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...
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH...
2018-09-06 Jim ProcterJAL-3105 reallocate quality and consensus annotation...
2018-06-21 gmungocJAL-3032 round Quality score for tooltip (as it becomes...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme...
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from...
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically...
2017-02-21 gmungocJAL-2416 quality calculation now only depends on loaded...
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62...
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
2016-12-16 gmungocJAL-1705 JAL-98 use SortedMap as more accurate type...
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold...
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis...
2016-11-02 gmungocJAL-98 wording "negatively conserved" now "absence...
2016-11-01 gmungocConservation now using ResidueCount; tests added
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-09-26 gmungocJAL-98 bug fix, string optimisation, sorted AA properties
2016-09-23 gmungocJAL-98 use SparseIntArray (wip)
2016-09-22 gmungocJAL-1421 use declared type of ResidueProperties.propHash
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-09-20 gmungocJAL-1306 calculate Quality also when Conservation not...
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation...
2016-05-26 gmungocJAL-1797 non-case-sensitive counting of residues /...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
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
2015-08-10 Jim ProcterJAL-736 relocate group associated conservation symbols...
2015-08-10 Jim ProcterJAL-736 source formatting
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-06-13 Jim ProcterMerge branch 'Release_2_8_2_Branch' into JAL-1483_featu...
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
2014-04-21 Jim ProcterJAL-736 hack to show the conserved property values...
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2011-10-21 jprocterstatic convenience methods for constructing and calcula...
2011-10-21 jprocteruse List rather than Vector
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_...
2011-09-27 jprocterapply version 2.7 copyright
2011-07-29 janengelhardtJAL-885; Implementation of StructureFrequency.java...
2011-02-18 jprocterfix for occasional race conditions
2010-09-23 jprocterJalview 2.6 source licence
2010-04-30 jprocterjalview 2.5 release banner
2009-08-21 jprocter1.1 compatibility
2009-08-21 jprocterstart/stop for per-group consensus calculation
2009-07-24 jproctercomplete alignment annotation row procedure
2009-06-08 jprocterapply gpl development license
2008-09-04 jproctermerge from 2_4_Release branch
2008-04-10 jprocterquick fix for conservation calculation when residue...
2007-02-07 amwaterhouseFormatting
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space
2006-12-14 amwaterhouseone less cast
2006-12-05 amwaterhousesequence is char []
2006-11-07 amwaterhousewarning note added to consequence
2006-11-06 amwaterhouseIf start is not zero, we need to put -- at the start
2006-10-26 amwaterhouseError message changed
2006-10-11 jprocterfixes exception (array index out of bounds - due to...
2006-10-10 amwaterhouseOptimized
2006-08-21 amwaterhouseheader updated
2006-04-10 amwaterhousedont need to set - to -
2006-04-07 amwaterhouseSet all gaps to - symbol
2005-08-18 amwaterhouseCharacter methods don't exist in java 1.1
2005-08-18 jproctervarious case sensitivity bugs fixed in residue comparis...
2005-08-15 amwaterhouseDeclare variables outside loops
2005-06-30 amwaterhouseFormatting changes
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2005-05-25 jproctertidied up system.out messages and moved many to stderr.
2005-05-03 amwaterhouse1.1 compatible
2005-04-11 jprocteradded the alignment quality calculation from the old...
2005-04-08 jprocterremember: do not check in quick bug fixes that you...
2005-04-08 jprocterAlignment quality with funky coloured histograms.
2005-03-23 amwaterhousedrawableSequence removed
2004-12-15 amwaterhouseisGap method added to utils
2004-12-14 amwaterhouseHastable is not used anywhere
2004-12-14 amwaterhouseHashtable size must allow for total-start
2004-11-16 amwaterhouseRemoved spaces
2004-11-02 amwaterhouseJalview Imported Sources start