format adapter should return AlignmentI
[jalview.git] / src / jalview / schemes /
2012-11-15 jproctersource formatting
2012-11-15 jprocterMerge branch 'develop' into menard
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-09-06 jprocterJAL-1027 JAL-1167 documentation and patched DNA/RNA...
2012-09-06 jprocterJAL-1167 method and simple tests for printing score...
2012-08-31 jprocterMerge branch 'develop' into menard
2012-08-28 jprocterJAL-1066 - per-sequence colouring with sequence associa...
2012-08-17 jprocterMerge branch 'develop' into menard
2012-08-14 Anne Menardlast version stay many bugs ..
2012-08-01 jprocterJAL-1066 patch regression ac33424148b2a4de29b3ca43f9411...
2012-07-16 Anne MenardLast version
2012-07-16 Anne MenardMerge branch 'develop' of https://source.jalview.org...
2012-07-10 Anne Menardv2
2012-07-05 Anne MenardAdd support RNAML format
2012-06-29 jprocterJAL-1065 JAL-1066 ensure non-residue based schemes...
2012-06-29 jprocterJAL-1065 JAL-1066 allow different lookup tables for...
2012-06-15 jprocterMerge branch 'JAL-1013_pca_rna_dna' into develop
2012-05-30 jprocterJAL-1109 JAL-1065 resolve t-coffee score scheme by...
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta...
2012-05-23 jproctertodo for JAL-1106
2012-05-23 jprocterJAL-1066,JAL-1068,JAL-961 - use alignment annotation...
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065...
2011-12-08 jprocter(JAL-1013) gap character index for each sequence alphabet
2011-12-08 jprocterJAL-1027 fixed up nucleotide subt matrix so it is symme...
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
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