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2012-12-07	jprocter	use new secstructure process algorithm	commit \| commitdiff \| tree
2012-12-07	jprocter	Anne's refined RNAML parser. Seems to have some bugs...	commit \| commitdiff \| tree
2012-12-07	jprocter	Anne reinstated general stockholm parser code but extended...	commit \| commitdiff \| tree
2012-12-07	jprocter	typing	commit \| commitdiff \| tree
2012-12-07	jprocter	consensus secondary structure algorithm (possibly came...	commit \| commitdiff \| tree
2012-12-07	jprocter	revised RNA stem/loop processing code that copes with...	commit \| commitdiff \| tree
2012-12-07	jprocter	update authors for RNA processing routines	commit \| commitdiff \| tree
2012-12-07	jprocter	menu for choosing between 'protein' and 'RNA' mode...	commit \| commitdiff \| tree
2012-12-07	jprocter	formatting and error report cleanup	commit \| commitdiff \| tree
2012-12-07	jprocter	gui hooks for contrafold and RNAfold services. commented...	commit \| commitdiff \| tree
2012-12-07	jprocter	Exception signature change (will be overwritten by...	commit \| commitdiff \| tree
2012-12-07	jprocter	formatting	commit \| commitdiff \| tree
2012-12-07	jprocter	tidy import	commit \| commitdiff \| tree
2012-12-07	jprocter	remove mentions of non-functional RNAInteraction colourscheme	commit \| commitdiff \| tree
2012-12-07	jprocter	tidy debug messages	commit \| commitdiff \| tree
2012-12-07	jprocter	proxy commit for Anne Menard <menard.annec@gmail.com...	commit \| commitdiff \| tree
2012-12-04	jprocter	bogus source dir for jmol (only for jim - fix for yourself!)	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1140 - handled VARNA specific RNA exceptions within...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1140 - handle VARNA specific RNA exceptions within...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1140 - IO classes should only raise generic IOExceptions	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1216 switch to official release of VARNA 3.9	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1213 JAL-674 robust test with an existing structure...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1214 todo	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1213 JAL-674 - import a PDB file using Jmol data...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-674 commented out annotate3d calling code for Jmol...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1028 JAL-674 hooks to call external processing...	commit \| commitdiff \| tree
2012-12-04	jprocter	Merge branch 'menard' into develop	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1028 tidy and refactor external processing and...	commit \| commitdiff \| tree
2012-11-21	jprocter	valid URLs in website menu frame and fixed GA code	commit \| commitdiff \| tree
2012-11-19	jprocter	bugfix	commit \| commitdiff \| tree
2012-11-18	jprocter	JAL-1205 JAL-1140 generalised exception for Anne's...	commit \| commitdiff \| tree
2012-11-17	jprocter	Merge branch 'develop' into menard	commit \| commitdiff \| tree
2012-11-17	jprocter	Merge branch 'Release_2_8_Branch' into develop	commit \| commitdiff \| tree
2012-11-17	jprocter	Merge branch 'master' into Release_2_8_Branch	commit \| commitdiff \| tree
2012-11-17	jprocter	FileParse adapter for reading directly from inputstreams	commit \| commitdiff \| tree
2012-11-17	jprocter	return alignmentI created from pdbfile class directly...	commit \| commitdiff \| tree
2012-11-17	jprocter	return annotated rna sequences from rnaml returned...	commit \| commitdiff \| tree
2012-11-17	jprocter	store chainid on pdbentry	commit \| commitdiff \| tree
2012-11-17	jprocter	format adapter should return AlignmentI	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	call annotate3d service and parse rnaml to alignment	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	sequence numbering from 1	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	store chaincode on pdbentry	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	simple HTTP multipart entity poster - may not be useful	commit \| commitdiff \| tree
2012-11-17	jprocter	tests for jalview.analysis.AlignSeq	commit \| commitdiff \| tree
2012-11-17	jprocter	openjdk7 returns null for default value selected format...	commit \| commitdiff \| tree
2012-11-17	jprocter	method to construct sequence mapping for matching positions...	commit \| commitdiff \| tree
2012-11-17	jprocter	convenience method for performing pairwise alignment	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting and javadoc	commit \| commitdiff \| tree
2012-11-15	jprocter	remove java7 plugin dependency	commit \| commitdiff \| tree
2012-11-15	jprocter	don't set background colour for menu bar	commit \| commitdiff \| tree
2012-11-15	jprocter	allow .rnaml as a filename extension	commit \| commitdiff \| tree
2012-11-15	jprocter	comment on jalview.io.AlignFile architecture	commit \| commitdiff \| tree
2012-11-15	jprocter	source formatting	commit \| commitdiff \| tree
2012-11-15	jprocter	Merge branch 'develop' into menard	commit \| commitdiff \| tree
2012-11-13	jprocter	Merge branch 'master' into develop	commit \| commitdiff \| tree
2012-11-12	jprocter	Merge branch 'Release_2_8_Branch'	commit \| commitdiff \| tree
2012-11-12	jprocter	final tweaks to help landing page	commit \| commitdiff \| tree
2012-11-12	jprocter	Merge branch 'Release_2_8_Branch'	commit \| commitdiff \| tree
2012-11-12	jprocter	update footer for static page	commit \| commitdiff \| tree
2012-11-12	jprocter	Merge branch 'Release_2_8_Branch'	commit \| commitdiff \| tree
2012-11-12	jprocter	tidy help	commit \| commitdiff \| tree
2012-11-09	jprocter	property to configure webstart image	commit \| commitdiff \| tree
2012-11-09	jprocter	tweak file association comment and make sure webstart...	commit \| commitdiff \| tree
2012-11-09	jprocter	push jalview v2.8 release date to monday 12th November	commit \| commitdiff \| tree
2012-11-09	jprocter	ga tracking, footers and footer link styles	commit \| commitdiff \| tree
2012-11-09	jprocter	more tweaking of static pages and rejigging applet...	commit \| commitdiff \| tree
2012-11-09	jprocter	tweak whats new again	commit \| commitdiff \| tree
2012-11-09	jprocter	tweaking welcome message and what's new	commit \| commitdiff \| tree
2012-11-09	jprocter	constructor takes settings from any existing feature...	commit \| commitdiff \| tree
2012-11-08	jprocter	JAL-1193 ensure the 'loadedComplete' method gets called...	commit \| commitdiff \| tree
2012-11-08	jprocter	update release notes for JAL-1202	commit \| commitdiff \| tree
2012-11-08	jprocter	remember to close input file!	commit \| commitdiff \| tree
2012-11-08	jprocter	tidy imports	commit \| commitdiff \| tree
2012-11-08	jprocter	embed links to major features in main page	commit \| commitdiff \| tree
2012-11-08	jprocter	tweak wording	commit \| commitdiff \| tree
2012-11-07	jprocter	patch broken link	commit \| commitdiff \| tree
2012-11-07	jprocter	and more tweaks.	commit \| commitdiff \| tree
2012-11-07	jprocter	JAL-1201 more layout tweaks	commit \| commitdiff \| tree
2012-11-07	jprocter	JAL-1201 tweak layout for applet page and allow monospace...	commit \| commitdiff \| tree
2012-11-07	jprocter	JAL-1201 more tweaks to page layout	commit \| commitdiff \| tree
2012-11-07	jprocter	Jalview 2.8 release notes and whats new! text	commit \| commitdiff \| tree
2012-11-07	jprocter	updated release notes for Jalview Version 2.8	commit \| commitdiff \| tree
2012-11-07	jprocter	JAL-1201 update pages to use new website design	commit \| commitdiff \| tree
2012-11-07	jprocter	JAL-957 manual update to applet authorlist - need to...	commit \| commitdiff \| tree
2012-10-31	jprocter	Merge branch 'Release_2_8_Branch' of https://source...	commit \| commitdiff \| tree
2012-10-31	jprocter	JAL-1130 fix gif palette (arggh!)	commit \| commitdiff \| tree
2012-10-30	jprocter	JAL-1130 JAL-1197 nice installer splashscreens and...	commit \| commitdiff \| tree
2012-10-30	jprocter	Merge branch 'Release_2_8_Branch' of https://source...	commit \| commitdiff \| tree
2012-10-30	jprocter	JAL-1130 fireworks editable huge jalview logo in RGB	commit \| commitdiff \| tree
2012-10-30	jprocter	JAL-1130 JAL-1197 update install anywhere installer...	commit \| commitdiff \| tree
2012-10-30	jprocter	JAL-1130 JAL-1197 update install anywhere installer...	commit \| commitdiff \| tree
2012-10-30	jprocter	JAL-1130 updated installAnywhere program logos	commit \| commitdiff \| tree
2012-10-30	jprocter	JAL-1130 preserved old installAnywhere installer logo...	commit \| commitdiff \| tree
2012-10-29	jprocter	JAL-1130 made background transparent for small logo...	commit \| commitdiff \| tree
2012-10-24	jprocter	JAL-1193 call setLoadingFromArchiveFinished(true) for...	commit \| commitdiff \| tree
2012-10-24	jprocter	JAL-1193 patch prevents JalviewJmolBinding from handling...	commit \| commitdiff \| tree
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