formatting
[jalview.git] / src / jalview / schemes /
2011-10-28 jprocter(JAL-889) ensure latest version of RNA pairlist is...
2011-10-28 jprocterrefactor to use model API
2011-10-28 jprocter(JAL-963) refactor RNA helix helper class to schemes
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
2011-07-25 janengelhardtStart merging of Laurens Code
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-08-04 jprocterreorganised colourscheme enumeration to make it easier...
2010-05-14 jprocterfix for JAL-533
2010-04-30 jprocterjalview 2.5 release banner
2010-04-16 jprocterdefault for colourBylabel is false
2010-04-14 jproctertodo and disable selection sharing between views on...
2010-04-02 jprocterjavadoc
2010-04-02 jproctermade threshold type enumaration into set of constants
2009-09-10 jprocterfix null pointer exception when using blosum colourscheme
2009-08-21 jprocterasparagine is polar but not charged
2009-07-24 jprocterfeature colour by label flag/style
2009-06-08 jprocterapply gpl development license
2009-06-01 jprocteradded graduated colourscheme support for feature file
2009-03-17 jprocterholds shading and range parameters rendering a feature...
2009-03-17 jprocterfixes launchApp bug where user defined colourscheme...
2008-11-12 jproctergracefully translate ambigous nucleotides as 'X'
2008-11-04 jprocterbugfix for transfer of user defined colourscheme from...
2008-09-04 jproctermerge from 2_4_Release branch
2008-08-11 jprocterEnsure 'None' translates into no colour scheme applied
2008-07-18 jprocterUser defined colourschemes are automatically generated...
2008-06-30 jprocterincluded includeGaps flag in clustalW colour calculatio...
2008-02-24 jproctersequenceId is a string, not an integer - allows generat...
2007-08-08 jprocterhistidine should be midblue (noticed by Peter Knight...
2007-04-30 jprocterdssp 7-state to three state lookup
2007-04-27 amwaterhouseAnnotation gradient will use direct colours if no graph...
2007-04-27 amwaterhouseAllow threshold to be min/max
2007-04-11 jprocterfixed base lookup bug in dna pairwise alignment and...
2007-03-19 jprocternote about selenocystine.
2007-02-27 amwaterhousecheck conservation length
2007-02-07 amwaterhouseFormatting
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space
2007-01-30 amwaterhouseconsensusColouring never used
2006-12-06 jproctergeneral pairwise substitution score models for pairwise...
2006-12-05 amwaterhouseSequence is char []
2006-11-28 amwaterhouseCurrentColour must not be accessed by multiple sequence...
2006-11-28 amwaterhouseCurrentColour must not be accessed by multiple sequence...
2006-11-14 amwaterhousewe already have c defined
2006-11-13 amwaterhouseEnable lower case colours
2006-11-09 amwaterhouseCheck conensus is not null
2006-10-12 amwaterhouseNull element checked
2006-10-10 amwaterhouseCheck on null consensus
2006-10-10 amwaterhouseaaIndex replaces aaHash
2006-10-06 amwaterhouseSet consensus as hashtble[]
2006-10-05 amwaterhouselower case available
2006-09-11 amwaterhouseComment out lower case colouring for bug fix release
2006-08-30 amwaterhouseGap added to aa3Hash
2006-08-30 amwaterhouseUser colours are case sensitive
2006-08-21 amwaterhouseheader updated
2006-06-14 amwaterhouseparseAppletParameter
2006-06-09 amwaterhousecreateColourFromName
2006-04-07 amwaterhouseMust check consensus length if autocalculate off
2006-04-05 amwaterhousepublic get methods
2006-03-24 amwaterhouseGroup colours not used
2006-03-16 amwaterhouseOut of bounds check
2006-02-16 amwaterhouseDont colour gaps
2006-02-16 amwaterhouseUse original colour scheme as base for annotation colouring
2006-02-15 amwaterhouseThreshold is a single element
2006-02-09 amwaterhouseIf conservation is zero, colour is white
2006-02-08 amwaterhouseColour above or below threshold
2006-02-03 amwaterhouseConservation colouring does what it should always have...
2006-02-03 amwaterhouseMake java 1.1 compatible
2006-01-30 amwaterhouseGet min and max colour added
2006-01-30 amwaterhouseNew files
2005-12-06 amwaterhouseafter merge
2005-11-18 jprocteradded 3 letter IUB codes for ambiguous residues/bases
2005-10-07 amwaterhousecomma separated rgb values
2005-09-22 amwaterhouseAdd nucleotide names
2005-09-15 amwaterhouseAdd Uracil as X unknown
2005-09-08 amwaterhouseIf vconsensus is null, return
2005-09-08 amwaterhouseAdd lowercase nucleotides to nucleotideHash
2005-08-30 amwaterhouseMake 24 colours to be sure
2005-08-29 amwaterhouseDefault user colour is 23 white colours
2005-08-22 amwaterhousefinalize all these hashtables
2005-08-22 amwaterhouseConservation colour scheme is no more
2005-08-18 amwaterhouseCharacter methods don't exist in java 1.1
2005-08-18 amwaterhouseProceed with upperCase residue Release_2_03
2005-08-18 amwaterhouseUse aa index for aboveThreshold as well as colour index
2005-08-17 amwaterhouseScheme name added
2005-08-15 amwaterhouseRemove null check
2005-08-15 amwaterhousesuper.setconsensus
2005-08-15 amwaterhousePercentage precalculated in aafrequency
2005-08-15 amwaterhouseAdd taylor to default colour check
2005-08-15 amwaterhouseHashtable now in array, not vector
2005-06-30 amwaterhouseFormatting changes
2005-06-13 amwaterhouseGet colourScheme with seqs and width
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2005-05-25 amwaterhousereset colours added
2005-05-25 amwaterhouseall can threshold
2005-05-25 jproctertidied up system.out messages and moved many to stderr.
2005-05-19 amwaterhousereturns name if given colourscheme
2005-05-03 amwaterhouse1.1 compatible, formatting changes
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