source.jalview.org Git - jalview.git/history

git://source.jalview.org / jalview.git / history

[jalview.git] / src / jalview / schemes /

2011-10-28	jprocter	(JAL-889) ensure latest version of RNA pairlist is...	tree \| commitdiff
2011-10-28	jprocter	refactor to use model API	tree \| commitdiff
2011-10-28	jprocter	(JAL-963) refactor RNA helix helper class to schemes	tree \| commitdiff
2011-10-10	jprocter	update author list in license for (JAL-826)	tree \| commitdiff
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	tree \| commitdiff
2011-09-27	jprocter	apply version 2.7 copyright	tree \| commitdiff
2011-07-25	janengelhardt	Start merging of Laurens Code	tree \| commitdiff
2010-09-23	jprocter	apply jalview code style	tree \| commitdiff
2010-09-23	jprocter	Jalview 2.6 source licence	tree \| commitdiff
2010-08-04	jprocter	reorganised colourscheme enumeration to make it easier...	tree \| commitdiff
2010-05-14	jprocter	fix for JAL-533	tree \| commitdiff
2010-04-30	jprocter	jalview 2.5 release banner	tree \| commitdiff
2010-04-16	jprocter	default for colourBylabel is false	tree \| commitdiff
2010-04-14	jprocter	todo and disable selection sharing between views on...	tree \| commitdiff
2010-04-02	jprocter	javadoc	tree \| commitdiff
2010-04-02	jprocter	made threshold type enumaration into set of constants	tree \| commitdiff
2009-09-10	jprocter	fix null pointer exception when using blosum colourscheme	tree \| commitdiff
2009-08-21	jprocter	asparagine is polar but not charged	tree \| commitdiff
2009-07-24	jprocter	feature colour by label flag/style	tree \| commitdiff
2009-06-08	jprocter	apply gpl development license	tree \| commitdiff
2009-06-01	jprocter	added graduated colourscheme support for feature file	tree \| commitdiff
2009-03-17	jprocter	holds shading and range parameters rendering a feature...	tree \| commitdiff
2009-03-17	jprocter	fixes launchApp bug where user defined colourscheme...	tree \| commitdiff
2008-11-12	jprocter	gracefully translate ambigous nucleotides as 'X'	tree \| commitdiff
2008-11-04	jprocter	bugfix for transfer of user defined colourscheme from...	tree \| commitdiff
2008-09-04	jprocter	merge from 2_4_Release branch	tree \| commitdiff
2008-08-11	jprocter	Ensure 'None' translates into no colour scheme applied	tree \| commitdiff
2008-07-18	jprocter	User defined colourschemes are automatically generated...	tree \| commitdiff
2008-06-30	jprocter	included includeGaps flag in clustalW colour calculatio...	tree \| commitdiff
2008-02-24	jprocter	sequenceId is a string, not an integer - allows generat...	tree \| commitdiff
2007-08-08	jprocter	histidine should be midblue (noticed by Peter Knight...	tree \| commitdiff
2007-04-30	jprocter	dssp 7-state to three state lookup	tree \| commitdiff
2007-04-27	amwaterhouse	Annotation gradient will use direct colours if no graph...	tree \| commitdiff
2007-04-27	amwaterhouse	Allow threshold to be min/max	tree \| commitdiff
2007-04-11	jprocter	fixed base lookup bug in dna pairwise alignment and...	tree \| commitdiff
2007-03-19	jprocter	note about selenocystine.	tree \| commitdiff
2007-02-27	amwaterhouse	check conservation length	tree \| commitdiff
2007-02-07	amwaterhouse	Formatting	tree \| commitdiff
2007-01-30	amwaterhouse	Any character non aa or nucleotide is a space	tree \| commitdiff
2007-01-30	amwaterhouse	consensusColouring never used	tree \| commitdiff
2006-12-06	jprocter	general pairwise substitution score models for pairwise...	tree \| commitdiff
2006-12-05	amwaterhouse	Sequence is char []	tree \| commitdiff
2006-11-28	amwaterhouse	CurrentColour must not be accessed by multiple sequence...	tree \| commitdiff
2006-11-28	amwaterhouse	CurrentColour must not be accessed by multiple sequence...	tree \| commitdiff
2006-11-14	amwaterhouse	we already have c defined	tree \| commitdiff
2006-11-13	amwaterhouse	Enable lower case colours	tree \| commitdiff
2006-11-09	amwaterhouse	Check conensus is not null	tree \| commitdiff
2006-10-12	amwaterhouse	Null element checked	tree \| commitdiff
2006-10-10	amwaterhouse	Check on null consensus	tree \| commitdiff
2006-10-10	amwaterhouse	aaIndex replaces aaHash	tree \| commitdiff
2006-10-06	amwaterhouse	Set consensus as hashtble[]	tree \| commitdiff
2006-10-05	amwaterhouse	lower case available	tree \| commitdiff
2006-09-11	amwaterhouse	Comment out lower case colouring for bug fix release	tree \| commitdiff
2006-08-30	amwaterhouse	Gap added to aa3Hash	tree \| commitdiff
2006-08-30	amwaterhouse	User colours are case sensitive	tree \| commitdiff
2006-08-21	amwaterhouse	header updated	tree \| commitdiff
2006-06-14	amwaterhouse	parseAppletParameter	tree \| commitdiff
2006-06-09	amwaterhouse	createColourFromName	tree \| commitdiff
2006-04-07	amwaterhouse	Must check consensus length if autocalculate off	tree \| commitdiff
2006-04-05	amwaterhouse	public get methods	tree \| commitdiff
2006-03-24	amwaterhouse	Group colours not used	tree \| commitdiff
2006-03-16	amwaterhouse	Out of bounds check	tree \| commitdiff
2006-02-16	amwaterhouse	Dont colour gaps	tree \| commitdiff
2006-02-16	amwaterhouse	Use original colour scheme as base for annotation colouring	tree \| commitdiff
2006-02-15	amwaterhouse	Threshold is a single element	tree \| commitdiff
2006-02-09	amwaterhouse	If conservation is zero, colour is white	tree \| commitdiff
2006-02-08	amwaterhouse	Colour above or below threshold	tree \| commitdiff
2006-02-03	amwaterhouse	Conservation colouring does what it should always have...	tree \| commitdiff
2006-02-03	amwaterhouse	Make java 1.1 compatible	tree \| commitdiff
2006-01-30	amwaterhouse	Get min and max colour added	tree \| commitdiff
2006-01-30	amwaterhouse	New files	tree \| commitdiff
2005-12-06	amwaterhouse	after merge	tree \| commitdiff
2005-11-18	jprocter	added 3 letter IUB codes for ambiguous residues/bases	tree \| commitdiff
2005-10-07	amwaterhouse	comma separated rgb values	tree \| commitdiff
2005-09-22	amwaterhouse	Add nucleotide names	tree \| commitdiff
2005-09-15	amwaterhouse	Add Uracil as X unknown	tree \| commitdiff
2005-09-08	amwaterhouse	If vconsensus is null, return	tree \| commitdiff
2005-09-08	amwaterhouse	Add lowercase nucleotides to nucleotideHash	tree \| commitdiff
2005-08-30	amwaterhouse	Make 24 colours to be sure	tree \| commitdiff
2005-08-29	amwaterhouse	Default user colour is 23 white colours	tree \| commitdiff
2005-08-22	amwaterhouse	finalize all these hashtables	tree \| commitdiff
2005-08-22	amwaterhouse	Conservation colour scheme is no more	tree \| commitdiff
2005-08-18	amwaterhouse	Character methods don't exist in java 1.1	tree \| commitdiff
2005-08-18	amwaterhouse	Proceed with upperCase residue Release_2_03	tree \| commitdiff
2005-08-18	amwaterhouse	Use aa index for aboveThreshold as well as colour index	tree \| commitdiff
2005-08-17	amwaterhouse	Scheme name added	tree \| commitdiff
2005-08-15	amwaterhouse	Remove null check	tree \| commitdiff
2005-08-15	amwaterhouse	super.setconsensus	tree \| commitdiff
2005-08-15	amwaterhouse	Percentage precalculated in aafrequency	tree \| commitdiff
2005-08-15	amwaterhouse	Add taylor to default colour check	tree \| commitdiff
2005-08-15	amwaterhouse	Hashtable now in array, not vector	tree \| commitdiff
2005-06-30	amwaterhouse	Formatting changes	tree \| commitdiff
2005-06-13	amwaterhouse	Get colourScheme with seqs and width	tree \| commitdiff
2005-06-08	amwaterhouse	Formatted source	tree \| commitdiff
2005-06-08	amwaterhouse	GPL license added	tree \| commitdiff
2005-05-25	amwaterhouse	reset colours added	tree \| commitdiff
2005-05-25	amwaterhouse	all can threshold	tree \| commitdiff
2005-05-25	jprocter	tidied up system.out messages and moved many to stderr.	tree \| commitdiff
2005-05-19	amwaterhouse	returns name if given colourscheme	tree \| commitdiff
2005-05-03	amwaterhouse	1.1 compatible, formatting changes	tree \| commitdiff
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