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JAL-2416 remove unused pep, dna alphabets, unused methods, code format
[jalview.git] / src / jalview /
2017-02-20 gmungocJAL-2416 remove unused pep, dna alphabets, unused metho... tree | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... tree | commitdiff
2017-02-17 gmungocJAL-2416 BLOSUM62 removed from ResidueProperties tree | commitdiff
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr... tree | commitdiff
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties tree | commitdiff
2017-02-17 gmungocJAL-2413 extracted new method SetUtils.countDisjunction() tree | commitdiff
2017-02-17 gmungocJAL-2423 refactored method to build panel title for... tree | commitdiff
2017-02-17 gmungocJAL-2416 SeqSpace PCA now provided as an alternative... tree | commitdiff
2017-02-17 gmungocJAL-2416 allow space in score matrix name tree | commitdiff
2017-02-17 gmungocJAL-2416 order score models by order of addition rather... tree | commitdiff
2017-02-17 gmungocJAL-2403 redundant 'implements' removed tree | commitdiff
2017-02-17 gmungocJAL-2403 extract method refactoring of FeatureScoreMode... tree | commitdiff
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV" tree | commitdiff
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop... tree | commitdiff
2017-02-13 gmungocJAL-2416 allow alphabet symbol (optional) in first... tree | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... tree | commitdiff
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... tree | commitdiff
2017-02-10 gmungocJAL-2371 small move of code, typo correction tree | commitdiff
2017-02-09 Jim ProcterMerge branch 'develop' into features/JAL-2316 features/JAL-2316 tree | commitdiff
2017-02-09 gmungocJAL-2401 change 'Lower Case Colour' to checkbox with... tree | commitdiff
2017-02-09 gmungocJAL-2371 ensure some colour scheme (may be None) is... tree | commitdiff
2017-02-09 gmungocJAL-2371 skip upper-casing consensus as it already is tree | commitdiff
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup... tree | commitdiff
2017-02-09 gmungocJAL-2405 set initial selection group alignment context tree | commitdiff
2017-02-09 gmungocJAL-2405 enable nucleotide/peptide colour schemes in... tree | commitdiff
2017-02-08 gmungocJAL-2405 set context on selection group for tailored... tree | commitdiff
2017-02-08 gmungocJAL-2401 fix for NPE on selectedButtons, tweak for... tree | commitdiff
2017-02-08 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-02-08 Jim ProcterJAL-2366 updated default URL to jalview.org/services... tree | commitdiff
2017-02-07 Jim ProcterMerge branch 'features/JAL-2371collectionColourScheme... tree | commitdiff
2017-02-07 gmungocJAL-2401 Lower Case Colour toggleable, help text added tree | commitdiff
2017-02-01 gmungocJAL-2371 (slight!) simplification of isApplicableTo() tree | commitdiff
2017-01-31 gmungocJAL-2371 commented code removed only tree | commitdiff
2017-01-31 gmungocJAL-2371 rename global/viewportColourScheme to residueS... tree | commitdiff
2017-01-31 gmungocJAL-2385 more tests/bug fixes mostly for gui.SliderPane... tree | commitdiff
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader... tree | commitdiff
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1 tree | commitdiff
2017-01-27 kiramtJAL-2366 Removed unneeded setEnabled calls tree | commitdiff
2017-01-26 gmungocJAL-2360 corrected comment tree | commitdiff
2017-01-26 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-01-26 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-26 kiramtJAL-2316 Updated to use identifiers jalview service tree | commitdiff
2017-01-26 gmungocJAL-2344 test fix and code tidy for review comments tree | commitdiff
2017-01-26 gmungocJAL-2380 code tidy after review tree | commitdiff
2017-01-25 gmungocJAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid... tree | commitdiff
2017-01-23 gmungocJAL-2386 unit tests for change colour (and minor refact... tree | commitdiff
2017-01-23 gmungocJAL-2386 simplify changeColour (doesn't change colour... tree | commitdiff
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-20 gmungocJAL-2385 tweak to applet 'switch colour slider context' tree | commitdiff
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-20 gmungocJAL-2385 update slider settings when switching slider... tree | commitdiff
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-20 gmungocJAL-2383 fixup from last merge tree | commitdiff
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-20 gmungocJAL-2383 check for null, spelling tree | commitdiff
2017-01-20 gmungocJAL-2383 make popup colour menu order and wording consi... tree | commitdiff
2017-01-20 gmungocJAL-2383 restore group conservation slider setting... tree | commitdiff
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-19 gmungocJAL-2383 restore PID colour threshold from project... tree | commitdiff
2017-01-19 gmungocJAL-2370 corrected applet mouse drag, refactored into... tree | commitdiff
2017-01-17 gmungocJAL-2370 fix bug when hiding a range including two... tree | commitdiff
2017-01-17 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-16 gmungocJAL-2380 fix Matrix.postMultiply() tree | commitdiff
2017-01-12 gmungocJAL-2379 null references to PCA model when panel is... tree | commitdiff
2017-01-12 gmungocJAL-2344 now flagging formats as 'identifiable' instead... tree | commitdiff
2017-01-11 gmungocJAL-2344 separated AlignmentFileI into AlignmentFileRea... tree | commitdiff
2017-01-11 gmungocJAL-2344 FileFormats singleton for formats, FileFormatI... tree | commitdiff
2017-01-11 gmungocJAL-2344 addSequence() method added to support Groovy... tree | commitdiff
2017-01-10 gmungocJAL-2377 avoid infinite loop formatting 1.0E-310 tree | commitdiff
2017-01-10 kiramtJAL-2316 Separate label/db name in UrlProviders. Unit... tree | commitdiff
2017-01-09 kiramtJAL-2316 Prevent applet from loading null links into... tree | commitdiff
2017-01-09 gmungocJAL-2371 pull up isNucleotide to SequenceCollectionI tree | commitdiff
2017-01-09 gmungocJAL-2371 remove ColourSchemeI.findColour(c), pure inter... tree | commitdiff
2017-01-09 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-01-06 gmungocJAL-2371 slight simplification of findColour overrides tree | commitdiff
2017-01-06 gmungocJAL-2371 correct Clustal, Blosum, PID colouring of... tree | commitdiff
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-06 gmungocJAL-2360 findColour() with no args removed from ColourS... tree | commitdiff
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-06 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-05 gmungocJAL-2374 fix popup out by one and multiple groups bugs tree | commitdiff
2017-01-05 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-05 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-05 gmungocJAL-2373 set state of Above PID, By Conservation in... tree | commitdiff
2017-01-05 gmungocJAL-2371 tests added tree | commitdiff
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI tree | commitdiff
2016-12-29 gmungocJAL-2630 first pass groovy colour scheme (with slight... tree | commitdiff
2016-12-23 gmungocJAL-2360 removed UserDefinedColours.userColourSchemes tree | commitdiff
2016-12-22 gmungocJAL-2360 fix bug that prematurely created a SequenceGroup tree | commitdiff
2016-12-22 gmungocJAL-2360 structure viewers now using ColourMenuHelper... tree | commitdiff
2016-12-21 gmungocJAL-2360 set new/loaded colour scheme name correctly tree | commitdiff
2016-12-21 gmungocJAL-2360 ColourMenuHelper now builds and selects items... tree | commitdiff
2016-12-21 gmungocJAL-2360 comment only tree | commitdiff
2016-12-21 gmungocJAL-2360 tidy up, simplify isApplicableTo test tree | commitdiff
2016-12-21 gmungocJAL-2360 no RNAHelices colouring for groups tree | commitdiff
2016-12-21 gmungocJAL-2361 Blosum is enabled for peptide tree | commitdiff
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