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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / analysis / AAFrequency.java
2024-09-16 Jim ProcterJAL-4392 autohide the secondary structure consensus... patch/JAL-4392_hide_ssconsensus_if_no_data commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks commit | commitdiff
2024-05-15 Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure commit | commitdiff
2024-05-13 Renia CorreyaJAL-4386 - Implementation of substitution matrix and... commit | commitdiff
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-06-18 gmungocJAL-3313 don't double count mapped codons commit | commitdiff
2019-04-18 hansonrexplicit Hashtable objects commit | commitdiff
2019-02-27 gmungocJAL-3202 discard zero percentages in extracted profile commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-03 Jim ProcterJAL-1933 show occupancy in tooltip for row commit | commitdiff
2017-04-27 Jim ProcterJAL-1933 shade occupancy from light grey to black for... commit | commitdiff
2017-04-27 Jim ProcterJAL-1933 don’t show symbol counts under histogram ... commit | commitdiff
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity commit | commitdiff
2016-12-04 Jim ProcterJAL-1933 show occupancy count as a tooltip commit | commitdiff
2016-12-04 Jim ProcterJAL-1933 switch from gap count to occupancy commit | commitdiff
2016-12-02 gmungocJAL-1933 gap value as description; minor formatting commit | commitdiff
2016-12-01 Jim ProcterJAL-1933 update the bounds for the Gap annotation row... commit | commitdiff
2016-12-01 Jim ProcterJAL-1933 basic hack to get gap counts shown as an annot... commit | commitdiff
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns commit | commitdiff
2016-11-02 gmungocJAL-98 ProfileI interface for Profile commit | commitdiff
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis... commit | commitdiff
2016-10-25 gmungocJAL-98 minor fixes to / tests for annotation derivation commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-25 gmungocJAL-98 javadoc / comments updated commit | commitdiff
2016-10-24 gmungocJAL-98 fixme comment removed - nothing to do commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount... commit | commitdiff
2016-09-26 gmungocJAL-98 don't include gaps in maxResidue! commit | commitdiff
2016-09-23 gmungocJAL-98 performance tweaks to use of SparseIntArray commit | commitdiff
2016-09-23 gmungocJAL-98 first working version commit | commitdiff
2016-09-23 gmungocJAL-98 use SparseIntArray (wip) commit | commitdiff
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co... commit | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop commit | commitdiff
2015-07-01 gmungocJAL-1681 more condensed tooltip where codons share... commit | commitdiff
2015-05-29 Jim ProcterJAL-1755 fix for NPE when setting up temporary variables commit | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-05-01 Jim Proctermake sure valid value for non-gapped calculation with... commit | commitdiff
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2013-10-16 Jim ProcterJAL-1395 do not calculate non-gap consensus when no... commit | commitdiff
2013-09-03 Jim ProcterJAL-1373 tweak precision calculation so alignments... commit | commitdiff
2013-09-03 Jim ProcterJAL-920 compute a consensus for single sequence commit | commitdiff
2013-09-02 Jim ProcterJAL-1373 generate percentages with appropriate precision commit | commitdiff
2013-09-02 Jim ProcterJAL-1373 pass size of sequence set to consensus renderi... commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-06-07 jprocterJAL-967, JAL-1114, JAL-1115 - modified render and calcu... commit | commitdiff
2012-05-31 jprocterformatting commit | commitdiff
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta... commit | commitdiff
2011-10-11 jprocternormalised logo rendering (JAL-958) commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2011-07-31 janengelhardtJAL-885; StructureConservation row is displayed at... commit | commitdiff
2011-07-29 janengelhardtJAL-885; Implementation of StructureFrequency.java... commit | commitdiff
2010-09-23 jprocterNPE race condition alert - see JAL-661 commit | commitdiff
2010-09-23 jprocterapply jalview code style commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-09-02 jprocterfix occasional arrayIndexOutOfBounds when sequences... commit | commitdiff
2010-06-29 jprocterpatch for npe that occurs for importing Jalview project... commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-08-21 jprocterstore symbol profile and extract it for display commit | commitdiff
2009-07-24 jproctercomplete alignment annotation row procedure commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2007-02-07 amwaterhouseFormatting commit | commitdiff
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space commit | commitdiff
2006-12-05 amwaterhousesequence is char [] commit | commitdiff
2006-11-28 amwaterhouseoff by one group consensus calculation commit | commitdiff
2006-11-15 amwaterhouseCheck if groupWidth is greater than sequence width commit | commitdiff
2006-10-10 amwaterhouseMaxResidue must be at least 2 commit | commitdiff
2006-10-10 amwaterhousestatic final strings for consensus keys commit | commitdiff
2006-10-06 amwaterhouseAAFrequency optimized commit | commitdiff
2006-08-21 amwaterhouseheader updated commit | commitdiff
2005-09-30 amwaterhouseRemove redundancy in Eclipse commit | commitdiff
2005-08-23 amwaterhouseFinalize calculate method commit | commitdiff
2005-08-18 amwaterhouseCharacter methods don't exist in java 1.1 commit | commitdiff
2005-08-18 jproctervarious case sensitivity bugs fixed in residue comparis... commit | commitdiff
2005-08-15 amwaterhouseCalculate gap and nogap ratio here commit | commitdiff
2005-06-30 amwaterhouseFormatting changes commit | commitdiff
2005-06-10 amwaterhouseRemove imports commit | commitdiff
2005-06-08 amwaterhouseFormatted source commit | commitdiff
2005-06-08 amwaterhouseGPL license added commit | commitdiff
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