JAL-1807 includes ?j2sdebug flag and DebugJS._(msg)

[jalviewjs.git] / bin / jalview / schemes / TCoffeeColourScheme.js

diff --git a/bin/jalview/schemes/TCoffeeColourScheme.js b/bin/jalview/schemes/TCoffeeColourScheme.js
index 0952425..6350ad9 100644 (file)
--- a/bin/jalview/schemes/TCoffeeColourScheme.js
+++ b/bin/jalview/schemes/TCoffeeColourScheme.js
@@ -1,45 +1,45 @@
-Clazz.declarePackage ("jalview.schemes");\r
-Clazz.load (["jalview.schemes.ResidueColourScheme", "java.awt.Color"], "jalview.schemes.TCoffeeColourScheme", ["jalview.datamodel.AlignmentI", "java.util.ArrayList", "$.IdentityHashMap"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.seqMap = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.schemes, "TCoffeeColourScheme", jalview.schemes.ResidueColourScheme);\r
-Clazz.makeConstructor (c$, \r
-function (alignment) {\r
-Clazz.superConstructor (this, jalview.schemes.TCoffeeColourScheme, []);\r
-this.alignmentChanged (alignment, null);\r
-}, "jalview.datamodel.AnnotatedCollectionI");\r
-Clazz.overrideMethod (c$, "alignmentChanged", \r
-function (alignment, hiddenReps) {\r
-var annots =  new java.util.ArrayList ();\r
-this.seqMap =  new java.util.IdentityHashMap ();\r
-var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext ();\r
-var w = 0;\r
-for (var al, $al = alcontext.findAnnotation ("TCoffeeScore").iterator (); $al.hasNext () && ((al = $al.next ()) || true);) {\r
-if (al.sequenceRef != null && !al.belowAlignment) {\r
-annots.add (al);\r
-if (w < al.annotations.length) {\r
-w = al.annotations.length;\r
-}var scores =  new Array (al.annotations.length);\r
-var i = 0;\r
-for (var an, $an = 0, $$an = al.annotations; $an < $$an.length && ((an = $$an[$an]) || true); $an++) {\r
-scores[i++] = (an != null) ? an.colour : java.awt.Color.white;\r
-}\r
-this.seqMap.put (al.sequenceRef, scores);\r
-}}\r
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
-Clazz.defineMethod (c$, "findColour", \r
-function (c, j, seq) {\r
-var cols;\r
-if (this.seqMap == null || (cols = this.seqMap.get (seq)) == null) {\r
-return java.awt.Color.white;\r
-}if (j < 0 || j >= cols.length) {\r
-return java.awt.Color.white;\r
-}return cols[j];\r
-}, "~S,~N,jalview.datamodel.SequenceI");\r
-Clazz.overrideMethod (c$, "applyTo", \r
-function (sg, hiddenRepSequences) {\r
-return  new jalview.schemes.TCoffeeColourScheme (sg);\r
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");\r
-c$.$colors = c$.prototype.$colors =  Clazz.newArray (-1, [ new java.awt.Color (102, 102, 255),  new java.awt.Color (0, 255, 0),  new java.awt.Color (102, 255, 0),  new java.awt.Color (204, 255, 0),  new java.awt.Color (255, 255, 0),  new java.awt.Color (255, 204, 0),  new java.awt.Color (255, 153, 0),  new java.awt.Color (255, 102, 0),  new java.awt.Color (255, 51, 0),  new java.awt.Color (255, 34, 0)]);\r
-});\r
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme", "java.awt.Color"], "jalview.schemes.TCoffeeColourScheme", ["jalview.datamodel.AlignmentI", "java.util.ArrayList", "$.IdentityHashMap"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.seqMap = null;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "TCoffeeColourScheme", jalview.schemes.ResidueColourScheme);
+Clazz.makeConstructor (c$, 
+function (alignment) {
+Clazz.superConstructor (this, jalview.schemes.TCoffeeColourScheme, []);
+this.alignmentChanged (alignment, null);
+}, "jalview.datamodel.AnnotatedCollectionI");
+Clazz.overrideMethod (c$, "alignmentChanged", 
+function (alignment, hiddenReps) {
+var annots =  new java.util.ArrayList ();
+this.seqMap =  new java.util.IdentityHashMap ();
+var alcontext = Clazz.instanceOf (alignment, jalview.datamodel.AlignmentI) ? alignment : alignment.getContext ();
+var w = 0;
+for (var al, $al = alcontext.findAnnotation ("TCoffeeScore").iterator (); $al.hasNext () && ((al = $al.next ()) || true);) {
+if (al.sequenceRef != null && !al.belowAlignment) {
+annots.add (al);
+if (w < al.annotations.length) {
+w = al.annotations.length;
+}var scores =  new Array (al.annotations.length);
+var i = 0;
+for (var an, $an = 0, $$an = al.annotations; $an < $$an.length && ((an = $$an[$an]) || true); $an++) {
+scores[i++] = (an != null) ? an.colour : java.awt.Color.white;
+}
+this.seqMap.put (al.sequenceRef, scores);
+}}
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.defineMethod (c$, "findColour", 
+function (c, j, seq) {
+var cols;
+if (this.seqMap == null || (cols = this.seqMap.get (seq)) == null) {
+return java.awt.Color.white;
+}if (j < 0 || j >= cols.length) {
+return java.awt.Color.white;
+}return cols[j];
+}, "~S,~N,jalview.datamodel.SequenceI");
+Clazz.overrideMethod (c$, "applyTo", 
+function (sg, hiddenRepSequences) {
+return  new jalview.schemes.TCoffeeColourScheme (sg);
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+c$.$colors = c$.prototype.$colors =  Clazz.newArray (-1, [ new java.awt.Color (102, 102, 255),  new java.awt.Color (0, 255, 0),  new java.awt.Color (102, 255, 0),  new java.awt.Color (204, 255, 0),  new java.awt.Color (255, 255, 0),  new java.awt.Color (255, 204, 0),  new java.awt.Color (255, 153, 0),  new java.awt.Color (255, 102, 0),  new java.awt.Color (255, 51, 0),  new java.awt.Color (255, 34, 0)]);
+});