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

2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff
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
2017-05-03	Jim Procter	JAL-1933 show occupancy in tooltip for row	blob \| commitdiff \| diff to current
2017-04-27	Jim Procter	JAL-1933 shade occupancy from light grey to black for...	blob \| commitdiff \| diff to current
2017-04-27	Jim Procter	JAL-1933 don’t show symbol counts under histogram ...	blob \| commitdiff \| diff to current
2017-03-16	Jim Procter	JAL-1933 refactor parameter for code clarity	blob \| commitdiff \| diff to current
2016-12-04	Jim Procter	JAL-1933 show occupancy count as a tooltip	blob \| commitdiff \| diff to current
2016-12-04	Jim Procter	JAL-1933 switch from gap count to occupancy	blob \| commitdiff \| diff to current
2016-12-02	gmungoc	JAL-1933 gap value as description; minor formatting	blob \| commitdiff \| diff to current
2016-12-01	Jim Procter	JAL-1933 update the bounds for the Gap annotation row...	blob \| commitdiff \| diff to current
2016-12-01	Jim Procter	JAL-1933 basic hack to get gap counts shown as an annot...	blob \| commitdiff \| diff to current
2016-11-17	gmungoc	JAL-98 ProfilesI container for profiles for columns	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 ProfileI interface for Profile	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 Profile and ResidueCount moved from analysis...	blob \| commitdiff \| diff to current
2016-10-25	gmungoc	JAL-98 minor fixes to / tests for annotation derivation	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
2016-10-25	gmungoc	JAL-98 javadoc / comments updated	blob \| commitdiff \| diff to current
2016-10-24	gmungoc	JAL-98 fixme comment removed - nothing to do	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-03	gmungoc	JAL-98 use Profile to store consensus, ResidueCount...	blob \| commitdiff \| diff to current
2016-09-26	gmungoc	JAL-98 don't include gaps in maxResidue!	blob \| commitdiff \| diff to current
2016-09-23	gmungoc	JAL-98 performance tweaks to use of SparseIntArray	blob \| commitdiff \| diff to current
2016-09-23	gmungoc	JAL-98 first working version	blob \| commitdiff \| diff to current
2016-09-23	gmungoc	JAL-98 use SparseIntArray (wip)	blob \| commitdiff \| diff to current
2016-07-20	gmungoc	JAL-2023 JAL-1681 fixed bug in computing '+' for co...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 AlignedCodonFrame internal refactor, merge...	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
2015-07-08	gmungoc	JAL-1759 merge from develop	blob \| commitdiff \| diff to current
2015-07-01	gmungoc	JAL-1681 more condensed tooltip where codons share...	blob \| commitdiff \| diff to current
2015-05-29	Jim Procter	JAL-1755 fix for NPE when setting up temporary variables	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	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
2014-05-01	Jim Procter	make sure valid value for non-gapped calculation with...	blob \| commitdiff \| diff to current
2014-02-03	Jim Procter	Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-10-16	Jim Procter	JAL-1395 do not calculate non-gap consensus when no...	blob \| commitdiff \| diff to current
2013-09-03	Jim Procter	JAL-1373 tweak precision calculation so alignments...	blob \| commitdiff \| diff to current
2013-09-03	Jim Procter	JAL-920 compute a consensus for single sequence	blob \| commitdiff \| diff to current
2013-09-02	Jim Procter	JAL-1373 generate percentages with appropriate precision	blob \| commitdiff \| diff to current
2013-09-02	Jim Procter	JAL-1373 pass size of sequence set to consensus renderi...	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
2012-06-07	jprocter	JAL-967, JAL-1114, JAL-1115 - modified render and calcu...	blob \| commitdiff \| diff to current
2012-05-31	jprocter	formatting	blob \| commitdiff \| diff to current
2012-05-30	jprocter	JAL-1114 - refactor methods handling Vectors and Hashta...	blob \| commitdiff \| diff to current
2011-10-11	jprocter	normalised logo rendering (JAL-958)	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-07-31	janengelhardt	JAL-885; StructureConservation row is displayed at...	blob \| commitdiff \| diff to current
2011-07-29	janengelhardt	JAL-885; Implementation of StructureFrequency.java...	blob \| commitdiff \| diff to current
2010-09-23	jprocter	NPE race condition alert - see JAL-661	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-09-02	jprocter	fix occasional arrayIndexOutOfBounds when sequences...	blob \| commitdiff \| diff to current
2010-06-29	jprocter	patch for npe that occurs for importing Jalview project...	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-08-21	jprocter	store symbol profile and extract it for display	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
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
2006-12-05	amwaterhouse	sequence is char []	blob \| commitdiff \| diff to current
2006-11-28	amwaterhouse	off by one group consensus calculation	blob \| commitdiff \| diff to current
2006-11-15	amwaterhouse	Check if groupWidth is greater than sequence width	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	MaxResidue must be at least 2	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	static final strings for consensus keys	blob \| commitdiff \| diff to current
2006-10-06	amwaterhouse	AAFrequency optimized	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2005-09-30	amwaterhouse	Remove redundancy in Eclipse	blob \| commitdiff \| diff to current
2005-08-23	amwaterhouse	Finalize calculate method	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	Calculate gap and nogap ratio here	blob \| commitdiff \| diff to current
2005-06-30	amwaterhouse	Formatting changes	blob \| commitdiff \| diff to current
2005-06-10	amwaterhouse	Remove imports	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
2005-04-13	jprocter	Gap characters are now properly detected in the conserv...	blob \| commitdiff \| diff to current
2005-04-07	amwaterhouse	checkfor gap characters	blob \| commitdiff \| diff to current
2004-11-02	amwaterhouse	Jalview Imported Sources start	blob \| commitdiff \| diff to current

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