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Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel / SequenceGroup.java
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2... blob | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 blob | commitdiff | diff to current
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... blob | commitdiff | diff to current
2019-06-05 tvaJAL-3285 add unmerged code to SequenceGroup blob | commitdiff | diff to current
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer blob | commitdiff | diff to current
2019-03-13 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2019-02-24 gmungocJAL-3198 SequenceGroup 'bulk constructor' without dupli... blob | commitdiff | diff to current
2019-02-04 hansonrrefactoring for DBMODList blob | commitdiff | diff to current
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... blob | commitdiff | diff to current
2018-12-17 Jim ProcterMerge branch 'bug/JAL-2750' into develop blob | commitdiff | diff to current
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of group without sequences... blob | commitdiff | diff to current
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of sequences from group... blob | commitdiff | diff to current
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not... blob | commitdiff | diff to current
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... blob | commitdiff | diff to current
2018-03-30 gmungocJAL-2939 field/method naming more consistent blob | commitdiff | diff to current
2018-03-26 gmungocJAL-2939 always store Information profile blob | commitdiff | diff to current
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and... blob | commitdiff | diff to current
2018-03-16 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group... blob | commitdiff | diff to current
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... blob | commitdiff | diff to current
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip) blob | commitdiff | diff to current
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc blob | commitdiff | diff to current
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and... blob | commitdiff | diff to current
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer blob | commitdiff | diff to current
2018-01-16 kjvdheideJAL-2750 startRes now directly assigned blob | commitdiff | diff to current
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) blob | commitdiff | diff to current
2017-11-10 Jim ProcterJAL-2828 refactored duplicate code for searching lists... blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-10-03 kjvdheideAdded checks for X mouse coordinate being >= 0 and... blob | commitdiff | diff to current
2017-10-02 kjvdhAdded check for negative start columns blob | commitdiff | diff to current
2017-08-28 tzvanaaltenJAL-2629 add option to set HMM Logo letter height to... blob | commitdiff | diff to current
2017-08-28 kiramtMerge remote-tracking branch 'origin/develop' into... blob | commitdiff | diff to current
2017-08-28 kiramtMerge remote-tracking branch 'origin/releases/Release_2... blob | commitdiff | diff to current
2017-08-28 kiramtJAL-2665 Changes for review comments; printing with... bug/JAL-2665 blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 remove sequence and group HMMER options blob | commitdiff | diff to current
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer blob | commitdiff | diff to current
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-08-16 kiramtJAL-2665 Added hidden columns group selection - almost... blob | commitdiff | diff to current
2017-08-16 kiramtJAL-2665 Added sequence group update event. blob | commitdiff | diff to current
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group blob | commitdiff | diff to current
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons blob | commitdiff | diff to current
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 blob | commitdiff | diff to current
2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics... features/hmmer_statistics blob | commitdiff | diff to current
2017-07-12 TZVanaaltentest HMM annotaTION blob | commitdiff | diff to current
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations blob | commitdiff | diff to current
2017-06-23 TZVanaaltenadd HMMER colour scheme blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-06-08 gmungocJAL-2386 JAL-2570 use ResidueShader copy constructor... bug/JAL-2386groupConservationColouring blob | commitdiff | diff to current
2017-06-07 gmungocJAL-2386 ensure group conservation shading is applied... blob | commitdiff | diff to current
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping... blob | commitdiff | diff to current
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup blob | commitdiff | diff to current
2017-04-27 Jim ProcterJAL-2494 fix: updated behaviour for SequenceGroup.findA... blob | commitdiff | diff to current
2017-03-31 gmungocJAL-2405 additional checks for circular reference in... blob | commitdiff | diff to current
2017-02-15 Jim ProcterJAL-2374 new contains methods for seq and seq,apos blob | commitdiff | diff to current
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup... blob | commitdiff | diff to current
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader... blob | commitdiff | diff to current
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1 blob | commitdiff | diff to current
2017-01-09 gmungocJAL-2371 pull up isNucleotide to SequenceCollectionI blob | commitdiff | diff to current
2017-01-05 gmungocJAL-2371 tests added blob | commitdiff | diff to current
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI blob | commitdiff | diff to current
2016-12-21 gmungocJAL-2360 Javadoc and test cases for findAnnotation blob | commitdiff | diff to current
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns blob | commitdiff | diff to current
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold... blob | commitdiff | diff to current
2016-11-02 gmungocJAL-98 ProfileI interface for Profile blob | commitdiff | diff to current
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis... blob | commitdiff | diff to current
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch blob | commitdiff | diff to current
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... blob | commitdiff | diff to current
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount... blob | commitdiff | diff to current
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... blob | commitdiff | diff to current
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns... blob | commitdiff | diff to current
2016-07-19 Jim ProcterMerge branch 'develop' into efficiency/JAL-2034_JAL... blob | commitdiff | diff to current
2016-06-20 Jim ProcterJAL-1551 tidy blob | commitdiff | diff to current
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus... blob | commitdiff | diff to current
2016-03-25 Jim ProcterJAL-2034 make colour scheme update optional when group... blob | commitdiff | diff to current
2016-03-25 Jim ProcterJAL-1551 blob | commitdiff | diff to current
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc... blob | commitdiff | diff to current
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 blob | commitdiff | diff to current
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... blob | commitdiff | diff to current
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports blob | commitdiff | diff to current
2015-04-01 gmungocJAL-845 fixed start/end range of a mapped SequenceGroup blob | commitdiff | diff to current
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch blob | commitdiff | diff to current
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... blob | commitdiff | diff to current
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... blob | commitdiff | diff to current
2015-02-12 Jim ProcterJAL-1115 List rather than vector for sequence groups... blob | commitdiff | diff to current
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 blob | commitdiff | diff to current
2014-12-15 Jim ProcterJAL-1620 version bump and release notes blob | commitdiff | diff to current
2014-11-28 gmungocJAL-1610 check reference annotations against alignment... blob | commitdiff | diff to current
2014-10-10 gmungocJAL-1264 reverted (removed added method) blob | commitdiff | diff to current
2014-10-07 gmungocJAL-1264 wip blob | commitdiff | diff to current
2014-09-23 gmungocJAL-1264 first cut of panel for annotation show/hide... blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 source formatting blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 blob | commitdiff | diff to current
2014-05-22 Jim ProcterJAL-1503 update version in GPL header blob | commitdiff | diff to current
2014-05-01 Jim ProcterJAL-1492 formatting and squash NPEs blob | commitdiff | diff to current
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