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2013-05-24	Jim Procter	JAL-???? notes on summarisation and analysis of annotation...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1291 reinstate fastPaint flag manipulation to make...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1291 TODO: revised graphGroup model so grouped...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1291 - don't touch the graphics object until after...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1291 conditional output of rendering debugging...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	patch for JAL-1300 fixes JAL-1294: read and write COMBINE...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1300 test and example data for parsing annotation...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1295 test to demonstrate JAL-1294 (caused by JAL...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1295 refactored Jws2 discovery bootstrap code to...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1295 relaxed test for Annotation element equivalence...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-381 Desktop.addInternalFrame cannot be called in...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1299 fix: ensure a new graphGroup is created if...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1295 JAL-1296 clearer assertion failed message	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1295 JAL-1297 enhance test to check graph visiblity...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	fix for JAL-1297: COMBINE output now follows specification...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1291 JAL-1297 JAL-1295 JAL-1294 allow alignment...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	javadoc and formatting	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1297 JAL-1295 JAL-1294 sensible toString for benefit...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1297 JAL-1295 JAL-1294 improve test logic for comparing...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1296 reinstated tab characters so example annotation...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1070 - [ not a real patch ] - include offending...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-966 paintrefresher should be abstract [ Merge branch...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1161 conditional parameters for controlling clipping	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1292 avoid exception by using bitset of arbitrary...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1161 changed signature to allow clipping bounds...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	formatting	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1161 only trigger an annotation repaint in unwrapped...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1161 enable fastPaint for nudges from scroll bars...	commit \| commitdiff \| tree
2013-05-24	Jim Procter	JAL-1161 stick to api	commit \| commitdiff \| tree
2013-05-24	Jim Procter	typo	commit \| commitdiff \| tree
2013-05-21	Jim Procter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-05-21	Jim Procter	split test for general Stockholm IO consistency (JAL...	commit \| commitdiff \| tree
2013-05-21	Jim Procter	JAL-1199 JAL-1272 remove main() method from test class	commit \| commitdiff \| tree
2013-05-21	Jim Procter	formatting	commit \| commitdiff \| tree
2013-05-21	Jim Procter	JAL-1199 JAL-1272 refactored Natasha's test to a generic...	commit \| commitdiff \| tree
2013-05-13	Jim Procter	Merge branch 'JAL-1289_initCallBack' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-05-13	Jim Procter	JAL-1289 call oninit callback even if no alignment...	commit \| commitdiff \| tree
2013-04-12	Jim Procter	Merge branch 'JAL-1286_gzip' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-04-12	Jim Procter	JAL-1286 URL stream reader tries to use a GZIPInputStream...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	(JAL-1016) noted position where race condition occurs	commit \| commitdiff \| tree
2012-02-12	Jim Procter	(JAL-1022) ensure all Jmol model filenames are normalised...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	(JAL-1022) reverted to original strategy of escaping...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	(JAL-1050) ensure all filenames passed in to the load...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	(JAL-1025 JAL-1022) File based equivalence used to...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	(JAL-1049) only store state reference for sequence...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	JAL-1025 JAL-1022 use File based equivalence to map...	commit \| commitdiff \| tree
2012-02-12	Jim Procter	JAL-715 - remove platform dependent includes	commit \| commitdiff \| tree
2011-05-05	jprocter	uncommentable debug message for JAL-771	commit \| commitdiff \| tree
2011-05-05	jprocter	html tags	commit \| commitdiff \| tree
2011-05-05	jprocter	improved javascript callback execution thread and provided...	commit \| commitdiff \| tree
2011-05-05	jprocter	separation of jmol script command generation from jmol...	commit \| commitdiff \| tree
2011-05-05	jprocter	javadoc and informative error message when external...	commit \| commitdiff \| tree
2011-05-05	jprocter	ensure feature renderer settings come from the given...	commit \| commitdiff \| tree
2011-05-05	jprocter	added simple stdout debug function	commit \| commitdiff \| tree
2011-04-25	jprocter	JAL-824 - additional methods to allow jmol colouring...	commit \| commitdiff \| tree
2011-04-25	jprocter	JAL-824 - patch to schema to allow jmol colouring state...	commit \| commitdiff \| tree
2011-04-25	jprocter	toggle of inclusion/exclusion of views for colouring...	commit \| commitdiff \| tree
2011-04-25	jprocter	JAL-824 - ensure Jmol colouring is a radio button	commit \| commitdiff \| tree
2011-04-25	jprocter	documentation for JAL-824 and JAL-621	commit \| commitdiff \| tree
2011-04-25	jprocter	documentation for JAL-732	commit \| commitdiff \| tree
2011-04-25	jprocter	htmlfix	commit \| commitdiff \| tree
2011-04-22	jprocter	formatting	commit \| commitdiff \| tree
2011-04-22	jprocter	removed useless flag (was always null for button press...	commit \| commitdiff \| tree
2011-04-22	jprocter	JAL-823 and JAL-824 - seqColour no longer the default...	commit \| commitdiff \| tree
2011-04-22	jprocter	comments re JAL-823 legacy issue	commit \| commitdiff \| tree
2011-04-22	jprocter	clarify tooltip	commit \| commitdiff \| tree
2011-04-22	jprocter	moved loadingFromArchive flag modification to after...	commit \| commitdiff \| tree
2011-04-22	jprocter	option for enabling Jmol colouring mode JAL-824	commit \| commitdiff \| tree
2011-04-21	jprocter	JAL-641 patch	commit \| commitdiff \| tree
2011-04-21	jprocter	patch for JAL-733	commit \| commitdiff \| tree
2011-04-21	jprocter	patch for JAL-820 and JAL-821	commit \| commitdiff \| tree
2011-04-21	jprocter	separated alignment annotation height calculation from...	commit \| commitdiff \| tree
2011-04-21	jprocter	moved to same place as in jalview.gui	commit \| commitdiff \| tree
2011-04-21	jprocter	save and recover graph height, visibility and row position...	commit \| commitdiff \| tree
2011-04-21	jprocter	allow an alignment annotation row to be removed and...	commit \| commitdiff \| tree
2011-04-21	jprocter	allow an existing alignment annotation row to be bound...	commit \| commitdiff \| tree
2011-04-21	jprocter	added graphHeight attribute to schema (JAL-784)	commit \| commitdiff \| tree
2011-04-19	jprocter	avoid race condition when featureRenderer for structure...	commit \| commitdiff \| tree
2011-04-19	jprocter	patched XML parser to ensure it properly escapes non...	commit \| commitdiff \| tree
2011-04-08	jprocter	todo	commit \| commitdiff \| tree
2011-04-08	jprocter	imported properties via -props should never be overwritten	commit \| commitdiff \| tree
2011-04-08	jprocter	allow groovy scripts to be run when in headless mode...	commit \| commitdiff \| tree
2011-04-07	jprocter	allow groovy scripts to be run when in headless mode...	commit \| commitdiff \| tree
2011-04-07	jprocter	allow groovy scripts to be run when in headless mode...	commit \| commitdiff \| tree
2011-04-07	jprocter	resolves JAL-805	commit \| commitdiff \| tree
2011-04-07	jprocter	resolves JAL-804	commit \| commitdiff \| tree
2011-02-28	jprocter	excess imports	commit \| commitdiff \| tree
2011-02-27	jprocter	patch for JAL-780	commit \| commitdiff \| tree
2011-02-27	jprocter	patch for occasional ArrayIndexOutOfBounds	commit \| commitdiff \| tree
2011-02-27	jprocter	patch for JAL-792	commit \| commitdiff \| tree
2011-02-27	jprocter	first patch for JAL-774 - ensure end is a valid bound...	commit \| commitdiff \| tree
2011-02-25	jprocter	first approximation for JAL-782 - hint that opaque...	commit \| commitdiff \| tree
2011-02-18	jprocter	JAL-777/JAL-641 debugging	commit \| commitdiff \| tree
2011-02-18	jprocter	new alignmentPanel api + JAL-777/JAL-641 debugging	commit \| commitdiff \| tree
2011-02-18	jprocter	fix scrolltoposition behaviour and new alignmentPanel api	commit \| commitdiff \| tree
2011-02-18	jprocter	fix scrolltoposition behaviour	commit \| commitdiff \| tree
2011-02-18	jprocter	JAL-574	commit \| commitdiff \| tree
2011-02-18	jprocter	convenience method to discover all Jmols	commit \| commitdiff \| tree
2011-02-18	jprocter	JAL-779 and some redraw refinements	commit \| commitdiff \| tree
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