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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / analysis / Conservation.java
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
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... commit | commitdiff
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH... commit | commitdiff
2018-09-06 Jim ProcterJAL-3105 reallocate quality and consensus annotation... commit | commitdiff
2018-06-21 gmungocJAL-3032 round Quality score for tooltip (as it becomes... 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
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme... commit | commitdiff
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from... commit | commitdiff
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically... commit | commitdiff
2017-02-21 gmungocJAL-2416 quality calculation now only depends on loaded... commit | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... commit | commitdiff
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties commit | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... commit | commitdiff
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI commit | commitdiff
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type... commit | commitdiff
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold... commit | commitdiff
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis... commit | commitdiff
2016-11-02 gmungocJAL-98 wording "negatively conserved" now "absence... commit | commitdiff
2016-11-01 gmungocConservation now using ResidueCount; tests added commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-09-26 gmungocJAL-98 bug fix, string optimisation, sorted AA properties commit | commitdiff
2016-09-23 gmungocJAL-98 use SparseIntArray (wip) commit | commitdiff
2016-09-22 gmungocJAL-1421 use declared type of ResidueProperties.propHash commit | commitdiff
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... commit | commitdiff
2016-09-20 gmungocJAL-1306 calculate Quality also when Conservation not... commit | commitdiff
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation... commit | commitdiff
2016-05-26 gmungocJAL-1797 non-case-sensitive counting of residues /... 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
2015-08-10 Jim ProcterJAL-736 relocate group associated conservation symbols... commit | commitdiff
2015-08-10 Jim ProcterJAL-736 source formatting commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-06-13 Jim ProcterMerge branch 'Release_2_8_2_Branch' into JAL-1483_featu... 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
2014-04-21 Jim ProcterJAL-736 hack to show the conserved property values... commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2011-10-21 jprocterstatic convenience methods for constructing and calcula... commit | commitdiff
2011-10-21 jprocteruse List rather than Vector commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_... commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2011-07-29 janengelhardtJAL-885; Implementation of StructureFrequency.java... commit | commitdiff
2011-02-18 jprocterfix for occasional race conditions commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-08-21 jprocter1.1 compatibility commit | commitdiff
2009-08-21 jprocterstart/stop for per-group consensus calculation 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
2008-04-10 jprocterquick fix for conservation calculation when residue... commit | commitdiff
2007-02-07 amwaterhouseFormatting commit | commitdiff
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space commit | commitdiff
2006-12-14 amwaterhouseone less cast commit | commitdiff
2006-12-05 amwaterhousesequence is char [] commit | commitdiff
2006-11-07 amwaterhousewarning note added to consequence commit | commitdiff
2006-11-06 amwaterhouseIf start is not zero, we need to put -- at the start commit | commitdiff
2006-10-26 amwaterhouseError message changed commit | commitdiff
2006-10-11 jprocterfixes exception (array index out of bounds - due to... commit | commitdiff
2006-10-10 amwaterhouseOptimized commit | commitdiff
2006-08-21 amwaterhouseheader updated commit | commitdiff
2006-04-10 amwaterhousedont need to set - to - commit | commitdiff
2006-04-07 amwaterhouseSet all gaps to - symbol 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 amwaterhouseDeclare variables outside loops commit | commitdiff
2005-06-30 amwaterhouseFormatting changes commit | commitdiff
2005-06-08 amwaterhouseFormatted source commit | commitdiff
2005-06-08 amwaterhouseGPL license added commit | commitdiff
2005-05-25 jproctertidied up system.out messages and moved many to stderr. commit | commitdiff
2005-05-03 amwaterhouse1.1 compatible commit | commitdiff
2005-04-11 jprocteradded the alignment quality calculation from the old... commit | commitdiff
2005-04-08 jprocterremember: do not check in quick bug fixes that you... commit | commitdiff
2005-04-08 jprocterAlignment quality with funky coloured histograms. commit | commitdiff
2005-03-23 amwaterhousedrawableSequence removed commit | commitdiff
2004-12-15 amwaterhouseisGap method added to utils commit | commitdiff
2004-12-14 amwaterhouseHastable is not used anywhere commit | commitdiff
2004-12-14 amwaterhouseHashtable size must allow for total-start commit | commitdiff
2004-11-16 amwaterhouseRemoved spaces commit | commitdiff
2004-11-02 amwaterhouseJalview Imported Sources start commit | commitdiff