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2012-09-06	jprocter	merge new 2.7.1 and 2.8 features into one	commit \| commitdiff \| tree
2012-09-06	jprocter	typo	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-958 flag indicating if visualization settings for...	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-958 store/recover normalised flag	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-958 store normalised flag in jalview project	commit \| commitdiff \| tree
2012-09-06	jprocter	PCA what's new and score matrix documentation page	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-1013 JAL-1167 JAL-1121 JAL-1125	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-1027 JAL-1167 documentation and patched DNA/RNA...	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-1013 - employ index parameter rather than hardcode...	commit \| commitdiff \| tree
2012-09-06	jprocter	JAL-1167 method and simple tests for printing score...	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-979 tidy up shmmr hardcoded WS definition	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-1136 give pre-existing custom settings a special...	commit \| commitdiff \| tree
2012-09-05	jprocter	formatting	commit \| commitdiff \| tree
2012-09-05	jprocter	patch for NPE when no services are available to resolve...	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-975 null any existing preset if user has supplied...	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-1162 catch security exception and just use bare...	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-994 fix when sequence is too short and no jobs run	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-1111 allow news reader window to be moved even...	commit \| commitdiff \| tree
2012-09-05	jprocter	JAL-976 fix AACon name typo in source and GUI	commit \| commitdiff \| tree
2012-09-04	jprocter	typo	commit \| commitdiff \| tree
2012-09-04	jprocter	JAL-976 documentation for disorder, AACon, ClustalO...	commit \| commitdiff \| tree
2012-09-04	jprocter	JAL-975 note about black colouring bug	commit \| commitdiff \| tree
2012-09-04	jprocter	JAL-1066 documentation for per-sequence annotation...	commit \| commitdiff \| tree
2012-09-04	jprocter	JAL-1060 new dialog box image	commit \| commitdiff \| tree
2012-09-04	jprocter	JAL-1060 documentation for new layout	commit \| commitdiff \| tree
2012-09-04	jprocter	off by one for sequence associated annotation	commit \| commitdiff \| tree
2012-09-04	jprocter	unused variable	commit \| commitdiff \| tree
2012-09-04	jprocter	JAL-974 JRonn thresholds	commit \| commitdiff \| tree
2012-09-03	jprocter	JAL-591 adapt option layout to width of dialog box	commit \| commitdiff \| tree
2012-09-03	jprocter	JAL-975 JAL-974 JAL-976 always adjust height after...	commit \| commitdiff \| tree
2012-09-03	jprocter	JAL-974 show thresholds for disorder predictor annotation...	commit \| commitdiff \| tree
2012-09-03	jprocter	JAL-1153 ensure _linecolour is copied in copy constructor	commit \| commitdiff \| tree
2012-09-03	jprocter	JAL-1111 news reader shouldn't be modal.	commit \| commitdiff \| tree
2012-09-03	jprocter	JAL-1111 doh - helps if you pass modality flag onto...	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-812 only trigger alignment redraw and calculation...	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-1007 refactored code and patched calculation bug	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-1015 documentation for basic HTML sequence annotation...	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-1075 JAL-1062 documentation and new figure for...	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-1158 - request focus after opening window.	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-659 cope with case insensitive accessions by forcing...	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-1062 JAL-659 correct start position for retrieved...	commit \| commitdiff \| tree
2012-09-02	jprocter	JAL-1062 use matching region or first section of sequence...	commit \| commitdiff \| tree
2012-09-01	jprocter	JAL-1075 sort nodes alphabetically	commit \| commitdiff \| tree
2012-09-01	jprocter	JAL-1160 support horizontal mouse wheel scrolling events	commit \| commitdiff \| tree
2012-09-01	jprocter	JAL-1161 JAL-1160 implement custom mousewheel listener...	commit \| commitdiff \| tree
2012-09-01	jprocter	javadoc	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-1015 equivalent menu items for applet - not visible...	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-1015 new menu items in desktop popup menu for creating...	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-1015 resolve dataset sequence before searching...	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-1157 new window for displaying HTML formatted text...	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-1015 refactor tooltip html generation code to jalview...	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-974 - ensure annotation created in local sequence...	commit \| commitdiff \| tree
2012-08-31	jprocter	JAL-1064 patch for NPE when registerd database names...	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-1155 fix panel length calculation for grouped graphs...	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-1066 limit available rows to per-sequence when...	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-974 skip empty rows	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-974 set GlobPlot raw/smooth score annotation rows...	commit \| commitdiff \| tree
2012-08-29	jprocter	formatting	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-1153 JAL-1155 improved layout and allowed labels...	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-1153 new runtime property set to first non-null...	commit \| commitdiff \| tree
2012-08-29	jprocter	JAL-48 patch NPE when encountering an alignment window...	commit \| commitdiff \| tree
2012-08-28	jprocter	remove contaminant imports	commit \| commitdiff \| tree
2012-08-28	jprocter	remove contaminant imports	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-676 JAL-1001 - simple menu item to access documentation...	commit \| commitdiff \| tree
2012-08-28	jprocter	formatting	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1066 basic gui and functionality for per-sequence...	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1066 - per-sequence colouring with sequence associated...	commit \| commitdiff \| tree
2012-08-28	jprocter	formatting	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1145 patch: sequence associated annotation with...	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-974 create mixture of sequence features marking...	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-974 refactored creation of Annotation rows from...	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-974 JAL-975 try to cope with temporary server errors...	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1136 sometimes there are no parameters associated...	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1001 - hack to extract the global URL for a service...	commit \| commitdiff \| tree
2012-08-28	jprocter	javadoc and note about broken semantics for findIndex	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1149 patch	commit \| commitdiff \| tree
2012-08-28	jprocter	JAL-1148 reinstate sequence references for annotation...	commit \| commitdiff \| tree
2012-08-24	jprocter	JAL-1087 skip processing any of the other command line...	commit \| commitdiff \| tree
2012-08-24	jprocter	JAL-1143 - ensure we revalidate annotation panel height...	commit \| commitdiff \| tree
2012-08-23	jprocter	JAL-975 JAL-951 test class for viewing layout for JABAWS...	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
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