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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
2005-05-27	jprocter	Response to bug mantis?id=8187 - some quick hacks to...	commit \| commitdiff \| tree
2005-05-27	jprocter	Old MSF Format writer now renamed.	commit \| commitdiff \| tree
2005-05-26	jprocter	fixed use of PID rather than 'Comparison' Alignment...	commit \| commitdiff \| tree
2005-05-26	jprocter	fairly pointless catch exception error information...	commit \| commitdiff \| tree
2005-05-26	jprocter	fixed redundancy Undo and allowed it to work on UNALIGNED...	commit \| commitdiff \| tree
2005-05-26	jprocter	bug fix in jpred client. TreeViewer display state and...	commit \| commitdiff \| tree
2005-05-26	jprocter	partially updated help. Added separate treeviewing...	commit \| commitdiff \| tree
2005-05-25	jprocter	added jalview.browser property so a linux user can...	commit \| commitdiff \| tree
2005-05-25	jprocter	doh - compile before commit!	commit \| commitdiff \| tree
2005-05-25	jprocter	tidied up system.out messages and moved many to stderr.	commit \| commitdiff \| tree
2005-05-25	jprocter	Improved consistency between JPredWS and MsaWS	commit \| commitdiff \| tree
2005-05-25	jprocter	base class for web service clients.	commit \| commitdiff \| tree
2005-05-24	jprocter	title parameter for single sequence prediction.	commit \| commitdiff \| tree
2005-05-24	jprocter	Added more firePropertyChange calls - mainly for sequence...	commit \| commitdiff \| tree
2005-05-24	jprocter	extended the UpdatePlaceholders to check for any new...	commit \| commitdiff \| tree
2005-05-24	jprocter	added PropertyChangeListeners for alignviewport.alignment...	commit \| commitdiff \| tree
2005-05-24	jprocter	formatting.	commit \| commitdiff \| tree
2005-05-24	jprocter	slight changes.	commit \| commitdiff \| tree
2005-05-24	jprocter	added sorting alignments documentation.	commit \| commitdiff \| tree
2005-05-24	jprocter	several ordering bug fixes.	commit \| commitdiff \| tree
2005-05-23	jprocter	Added PadGaps and made treeSortMenu dynamic (it gets...	commit \| commitdiff \| tree
2005-05-23	jprocter	added some assertions and rangechecks for insert/deleteChar...	commit \| commitdiff \| tree
2005-05-23	jprocter	added getSequencesInOrder (part of refactor from AlignPanel...	commit \| commitdiff \| tree
2005-05-23	jprocter	editMenuPadGaps and sortByTree/sort items	commit \| commitdiff \| tree
2005-05-23	jprocter	fixed window title names for prediction on MSA or Sequence.	commit \| commitdiff \| tree
2005-05-23	jprocter	Ugly but improved recovery of sequence names, starts...	commit \| commitdiff \| tree
2005-05-23	jprocter	bug fix for wierdness retrieving QUERY sequence index.	commit \| commitdiff \| tree
2005-05-22	jprocter	include MsaWS ordering but not perfect (undo destroys...	commit \| commitdiff \| tree
2005-05-22	jprocter	marginal improvements - still no automated client constructor.	commit \| commitdiff \| tree
2005-05-22	jprocter	Added alignment ordering option to 'Sort by' and implemented...	commit \| commitdiff \| tree
2005-05-22	jprocter	later version of client-side WSDL2Java generated simple...	commit \| commitdiff \| tree
2005-05-20	jprocter	Semiworking generic MSA client	commit \| commitdiff \| tree
2005-05-20	jprocter	added placeholder indicators and menu item	commit \| commitdiff \| tree
2005-05-20	jprocter	Various sort methods added and bugs fixed (coping with...	commit \| commitdiff \| tree
2005-05-20	jprocter	sequence place holder reveal menu item.	commit \| commitdiff \| tree
2005-05-20	jprocter	added tree node property for sequence placeholders.	commit \| commitdiff \| tree
2005-05-20	jprocter	xml-apis from the same place as xercesImpl.jar	commit \| commitdiff \| tree
2005-05-20	jprocter	This is the xercesImpl.jar from xerces-2_6_2	commit \| commitdiff \| tree
2005-05-20	jprocter	Fixing the broken cvs.	commit \| commitdiff \| tree
2005-05-19	jprocter	The archetypal Multiple Sequence Alignment Web Service	commit \| commitdiff \| tree
2005-05-05	jprocter	Added cancel interface for JPred Client and fixed some...	commit \| commitdiff \| tree
2005-05-05	jprocter	Moved tree leafname to alignment set matching into...	commit \| commitdiff \| tree
2005-05-05	jprocter	<No Comment Entered>	commit \| commitdiff \| tree
2005-05-03	jprocter	Better treatment of error states and cancellability...	commit \| commitdiff \| tree
2005-04-29	jprocter	stopped duplicate jars appearing in jalview.jar	commit \| commitdiff \| tree
2005-04-28	jprocter	Added MuscleWS back in	commit \| commitdiff \| tree
2005-04-28	jprocter	First try with MuscleWS and vamsas.simple.objects	commit \| commitdiff \| tree
2005-04-28	jprocter	First try with MuscleWS	commit \| commitdiff \| tree
2005-04-28	jprocter	added MuscleWS and did a bit more standardisation of...	commit \| commitdiff \| tree
2005-04-14	jprocter	consistent percentage gaps filter for conservation...	commit \| commitdiff \| tree
2005-04-14	jprocter	added quality calculation from Jalview118, and scale...	commit \| commitdiff \| tree
2005-04-13	jprocter	Gap characters are now properly detected in the conservation...	commit \| commitdiff \| tree
2005-04-13	jprocter	Fixed so that all alternate residues are used to calculate...	commit \| commitdiff \| tree
2005-04-13	jprocter	Added order-preservation for clustalW alignment. No...	commit \| commitdiff \| tree
2005-04-11	jprocter	added the alignment quality calculation from the old...	commit \| commitdiff \| tree
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