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JAL-2629 adjust placement and optionality of arguments/options
[jalview.git]
/
src
/
jalview
/
schemes
/
2018-04-17
gmungoc
JAL-2629 choice of hmm profile now a parameter not...
tree
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commitdiff
2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2938 revisions to implementation details
tree
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commitdiff
2018-03-23
gmungoc
JAL-2938 update colour schemes enum for class name...
tree
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commitdiff
2018-03-23
gmungoc
JAL-2938 extracted base class for Hmmer colour schems
tree
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commitdiff
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
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commitdiff
2018-02-27
gmungoc
JAL-2668 method name change for clarity
tree
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commitdiff
2018-02-27
gmungoc
JAL-2668 fix broken factory method for colour scheme
tree
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commitdiff
2018-02-27
gmungoc
JAL-2717 JAL-2668 fixes to HMMER colour scheme display...
tree
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commitdiff
2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
tree
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commitdiff
2018-01-10
gmungoc
JAL-1793 update spike branch to latest
tree
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commitdiff
2017-12-11
gmungoc
JAL-2843 add colour by attribute, and no value colour...
tree
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commitdiff
2017-11-22
gmungoc
JAL-2069 spike updated with latest (FeatureTypeSettings)
tree
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commitdiff
2017-11-22
gmungoc
JAL-2069 Javadoc added only
tree
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commitdiff
2017-11-16
gmungoc
JAL-2069 removed unused and redundant thresholdIsMinMax
tree
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commitdiff
2017-11-15
gmungoc
JAL-2816 exclude filtered / thresholded out features...
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 spike updated with latest
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 support filter/colour by nested attribute...
tree
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commitdiff
2017-11-07
gmungoc
JAL-2069 update spike with latest
tree
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commitdiff
2017-11-07
gmungoc
JAL-2069 corrected overloaded constructor behaviour
tree
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commitdiff
2017-11-07
gmungoc
JAL-2069 update spike branch with latest
tree
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commitdiff
2017-11-07
gmungoc
JAL-2069 add attributeName and noValueColour to Feature...
tree
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commitdiff
2017-11-02
gmungoc
JAL-2808 reverted to develop (attribute filters removed)
tree
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commitdiff
2017-10-31
gmungoc
JAL-2808 revised util.matcher package, 2 filter conditi...
tree
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commitdiff
2017-10-30
gmungoc
JAL-2808 add attribute filter(s) to FeatureColour
tree
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commitdiff
2017-10-24
gmungoc
JAL-2738 update spike branch with latest
tree
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commitdiff
2017-10-12
Jim Procter
JAL-2773 add new flag to paintAlignment(updateOverview...
features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
tree
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commitdiff
2017-09-03
Jim Procter
Merge branch 'documentation/JAL-2675_release2102b1...
tree
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commitdiff
2017-08-28
TZVanaalten
JAL-2629 HMMER alignment background colour scheme is...
tree
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commitdiff
2017-08-25
TZVanaalten
JAl-2629 add new HMMER colour scheme class
tree
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commitdiff
2017-08-25
TZVanaalten
JAL-2629 add multiple options for running hmmbuild...
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
tree
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commitdiff
2017-08-18
Jim Procter
Merge branch 'feature/2588' into merge/develop_feature...
tree
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commitdiff
2017-08-18
TZVanaalten
JAL-2668 add tests for HMMER commands, annotation and io
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2599 fix background frequency storage and correct...
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2599 fix HMMER scheme not colouring inserts and...
tree
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commitdiff
2017-08-09
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 moved HMM storage location to placeholder...
tree
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commitdiff
2017-07-24
gmungoc
spike branch updated from latest features/JAL-2446
tree
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commitdiff
2017-07-24
gmungoc
JAL-2624 additional tests for FeatureColour.getColour(),
tree
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commitdiff
2017-07-23
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2599 add ability to process RNA HMMer files
tree
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commitdiff
2017-07-14
TZVanaalten
add partial button fix to annotation and statistics...
features/hmmer_statistics
tree
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commitdiff
2017-07-11
TZVanaalten
complete Information Content annotation
tree
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commitdiff
2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
tree
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commitdiff
2017-06-28
kiramt
JAL-2588 Gap colour scheme now shown in overview
tree
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commitdiff
2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-23
TZVanaalten
test HMMER colour scheme
tree
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commitdiff
2017-06-23
TZVanaalten
add HMMER colour scheme
tree
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commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
tree
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
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commitdiff
2017-06-09
gmungoc
JAL-2592 distinguish "User Defined" (scheme name) from...
bug/JAL-2592userDefinedScheme
tree
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commitdiff
2017-06-06
gmungoc
JAL-2589 correct colour for Gap in Score and User Defin...
tree
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commitdiff
2017-04-07
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-04-05
gmungoc
JAL-2361 apply any saved changes to current colour...
tree
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commitdiff
2017-03-30
gmungoc
Merge branch 'develop' into bug/JAL-2346annotationChoice
tree
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commitdiff
2017-03-24
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-03-24
Jim Procter
JAL-2360 fix applet build by separating castor XML...
tree
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commitdiff
2017-02-23
gmungoc
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
tree
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commitdiff
2017-02-20
gmungoc
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
tree
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commitdiff
2017-02-20
Jim Procter
Merge branch 'features/JAL-2379pcaMemory' into develop
tree
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commitdiff
2017-02-18
gmungoc
JAL-2416 better encapsulated 'constants' for BLOSUM62...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 BLOSUM62 removed from ResidueProperties
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 removed DNA and PAM250 matrices from ResiduePr...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 scoreMatrices removed from ResidueProperties
tree
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commitdiff
2017-02-14
gmungoc
JAL-2346 remove refactored fields, fix test for above...
tree
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commitdiff
2017-02-14
gmungoc
Merge branch 'develop' into bug/JAL-2346annotationChoice
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 first cut of Tree chooser dialog and ScoreMode...
tree
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commitdiff
2017-02-09
gmungoc
JAL-2401 change 'Lower Case Colour' to checkbox with...
tree
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commitdiff
2017-02-09
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
features/JAL-2379pcaMemory
tree
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commitdiff
2017-02-09
gmungoc
JAL-2371 skip upper-casing consensus as it already is
tree
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commitdiff
2017-02-07
gmungoc
JAL-2397 PCA gap cost uses last column of score matrix
tree
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commitdiff
2017-02-07
gmungoc
JAL-2398 corrected entry for C->R in Blosum62 matrix
tree
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commitdiff
2017-02-06
gmungoc
JAL-2379 computePairwiseScores() moved to ScoreMatrix
tree
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commitdiff
2017-02-03
gmungoc
JAL-2379 'direct' pairwise score calculation for PCA...
tree
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commitdiff
2017-02-01
gmungoc
JAL-2371 (slight!) simplification of isApplicableTo()
tree
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commitdiff
2017-01-31
gmungoc
JAL-2385 more tests/bug fixes mostly for gui.SliderPane...
tree
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commitdiff
2017-01-27
gmungoc
JAL-2371 CollectionColourScheme renamed ResidueShader...
tree
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commitdiff
2017-01-27
gmungoc
JAL-2360 JAL-2371 updates from review CR-JAL-1
tree
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commitdiff
2017-01-26
gmungoc
JAL-2360 corrected comment
tree
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commitdiff
2017-01-09
gmungoc
JAL-2371 remove ColourSchemeI.findColour(c), pure inter...
tree
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commitdiff
2017-01-06
gmungoc
JAL-2371 slight simplification of findColour overrides
tree
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commitdiff
2017-01-06
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-06
gmungoc
JAL-2360 findColour() with no args removed from ColourS...
tree
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commitdiff
2017-01-04
gmungoc
JAL-2371 CollectionColourScheme wraps ColourSchemeI
tree
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commitdiff
2016-12-29
gmungoc
JAL-2630 first pass groovy colour scheme (with slight...
tree
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commitdiff
2016-12-23
gmungoc
JAL-2360 removed UserDefinedColours.userColourSchemes
tree
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commitdiff
2016-12-22
gmungoc
JAL-2360 structure viewers now using ColourMenuHelper...
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 ColourMenuHelper now builds and selects items...
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 comment only
tree
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commitdiff
2016-12-21
gmungoc
JAL-2360 tidy up, simplify isApplicableTo test
tree
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commitdiff
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