Merge branch 'master' of https://source.jalview.org/git/jalviewjs.git

[jalviewjs.git] / site / j2s / jalview / schemes / PIDColourScheme.js

diff --git a/site/j2s/jalview/schemes/PIDColourScheme.js b/site/j2s/jalview/schemes/PIDColourScheme.js
index 093328c..bdf6f24 100644 (file)
--- a/site/j2s/jalview/schemes/PIDColourScheme.js
+++ b/site/j2s/jalview/schemes/PIDColourScheme.js
@@ -1,39 +1,39 @@
-Clazz.declarePackage ("jalview.schemes");\r
-Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PIDColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.pidColours = null;\r
-this.thresholds = null;\r
-this.group = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.schemes, "PIDColourScheme", jalview.schemes.ResidueColourScheme);\r
-Clazz.makeConstructor (c$, \r
-function () {\r
-Clazz.superConstructor (this, jalview.schemes.PIDColourScheme, []);\r
-this.pidColours = jalview.schemes.ResidueProperties.pidColours;\r
-this.thresholds = jalview.schemes.ResidueProperties.pidThresholds;\r
-});\r
-Clazz.defineMethod (c$, "findColour", \r
-function (c, j, seq) {\r
-if ('a' <= c && c <= 'z') {\r
-c = String.fromCharCode (c.charCodeAt (0) - (32));\r
-}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null) {\r
-return java.awt.Color.white;\r
-}if ((this.threshold != 0) && !this.aboveThreshold (c, j)) {\r
-return java.awt.Color.white;\r
-}var currentColour = java.awt.Color.white;\r
-var sc = 0;\r
-if (this.consensus.length <= j) {\r
-return java.awt.Color.white;\r
-}if ((Integer.parseInt (this.consensus[j].get ("C").toString ()) != -1) && this.consensus[j].contains (String.valueOf (c))) {\r
-sc = (this.consensus[j].get (this.ignoreGaps)).floatValue ();\r
-if (!jalview.util.Comparison.isGap (c)) {\r
-for (var i = 0; i < this.thresholds.length; i++) {\r
-if (sc > this.thresholds[i]) {\r
-currentColour = this.pidColours[i];\r
-break;\r
-}}\r
-}}if (this.conservationColouring) {\r
-currentColour = this.applyConservation (currentColour, j);\r
-}return currentColour;\r
-}, "~S,~N,jalview.datamodel.SequenceI");\r
-});\r
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PIDColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.pidColours = null;
+this.thresholds = null;
+this.group = null;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "PIDColourScheme", jalview.schemes.ResidueColourScheme);
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.schemes.PIDColourScheme, []);
+this.pidColours = jalview.schemes.ResidueProperties.pidColours;
+this.thresholds = jalview.schemes.ResidueProperties.pidThresholds;
+});
+Clazz.defineMethod (c$, "findColour", 
+function (c, j, seq) {
+if ('a' <= c && c <= 'z') {
+c = String.fromCharCode (c.charCodeAt (0) - (32));
+}if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null) {
+return java.awt.Color.white;
+}if ((this.threshold != 0) && !this.aboveThreshold (c, j)) {
+return java.awt.Color.white;
+}var currentColour = java.awt.Color.white;
+var sc = 0;
+if (this.consensus.length <= j) {
+return java.awt.Color.white;
+}if ((Integer.parseInt (this.consensus[j].get ("C").toString ()) != -1) && this.consensus[j].contains (String.valueOf (c))) {
+sc = (this.consensus[j].get (this.ignoreGaps)).floatValue ();
+if (!jalview.util.Comparison.isGap (c)) {
+for (var i = 0; i < this.thresholds.length; i++) {
+if (sc > this.thresholds[i]) {
+currentColour = this.pidColours[i];
+break;
+}}
+}}if (this.conservationColouring) {
+currentColour = this.applyConservation (currentColour, j);
+}return currentColour;
+}, "~S,~N,jalview.datamodel.SequenceI");
+});