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2012-08-21	jprocter	JAL-1142 - test to demonstrate mismatch between rnaview...	commit \| commitdiff \| tree
2012-08-20	jprocter	JAL-1140 test Annotate3D methods for SAM Riboswitch...	commit \| commitdiff \| tree
2012-08-20	jprocter	JAL-1140 library methods for accessing the Annotate3d...	commit \| commitdiff \| tree
2012-08-20	jprocter	JAL-1028 utilities package for accessing synchronous...	commit \| commitdiff \| tree
2012-08-20	jprocter	JAL-1140 bugfix - getDataName throws errors - prefer...	commit \| commitdiff \| tree
2012-08-20	jprocter	JAL-1140 use the Reader provided by the jalview.io...	commit \| commitdiff \| tree
2012-08-17	jprocter	Merge branch 'develop' into menard	commit \| commitdiff \| tree
2012-08-14	jprocter	do not commit .settings to .git	commit \| commitdiff \| tree
2012-08-07	jprocter	JAL-1137 clean up old-style menu code and look	commit \| commitdiff \| tree
2012-08-07	jprocter	JAL-1137 JAL-975 simpler menu for the AACon service...	commit \| commitdiff \| tree
2012-08-07	jprocter	Debug message associated with TODO for JAL-1136 - re...	commit \| commitdiff \| tree
2012-08-07	jprocter	JAL-975 JAL-1137 debug messages for web service client...	commit \| commitdiff \| tree
2012-08-05	jprocter	JAL-1131 - todos for later versions	commit \| commitdiff \| tree
2012-08-05	jprocter	JAL-1131 ensure new dataset sequence is created if...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 Ensure asynchronously calculated autoannotation...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 JAL-811 JAL-812 store/recover autocalc alignment...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 fix logic for recovering AACons params	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 store ws-parameter list as XML element content...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 allow parameter sets to be transferred across...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 less code-dependent formula for creating server...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1136 - fix abstraction for parameter container...	commit \| commitdiff \| tree
2012-08-03	jprocter	JAL-1115 reference to List<SequenceI> passed in 'alignment...	commit \| commitdiff \| tree
2012-08-02	jprocter	JAL-976 better logging/error reporting for disorder...	commit \| commitdiff \| tree
2012-08-02	jprocter	JAL-976 JAL-958 todo list for release	commit \| commitdiff \| tree
2012-08-01	jprocter	JAL-976 ensure protein disorder services appears in...	commit \| commitdiff \| tree
2012-08-01	jprocter	JAL-976 don't clear menu out before adding jabaws services...	commit \| commitdiff \| tree
2012-08-01	jprocter	JAL-1066 patch regression ac33424148b2a4de29b3ca43f941162e8b...	commit \| commitdiff \| tree
2012-07-08	jprocter	documentation for PCA calculation parameters and reset...	commit \| commitdiff \| tree
2012-07-08	jprocter	a209409239 (JAL-976 - add support for storing service...	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-976 clean out associated annotation	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-976 implement additional calcId method	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-976 simpler parameter update model	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-961 JAL-976 allow access to service URI for parameter...	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-961 JAL-976 recover current settings from associated...	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-976 pick an available instance of a service based...	commit \| commitdiff \| tree
2012-07-08	jprocter	bugfix - use currently held parameters	commit \| commitdiff \| tree
2012-07-08	jprocter	JAL-976 - storing service parameters on the view model	commit \| commitdiff \| tree
2012-07-06	jprocter	JAL-976 test if the sliders have been modified from...	commit \| commitdiff \| tree
2012-07-06	jprocter	unique URI for service type	commit \| commitdiff \| tree
2012-07-06	jprocter	JAL-961 JAL-976 abstracted container for dynamic calculation...	commit \| commitdiff \| tree
2012-07-06	jprocter	tidy imports	commit \| commitdiff \| tree
2012-07-06	jprocter	JAL-976 - add support for storing service parameter...	commit \| commitdiff \| tree
2012-07-03	jprocter	JAL-961 allow calcId to be specified independently...	commit \| commitdiff \| tree
2012-07-03	jprocter	JAL-974 - broken copy of feature settings	commit \| commitdiff \| tree
2012-07-02	jprocter	JAL-1129 progress bar - this patch doesn't provide...	commit \| commitdiff \| tree
2012-07-02	jprocter	JAL-968 incremental - PNG/EPS output has annotation...	commit \| commitdiff \| tree
2012-07-02	jprocter	tidy imports	commit \| commitdiff \| tree
2012-07-02	jprocter	JAL-974 create graduated feature colours for annotation...	commit \| commitdiff \| tree
2012-07-02	jprocter	JAL-974 - use refactored methods on AlignmentPanel	commit \| commitdiff \| tree
2012-07-02	jprocter	JAL-974 - refactor FeatureRenderer constructor to AlignmentP...	commit \| commitdiff \| tree
2012-07-01	jprocter	JAL-1117 alleviate lock starvation	commit \| commitdiff \| tree
2012-07-01	jprocter	ensure all annotation dependent rendering gets refreshed	commit \| commitdiff \| tree
2012-06-29	jprocter	JAL-1065 JAL-1066 ensure non-residue based schemes...	commit \| commitdiff \| tree
2012-06-29	jprocter	JAL-1065 JAL-1066 allow different lookup tables for...	commit \| commitdiff \| tree
2012-06-26	jprocter	JAL-899 added groovy support to develop branch	commit \| commitdiff \| tree
2012-06-20	jprocter	formatting	commit \| commitdiff \| tree
2012-06-19	jprocter	JAL-976 JAL-975 JAL-1119 - pass on any existing parameters...	commit \| commitdiff \| tree
2012-06-19	jprocter	JAL-975 JAL-1119 - prototype adjustable AACons parameters...	commit \| commitdiff \| tree
2012-06-19	jprocter	JAL-975 - doh! valid result if width matches *ungapped...	commit \| commitdiff \| tree
2012-06-19	jprocter	JAL-975 - bespoke AACons settings object to save current...	commit \| commitdiff \| tree
2012-06-19	jprocter	patch for JAL-1172 ensure option's default value is...	commit \| commitdiff \| tree
2012-06-19	jprocter	JAL-961 JAL-975 extend api to support removal of workers...	commit \| commitdiff \| tree
2012-06-19	jprocter	JAL-975 - ensure we only submit ungapped, padded alignment...	commit \| commitdiff \| tree
2012-06-15	jprocter	formatting	commit \| commitdiff \| tree
2012-06-15	jprocter	JAL-1125 option to switch between Jalview and SeqSpace...	commit \| commitdiff \| tree
2012-06-15	jprocter	fix JAL-1122	commit \| commitdiff \| tree
2012-06-15	jprocter	JAL-1123 - make clear where off-by-one error was occuring...	commit \| commitdiff \| tree
2012-06-15	jprocter	JAL-535 - refactored core PCA viewer code to viewmodel	commit \| commitdiff \| tree
2012-06-15	jprocter	JAL-535 refactored core code from PCA viewer to viewmodel.	commit \| commitdiff \| tree
2012-06-15	jprocter	JAL-1120 patch for desktop	commit \| commitdiff \| tree
2012-06-15	jprocter	patch for JAL-1121 - reset button and slightly wider...	commit \| commitdiff \| tree
2012-06-15	jprocter	JAL-535 refactoring todo	commit \| commitdiff \| tree
2012-06-15	jprocter	Extended IProgressIndicator with method to check if...	commit \| commitdiff \| tree
2012-06-15	jprocter	Merge branch 'JAL-1013_pca_rna_dna' into develop	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-975 JAL-1002 ensure custom parameters are actually...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-1115 - synchronized access to group list	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-976 - make sure annotation panel is updated to...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-961 JAL-976 kill any existing AACon job if a new...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-1003 visual delay when running a sequence or alignment...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-961 JAL-976 tweaked way that AACons client is registered...	commit \| commitdiff \| tree
2012-06-14	jprocter	formatting	commit \| commitdiff \| tree
2012-06-14	jprocter	formatting	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-1118 - hack to try and get rid of flicker. consider...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-1118 WIP - flag to mark if image buffer has just...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-1115 trap exception arising from race condition...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-968 javadoc and return flag indicating if any of...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-961 ensure we only add one instance of a worker...	commit \| commitdiff \| tree
2012-06-14	jprocter	JAL-961 potentially helpful println statements when...	commit \| commitdiff \| tree
2012-06-13	jprocter	JAL-1115 refactor base collection for Alignment from...	commit \| commitdiff \| tree
2012-06-13	jprocter	JAL-1116 - location where vamsas sync failure occurs	commit \| commitdiff \| tree
2012-06-13	jprocter	javatidy	commit \| commitdiff \| tree
2012-06-12	jprocter	JAL-1115 refactor reordering code operating directly...	commit \| commitdiff \| tree
2012-06-12	jprocter	JAL-1115 refactor base collection for Alignment from...	commit \| commitdiff \| tree
2012-06-12	jprocter	JAL-1115 - use local reference for annotation row	commit \| commitdiff \| tree
2012-06-12	jprocter	JAL-961, JAL-1115 - pending test to ensure only one...	commit \| commitdiff \| tree
2012-06-07	jprocter	javatidy	commit \| commitdiff \| tree
2012-06-07	jprocter	JAL-967, JAL-1114, JAL-1115 more concurrent access...	commit \| commitdiff \| tree
2012-06-07	jprocter	javatidy	commit \| commitdiff \| tree
2012-06-07	jprocter	fix for bug introduced with commit:b81d4d7d46ea8b1c89df086fb...	commit \| commitdiff \| tree
2012-06-07	jprocter	javatidy	commit \| commitdiff \| tree
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