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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
2005-04-11	jprocter	Conservation symbols : + = all props are conserved...	commit \| commitdiff \| tree
2005-04-11	jprocter	Fixed the job-failed message.	commit \| commitdiff \| tree
2005-04-11	jprocter	Now tries to set viewing parameters for distances and...	commit \| commitdiff \| tree
2005-04-08	jprocter	slight mods again.	commit \| commitdiff \| tree
2005-04-08	jprocter	WebStartLocation form.	commit \| commitdiff \| tree
2005-04-08	jprocter	trival.	commit \| commitdiff \| tree
2005-04-08	jprocter	Fixed broken jnlp creation.	commit \| commitdiff \| tree
2005-04-08	jprocter	remember: do not check in quick bug fixes that you...	commit \| commitdiff \| tree
2005-04-08	jprocter	recent rebuild of the JPred client from WSDL2Java	commit \| commitdiff \| tree
2005-04-08	jprocter	Alignment quality with funky coloured histograms.	commit \| commitdiff \| tree
2005-04-08	jprocter	updated build strategy and checking for portability.	commit \| commitdiff \| tree
2005-04-06	jprocter	next version of Jpred functionality using new client...	commit \| commitdiff \| tree
2005-04-06	jprocter	New method for helping to quickly map different aligned...	commit \| commitdiff \| tree
2005-04-06	jprocter	New client code for JPred service includes return of...	commit \| commitdiff \| tree
2005-03-31	jprocter	doh - stupid jim.	commit \| commitdiff \| tree
2005-03-31	jprocter	utility classes used in build.xml, and a dodgy perl...	commit \| commitdiff \| tree
2005-03-31	jprocter	JavaC target set to 1.4 for proper compilation of 1...	commit \| commitdiff \| tree
2005-03-31	jprocter	Added a flag to control if the "/<seq_start>-<seq_end...	commit \| commitdiff \| tree
2005-03-31	jprocter	added a an axis log4j appender property to the jalview...	commit \| commitdiff \| tree
2005-03-30	jprocter	new libraries for soap bits.	commit \| commitdiff \| tree
2005-03-30	jprocter	fixed the log4j messages.	commit \| commitdiff \| tree
2005-03-30	jprocter	cleaned up some comments and exception messages.	commit \| commitdiff \| tree
2005-03-30	jprocter	Updated version of axis to fix the j1.5 webstart problems.	commit \| commitdiff \| tree
2005-03-30	jprocter	Fixed a sensible default leaf distance (for files where...	commit \| commitdiff \| tree
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