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2017-05-15	Jim Procter	JAL-2507 - required callers to specify exact ignore...	commit \| commitdiff \| tree
2017-05-15	Jim Procter	JAL-2535 quick hack to implement posterior probabilities...	commit \| commitdiff \| tree
2017-05-11	Jim Procter	JAL-2509 JAL-2507 allow whitespace in GS annotation...	commit \| commitdiff \| tree
2017-05-11	Jim Procter	JAL-2507 JAL-2509 allow whitespace==null for annotation...	commit \| commitdiff \| tree
2017-05-11	Jim Procter	JAL-2507 test if an annotation is ‘whitespace’	commit \| commitdiff \| tree
2017-05-11	Jim Procter	JAL-2507 Annotation.EMPTY_ANNOTATION - non-null whitespace...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2507 spit out tests for ‘{‘ WUSS io from ‘[‘ WUSS...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2509 verify stockholm parser’s bracket regex is...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2509 extend set of brackets recognised by stockholm...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2507 JAL-2509 extend test to cover round trip of...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2507 output secondary structure regardless of presence...	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2507 simplify round trip test via AppletFormatAdapter	commit \| commitdiff \| tree
2017-05-09	Jim Procter	JAL-2507 test for alignment+rna annotation -> Stockholm...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	Merge branch 'bug/JAL-2507_rnasecstrstockholmoutput...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	Merge branch 'features/JAL-2503_filteronquantitativeannotati...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	Merge branch 'features/JAL-2393customMatrices' into...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	JAL-1656 make RNAML->Stockholm round trip test pass...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	JAL-2507 JAL-2509 allow differences in visibility of...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	JAL-2507 JAL-2509 new assert to compare secondary structure...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	fix for JAL-2509 - don’t replace all bracket types...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	fix for JAL-2507 - resolve stockholm per residue annotation...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	Merge branch 'features/JAL-2503_filteronquantitativeannotati...	commit \| commitdiff \| tree
2017-05-04	Jim Procter	Merge branch 'features/JAL-2393customMatrices' into...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2393 JAL-2416 refresh the score model menu when...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2503 show threshold slider for quantitative annotation...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2503 AlignmentAnnotation.isQuantitative() test	commit \| commitdiff \| tree
2017-05-03	Jim Procter	Merge branch 'features/JAL-2432_annotbypercent' into...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-1933 JAL-2501 i18n for all auto calculated descriptions	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-1933 show occupancy in tooltip for row	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2432 honour percentage checkbox when entering values...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2432 applet: only enable percent checkbox when...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2432 percentage checkbox follows threshold value...	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2432 recover state for ‘display percentage’ checkbox	commit \| commitdiff \| tree
2017-05-03	Jim Procter	JAL-2432 simplify code	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-1632 validate CalculationChooser when selection...	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-1632 enable/disable CalculationChooser buttons...	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-1632 compare size of input against minimums for...	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-1632 OK->Calculate, Cancel->Close buttons	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-1632 removed ‘tree’ option and changed dialog layout	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-2424 fixme’s removed	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-2424 update assert to correct width for normalising...	commit \| commitdiff \| tree
2017-05-02	Jim Procter	JAL-2424 resolved, assert updated to pass (1f != 1d)	commit \| commitdiff \| tree
2017-05-02	Jim Procter	Merge branch 'develop' into features/JAL-2393customMatrices	commit \| commitdiff \| tree
2017-05-02	Jim Procter	Merge branch 'bug/JAL-2424getVisibleContigs' into develop	commit \| commitdiff \| tree
2017-04-27	Jim Procter	Merge branch 'features/JAL-1933_occupancy' into develop	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 patch jalview/io/testProps.jvprops to show...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 patch jalview/io/testProps.jvprops to show...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	Merge branch 'features/JAL-1933_occupancy' into develop	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 don't show occupancy row when testing conservation...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	Merge branch 'features/JAL-1933_occupancy' into develop	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 applet doc for showOccupancy parameter	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 desktop documentation for show occupancy preference	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 use constant for preference token	commit \| commitdiff \| tree
2017-04-27	Jim Procter	Merge branch 'features/JAL-1933_occupancy' into develop	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 consensus calculation doesn’t depend on occupancy...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 desktop preferences for occupancy	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 action and label for occupancy	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 test for SHOW_OCCUPANCY .jalview_properties...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 showOccupancy applet parameter and SHOW_OCCUPANCY...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 only create and add occupancy row to alignment...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-2494 fix: updated behaviour for SequenceGroup.findAnnota...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-2494 fixed behaviour for null parameters in line...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-2494 javadoc for AnnotatedCollectionI.findAnnotations	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-2494 test to cover AnnotatedCollectionI.findAnnotations	commit \| commitdiff \| tree
2017-04-27	Jim Procter	Merge branch 'features/JAL-1933_occupancy' into develop	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-2432 desktop: filter/select columns by threshold...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 JAL-2432 code tidy	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-2432 left justify value shown after adjusting threshold...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 JAL-2432 percentile filter for select/hide...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 shade occupancy from light grey to black for...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 don’t show symbol counts under histogram ...	commit \| commitdiff \| tree
2017-04-27	Jim Procter	JAL-1933 occupancy row has a space below it for counts	commit \| commitdiff \| tree
2017-04-27	Jim Procter	Merge branch 'develop' into features/JAL-1933_occupancy	commit \| commitdiff \| tree
2017-03-24	Jim Procter	JAL-2360 fix applet build by separating castor XML...	commit \| commitdiff \| tree
2017-03-21	Jim Procter	Merge branch 'features/JAL-2388OverviewWindow' into...	commit \| commitdiff \| tree
2017-03-20	Jim Procter	Merge branch 'bug/JAL-2421overviewboxflicker' into...	commit \| commitdiff \| tree
2017-03-16	Jim Procter	Merge branch 'merges/develop_JAL2295setChimeraAttributes...	commit \| commitdiff \| tree
2017-03-16	Jim Procter	JAL-1933 refactor parameter for code clarity	commit \| commitdiff \| tree
2017-03-06	Jim Procter	Merge branch 'merges/develop_JAL2295setChimeraAttributes...	commit \| commitdiff \| tree
2017-02-20	Jim Procter	Merge branch 'features/JAL-2379pcaMemory' into develop	commit \| commitdiff \| tree
2017-02-16	Jim Procter	Merge branch 'bug/JAL-2374_JAL-2419_overlappinggroups_curren...	commit \| commitdiff \| tree
2017-02-15	Jim Procter	JAL-2374 JAL-2419 - TODO suspiciously redundant nested...	commit \| commitdiff \| tree
2017-02-15	Jim Procter	fix for JAL-2419 - don’t trash the current selection	commit \| commitdiff \| tree
2017-02-15	Jim Procter	JAL-2374 don’t search twice for containing group to...	commit \| commitdiff \| tree
2017-02-15	Jim Procter	JAL-2374 tests for SequenceGroup.contains	commit \| commitdiff \| tree
2017-02-15	Jim Procter	JAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functional’	commit \| commitdiff \| tree
2017-02-15	Jim Procter	JAL-2374 new contains methods for seq and seq,apos	commit \| commitdiff \| tree
2017-02-15	Jim Procter	JAL-2374 javadoc - qualify that sequence argument to...	commit \| commitdiff \| tree
2017-02-09	Jim Procter	Merge branch 'features/JAL-2316' into develop	commit \| commitdiff \| tree
2017-02-09	Jim Procter	Merge branch 'develop' into features/JAL-2316	commit \| commitdiff \| tree
2017-02-08	Jim Procter	JAL-2316 tidying preferences help page	commit \| commitdiff \| tree
2017-02-08	Jim Procter	JAL-2316 tidied up documentation for Links tab	commit \| commitdiff \| tree
2017-02-08	Jim Procter	JAL-2366 updated default URL to www.jalview.org/services...	commit \| commitdiff \| tree
2017-02-07	Jim Procter	Merge branch 'features/JAL-2371collectionColourScheme...	commit \| commitdiff \| tree
2016-12-16	Jim Procter	JAL-2360 report line number when threshold cannot be...	commit \| commitdiff \| tree
2016-12-14	Jim Procter	Merge branch 'patch/JAL-2197_jpredforjnets' into develop	commit \| commitdiff \| tree
2016-12-04	Jim Procter	JAL-1933 show occupancy count as a tooltip	commit \| commitdiff \| tree
2016-12-04	Jim Procter	JAL-1933 switch from gap count to occupancy	commit \| commitdiff \| tree
2016-12-01	Jim Procter	JAL-1933 update the bounds for the Gap annotation row...	commit \| commitdiff \| tree
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