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[jalview.git] / src / jalview / analysis / Conservation.java

2021-09-21	Ben Soares	JAL-3691 automatic insertion of Locale.ROOT to toUpperC...	blob \| commitdiff
2019-07-16	gmungoc	JAL-3210 Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-03-20	Ben Soares	JAL-3130 Lots of deprecation fixes. See utils/deprecat...	blob \| commitdiff \| diff to current
2018-10-17	Jim Procter	Merge branch 'feature/JAL-3063JAXB' into Jalview-BH...	blob \| commitdiff \| diff to current
2018-09-06	Jim Procter	JAL-3105 reallocate quality and consensus annotation...	blob \| commitdiff \| diff to current
2018-06-21	gmungoc	JAL-3032 round Quality score for tooltip (as it becomes...	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-14	gmungoc	JAL-2598 Sequence.getSequence return a copy of the...	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-03-29	gmungoc	JAL-2416 JAL-728 reduced dependency on Blosum62 impleme...	blob \| commitdiff \| diff to current
2017-03-28	gmungoc	JAL-2416 JAL-2403 remove unused '*' row/column from...	blob \| commitdiff \| diff to current
2017-03-27	gmungoc	JAL-2416 score matrix gap symbol (if any) dynamically...	blob \| commitdiff \| diff to current
2017-02-21	gmungoc	JAL-2416 quality calculation now only depends on loaded...	blob \| commitdiff \| diff to current
2017-02-18	gmungoc	JAL-2416 better encapsulated 'constants' for BLOSUM62...	blob \| commitdiff \| diff to current
2017-02-17	gmungoc	JAL-2416 BLOSUM62 removed from ResidueProperties	blob \| commitdiff \| diff to current
2017-02-13	gmungoc	JAL-1632 JAL-2416 load score matrices from file, as...	blob \| commitdiff \| diff to current
2017-01-04	gmungoc	JAL-2371 CollectionColourScheme wraps ColourSchemeI	blob \| commitdiff \| diff to current
2016-12-16	gmungoc	JAL-1705 JAL-98 use SortedMap as more accurate type...	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 JAL-1854 encapsulate 'magic number' threshold...	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 Profile and ResidueCount moved from analysis...	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 wording "negatively conserved" now "absence...	blob \| commitdiff \| diff to current
2016-11-01	gmungoc	Conservation now using ResidueCount; tests added	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	gmungoc	Merge branch 'develop' into bug/JAL-98consensusMemory	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-09-26	gmungoc	JAL-98 bug fix, string optimisation, sorted AA properties	blob \| commitdiff \| diff to current
2016-09-23	gmungoc	JAL-98 use SparseIntArray (wip)	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-1421 use declared type of ResidueProperties.propHash	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-1421 typed ResidueProperties.propHash; JAL-2176...	blob \| commitdiff \| diff to current
2016-09-20	gmungoc	JAL-1306 calculate Quality also when Conservation not...	blob \| commitdiff \| diff to current
2016-07-18	Jim Procter	JAL-2145 improvement: ensure conservation calculation...	blob \| commitdiff \| diff to current
2016-05-26	gmungoc	JAL-1797 non-case-sensitive counting of residues /...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-08-10	Jim Procter	JAL-736 relocate group associated conservation symbols...	blob \| commitdiff \| diff to current
2015-08-10	Jim Procter	JAL-736 source formatting	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-13	Jim Procter	Merge branch 'Release_2_8_2_Branch' into JAL-1483_featu...	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	JAL-736 hack to show the conserved property values...	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2011-10-21	jprocter	static convenience methods for constructing and calcula...	blob \| commitdiff \| diff to current
2011-10-21	jprocter	use List rather than Vector	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-07-29	janengelhardt	JAL-885; Implementation of StructureFrequency.java...	blob \| commitdiff \| diff to current
2011-02-18	jprocter	fix for occasional race conditions	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-08-21	jprocter	1.1 compatibility	blob \| commitdiff \| diff to current
2009-08-21	jprocter	start/stop for per-group consensus calculation	blob \| commitdiff \| diff to current
2009-07-24	jprocter	complete alignment annotation row procedure	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-04-10	jprocter	quick fix for conservation calculation when residue...	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-01-30	amwaterhouse	Any character non aa or nucleotide is a space	blob \| commitdiff \| diff to current
2006-12-14	amwaterhouse	one less cast	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	sequence is char []	blob \| commitdiff \| diff to current
2006-11-07	amwaterhouse	warning note added to consequence	blob \| commitdiff \| diff to current
2006-11-06	amwaterhouse	If start is not zero, we need to put -- at the start	blob \| commitdiff \| diff to current
2006-10-26	amwaterhouse	Error message changed	blob \| commitdiff \| diff to current
2006-10-11	jprocter	fixes exception (array index out of bounds - due to...	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	Optimized	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-04-10	amwaterhouse	dont need to set - to -	blob \| commitdiff \| diff to current
2006-04-07	amwaterhouse	Set all gaps to - symbol	blob \| commitdiff \| diff to current
2005-08-18	amwaterhouse	Character methods don't exist in java 1.1	blob \| commitdiff \| diff to current
2005-08-18	jprocter	various case sensitivity bugs fixed in residue comparis...	blob \| commitdiff \| diff to current
2005-08-15	amwaterhouse	Declare variables outside loops	blob \| commitdiff \| diff to current
2005-06-30	amwaterhouse	Formatting changes	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	Formatted source	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	GPL license added	blob \| commitdiff \| diff to current
2005-05-25	jprocter	tidied up system.out messages and moved many to stderr.	blob \| commitdiff \| diff to current
2005-05-03	amwaterhouse	1.1 compatible	blob \| commitdiff \| diff to current
2005-04-11	jprocter	added the alignment quality calculation from the old...	blob \| commitdiff \| diff to current
2005-04-08	jprocter	remember: do not check in quick bug fixes that you...	blob \| commitdiff \| diff to current
2005-04-08	jprocter	Alignment quality with funky coloured histograms.	blob \| commitdiff \| diff to current
2005-03-23	amwaterhouse	drawableSequence removed	blob \| commitdiff \| diff to current
2004-12-15	amwaterhouse	isGap method added to utils	blob \| commitdiff \| diff to current
2004-12-14	amwaterhouse	Hastable is not used anywhere	blob \| commitdiff \| diff to current
2004-12-14	amwaterhouse	Hashtable size must allow for total-start	blob \| commitdiff \| diff to current
2004-11-16	amwaterhouse	Removed spaces	blob \| commitdiff \| diff to current
2004-11-02	amwaterhouse	Jalview Imported Sources start	blob \| commitdiff \| diff to current

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