X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fschemes%2FPIDColourScheme.js;fp=site%2Fj2s%2Fjalview%2Fschemes%2FPIDColourScheme.js;h=bdf6f2406834e2b9b13833f442457697494efe09;hp=093328cafadee08d54929f4af29ec18e96007e88;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/schemes/PIDColourScheme.js b/site/j2s/jalview/schemes/PIDColourScheme.js
index 093328c..bdf6f24 100644
--- a/site/j2s/jalview/schemes/PIDColourScheme.js
+++ b/site/j2s/jalview/schemes/PIDColourScheme.js
@@ -1,39 +1,39 @@
-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");
-});
+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");
+});