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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
2016-12-01	Jim Procter	JAL-1933 basic hack to get gap counts shown as an annotation...	commit \| commitdiff \| tree
2016-11-30	Jim Procter	Merge branch 'features/JAL-2320_closeChimeraAction...	commit \| commitdiff \| tree
2016-11-29	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-29	Jim Procter	JAL-2325 update release date in whatsNew	commit \| commitdiff \| tree
2016-11-29	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-11-29	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-28	Jim Procter	JAL-2325 JAL-1878 update minimum versions of JRE for...	commit \| commitdiff \| tree
2016-11-28	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-28	Jim Procter	JAL-2325 finalise release notes	commit \| commitdiff \| tree
2016-11-25	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-25	Jim Procter	JAL-2325 JAL-2273 update vms bound to different installers	commit \| commitdiff \| tree
2016-11-25	Jim Procter	JAL-2325 more ignores on sourcedist build	commit \| commitdiff \| tree
2016-11-24	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-24	Jim Procter	JAL-2325 exclude .class and .* files (install anywhere...	commit \| commitdiff \| tree
2016-11-24	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-24	Jim Procter	JAL-2325 applied BSD license for chimera/StrucViz2...	commit \| commitdiff \| tree
2016-11-24	Jim Procter	JAL-2325 apply license to new source files	commit \| commitdiff \| tree
2016-11-24	Jim Procter	JAL-2325 update release date to next Tuesday	commit \| commitdiff \| tree
2016-11-24	Jim Procter	JAL-2325 tidy up release notes	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 remove 2.10.0 what’s new	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 latest release to 2.10	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-1738 Ctrl/Cmd/Alt modifiers and mention that B...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-1738 hint about using the task switching key combination...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-1738 mention Ctrl/Cmd/Alt modifiers and mention...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-1738 mention Ctrl or Cmd for toggle behaviour in...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 updated what’s new for 2.10.1	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 reword ‘tame tooltip’ JAL-1723 release note	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 rejig authors and add Kira	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2282 JAL-2325 added link to help text from release...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 updated what’s new for 2.10.1	commit \| commitdiff \| tree
2016-11-23	Jim Procter	Merge branch 'develop' of http://source.jalview.org...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2282 revised docs about warning message.	commit \| commitdiff \| tree
2016-11-23	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 JAL-2332 release notes	commit \| commitdiff \| tree
2016-11-23	Jim Procter	Merge branch 'documentation/JAL-2325_release2101' into...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	Merge branch 'bug/JAL-2323disulfideOverview' into develop	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 moved disulphide/contact bug fixes (JAL-2323...	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 release notes formatting	commit \| commitdiff \| tree
2016-11-23	Jim Procter	JAL-2325 release notes	commit \| commitdiff \| tree
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