tree
2008-11-12	jprocter	todo for documenting selection sharing	commit \| commitdiff \| tree
2008-11-12	jprocter	autoscroll option	commit \| commitdiff \| tree
2008-11-12	jprocter	new capabilities and note on 'try vamsas'	commit \| commitdiff \| tree
2008-11-12	jprocter	new features/resolved for 2.4.1.	commit \| commitdiff \| tree
2008-11-12	jprocter	refactored to propery separate addToDocument,addFromDocument...	commit \| commitdiff \| tree
2008-11-12	jprocter	new viewport IDs and jalview XML storage/sync in vamsas...	commit \| commitdiff \| tree
2008-11-12	jprocter	selection sending and receiving, autoscrolling to highlighte...	commit \| commitdiff \| tree
2008-11-12	jprocter	selection sending and receiving, autoscrolling to highlighte...	commit \| commitdiff \| tree
2008-11-12	jprocter	selection sending	commit \| commitdiff \| tree
2008-11-12	jprocter	new ID constructor and selection sending	commit \| commitdiff \| tree
2008-11-12	jprocter	new constructors for setting IDs	commit \| commitdiff \| tree
2008-11-12	jprocter	new window discovery and alignment view navigation...	commit \| commitdiff \| tree
2008-11-12	jprocter	jar inputstream provider enabling multiple jar entries...	commit \| commitdiff \| tree
2008-11-12	jprocter	automatic scrolling switch	commit \| commitdiff \| tree
2008-11-12	jprocter	updated library supporting exchange of selection messages	commit \| commitdiff \| tree
2008-11-12	jprocter	automatic scrolling option added to view	commit \| commitdiff \| tree
2008-11-12	jprocter	jdk1.2 compatibility	commit \| commitdiff \| tree
2008-11-12	jprocter	minor translation bug	commit \| commitdiff \| tree
2008-11-12	jprocter	javadoc	commit \| commitdiff \| tree
2008-11-12	jprocter	jalview XML schema update for 2.4.1 (or 2.5?) introducing...	commit \| commitdiff \| tree
2008-11-12	jprocter	new listener/sender for selection events	commit \| commitdiff \| tree
2008-11-12	jprocter	gracefully translate ambigous nucleotides as 'X'	commit \| commitdiff \| tree
2008-11-12	jprocter	bugfix to safely deal with server exception resulting...	commit \| commitdiff \| tree
2008-11-12	jprocter	added todo regarding import of GFF2 key=value attributes	commit \| commitdiff \| tree
2008-11-12	jprocter	avoid exception if search returns valid object but...	commit \| commitdiff \| tree
2008-11-12	jprocter	new copy constructor and intersect method	commit \| commitdiff \| tree
2008-11-12	jprocter	involvesSequence to check if searchResults intersect...	commit \| commitdiff \| tree
2008-11-12	jprocter	javadoc and new method to get alignment sequence index...	commit \| commitdiff \| tree
2008-11-04	jprocter	bugfix db ref retrieve routine so it removes dead query...	commit \| commitdiff \| tree
2008-11-04	jprocter	implemented embl validation properly	commit \| commitdiff \| tree
2008-11-04	jprocter	implemented embl validation properly	commit \| commitdiff \| tree
2008-11-04	jprocter	links for non-positional features	commit \| commitdiff \| tree
2008-11-04	jprocter	comment about escaping regex properly	commit \| commitdiff \| tree
2008-11-04	jprocter	optional display of database refs and non-positional...	commit \| commitdiff \| tree
2008-11-04	jprocter	optional display of database refs and non-positional...	commit \| commitdiff \| tree
2008-11-04	jprocter	beginning of implementation of new properties for hide...	commit \| commitdiff \| tree
2008-11-04	jprocter	bugfix for transfer of user defined colourscheme from...	commit \| commitdiff \| tree
2008-11-04	jprocter	application specific validIOformat method	commit \| commitdiff \| tree
2008-09-26	jprocter	added .DSA files to list of jar signatures to be removed...	commit \| commitdiff \| tree
2008-09-24	jprocter	fixed sequence associated annotation reading bug where...	commit \| commitdiff \| tree
2008-09-16	jprocter	added bugfix note for 2.4	commit \| commitdiff \| tree
2008-09-16	jprocter	java 1.1 compatibility	commit \| commitdiff \| tree
2008-09-16	jprocter	fix exception raised when JNet concise files with no...	commit \| commitdiff \| tree
2008-09-09	jprocter	links associated with non-positional features do not...	commit \| commitdiff \| tree
2008-09-09	jprocter	show non-positional features with same code as positonal...	commit \| commitdiff \| tree
2008-09-09	jprocter	refactored feature tooltip generation code to static...	commit \| commitdiff \| tree
2008-09-09	jprocter	non-positional features are displayed with additional...	commit \| commitdiff \| tree
2008-09-09	jprocter	tooltip contains non-positional features and popup...	commit \| commitdiff \| tree
2008-09-09	jprocter	make URL links from description string when link is...	commit \| commitdiff \| tree
2008-09-08	jprocter	view settings in view submenu and user preferences...	commit \| commitdiff \| tree
2008-09-08	jprocter	introduced and commented out code for generating URLs...	commit \| commitdiff \| tree
2008-09-04	jprocter	release property includes -b or -t to indicate what...	commit \| commitdiff \| tree
2008-09-04	jprocter	merge from 2_4_Release branch	commit \| commitdiff \| tree
2008-08-27	jprocter	no newline after licence comment	commit \| commitdiff \| tree
2008-08-27	jprocter	added Release_2_4_branch	commit \| commitdiff \| tree
2008-08-27	jprocter	fix vamas homedir link	commit \| commitdiff \| tree
2008-08-27	jprocter	added keystore config properties	commit \| commitdiff \| tree
2008-08-26	jprocter	update and test release build system	commit \| commitdiff \| tree
2008-08-26	jprocter	2.4 release documentation update menus, service refs...	commit \| commitdiff \| tree
2008-08-26	jprocter	update Jpred3 service referenec	commit \| commitdiff \| tree
2008-08-26	jprocter	allow '\|' to be entered in URL text box and added regex...	commit \| commitdiff \| tree
2008-08-26	jprocter	set title of viewer frame after file has been loaded...	commit \| commitdiff \| tree
2008-08-26	jprocter	future bug fix todo	commit \| commitdiff \| tree
2008-08-26	jprocter	new thread for initting of DBRefFetcher with latest...	commit \| commitdiff \| tree
2008-08-26	jprocter	uses shared singleton from jalview.gui.SequenceFetcher...	commit \| commitdiff \| tree
2008-08-26	jprocter	added singleton access method to retrieve the latest...	commit \| commitdiff \| tree
2008-08-26	jprocter	bugfix todo for the 'edit sequence' command	commit \| commitdiff \| tree
2008-08-26	jprocter	tooltip for fetch db refs and more generic regex for...	commit \| commitdiff \| tree
2008-08-26	jprocter	pdb xrefs added as dbrefs and as PDB file links	commit \| commitdiff \| tree
2008-08-26	jprocter	ensure successive matches to a regex have distinct...	commit \| commitdiff \| tree
2008-08-20	jprocter	Use 0f rather than NaN to specify non-valued annotation...	commit \| commitdiff \| tree
2008-08-20	jprocter	tooltip displays formatted annotation row description...	commit \| commitdiff \| tree
2008-08-19	jprocter	beginning of fix for embl/cds/highlighting IO in https...	commit \| commitdiff \| tree
2008-08-19	jprocter	fix for arrayoutofbounds bug when secondary structure...	commit \| commitdiff \| tree
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