JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs
[jalview.git] / src / jalview / schemes /
2020-02-06 gmungocJAL-3509 coerce RESNUM to hidden (really) after fetchin...
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with...
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2019-03-19 Ben SoaresJAL-3130 Merge of JAL-3130_Java_11_investigations-Ben...
2019-03-12 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into...
2019-03-12 gmungocJAL-3127 check for null viewport feature/JAL-3127_seqidChainshading
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into...
2019-03-11 gmungocJAL-3206 strict above/below threshold test restored
2019-03-07 gmungocMerge branch 'feature/JAL-3180colourAnnotationMenu...
2019-03-07 Ben SoaresJAL-3130 deprecation change preparation
2019-03-05 gmungocMerge remote-tracking branch 'origin/features/JAL-2620a...
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-3049colour...
2019-03-04 gmungocJAL-3206 avoid divide by zero when threshold is graphMi...
2019-03-04 gmungocMerge branch 'bug/JAL-3120restoreFeatureColour' into...
2019-03-01 gmungocMerge branch 'bug/JAL-2791exportFilteredFeature' into...
2019-02-28 gmungocMerge remote-tracking branch 'origin/feature/JAL-3141_b...
2019-02-28 Jim ProcterMerge branch 'feature/JAL-3141_backupfiles_for211'... merge/develop_feature/JAL-3141_backupfiles_for211
2019-02-25 gmungocJAL-3200 fast lookup of DSSP3 notation
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA...
2019-01-04 gmungocJAL-3180 fix By Annotation selection state in colour...
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
2018-12-03 gmungocJAL-3063 Castor removed from codebase
2018-12-03 gmungocMerge branch 'feature/JAL-3063JAXB' into feature/JAL...
2018-11-20 Jim ProcterJAL-3127 Sequence ID Colour and nominal spanish translation
2018-11-19 Jim ProcterJAL-3127 javadoc, don’t darken white when shading resid...
2018-11-19 Jim ProcterJAL-3127 drop redundant hidden representative sequences...
2018-10-16 Jim ProcterJAL-3127 always look up sequence ID colour from view...
2018-10-09 Jim ProcterJAL-3127 Colour sequences by ID - need to check that...
2018-10-09 Jim ProcterJAL-3127 pass reference to AlignViewportI when creating...
2018-09-27 gmungocJAL-2791 new method to test if feature fails colour...
2018-09-21 gmungocJAL-3120 preserve feature colour/mincolour/maxcolour... bug/JAL-3120restoreFeatureColour
2018-09-20 gmungocJAL-2843 help text for colour by attribute, feature...
2018-09-18 gmungocJAL-3063 Save/Load user defined colours using JAXB
2018-06-29 gmungocJAL-3049 JAL-2069 colour icon tooltip including by...
2018-03-16 gmungocJAL-2620 alternative genetic code translation tables
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
2018-01-10 gmungocJAL-1793 update spike branch to latest
2017-12-11 gmungocJAL-2843 add colour by attribute, and no value colour...
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings)
2017-11-22 gmungocJAL-2069 Javadoc added only
2017-11-16 gmungocJAL-2069 removed unused and redundant thresholdIsMinMax
2017-11-15 gmungocJAL-2816 exclude filtered / thresholded out features...
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-15 gmungocJAL-2835 support filter/colour by nested attribute...
2017-11-07 gmungocJAL-2069 update spike with latest
2017-11-07 gmungocJAL-2069 corrected overloaded constructor behaviour
2017-11-07 gmungocJAL-2069 update spike branch with latest
2017-11-07 gmungocJAL-2069 add attributeName and noValueColour to Feature...
2017-11-02 gmungocJAL-2808 reverted to develop (attribute filters removed)
2017-10-31 gmungocJAL-2808 revised util.matcher package, 2 filter conditi...
2017-10-30 gmungocJAL-2808 add attribute filter(s) to FeatureColour
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-03 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1...
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-18 Jim ProcterMerge branch 'feature/2588' into merge/develop_feature...
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-09 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-07-24 gmungocspike branch updated from latest features/JAL-2446
2017-07-24 gmungocJAL-2624 additional tests for FeatureColour.getColour(),
2017-07-23 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-28 kiramtJAL-2588 Gap colour scheme now shown in overview
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-09 gmungocJAL-2592 distinguish "User Defined" (scheme name) from... bug/JAL-2592userDefinedScheme
2017-06-06 gmungocJAL-2589 correct colour for Gap in Score and User Defin...
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
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