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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/ schemes
2024-09-16
Jim Procter
JAL-4392 autohide the secondary structure consensus...
patch/JAL-4392_hide_ssconsensus_if_no_data
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commitdiff
2024-08-05
Jim Procter
JAL-1551 gradle spotlessApply and doc tweaks
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commitdiff
2024-05-13
Renia Correya
JAL-4386 - Implementation of substitution matrix and...
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commitdiff
2023-12-06
James Procter
Merge branch 'patch/JAL-840_clustalx_docs_fix' into...
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commitdiff
2023-11-13
James Procter
JAL-4090 JAL-1551 source license
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commitdiff
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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commitdiff
2023-04-28
Ben Soares
JAL-629 Change colour scheme shortnames to something...
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commitdiff
2023-02-10
James Procter
JAL-840 generate fragments of clustal.html documentatio...
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commitdiff
2022-11-13
Ben Soares
JAL-4019 small but important corrections to array order...
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commitdiff
2022-11-13
Ben Soares
JAL-4019 improvement to short sequence nucleotide detec...
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commitdiff
2022-11-10
Ben Soares
JAL-4019 Nucleotide Ambiguity Colour Scheme added....
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commitdiff
2022-05-12
Ben Soares
JAL-4014 4 gecos colour schemes added
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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commitdiff
2021-09-15
gmungoc
JAL-3788 synchronize concurrent findColour() and alignm...
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commitdiff
2021-09-02
gmungoc
JAL-3509 coerce RESNUM to hidden (really) after fetchin...
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commitdiff
2020-02-06
gmungoc
JAL-3509 coerce RESNUM to hidden (really) after fetchin...
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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commitdiff
2019-04-04
gmungoc
JAL-3220 j2sIgnore on main methods on test / utility...
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
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commitdiff
2019-03-19
Ben Soares
JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben...
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commitdiff
2019-03-12
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
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commitdiff
2019-03-12
gmungoc
JAL-3127 check for null viewport
feature/JAL-3127_seqidChainshading
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commitdiff
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
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commitdiff
2019-03-11
gmungoc
JAL-3206 strict above/below threshold test restored
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commitdiff
2019-03-07
gmungoc
Merge branch 'feature/JAL-3180colourAnnotationMenu...
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commitdiff
2019-03-07
Ben Soares
JAL-3130 deprecation change preparation
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/features/JAL-2620a...
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3049colour...
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commitdiff
2019-03-04
gmungoc
JAL-3206 avoid divide by zero when threshold is graphMi...
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3120restoreFeatureColour' into...
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-2791exportFilteredFeature' into...
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commitdiff
2019-02-28
gmungoc
Merge remote-tracking branch 'origin/feature/JAL-3141_b...
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commitdiff
2019-02-28
Jim Procter
Merge branch 'feature/JAL-3141_backupfiles_for211'...
merge/develop_feature/JAL-3141_backupfiles_for211
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commitdiff
2019-02-25
gmungoc
JAL-3200 fast lookup of DSSP3 notation
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commitdiff
2019-01-16
Jim Procter
Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA...
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commitdiff
2019-01-04
gmungoc
JAL-3180 fix By Annotation selection state in colour...
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commitdiff
2018-12-06
Ben Soares
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
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commitdiff
2018-12-03
gmungoc
JAL-3063 Castor removed from codebase
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commitdiff
2018-12-03
gmungoc
Merge branch 'feature/JAL-3063JAXB' into feature/JAL...
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commitdiff
2018-11-20
Jim Procter
JAL-3127 Sequence ID Colour and nominal spanish translation
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commitdiff
2018-11-19
Jim Procter
JAL-3127 javadoc, don’t darken white when shading resid...
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commitdiff
2018-11-19
Jim Procter
JAL-3127 drop redundant hidden representative sequences...
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commitdiff
2018-11-01
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into
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commitdiff
2018-10-17
Jim Procter
Merge branch 'feature/JAL-3063JAXB' into Jalview-BH...
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commitdiff
2018-10-16
Jim Procter
JAL-3127 always look up sequence ID colour from view...
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commitdiff
2018-10-09
Jim Procter
JAL-3127 Colour sequences by ID - need to check that...
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commitdiff
2018-10-09
Jim Procter
JAL-3127 pass reference to AlignViewportI when creating...
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commitdiff
2018-09-27
gmungoc
JAL-2791 new method to test if feature fails colour...
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commitdiff
2018-09-21
gmungoc
JAL-3120 preserve feature colour/mincolour/maxcolour...
bug/JAL-3120restoreFeatureColour
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commitdiff
2018-09-20
gmungoc
JAL-2843 help text for colour by attribute, feature...
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commitdiff
2018-09-18
gmungoc
JAL-3063 Save/Load user defined colours using JAXB
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commitdiff
2018-06-29
gmungoc
JAL-3049 JAL-2069 colour icon tooltip including by...
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commitdiff
2018-03-16
gmungoc
JAL-2620 alternative genetic code translation tables
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
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commitdiff
2018-01-10
gmungoc
JAL-1793 update spike branch to latest
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commitdiff
2017-12-11
gmungoc
JAL-2843 add colour by attribute, and no value colour...
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commitdiff
2017-11-22
gmungoc
JAL-2069 spike updated with latest (FeatureTypeSettings)
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commitdiff
2017-11-22
gmungoc
JAL-2069 Javadoc added only
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commitdiff
2017-11-16
gmungoc
JAL-2069 removed unused and redundant thresholdIsMinMax
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commitdiff
2017-11-15
gmungoc
JAL-2816 exclude filtered / thresholded out features...
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commitdiff
2017-11-15
gmungoc
JAL-2835 spike updated with latest
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commitdiff
2017-11-15
gmungoc
JAL-2835 support filter/colour by nested attribute...
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commitdiff
2017-11-07
gmungoc
JAL-2069 update spike with latest
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commitdiff
2017-11-07
gmungoc
JAL-2069 corrected overloaded constructor behaviour
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commitdiff
2017-11-07
gmungoc
JAL-2069 update spike branch with latest
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commitdiff
2017-11-07
gmungoc
JAL-2069 add attributeName and noValueColour to Feature...
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commitdiff
2017-11-02
gmungoc
JAL-2808 reverted to develop (attribute filters removed)
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commitdiff
2017-10-31
gmungoc
JAL-2808 revised util.matcher package, 2 filter conditi...
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commitdiff
2017-10-30
gmungoc
JAL-2808 add attribute filter(s) to FeatureColour
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commitdiff
2017-10-24
gmungoc
JAL-2738 update spike branch with latest
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commitdiff
2017-10-12
Jim Procter
JAL-2773 add new flag to paintAlignment(updateOverview...
features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
2017-09-03
Jim Procter
Merge branch 'documentation/JAL-2675_release2102b1...
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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commitdiff
2017-08-18
Jim Procter
Merge branch 'feature/2588' into merge/develop_feature...
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
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commitdiff
2017-08-09
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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commitdiff
2017-07-24
gmungoc
spike branch updated from latest features/JAL-2446
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commitdiff
2017-07-24
gmungoc
JAL-2624 additional tests for FeatureColour.getColour(),
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commitdiff
2017-07-23
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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commitdiff
2017-06-28
kiramt
JAL-2588 Gap colour scheme now shown in overview
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commitdiff
2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
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commitdiff
2017-06-09
gmungoc
JAL-2592 distinguish "User Defined" (scheme name) from...
bug/JAL-2592userDefinedScheme
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commitdiff
2017-06-06
gmungoc
JAL-2589 correct colour for Gap in Score and User Defin...
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commitdiff
2017-04-07
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
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commitdiff
2017-04-05
gmungoc
JAL-2361 apply any saved changes to current colour...
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commitdiff
2017-03-30
gmungoc
Merge branch 'develop' into bug/JAL-2346annotationChoice
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commitdiff
2017-03-24
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
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commitdiff
2017-03-24
Jim Procter
JAL-2360 fix applet build by separating castor XML...
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commitdiff
2017-02-23
gmungoc
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
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commitdiff
2017-02-20
gmungoc
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
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commitdiff
2017-02-20
Jim Procter
Merge branch 'features/JAL-2379pcaMemory' into develop
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commitdiff
2017-02-18
gmungoc
JAL-2416 better encapsulated 'constants' for BLOSUM62...
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