JAL-2473 revised default minimum dimension for Alignment Frame windows
[jalview.git] / src / jalview / schemes /
2017-04-07 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-04-05 gmungocJAL-2361 apply any saved changes to current colour...
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice
2017-03-24 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-03-24 Jim ProcterJAL-2360 fix applet build by separating castor XML...
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
2017-02-20 Jim ProcterMerge branch 'features/JAL-2379pcaMemory' into develop
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62...
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr...
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties
2017-02-14 gmungocJAL-2346 remove refactored fields, fix test for above...
2017-02-14 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode...
2017-02-09 gmungocJAL-2401 change 'Lower Case Colour' to checkbox with...
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory
2017-02-09 gmungocJAL-2371 skip upper-casing consensus as it already is
2017-02-07 gmungocJAL-2397 PCA gap cost uses last column of score matrix
2017-02-07 gmungocJAL-2398 corrected entry for C->R in Blosum62 matrix
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA...
2017-02-01 gmungocJAL-2371 (slight!) simplification of isApplicableTo()
2017-01-31 gmungocJAL-2385 more tests/bug fixes mostly for gui.SliderPane...
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader...
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1
2017-01-26 gmungocJAL-2360 corrected comment
2017-01-09 gmungocJAL-2371 remove ColourSchemeI.findColour(c), pure inter...
2017-01-06 gmungocJAL-2371 slight simplification of findColour overrides
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit...
2017-01-06 gmungocJAL-2360 findColour() with no args removed from ColourS...
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
2016-12-29 gmungocJAL-2630 first pass groovy colour scheme (with slight...
2016-12-23 gmungocJAL-2360 removed UserDefinedColours.userColourSchemes
2016-12-22 gmungocJAL-2360 structure viewers now using ColourMenuHelper...
2016-12-21 gmungocJAL-2360 ColourMenuHelper now builds and selects items...
2016-12-21 gmungocJAL-2360 comment only
2016-12-21 gmungocJAL-2360 tidy up, simplify isApplicableTo test
2016-12-21 gmungocJAL-2360 no RNAHelices colouring for groups
2016-12-21 gmungocJAL-2361 Blosum is enabled for peptide
2016-12-21 gmungocJAL-1421 add types to Map
2016-12-20 gmungocJAL-2360 ColourSchemes holds configured schemes, AlignF...
2016-12-19 gmungocJAL-2360 amended toAppletParameter() for reproducible...
2016-12-16 gmungocJAL-2360 added UserColourScheme.toAppletParameter+test...
2016-12-16 gmungocJAL-2360 getColour() renamed to getColourScheme(),...
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum,
2016-12-13 gmungocJAL-2365 test for lightgray, darkgray not lightGray...
2016-12-13 gmungocJAL-2360 code formatting only and if-else changed to...
2016-12-12 gmungocJAL-2362 return correct lower-case colour; Javadoc...
2016-12-02 gmungocJAL-2346 Javadoc correction
2016-12-02 gmungocJAL-2346 fixed bug (in code not reached by Jalview)
2016-12-01 gmungocJAL-2346 restore choice of annotation for colouring...
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-08 gmungocJAL-2301 made T hydrophobic as per the cited conservati...
2016-11-02 gmungocJAL-98 ProfileI interface for Profile
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis...
2016-11-01 gmungocJAL-98 use Integer constants; tests added for propHash...
2016-10-27 gmungocJAL-98 refactor bleachColour() to ColorUtils
2016-10-26 gmungocJAL-2286 modal residue check + commenting
2016-10-26 gmungocJAL-2286 javadoc, refactor, unit tests for threshold...
2016-10-25 gmungocJAL-2286 use constant for fixed colours
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-25 gmungocJAL-98 field comments updated
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-09-29 Jim ProcterJAL-2236 fix: bail if no context available for subgroup
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2016-06-22 gmungocJAL-2015 fixed bug in copy constructor and added tests
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-03-15 gmungocJAL-2016 FeatureSettingsI now FeatureSettingsModelI
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-02-25 gmungocJAL-2015 parse/write Jalview feature format pushed...
2016-02-24 gmungocJAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles
2016-02-22 gmungocJAL-1705 first pass at applying preset feature colourin...
2016-02-20 gmungocMerge branch 'JAL-1956_featureStyles' into features...
2016-02-20 gmungocJAL-2016 first draft of pre-set feature colour scheme
2016-02-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2016-01-21 tcofoegbuJAL-1479 JAL-1979 updated the modified-aminoacid triple...
2015-12-22 gmungocJAL-1421 parameterised map constructor used
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-08 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-30 tcofoegbuJAL-1912 added support of tcoffee annotation and other...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-09-07 gmungocJAL-1636 translate stop codon as '*', mouseover * as...
2015-09-05 Jim ProcterJAL-1871 choose a new RNA Helices palette when annotati...
2015-09-05 Jim ProcterJAL-1871 don’t change the palette every time an edit...
2015-09-05 Jim ProcterJAL-1871 reinstate random generation of palette when...
2015-09-05 Jim ProcterJAL-1869 make per-sequence RNA helix colours each time...
2015-09-05 Jim ProcterJAL-1233 tidy up and use same RNA helix colours in...
2015-09-05 Jim ProcterJAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection...
2015-09-03 Jim ProcterJAL-1680 JAL-1576 JAL-1233 all conservation and consens...
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