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[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff
2016-12-04	Jim Procter	JAL-1933 switch from gap count to occupancy	blob \| commitdiff \| diff to current
2016-12-02	gmungoc	JAL-1933 gap value as description; minor formatting	blob \| commitdiff \| diff to current
2016-12-01	Jim Procter	JAL-1933 basic hack to get gap counts shown as an annot...	blob \| commitdiff \| diff to current
2016-11-22	Jim Procter	Merge branch 'features/JAL-1738_JAL-345_selectionfromhi...	blob \| commitdiff \| diff to current
2016-11-17	gmungoc	JAL-98 ProfilesI container for profiles for columns	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 JAL-1854 encapsulate 'magic number' threshold...	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 ProfileI interface for Profile	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 Profile and ResidueCount moved from analysis...	blob \| commitdiff \| diff to current
2016-10-28	Jim Procter	JAL-966 SearchResultsI now on viewmodels.AlignmentViewp...	blob \| commitdiff \| diff to current
2016-10-28	Jim Procter	JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...	blob \| commitdiff \| diff to current
2016-10-26	gmungoc	Merge branch 'bug/JAL-98consensusMemory' into develop	blob \| commitdiff \| diff to current
2016-10-26	gmungoc	JAL-98 null reference to globalColourScheme as it has...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-24	Jim Procter	Merge branch 'releases/Release_2_10_0_Branch'	blob \| commitdiff \| diff to current
2016-10-24	gmungoc	JAL-2283 set 'by conservation' correctly when changing...	blob \| commitdiff \| diff to current
2016-10-06	gmungoc	Merge branch 'develop' into bug/JAL-98consensusMemory	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-10-03	gmungoc	JAL-98 use Profile to store consensus, ResidueCount...	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-1421 typed ResidueProperties.propHash; JAL-2176...	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-2216 new dispose() method to null references	blob \| commitdiff \| diff to current
2016-09-20	gmungoc	JAL-1306 calculate Quality also when Conservation not...	blob \| commitdiff \| diff to current
2016-09-19	gmungoc	JAL-2172 test and code updates for readonly selection...	blob \| commitdiff \| diff to current
2016-09-07	Jim Procter	Merge branch 'develop' into bug/JAL-1803_JAL-2157	blob \| commitdiff \| diff to current
2016-09-06	gmungoc	JAL-2147 additional test coverage for findMappingsForSe...	blob \| commitdiff \| diff to current
2016-09-01	Jim Procter	JAL-2034 check context of selection group to catch...	blob \| commitdiff \| diff to current
2016-08-31	Jim Procter	JAL-2034 moved ‘isDefinedGroup’ flag to a test method...	blob \| commitdiff \| diff to current
2016-07-20	gmungoc	JAL-2023 stronger check for whether to start cdna consensus	blob \| commitdiff \| diff to current
2016-07-14	Jim Procter	fix for JAL-2147	blob \| commitdiff \| diff to current
2016-06-27	gmungoc	JAL-2133 refactored duplicated code to AlignmentViewport	blob \| commitdiff \| diff to current
2016-06-22	gmungoc	JAL-1982 defensive checks for null annotations array	blob \| commitdiff \| diff to current
2016-06-02	tcofoegbu	JAL-1944 java doc update and minor house keeping	blob \| commitdiff \| diff to current
2016-06-01	tcofoegbu	JAL-1944 updated bugfix implementation	blob \| commitdiff \| diff to current
2016-05-31	tcofoegbu	JAL-1944 fix for visible seqs sometimes been replaced...	blob \| commitdiff \| diff to current
2016-05-27	gmungoc	JAL-1989 tightened up use of flag for 'column selection...	blob \| commitdiff \| diff to current
2016-04-27	Jim Procter	JAL-2085 JAL-2086 fix hiddenRepSequence and new referen...	blob \| commitdiff \| diff to current
2016-04-04	Jim Procter	JAL-969 refactor columnselection operation (during...	blob \| commitdiff \| diff to current
2016-03-07	gmungoc	JAL-2023 CDS sequences added to / share alignment dataset	blob \| commitdiff \| diff to current
2016-03-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2016-02-26	tcofoegbu	JAL-1994 updated implementation for broken tests	blob \| commitdiff \| diff to current
2016-02-26	tcofoegbu	JAL-1994 fix for broken tests	blob \| commitdiff \| diff to current
2016-02-25	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2016-02-22	tcofoegbu	JAL-1944 bugfix for error when exporting hidden sequenc...	blob \| commitdiff \| diff to current
2016-02-22	gmungoc	JAL-1705 first pass at applying preset feature colourin...	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-11	gmungoc	JAL-1989 more unit tests and encapsulation for ColumnSe...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 realise virtual mappings and align when adding...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-03	Jim Procter	JAL-961 TODO use workers for calculations supporting...	blob \| commitdiff \| diff to current
2015-09-03	Jim Procter	JAL-1551 source tidy	blob \| commitdiff \| diff to current
2015-08-17	gmungoc	JAL-1691 scan full width and depth of alignment for...	blob \| commitdiff \| diff to current
2015-06-30	gmungoc	JAL-1691 trackpad scrolling goes to full width even...	blob \| commitdiff \| diff to current
2015-06-19	Jim Procter	JAL-653 JAL-1780 dropped av.setHasHiddenRows() and...	blob \| commitdiff \| diff to current
2015-06-19	Jim Procter	JAL-1780 JAL-653 organise imports	blob \| commitdiff \| diff to current
2015-06-10	tcofoegbu	JAL-1641 updated applet version	blob \| commitdiff \| diff to current
2015-04-28	gmungoc	JAL-1684 removed reflection from ViewStyle (to Junit...	blob \| commitdiff \| diff to current
2015-04-27	gmungoc	JAL-1691 more stable linked scrolling across split...	blob \| commitdiff \| diff to current
2015-04-08	gmungoc	JAL-1691 applet SplitFrame scrolling; pull up of 5...	blob \| commitdiff \| diff to current
2015-04-02	gmungoc	JAL-1690 'scale protein as cDNA' options in Preferences...	blob \| commitdiff \| diff to current
2015-04-01	gmungoc	JAL-1264 reinstate Show annotations menu item	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-969 hasHiddenRows is now an interface method	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-969 drop the hiddenColumns flag in favour of checki...	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-969 javadoc and mark interface overrides for clarity	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-1628 drop getShowAnnotation accessor in favour...	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1628 method to hide insertions to current sequence...	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1628 wrappers for common checks on ColumnSelection	blob \| commitdiff \| diff to current
2015-01-09	Jim Procter	Merge branch 'JAL-1372_referenceseq' into feature_29...	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-17	gmungoc	JAL-1293 hide/show sequence annotations with hide/revea...	blob \| commitdiff \| diff to current
2014-11-14	Jim Procter	Merge branch 'develop' into JAL-1483_featureBasedTreeCalc	blob \| commitdiff \| diff to current
2014-09-12	j.procter@dundee...	JAL-1486 JAL-535 refactor code for trimming alignment...	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1483 move show sequence feature and sequence featur...	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1483 model and api for feature display list on...	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-05-02	Jim Procter	Merge branch 'Release_2_8_1_Branch' into JAL-1372_refer...	blob \| commitdiff \| diff to current
2014-05-01	Jim Procter	JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and...	blob \| commitdiff \| diff to current
2014-05-01	Jim Procter	JAL-961 store result of conservation analysis worker...	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	don't unhook existing group associated annotation JAL...	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	don't finness the alignment annotation modification...	blob \| commitdiff \| diff to current
2014-02-03	Jim Procter	Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-10-11	Jim Procter	JAL-1164 regression on JAL-1292 use bitset to mark...	blob \| commitdiff \| diff to current
2013-10-11	Jim Procter	JAL-1164 regression on JAL-1292 use bitset to mark...	blob \| commitdiff \| diff to current
2013-10-11	Jim Procter	JAL-1385 expose core view model methods in interface	blob \| commitdiff \| diff to current
2013-10-07	Jim Procter	JAL-1385 JAL-535 refactor sequence colour settings...	blob \| commitdiff \| diff to current
2013-10-07	Jim Procter	JAL-1385 expose core view model methods in interface	blob \| commitdiff \| diff to current
2013-08-30	Jim Procter	JAL-1367 allow reference sequence to be shown in bold...	blob \| commitdiff \| diff to current
2013-08-30	Jim Procter	JAL-1370 JAL-1371 flags for display and colour of view...	blob \| commitdiff \| diff to current
2013-06-23	Jim Procter	JAL-1230 simplify initialisation of consensus, conserva...	blob \| commitdiff \| diff to current
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