Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / datamodel / SequenceGroup.java
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2023-05-25 James ProcterJAL-2381 don’t need to set description, dbrefs etc...
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact...
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
2022-10-15 Jim ProcterJAL-2349 reusable contact map holder for SequenceI...
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2019-03-13 gmungocMerge branch 'develop' into trialMerge
2019-02-24 gmungocJAL-3198 SequenceGroup 'bulk constructor' without dupli...
2019-02-04 hansonrrefactoring for DBMODList
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
2018-12-17 Jim ProcterMerge branch 'bug/JAL-2750' into develop
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group...
2018-01-16 kjvdheideJAL-2750 startRes now directly assigned
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings)
2017-11-10 Jim ProcterJAL-2828 refactored duplicate code for searching lists...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-10-03 kjvdheideAdded checks for X mouse coordinate being >= 0 and...
2017-10-02 kjvdhAdded check for negative start columns
2017-08-28 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-08-28 kiramtMerge remote-tracking branch 'origin/releases/Release_2...
2017-08-28 kiramtJAL-2665 Changes for review comments; printing with... bug/JAL-2665
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-16 kiramtJAL-2665 Added hidden columns group selection - almost...
2017-08-16 kiramtJAL-2665 Added sequence group update event.
2017-07-24 gmungocspike branch updated from latest features/JAL-2446
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-08 gmungocJAL-2386 JAL-2570 use ResidueShader copy constructor... bug/JAL-2386groupConservationColouring
2017-06-07 gmungocJAL-2386 ensure group conservation shading is applied...
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping...
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup
2017-04-27 Jim ProcterJAL-2494 fix: updated behaviour for SequenceGroup.findA...
2017-03-31 gmungocJAL-2405 additional checks for circular reference in...
2017-02-15 Jim ProcterJAL-2374 new contains methods for seq and seq,apos
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup...
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader...
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1
2017-01-09 gmungocJAL-2371 pull up isNucleotide to SequenceCollectionI
2017-01-05 gmungocJAL-2371 tests added
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
2016-12-21 gmungocJAL-2360 Javadoc and test cases for findAnnotation
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold...
2016-11-02 gmungocJAL-98 ProfileI interface for Profile
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns...
2016-07-19 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL...
2016-06-20 Jim ProcterJAL-1551 tidy
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus...
2016-03-25 Jim ProcterJAL-2034 make colour scheme update optional when group...
2016-03-25 Jim ProcterJAL-1551
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-04-01 gmungocJAL-845 fixed start/end range of a mapped SequenceGroup
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-02-12 Jim ProcterJAL-1115 List rather than vector for sequence groups...
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-11-28 gmungocJAL-1610 check reference annotations against alignment...
2014-10-10 gmungocJAL-1264 reverted (removed added method)
2014-10-07 gmungocJAL-1264 wip
2014-09-23 gmungocJAL-1264 first cut of panel for annotation show/hide...
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-05-01 Jim ProcterJAL-1492 formatting and squash NPEs
2014-05-01 Jim ProcterJAL-1492 JAL-1397 make AnnotatedCollectionI context...
2014-05-01 Jim ProcterJAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and...
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-10-11 Jim ProcterMerge branch 'JAL-1164_disorderforselection' into Relea...
2013-10-11 Jim ProcterJAL-1114 javadoc
2013-09-02 Jim ProcterJAL-1373 pass size of sequence set to consensus renderi...
2013-07-11 Jim ProcterJAL-1347 make it efficient to call getConsensus to...
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta...
2012-05-23 jprocterJAL-961 - annotatable datamodel objects can be queried...
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065...
2011-10-11 jprocternormalised logo rendering (JAL-958)
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2011-08-17 jprocterJAL-813 fix - check whether conservation is applied...
2011-04-21 jprocterallow an existing alignment annotation row to be bound...
2010-12-17 jprocterjavadoc
2010-12-09 jprocterjavadoc and additional convenience method for JAL-716
2010-09-23 jprocterapply jalview code style
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