jalview.git
7 years agoJAL-2403 additional methods to support distance/similarity score
gmungoc [Thu, 23 Feb 2017 15:39:01 +0000 (15:39 +0000)]
JAL-2403 additional methods to support distance/similarity score
conversion

7 years agoJAL-2416 typo
gmungoc [Tue, 21 Feb 2017 17:02:51 +0000 (17:02 +0000)]
JAL-2416 typo

7 years agoJAL-2416 ScoreMatrix.getMatrix() returns a defensive copy to keep the
gmungoc [Tue, 21 Feb 2017 17:01:37 +0000 (17:01 +0000)]
JAL-2416 ScoreMatrix.getMatrix() returns a defensive copy to keep the
class invariant

7 years agoJAL-2416 support roundtrip print/parse of ScoreMatrix
gmungoc [Tue, 21 Feb 2017 13:36:59 +0000 (13:36 +0000)]
JAL-2416 support roundtrip print/parse of ScoreMatrix

7 years agoMerge branch 'develop' into features/JAL-2393customMatrices
gmungoc [Tue, 21 Feb 2017 11:56:39 +0000 (11:56 +0000)]
Merge branch 'develop' into features/JAL-2393customMatrices

Conflicts:
src/jalview/analysis/PCA.java
src/jalview/schemes/ResidueProperties.java
src/jalview/schemes/ScoreMatrix.java

7 years agoJAL-2416 quality calculation now only depends on loaded score matrix
gmungoc [Tue, 21 Feb 2017 10:40:02 +0000 (10:40 +0000)]
JAL-2416 quality calculation now only depends on loaded score matrix

7 years agoJAL-2416 more validation in ScoreMatrix constructor
gmungoc [Tue, 21 Feb 2017 10:13:06 +0000 (10:13 +0000)]
JAL-2416 more validation in ScoreMatrix constructor

7 years agoJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
gmungoc [Mon, 20 Feb 2017 16:07:45 +0000 (16:07 +0000)]
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
PairwiseDistanceModel

7 years agoJAL-2416 replaced dependency on ResidueProperties with loaded score
gmungoc [Mon, 20 Feb 2017 16:04:08 +0000 (16:04 +0000)]
JAL-2416 replaced dependency on ResidueProperties with loaded score
matrix

7 years agoMerge branch 'features/JAL-2379pcaMemory' into develop
Jim Procter [Mon, 20 Feb 2017 11:36:39 +0000 (11:36 +0000)]
Merge branch 'features/JAL-2379pcaMemory' into develop

7 years agoJAL-2416 public constant for space gap character
gmungoc [Mon, 20 Feb 2017 10:36:41 +0000 (10:36 +0000)]
JAL-2416 public constant for space gap character

7 years agoJAL-2416 remove unused pep, dna alphabets, unused methods, code format
gmungoc [Mon, 20 Feb 2017 10:35:32 +0000 (10:35 +0000)]
JAL-2416 remove unused pep, dna alphabets, unused methods, code format
tidy

7 years agoJAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250
gmungoc [Sat, 18 Feb 2017 08:21:41 +0000 (08:21 +0000)]
JAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250

7 years agoJAL-2416 BLOSUM62 removed from ResidueProperties
gmungoc [Fri, 17 Feb 2017 19:26:26 +0000 (19:26 +0000)]
JAL-2416 BLOSUM62 removed from ResidueProperties

7 years agoJAL-2416 removed DNA and PAM250 matrices from ResidueProperties
gmungoc [Fri, 17 Feb 2017 17:44:56 +0000 (17:44 +0000)]
JAL-2416 removed DNA and PAM250 matrices from ResidueProperties

7 years agoJAL-2416 scoreMatrices removed from ResidueProperties
gmungoc [Fri, 17 Feb 2017 16:28:44 +0000 (16:28 +0000)]
JAL-2416 scoreMatrices removed from ResidueProperties

7 years agoJAL-2413 extracted new method SetUtils.countDisjunction()
gmungoc [Fri, 17 Feb 2017 15:41:39 +0000 (15:41 +0000)]
JAL-2413 extracted new method SetUtils.countDisjunction()

7 years agoJAL-2423 refactored method to build panel title for tree either
gmungoc [Fri, 17 Feb 2017 15:14:19 +0000 (15:14 +0000)]
JAL-2423 refactored method to build panel title for tree either
calculated or read from file

7 years agoJAL-2416 SeqSpace PCA now provided as an alternative score matrix rather
gmungoc [Fri, 17 Feb 2017 13:31:49 +0000 (13:31 +0000)]
JAL-2416 SeqSpace PCA now provided as an alternative score matrix rather
than an alternative method (+code tidying)

7 years agoJAL-2416 score models now held in order added
gmungoc [Fri, 17 Feb 2017 13:30:39 +0000 (13:30 +0000)]
JAL-2416 score models now held in order added

7 years agoJAL-2416 allow space in score matrix name
gmungoc [Fri, 17 Feb 2017 13:30:01 +0000 (13:30 +0000)]
JAL-2416 allow space in score matrix name

7 years agoJAL-2416 order score models by order of addition rather than name
gmungoc [Fri, 17 Feb 2017 13:27:33 +0000 (13:27 +0000)]
JAL-2416 order score models by order of addition rather than name

7 years agoJAL-2403 redundant 'implements' removed
gmungoc [Fri, 17 Feb 2017 13:26:39 +0000 (13:26 +0000)]
JAL-2403 redundant 'implements' removed

7 years agoJAL-2403 extract method refactoring of FeatureScoreModel + test
gmungoc [Fri, 17 Feb 2017 13:25:42 +0000 (13:25 +0000)]
JAL-2403 extract method refactoring of FeatureScoreModel + test

7 years agoJAL-2403 constants for "NJ", "AV"
gmungoc [Fri, 17 Feb 2017 10:31:11 +0000 (10:31 +0000)]
JAL-2403 constants for "NJ", "AV"

7 years agoMerge branch 'bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu...
Jim Procter [Thu, 16 Feb 2017 11:49:57 +0000 (11:49 +0000)]
Merge branch 'bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu' into develop

7 years agoJAL-2374 JAL-2419 - TODO suspiciously redundant nested if clauses probably need a... bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu
Jim Procter [Wed, 15 Feb 2017 17:13:26 +0000 (17:13 +0000)]
JAL-2374 JAL-2419 - TODO suspiciously redundant nested if clauses probably need a cleanup

7 years agofix for JAL-2419 - don’t trash the current selection
Jim Procter [Wed, 15 Feb 2017 17:12:02 +0000 (17:12 +0000)]
fix for JAL-2419 - don’t trash the current selection

7 years agoJAL-2374 don’t search twice for containing group to assign to stretchGroup
Jim Procter [Wed, 15 Feb 2017 16:47:34 +0000 (16:47 +0000)]
JAL-2374 don’t search twice for containing group to assign to stretchGroup

7 years agoJAL-2374 tests for SequenceGroup.contains
Jim Procter [Wed, 15 Feb 2017 15:45:06 +0000 (15:45 +0000)]
JAL-2374 tests for SequenceGroup.contains

7 years agoJAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functional’
Jim Procter [Wed, 15 Feb 2017 15:43:06 +0000 (15:43 +0000)]
JAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functional’

7 years agoJAL-2374 new contains methods for seq and seq,apos
Jim Procter [Wed, 15 Feb 2017 15:41:58 +0000 (15:41 +0000)]
JAL-2374 new contains methods for seq and seq,apos

7 years agoJAL-2374 javadoc - qualify that sequence argument to findGroup must be in the Alignme...
Jim Procter [Wed, 15 Feb 2017 15:38:49 +0000 (15:38 +0000)]
JAL-2374 javadoc - qualify that sequence argument to findGroup must be in the Alignment, not share the same dataset sequence

7 years agoJAL-2393 example (unvalidated) blosum80 matrix to play with drag and
gmungoc [Tue, 14 Feb 2017 16:48:32 +0000 (16:48 +0000)]
JAL-2393 example (unvalidated) blosum80 matrix to play with drag and
drop

7 years agoParsing moved to (new) ScoreMatrixFile, drag and drop to alignment now
gmungoc [Tue, 14 Feb 2017 16:47:52 +0000 (16:47 +0000)]
Parsing moved to (new) ScoreMatrixFile, drag and drop to alignment now
supported

7 years agoJAL-2416 allow alphabet symbol (optional) in first column of score table
gmungoc [Mon, 13 Feb 2017 17:00:37 +0000 (17:00 +0000)]
JAL-2416 allow alphabet symbol (optional) in first column of score table

7 years agoJAL-1632 JAL-2416 load score matrices from file, as float[][]
gmungoc [Mon, 13 Feb 2017 16:00:59 +0000 (16:00 +0000)]
JAL-1632 JAL-2416 load score matrices from file, as float[][]

7 years agoJAL-1632 first cut of Tree chooser dialog and ScoreModels singleton
gmungoc [Mon, 13 Feb 2017 09:01:54 +0000 (09:01 +0000)]
JAL-1632 first cut of Tree chooser dialog and ScoreModels singleton

7 years agoJAL-2371 small move of code, typo correction
gmungoc [Fri, 10 Feb 2017 11:03:15 +0000 (11:03 +0000)]
JAL-2371 small move of code, typo correction

7 years agoMerge branch 'features/JAL-2316' into develop
Jim Procter [Thu, 9 Feb 2017 12:49:33 +0000 (12:49 +0000)]
Merge branch 'features/JAL-2316' into develop

7 years agoMerge branch 'develop' into features/JAL-2316 features/JAL-2316
Jim Procter [Thu, 9 Feb 2017 11:50:07 +0000 (11:50 +0000)]
Merge branch 'develop' into features/JAL-2316

7 years agoJAL-2401 tweaked button text, added Spanish
gmungoc [Thu, 9 Feb 2017 11:40:09 +0000 (11:40 +0000)]
JAL-2401 tweaked button text, added Spanish

7 years agoJAL-2401 change 'Lower Case Colour' to checkbox with tooltip
gmungoc [Thu, 9 Feb 2017 10:39:22 +0000 (10:39 +0000)]
JAL-2401 change 'Lower Case Colour' to checkbox with tooltip

7 years agoJAL-2371 no test for lower case consensus as not expected or handled
gmungoc [Thu, 9 Feb 2017 10:05:21 +0000 (10:05 +0000)]
JAL-2371 no test for lower case consensus as not expected or handled

7 years agoJAL-2371 ensure some colour scheme (may be None) is set on startup
gmungoc [Thu, 9 Feb 2017 10:04:13 +0000 (10:04 +0000)]
JAL-2371 ensure some colour scheme (may be None) is set on startup

7 years agoMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory
gmungoc [Thu, 9 Feb 2017 09:05:30 +0000 (09:05 +0000)]
Merge branch 'develop' into features/JAL-2379pcaMemory

7 years agoJAL-2371 skip upper-casing consensus as it already is
gmungoc [Thu, 9 Feb 2017 09:01:13 +0000 (09:01 +0000)]
JAL-2371 skip upper-casing consensus as it already is

7 years agoJAL-2405 check for circular reference in SequenceGroup.context
gmungoc [Thu, 9 Feb 2017 08:49:38 +0000 (08:49 +0000)]
JAL-2405 check for circular reference in SequenceGroup.context

7 years agoJAL-2405 set initial selection group alignment context
gmungoc [Thu, 9 Feb 2017 08:41:33 +0000 (08:41 +0000)]
JAL-2405 set initial selection group alignment context

7 years agoJAL-2405 enable nucleotide/peptide colour schemes in applet menus
gmungoc [Thu, 9 Feb 2017 08:41:02 +0000 (08:41 +0000)]
JAL-2405 enable nucleotide/peptide colour schemes in applet menus

7 years agoJAL-2316 tidying preferences help page
Jim Procter [Wed, 8 Feb 2017 16:33:51 +0000 (16:33 +0000)]
JAL-2316 tidying preferences help page

7 years agoJAL-2316 tidied up documentation for Links tab
Jim Procter [Wed, 8 Feb 2017 16:33:35 +0000 (16:33 +0000)]
JAL-2316 tidied up documentation for Links tab

7 years agoJAL-2405 set context on selection group for tailored colour options
gmungoc [Wed, 8 Feb 2017 15:30:42 +0000 (15:30 +0000)]
JAL-2405 set context on selection group for tailored colour options

7 years agoJAL-2401 fix for NPE on selectedButtons, tweak for button appearance
gmungoc [Wed, 8 Feb 2017 14:43:36 +0000 (14:43 +0000)]
JAL-2401 fix for NPE on selectedButtons, tweak for button appearance

7 years agoMerge remote-tracking branch 'origin/develop' into features/JAL-2316
kiramt [Wed, 8 Feb 2017 11:59:19 +0000 (11:59 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2316

7 years agoJAL-2366 updated default URL to www.jalview.org/services/identifiers
Jim Procter [Wed, 8 Feb 2017 09:53:10 +0000 (09:53 +0000)]
JAL-2366 updated default URL to jalview.org/services/identifiers

7 years agoMerge branch 'features/JAL-2371collectionColourScheme' into develop
Jim Procter [Tue, 7 Feb 2017 18:15:14 +0000 (18:15 +0000)]
Merge branch 'features/JAL-2371collectionColourScheme' into develop

7 years agoJAL-2401 Lower Case Colour toggleable, help text added
gmungoc [Tue, 7 Feb 2017 15:59:37 +0000 (15:59 +0000)]
JAL-2401 Lower Case Colour toggleable, help text added

7 years agoJAL-2379 removed unused commented code
gmungoc [Tue, 7 Feb 2017 13:20:31 +0000 (13:20 +0000)]
JAL-2379 removed unused commented code

7 years agoJAL-2397 flag provided for 2.10.1 PCA gap calculation treatment
gmungoc [Tue, 7 Feb 2017 13:20:12 +0000 (13:20 +0000)]
JAL-2397 flag provided for 2.10.1 PCA gap calculation treatment

7 years agoJAL-2398 include 'compatibility mode' for C->R score correction
gmungoc [Tue, 7 Feb 2017 12:50:49 +0000 (12:50 +0000)]
JAL-2398 include 'compatibility mode' for C->R score correction

7 years agoJAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode
gmungoc [Tue, 7 Feb 2017 12:44:01 +0000 (12:44 +0000)]
JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode

7 years agoJAL-2397 PCA gap cost uses last column of score matrix
gmungoc [Tue, 7 Feb 2017 12:43:19 +0000 (12:43 +0000)]
JAL-2397 PCA gap cost uses last column of score matrix

7 years agoJAL-2398 corrected entry for C->R in Blosum62 matrix
gmungoc [Tue, 7 Feb 2017 11:50:00 +0000 (11:50 +0000)]
JAL-2398 corrected entry for C->R in Blosum62 matrix

7 years agoJAL-2379 computePairwiseScores() moved to ScoreMatrix
gmungoc [Mon, 6 Feb 2017 14:50:11 +0000 (14:50 +0000)]
JAL-2379 computePairwiseScores() moved to ScoreMatrix

7 years agoJAL-2379 'direct' pairwise score calculation for PCA (no encoding)
gmungoc [Fri, 3 Feb 2017 16:13:24 +0000 (16:13 +0000)]
JAL-2379 'direct' pairwise score calculation for PCA (no encoding)

7 years agoJAL-2371 (slight!) simplification of isApplicableTo()
gmungoc [Wed, 1 Feb 2017 13:02:56 +0000 (13:02 +0000)]
JAL-2371 (slight!) simplification of isApplicableTo()

7 years agoJAL-2383 and Spanish!
gmungoc [Wed, 1 Feb 2017 11:37:04 +0000 (11:37 +0000)]
JAL-2383 and Spanish!

7 years agoJAL-2371 commented code removed only
gmungoc [Tue, 31 Jan 2017 15:23:06 +0000 (15:23 +0000)]
JAL-2371 commented code removed only

7 years agoJAL-2371 rename global/viewportColourScheme to residueShading
gmungoc [Tue, 31 Jan 2017 14:40:51 +0000 (14:40 +0000)]
JAL-2371 rename global/viewportColourScheme to residueShading

7 years agoJAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some
gmungoc [Tue, 31 Jan 2017 14:38:38 +0000 (14:38 +0000)]
JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some
JAL-2371 tidying

7 years agoJAL-2379 commented out code removed
gmungoc [Fri, 27 Jan 2017 15:46:02 +0000 (15:46 +0000)]
JAL-2379 commented out code removed

7 years agoJAL-2371 CollectionColourScheme renamed ResidueShader and moved to
gmungoc [Fri, 27 Jan 2017 15:37:30 +0000 (15:37 +0000)]
JAL-2371 CollectionColourScheme renamed ResidueShader and moved to
jalview.renderer

7 years agoJAL-2099 belated unit test
gmungoc [Fri, 27 Jan 2017 15:30:49 +0000 (15:30 +0000)]
JAL-2099 belated unit test

7 years agoJAL-2360 JAL-2371 updates from review CR-JAL-1
gmungoc [Fri, 27 Jan 2017 10:40:43 +0000 (10:40 +0000)]
JAL-2360 JAL-2371 updates from review CR-JAL-1

7 years agoJAL-2366 Removed unneeded setEnabled calls
kiramt [Fri, 27 Jan 2017 09:52:40 +0000 (09:52 +0000)]
JAL-2366 Removed unneeded setEnabled calls

7 years agoJAL-2360 corrected comment
gmungoc [Thu, 26 Jan 2017 14:35:28 +0000 (14:35 +0000)]
JAL-2360 corrected comment

7 years agoJAL-2360 C is Pink with consensus > 85% (not 100%)
gmungoc [Thu, 26 Jan 2017 14:24:38 +0000 (14:24 +0000)]
JAL-2360 C is Pink with consensus > 85% (not 100%)

7 years agoMerge remote-tracking branch 'origin/develop' into features/JAL-2316
kiramt [Thu, 26 Jan 2017 11:40:39 +0000 (11:40 +0000)]
Merge remote-tracking branch 'origin/develop' into features/JAL-2316

7 years agoMerge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...
gmungoc [Thu, 26 Jan 2017 11:34:46 +0000 (11:34 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme

7 years agoMerge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Thu, 26 Jan 2017 11:34:04 +0000 (11:34 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

Conflicts:
src/jalview/gui/UserDefinedColours.java

7 years agoJAL-2316 Updated to use identifiers jalview service
kiramt [Thu, 26 Jan 2017 11:27:08 +0000 (11:27 +0000)]
JAL-2316 Updated to use identifiers jalview service

7 years agoMerge branch 'develop' into features/JAL-2379pcaMemory
gmungoc [Thu, 26 Jan 2017 09:47:42 +0000 (09:47 +0000)]
Merge branch 'develop' into features/JAL-2379pcaMemory

Conflicts:
src/jalview/analysis/PCA.java
src/jalview/math/Matrix.java
test/jalview/math/MatrixTest.java

7 years agoJAL-2344 test fix and code tidy for review comments
gmungoc [Thu, 26 Jan 2017 09:38:31 +0000 (09:38 +0000)]
JAL-2344 test fix and code tidy for review comments

7 years agoJAL-2380 code tidy after review
gmungoc [Thu, 26 Jan 2017 09:20:46 +0000 (09:20 +0000)]
JAL-2380 code tidy after review

7 years agoJAL-2344 push Cache.getProperty("LAST_DIRECTORY") inside method
gmungoc [Wed, 25 Jan 2017 12:15:43 +0000 (12:15 +0000)]
JAL-2344 push Cache.getProperty("LAST_DIRECTORY") inside method

7 years agoJAL-2379 made SparseMatrix.divide() so as to exactly match
gmungoc [Mon, 23 Jan 2017 20:25:42 +0000 (20:25 +0000)]
JAL-2379 made SparseMatrix.divide() so as to exactly match
Matrix.divide()

7 years agoJAL-2386 unit tests for change colour (and minor refactoring for
gmungoc [Mon, 23 Jan 2017 13:26:24 +0000 (13:26 +0000)]
JAL-2386 unit tests for change colour (and minor refactoring for
testability)

7 years agoJAL-2386 simplify changeColour (doesn't change colour thresholds)
gmungoc [Mon, 23 Jan 2017 09:11:36 +0000 (09:11 +0000)]
JAL-2386 simplify changeColour (doesn't change colour thresholds)

7 years agoMerge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...
gmungoc [Fri, 20 Jan 2017 14:49:29 +0000 (14:49 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme

7 years agoMerge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Fri, 20 Jan 2017 14:48:43 +0000 (14:48 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

7 years agoJAL-2385 tweak to applet 'switch colour slider context'
gmungoc [Fri, 20 Jan 2017 14:48:16 +0000 (14:48 +0000)]
JAL-2385 tweak to applet 'switch colour slider context'

7 years agoMerge branch 'features/JAL-2360colourSchemeApplicability' into
gmungoc [Fri, 20 Jan 2017 14:44:02 +0000 (14:44 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into
features/JAL-2371collectionColourScheme

Conflicts:
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/SliderPanel.java

7 years agoMerge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Fri, 20 Jan 2017 14:25:58 +0000 (14:25 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

7 years agoJAL-2385 update slider settings when switching slider panel focus
gmungoc [Fri, 20 Jan 2017 14:20:48 +0000 (14:20 +0000)]
JAL-2385 update slider settings when switching slider panel focus

7 years agoMerge branch 'features/JAL-2360colourSchemeApplicability' into
gmungoc [Fri, 20 Jan 2017 12:21:42 +0000 (12:21 +0000)]
Merge branch 'features/JAL-2360colourSchemeApplicability' into
features/JAL-2371collectionColourScheme

Conflicts:
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/Jalview2XML.java
src/jalview/gui/SliderPanel.java

7 years agoJAL-2383 fixup from last merge
gmungoc [Fri, 20 Jan 2017 12:03:39 +0000 (12:03 +0000)]
JAL-2383 fixup from last merge

7 years agoMerge branch 'develop' into features/JAL-2360colourSchemeApplicability
gmungoc [Fri, 20 Jan 2017 11:56:07 +0000 (11:56 +0000)]
Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

Conflicts:
src/jalview/appletgui/APopupMenu.java
src/jalview/appletgui/SliderPanel.java
src/jalview/gui/PopupMenu.java

7 years agoJAL-2383 check for null, spelling
gmungoc [Fri, 20 Jan 2017 10:55:50 +0000 (10:55 +0000)]
JAL-2383 check for null, spelling

7 years agoJAL-2383 make popup colour menu order and wording consistent
gmungoc [Fri, 20 Jan 2017 10:55:24 +0000 (10:55 +0000)]
JAL-2383 make popup colour menu order and wording consistent