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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git] / src / jalview / analysis / AAFrequency.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
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge blob | commitdiff | diff to current
2019-07-10 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... blob | commitdiff | diff to current
2019-06-18 gmungocJAL-3313 don't double count mapped codons blob | commitdiff | diff to current
2019-06-05 tvaJAL-3285 change method declaration in AAFrequency to... blob | commitdiff | diff to current
2019-04-18 hansonrexplicit Hashtable objects blob | commitdiff | diff to current
2019-02-27 gmungocJAL-3202 discard zero percentages in extracted profile blob | commitdiff | diff to current
2018-03-30 gmungocJAL-2939 simplified way of getting hmm consensus residue 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
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... blob | commitdiff | diff to current
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) blob | commitdiff | diff to current
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double... blob | commitdiff | diff to current
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc blob | commitdiff | diff to current
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-08-28 tzvanaaltenJAL-2629 add option to set HMM Logo letter height to... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 hmm annotation consensus characters are now... blob | commitdiff | diff to current
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer blob | commitdiff | diff to current
2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io 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 TZVanaaltenJAL-2599 HMM annotation now shows consensus characters... blob | commitdiff | diff to current
2017-08-16 TZVanaaltenJAL-2599 fix background frequency storage and correct... blob | commitdiff | diff to current
2017-08-02 TZVanaaltenJAL-2599 fix for HMM logo not normalising correctly blob | commitdiff | diff to current
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons blob | commitdiff | diff to current
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... blob | commitdiff | diff to current
2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files blob | commitdiff | diff to current
2017-07-18 TZVanaaltenJAL-2599 complete documentation for HMM and HMMFile... 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
2017-07-11 TZVanaaltencomplete Information Content annotation blob | commitdiff | diff to current
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-05-03 Jim ProcterJAL-1933 show occupancy in tooltip for row blob | commitdiff | diff to current
2017-04-27 Jim ProcterJAL-1933 shade occupancy from light grey to black for... blob | commitdiff | diff to current
2017-04-27 Jim ProcterJAL-1933 don’t show symbol counts under histogram ... blob | commitdiff | diff to current
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity blob | commitdiff | diff to current
2016-12-04 Jim ProcterJAL-1933 show occupancy count as a tooltip blob | commitdiff | diff to current
2016-12-04 Jim ProcterJAL-1933 switch from gap count to occupancy blob | commitdiff | diff to current
2016-12-02 gmungocJAL-1933 gap value as description; minor formatting blob | commitdiff | diff to current
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row... blob | commitdiff | diff to current
2016-12-01 Jim ProcterJAL-1933 basic hack to get gap counts shown as an annot... 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 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 gmungocJAL-98 minor fixes to / tests for annotation derivation 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
2016-10-25 gmungocJAL-98 javadoc / comments updated blob | commitdiff | diff to current
2016-10-24 gmungocJAL-98 fixme comment removed - nothing to do 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
2016-09-26 gmungocJAL-98 don't include gaps in maxResidue! blob | commitdiff | diff to current
2016-09-23 gmungocJAL-98 performance tweaks to use of SparseIntArray blob | commitdiff | diff to current
2016-09-23 gmungocJAL-98 first working version blob | commitdiff | diff to current
2016-09-23 gmungocJAL-98 use SparseIntArray (wip) blob | commitdiff | diff to current
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co... blob | commitdiff | diff to current
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... 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
2015-10-08 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
2015-07-08 gmungocJAL-1759 merge from develop blob | commitdiff | diff to current
2015-07-01 gmungocJAL-1681 more condensed tooltip where codons share... blob | commitdiff | diff to current
2015-05-29 Jim ProcterJAL-1755 fix for NPE when setting up temporary variables 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
2014-12-15 Jim ProcterJAL-1620 version bump and release notes 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 Proctermake sure valid value for non-gapped calculation with... blob | commitdiff | diff to current
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge blob | commitdiff | diff to current
2014-01-29 Jim ProcterJAL-1432 updated copyright notices blob | commitdiff | diff to current
2013-10-16 Jim ProcterJAL-1395 do not calculate non-gap consensus when no... blob | commitdiff | diff to current
2013-09-03 Jim ProcterJAL-1373 tweak precision calculation so alignments... blob | commitdiff | diff to current
2013-09-03 Jim ProcterJAL-920 compute a consensus for single sequence blob | commitdiff | diff to current
2013-09-02 Jim ProcterJAL-1373 generate percentages with appropriate precision blob | commitdiff | diff to current
2013-09-02 Jim ProcterJAL-1373 pass size of sequence set to consensus renderi... blob | commitdiff | diff to current
2012-10-22 jprocterJalview 2.8 Source Header blob | commitdiff | diff to current
2012-10-03 jprocterformatting blob | commitdiff | diff to current
2012-06-07 jprocterJAL-967, JAL-1114, JAL-1115 - modified render and calcu... blob | commitdiff | diff to current
2012-05-31 jprocterformatting blob | commitdiff | diff to current
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta... blob | commitdiff | diff to current
2011-10-11 jprocternormalised logo rendering (JAL-958) blob | commitdiff | diff to current
2011-10-10 jprocterupdate author list in license for (JAL-826) blob | commitdiff | diff to current
2011-09-27 jprocterapply version 2.7 copyright blob | commitdiff | diff to current
2011-07-31 janengelhardtJAL-885; StructureConservation row is displayed at... blob | commitdiff | diff to current
2011-07-29 janengelhardtJAL-885; Implementation of StructureFrequency.java... blob | commitdiff | diff to current
2010-09-23 jprocterNPE race condition alert - see JAL-661 blob | commitdiff | diff to current
2010-09-23 jprocterapply jalview code style blob | commitdiff | diff to current
2010-09-23 jprocterJalview 2.6 source licence blob | commitdiff | diff to current
2010-09-02 jprocterfix occasional arrayIndexOutOfBounds when sequences... blob | commitdiff | diff to current
2010-06-29 jprocterpatch for npe that occurs for importing Jalview project... blob | commitdiff | diff to current
2010-04-30 jprocterjalview 2.5 release banner blob | commitdiff | diff to current
2009-08-21 jprocterstore symbol profile and extract it for display blob | commitdiff | diff to current
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