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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
2005-03-18	jprocter	rough JPredService client copied from WebServices project.	commit \| commitdiff \| tree
2005-03-18	jprocter	various loadTree bits for loading and saving trees.	commit \| commitdiff \| tree
2005-03-18	jprocter	merged Loadtree and EPSfile and changed crlf.	commit \| commitdiff \| tree
2005-03-18	jprocter	Save tree.	commit \| commitdiff \| tree
2005-03-18	jprocter	Load and Save trees.	commit \| commitdiff \| tree
2005-03-18	jprocter	Tree io modifications, including support for polytomous...	commit \| commitdiff \| tree
2005-03-18	jprocter	New constructors for turning NewickFile objects into...	commit \| commitdiff \| tree
2005-03-17	jprocter	Newick/New Hampshire tree format parser and generator.	commit \| commitdiff \| tree
2005-03-08	jprocter	fixed interface for PID method.	commit \| commitdiff \| tree
2005-03-08	jprocter	fixed so that alignment percentage ID is used for distance...	commit \| commitdiff \| tree
2005-03-08	jprocter	fixed signing bug (also updated to latest javahelp...	commit \| commitdiff \| tree
2005-03-08	jprocter	more precise methods information in help description.	commit \| commitdiff \| tree
2005-03-08	jprocter	fixed some of the jar/wsdl deployment problems.	commit \| commitdiff \| tree
2005-03-08	jprocter	removed conservation calculation from calculations.	commit \| commitdiff \| tree
2005-03-01	jprocter	Obsolete. Explanation within the conservation colourscheme...	commit \| commitdiff \| tree
2005-02-28	jprocter	added uniquify sequence id assertion.	commit \| commitdiff \| tree
2005-02-28	jprocter	partial implementation of JNet server prediction.	commit \| commitdiff \| tree
2005-02-28	jprocter	first stab at a JPredClient.	commit \| commitdiff \| tree
2005-02-23	jprocter	basic jpred concise prediction reader.	commit \| commitdiff \| tree
2005-02-23	jprocter	new resources location.	commit \| commitdiff \| tree
2005-02-23	jprocter	rearranged project structure	commit \| commitdiff \| tree
2005-02-23	jprocter	making Jemboss client more configurable.	commit \| commitdiff \| tree
2005-02-23	jprocter	bug fix for unaligned sequence sets and clustal colours...	commit \| commitdiff \| tree
2005-02-23	jprocter	rearranged project structure	commit \| commitdiff \| tree
2005-02-23	jprocter	new ant build for Jalview.	commit \| commitdiff \| tree
2005-02-08	jprocter	formatting imports.	commit \| commitdiff \| tree
2005-01-15	jprocter	JBuilder Project file update	commit \| commitdiff \| tree
2005-01-15	jprocter	Jemboss(emboss 2.9.0) classes to provide client functionality to	commit \| commitdiff \| tree
2005-01-15	jprocter	first jemboss clustalw client for jalview.	commit \| commitdiff \| tree
2005-01-15	jprocter	support for jemboss server interaction.	commit \| commitdiff \| tree
2005-01-15	jprocter	bugfix for writing fasta file without gap characters.	commit \| commitdiff \| tree
2005-01-15	jprocter	Implemented clustal alignment via jemboss.	commit \| commitdiff \| tree
2005-01-12	jprocter	random change 3	commit \| commitdiff \| tree
2005-01-12	jprocter	another dummy.	commit \| commitdiff \| tree
2005-01-12	jprocter	irrelevant comment.	commit \| commitdiff \| tree

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