JAL-2403 additional methods to support distance/similarity score
conversion

JAL-2416 typo

JAL-2416 ScoreMatrix.getMatrix() returns a defensive copy to keep the
class invariant

JAL-2416 support roundtrip print/parse of ScoreMatrix

Merge branch 'develop' into features/JAL-2393customMatrices

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

JAL-2416 quality calculation now only depends on loaded score matrix

JAL-2416 more validation in ScoreMatrix constructor

JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of
PairwiseDistanceModel

JAL-2416 replaced dependency on ResidueProperties with loaded score
matrix

Merge branch 'features/JAL-2379pcaMemory' into develop

JAL-2416 public constant for space gap character

JAL-2416 remove unused pep, dna alphabets, unused methods, code format
tidy

JAL-2416 better encapsulated 'constants' for BLOSUM62, PAM250

JAL-2416 BLOSUM62 removed from ResidueProperties

JAL-2416 removed DNA and PAM250 matrices from ResidueProperties

JAL-2416 scoreMatrices removed from ResidueProperties

JAL-2413 extracted new method SetUtils.countDisjunction()

JAL-2423 refactored method to build panel title for tree either
calculated or read from file

JAL-2416 SeqSpace PCA now provided as an alternative score matrix rather
than an alternative method (+code tidying)

JAL-2416 score models now held in order added

JAL-2416 allow space in score matrix name

JAL-2416 order score models by order of addition rather than name

JAL-2403 redundant 'implements' removed

JAL-2403 extract method refactoring of FeatureScoreModel + test

JAL-2403 constants for "NJ", "AV"

Merge branch 'bug/JAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu' into develop

JAL-2374 JAL-2419 - TODO suspiciously redundant nested if clauses probably need a cleanup

fix for JAL-2419 - don’t trash the current selection

JAL-2374 don’t search twice for containing group to assign to stretchGroup

JAL-2374 tests for SequenceGroup.contains

JAL-2374 JAL-1270 assign SequenceGroup tests to ‘Functional’

JAL-2374 new contains methods for seq and seq,apos

JAL-2374 javadoc - qualify that sequence argument to findGroup must be in the Alignment, not share the same dataset sequence

JAL-2393 example (unvalidated) blosum80 matrix to play with drag and
drop

Parsing moved to (new) ScoreMatrixFile, drag and drop to alignment now
supported

JAL-2416 allow alphabet symbol (optional) in first column of score table

JAL-1632 JAL-2416 load score matrices from file, as float[][]

JAL-1632 first cut of Tree chooser dialog and ScoreModels singleton

JAL-2371 small move of code, typo correction

Merge branch 'features/JAL-2316' into develop

Merge branch 'develop' into features/JAL-2316

JAL-2401 tweaked button text, added Spanish

JAL-2401 change 'Lower Case Colour' to checkbox with tooltip

JAL-2371 no test for lower case consensus as not expected or handled

JAL-2371 ensure some colour scheme (may be None) is set on startup

Merge branch 'develop' into features/JAL-2379pcaMemory

JAL-2371 skip upper-casing consensus as it already is

JAL-2405 check for circular reference in SequenceGroup.context

JAL-2405 set initial selection group alignment context

JAL-2405 enable nucleotide/peptide colour schemes in applet menus

JAL-2316 tidying preferences help page

JAL-2316 tidied up documentation for Links tab

JAL-2405 set context on selection group for tailored colour options

JAL-2401 fix for NPE on selectedButtons, tweak for button appearance

Merge remote-tracking branch 'origin/develop' into features/JAL-2316

JAL-2366 updated default URL to jalview.org/services/identifiers

Merge branch 'features/JAL-2371collectionColourScheme' into develop

JAL-2401 Lower Case Colour toggleable, help text added

JAL-2379 removed unused commented code

JAL-2397 flag provided for 2.10.1 PCA gap calculation treatment

JAL-2398 include 'compatibility mode' for C->R score correction

JAL-2397 scripts to toggle 2.10.1 / 2.10.2 PCA calculation mode

JAL-2397 PCA gap cost uses last column of score matrix

JAL-2398 corrected entry for C->R in Blosum62 matrix

JAL-2379 computePairwiseScores() moved to ScoreMatrix

JAL-2379 'direct' pairwise score calculation for PCA (no encoding)

JAL-2371 (slight!) simplification of isApplicableTo()

JAL-2383 and Spanish!

JAL-2371 commented code removed only

JAL-2371 rename global/viewportColourScheme to residueShading

JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some
JAL-2371 tidying

JAL-2379 commented out code removed

JAL-2371 CollectionColourScheme renamed ResidueShader and moved to
jalview.renderer

JAL-2099 belated unit test

JAL-2360 JAL-2371 updates from review CR-JAL-1

JAL-2366 Removed unneeded setEnabled calls

JAL-2360 corrected comment

JAL-2360 C is Pink with consensus > 85% (not 100%)

Merge remote-tracking branch 'origin/develop' into features/JAL-2316

Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme

Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

Conflicts:
src/jalview/gui/UserDefinedColours.java

JAL-2316 Updated to use identifiers jalview service

Merge branch 'develop' into features/JAL-2379pcaMemory

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

JAL-2344 test fix and code tidy for review comments

JAL-2380 code tidy after review

JAL-2344 push Cache.getProperty("LAST_DIRECTORY") inside method

JAL-2379 made SparseMatrix.divide() so as to exactly match
Matrix.divide()

JAL-2386 unit tests for change colour (and minor refactoring for
testability)

JAL-2386 simplify changeColour (doesn't change colour thresholds)

Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371collectionColourScheme

Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

JAL-2385 tweak to applet 'switch colour slider context'

Merge branch 'features/JAL-2360colourSchemeApplicability' into
features/JAL-2371collectionColourScheme

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

Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

JAL-2385 update slider settings when switching slider panel focus

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

JAL-2383 fixup from last merge

Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

JAL-2383 check for null, spelling

JAL-2383 make popup colour menu order and wording consistent