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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
2005-06-14	jprocter	removes jarsign.	commit \| commitdiff \| tree
2005-06-14	jprocter	help file bits.	commit \| commitdiff \| tree
2005-06-14	jprocter	pad-1 gaps fixed.	commit \| commitdiff \| tree
2005-06-14	jprocter	slight modification to srs query so it takes both uniprot...	commit \| commitdiff \| tree
2005-06-14	jprocter	Arbitrary decision to keep friendly id name when reading...	commit \| commitdiff \| tree
2005-06-13	jprocter	null pointer fix.	commit \| commitdiff \| tree
2005-06-10	jprocter	added logs.Castor.level	commit \| commitdiff \| tree
2005-06-10	jprocter	added castor logger configuration.	commit \| commitdiff \| tree
2005-06-10	jprocter	removed exception name from server error state (to...	commit \| commitdiff \| tree
2005-06-08	jprocter	style change.	commit \| commitdiff \| tree
2005-06-08	jprocter	heading	commit \| commitdiff \| tree
2005-06-08	jprocter	punctuation (sorry ;-)	commit \| commitdiff \| tree
2005-06-08	jprocter	grammar.	commit \| commitdiff \| tree
2005-06-08	jprocter	unterminated ul	commit \| commitdiff \| tree
2005-06-08	jprocter	nicer help.	commit \| commitdiff \| tree
2005-06-07	jprocter	more truthful comment.	commit \| commitdiff \| tree
2005-06-07	jprocter	quickie build instructions.	commit \| commitdiff \| tree
2005-06-07	jprocter	very basic code convention. no licensing/stripping...	commit \| commitdiff \| tree
2005-06-07	jprocter	better code convention name	commit \| commitdiff \| tree
2005-06-07	jprocter	jalopy is used for sourcescrub target of build.xml...	commit \| commitdiff \| tree
2005-06-07	jprocter	removed signature for this jar	commit \| commitdiff \| tree
2005-06-07	jprocter	loads of changes. Jalopy source formatting, better...	commit \| commitdiff \| tree
2005-06-07	jprocter	added a couple of debug statements for unix browser...	commit \| commitdiff \| tree
2005-06-05	jprocter	made error for browser configuration on unix a bit...	commit \| commitdiff \| tree
2005-06-05	jprocter	firefox now default for unixen.	commit \| commitdiff \| tree
2005-06-05	jprocter	more subtle rearrangements	commit \| commitdiff \| tree
2005-06-03	jprocter	Reinstated 'create tree from selected region only'...	commit \| commitdiff \| tree
2005-06-02	jprocter	tidied the exceptions and ws server error behaviour	commit \| commitdiff \| tree
2005-06-02	jprocter	minor changes to make jalopy happy	commit \| commitdiff \| tree
2005-06-02	jprocter	minor changes to try and make jalopy happy	commit \| commitdiff \| tree
2005-05-31	jprocter	Moved comment so it doesn't break jalopy (this is not...	commit \| commitdiff \| tree
2005-05-30	jprocter	added the sorting entry to calculations, and corrected...	commit \| commitdiff \| tree
2005-05-30	jprocter	Changed sortByPID to use the gapped PID function.	commit \| commitdiff \| tree
2005-05-30	jprocter	comments	commit \| commitdiff \| tree
2005-05-30	jprocter	Added clustalW 'realignment' (primitive)	commit \| commitdiff \| tree
2005-05-30	jprocter	added default ClustalWS or MuscleWS to remove gaps.	commit \| commitdiff \| tree
2005-05-30	jprocter	propagated use of jalview.util.GapChars for gap removal.	commit \| commitdiff \| tree
2005-05-30	jprocter	more robust parsing for DBset/DBname\|id1\|id2 type ids	commit \| commitdiff \| tree
2005-05-30	jprocter	modified history for redundancy removal.	commit \| commitdiff \| tree
2005-05-30	jprocter	fixed stacktrace potential for pairwise alignment action.	commit \| commitdiff \| tree
2005-05-30	jprocter	Modified output on stdout for similarity matrix.	commit \| commitdiff \| tree
2005-05-27	jprocter	fixed brain interruption bug.	commit \| commitdiff \| tree
2005-05-27	jprocter	right ordering for RedundancyPanel constructor	commit \| commitdiff \| tree
2005-05-27	jprocter	added proper state check for failedJob flag.	commit \| commitdiff \| tree
2005-05-27	jprocter	Added jobFail state	commit \| commitdiff \| tree
2005-05-27	jprocter	better recognition of MSF files.	commit \| commitdiff \| tree
2005-05-27	jprocter	Added nicer header formatting for MSFfile output.	commit \| commitdiff \| tree
2005-05-27	jprocter	recovered changes from v 1.84	commit \| commitdiff \| tree
2005-05-27	jprocter	Jpredfile now uses the PileUpfile io class.	commit \| commitdiff \| tree
2005-05-27	jprocter	Addred GapChar string for convenient regex construction	commit \| commitdiff \| tree
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