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2013-06-09	Jim Procter	JAL-674 - update applet build dependency on VARNA	commit \| commitdiff \| tree
2013-06-09	Jim Procter	Merge branch '2_8_1_patch_multiharmony' into develop	commit \| commitdiff \| tree
2013-06-09	Jim Procter	fix for JAL-1298	commit \| commitdiff \| tree
2013-06-09	Jim Procter	JAL-715 - TODO	commit \| commitdiff \| tree
2013-06-07	Jim Procter	Merge branch '2_8_1_patch_multiharmony' into develop	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-1309 fix broken partition computation for adding...	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-945 uniquify prior to submission	commit \| commitdiff \| tree
2013-06-07	Jim Procter	formatting	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-715 allow headless construction for testing	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-724 JAL-715 refactor and create new test for RSBS...	commit \| commitdiff \| tree
2013-06-07	Jim Procter	fix for JAL-1246	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-1307 patch to squash number format exceptions when...	commit \| commitdiff \| tree
2013-06-07	Jim Procter	JAL-1300 documentation	commit \| commitdiff \| tree
2013-06-07	Jim Procter	Merge branch 'JAL-1161_optimisingAnnotationPanel' into...	commit \| commitdiff \| tree
2013-05-31	Jim Procter	JAL-1259 patch to avoid NPE	commit \| commitdiff \| tree
2013-05-31	Jim Procter	Merge branch 'JAL-1259_hotfix' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-05-31	Jim Procter	JAL-1259 patch to avoid NPE	commit \| commitdiff \| tree
2013-05-24	Jim Procter	Merge branch 'JAL-1161_optimisingAnnotationPanel' ...	commit \| commitdiff \| tree
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	JAL-1286 URL stream reader tries to use a GZIPInputStream...	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	Merge branch 'JAL-1289_initCallBack' into develop	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
2013-02-06	jprocter	Merge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing	commit \| commitdiff \| tree
2013-02-06	jprocter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-02-06	jprocter	JAL-1265 basic support for parsing database accessions...	commit \| commitdiff \| tree
2013-02-06	jprocter	JAL-1199 added test for Rfam Stockholm file example	commit \| commitdiff \| tree
2013-02-06	jprocter	JAL-1199 refactored stockholm test code from main class...	commit \| commitdiff \| tree
2013-02-05	jprocter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-02-05	jprocter	formatting	commit \| commitdiff \| tree
2013-02-05	jprocter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-01-20	jprocter	Merge branch 'Dbfetch_hotfix-JAL-1238' into develop	commit \| commitdiff \| tree
2013-01-20	jprocter	Merge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 test to see if the primary Uniprot source...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 order to place primary sources before lower...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 method to test if DAS source is a primary...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 tier index indicating distance of a source...	commit \| commitdiff \| tree
2013-01-18	jprocter	Merge branch 'JAL-1254-hotfix' into develop	commit \| commitdiff \| tree
2013-01-18	jprocter	Merge branch 'JAL-1254-hotfix' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1255 don't show 'Right click to add annotations...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1254 patch for NPE in annotation renderer when...	commit \| commitdiff \| tree
2012-12-11	jprocter	JAL-1217 check and avoid NPE if no datastore object...	commit \| commitdiff \| tree
2012-12-11	jprocter	JAL-1217 report exception for service when no datastore...	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
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