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2006-05-17	jprocter	added the jnetfile parameter to specify a JNet concise...	commit \| commitdiff \| tree
2006-05-17	jprocter	added unofficial support for concise output parsing...	commit \| commitdiff \| tree
2006-05-17	jprocter	refactored code for creating JNet annotations	commit \| commitdiff \| tree
2006-05-17	jprocter	Refactored code for creating annotation objects from...	commit \| commitdiff \| tree
2006-05-16	jprocter	added popup warning when proxy settings must be configured.	commit \| commitdiff \| tree
2006-05-12	jprocter	rearranged discoverer to dynamically update on demand	commit \| commitdiff \| tree
2006-04-10	jprocter	load features/annotations typo.	commit \| commitdiff \| tree
2006-04-10	jprocter	added note about cursor mode disabling the popup menu.	commit \| commitdiff \| tree
2006-04-10	jprocter	typo and explanation for ignore gaps in consensus	commit \| commitdiff \| tree
2006-04-10	jprocter	reworded pad gaps	commit \| commitdiff \| tree
2006-04-10	jprocter	reworded pad gaps.	commit \| commitdiff \| tree
2006-04-10	jprocter	put modellerpir in correct place!	commit \| commitdiff \| tree
2006-04-10	jprocter	updated menus and rearranged seqfeatures (again)	commit \| commitdiff \| tree
2006-04-10	jprocter	fix links to complex html (that don't display) by quoting...	commit \| commitdiff \| tree
2006-04-10	jprocter	moved Modeller/PIR description to its own home.	commit \| commitdiff \| tree
2006-04-10	jprocter	moved modellerpir to io	commit \| commitdiff \| tree
2006-04-10	jprocter	describing the Modeller/PIR output.	commit \| commitdiff \| tree
2006-04-10	jprocter	Fixed table border and updated restrictions	commit \| commitdiff \| tree
2006-04-10	jprocter	added bit about modeller/pir	commit \| commitdiff \| tree
2006-04-10	jprocter	added annotationColouring to whats new and updated...	commit \| commitdiff \| tree
2006-04-10	jprocter	extended preamble and added new heading for user defined...	commit \| commitdiff \| tree
2006-04-10	jprocter	doco	commit \| commitdiff \| tree
2006-04-10	jprocter	doco changes.	commit \| commitdiff \| tree
2006-04-10	jprocter	added 2.08 application version dialog box.	commit \| commitdiff \| tree
2006-04-10	jprocter	feature settings dialog box for jalview 2.08 application	commit \| commitdiff \| tree
2006-04-09	jprocter	doco writing.	commit \| commitdiff \| tree
2006-04-07	jprocter	added full keyset for cursorMode	commit \| commitdiff \| tree
2006-04-06	jprocter	added cursorMode feature page and rearranged keystrokes...	commit \| commitdiff \| tree
2006-04-06	jprocter	removed dross, added a safety check to buildextclients...	commit \| commitdiff \| tree
2006-03-20	jprocter	added example jnlp to memory settings help	commit \| commitdiff \| tree
2006-03-20	jprocter	added link to example jnlp file	commit \| commitdiff \| tree
2006-03-20	jprocter	example jnlp file for users to edit and save locally	commit \| commitdiff \| tree
2006-03-17	jprocter	jnet method description correction.	commit \| commitdiff \| tree
2006-03-16	jprocter	added description of alignment quality scores and separated	commit \| commitdiff \| tree
2006-03-14	jprocter	methods for searching DBRef lists	commit \| commitdiff \| tree
2006-03-13	jprocter	fixes bug 0013013 but reveals lack of a 'features retrieved...	commit \| commitdiff \| tree
2006-03-13	jprocter	bug fix for 0013013	commit \| commitdiff \| tree
2006-03-01	jprocter	fixed after refactoring of SequenceFeature[] seq.getSequence...	commit \| commitdiff \| tree
2006-03-01	jprocter	propagate SearchResult object use to MCView's highlighted...	commit \| commitdiff \| tree
2006-01-12	jprocter	PIR file IO now preserves and parses Modeller style...	commit \| commitdiff \| tree
2006-01-12	jprocter	DBRefEntry made for sequences retrieved from the PDB	commit \| commitdiff \| tree
2006-01-12	jprocter	<No Comment Entered>	commit \| commitdiff \| tree
2006-01-12	jprocter	ensured properties are loaded before loggers are initialised.	commit \| commitdiff \| tree
2006-01-11	jprocter	refactored Alignframe padGaps code to Alignment and...	commit \| commitdiff \| tree
2005-12-16	jprocter	Todo notes for feature issue: 0011711	commit \| commitdiff \| tree
2005-12-09	jprocter	added description of how PDB structures can be associated...	commit \| commitdiff \| tree
2005-12-09	jprocter	Rearranged 'What's new' and debugged/verified the sequence...	commit \| commitdiff \| tree
2005-12-09	jprocter	fixed pdbentry creation and multiple uniprot or pdb...	commit \| commitdiff \| tree
2005-12-08	jprocter	context dependent title for when called from desktop...	commit \| commitdiff \| tree
2005-12-08	jprocter	changed WhatsNew to a folder and modified preferences...	commit \| commitdiff \| tree
2005-12-08	jprocter	added some error checking and instruction dialogs	commit \| commitdiff \| tree
2005-12-08	jprocter	modified jnet parsing exception report string.	commit \| commitdiff \| tree
2005-12-08	jprocter	exception checks for (de)uniquify	commit \| commitdiff \| tree
2005-11-18	jprocter	Fixed bug http://dragonfly.compbio.dundee.ac.uk/mantis...	commit \| commitdiff \| tree
2005-11-18	jprocter	added 3 letter IUB codes for ambiguous residues/bases	commit \| commitdiff \| tree
2005-09-15	jprocter	Fixed so job submission and job failure errors are...	commit \| commitdiff \| tree
2005-09-05	jprocter	More informative error messages.	commit \| commitdiff \| tree
2005-08-25	jprocter	html typo	commit \| commitdiff \| tree
2005-08-25	jprocter	more informative clustal colourscheme doco.	commit \| commitdiff \| tree
2005-08-22	jprocter	jalview-dev doesn't exist.	commit \| commitdiff \| tree
2005-08-22	jprocter	regenerated stubs from wsdl and removed old vamsas...	commit \| commitdiff \| tree
2005-08-22	jprocter	regenerated from wsdl.	commit \| commitdiff \| tree
2005-08-22	jprocter	Replaced by jpred.java and associated stubs.	commit \| commitdiff \| tree
2005-08-22	jprocter	fixed hanging on job finished bug.	commit \| commitdiff \| tree
2005-08-22	jprocter	tidied client and fixed non-unique msa bug (lead to...	commit \| commitdiff \| tree
2005-08-22	jprocter	fixed uniquify seq[]	commit \| commitdiff \| tree
2005-08-22	jprocter	regenerated Jpred stubs and tidied client thread.	commit \| commitdiff \| tree
2005-08-22	jprocter	comment on WORD_SEP values	commit \| commitdiff \| tree
2005-08-18	jprocter	made changes to DEFAULT_BROWSER in user preferences...	commit \| commitdiff \| tree
2005-08-18	jprocter	changed first clicked to nearest the top of the alignment.	commit \| commitdiff \| tree
2005-08-18	jprocter	typo	commit \| commitdiff \| tree
2005-08-18	jprocter	moved to clustalw.html	commit \| commitdiff \| tree
2005-08-18	jprocter	typo fixes.	commit \| commitdiff \| tree
2005-08-18	jprocter	error checking, sanitization and properties support.	commit \| commitdiff \| tree
2005-08-18	jprocter	GUI typo	commit \| commitdiff \| tree
2005-08-18	jprocter	typo - Muscle->JNet	commit \| commitdiff \| tree
2005-08-18	jprocter	Jpred to JNet	commit \| commitdiff \| tree
2005-08-18	jprocter	various case sensitivity bugs fixed in residue comparison...	commit \| commitdiff \| tree
2005-08-17	jprocter	Client threads for discovered web services.	commit \| commitdiff \| tree
2005-08-17	jprocter	GUI modifications for service discovery.	commit \| commitdiff \| tree
2005-08-17	jprocter	Gui Modifications for Service Discovery.	commit \| commitdiff \| tree
2005-08-17	jprocter	<No Comment Entered>	commit \| commitdiff \| tree
2005-08-17	jprocter	Maintain list of webservices and query any Service...	commit \| commitdiff \| tree
2005-08-17	jprocter	Simple Registry Service stubs	commit \| commitdiff \| tree
2005-08-17	jprocter	Fixed basic name to sequence ID matching (bug http...	commit \| commitdiff \| tree
2005-08-12	jprocter	fixed leafMapping bug for Id's like SequenceX (where...	commit \| commitdiff \| tree
2005-07-11	jprocter	added help and documentation for annotation editing.	commit \| commitdiff \| tree
2005-06-16	jprocter	jalview-dev@jalview.org is the right email address?	commit \| commitdiff \| tree
2005-06-16	jprocter	renamed menu for jPred to Jnet.	commit \| commitdiff \| tree
2005-06-16	jprocter	separated alignment menu bits.	commit \| commitdiff \| tree
2005-06-16	jprocter	more doco.	commit \| commitdiff \| tree
2005-06-16	jprocter	moved clustal to clustalw	commit \| commitdiff \| tree
2005-06-16	jprocter	lots of tidying in doco.	commit \| commitdiff \| tree
2005-06-16	jprocter	better clustalw reference	commit \| commitdiff \| tree
2005-06-16	jprocter	export moved to its own file.	commit \| commitdiff \| tree
2005-06-16	jprocter	export alignment	commit \| commitdiff \| tree
2005-06-16	jprocter	feredoxin startup alignment with a tree.	commit \| commitdiff \| tree
2005-06-16	jprocter	more menu doco.	commit \| commitdiff \| tree
2005-06-15	jprocter	first jalarchive entry.	commit \| commitdiff \| tree
2005-06-14	jprocter	de-os-specificised some bits. Commented the file association...	commit \| commitdiff \| tree
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