JAL-1807 still testing

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

diff --git a/bin/jalview/schemes/CovariationColourScheme.js b/bin/jalview/schemes/CovariationColourScheme.js
index 68c8f15..3d75e42 100644 (file)
--- a/bin/jalview/schemes/CovariationColourScheme.js
+++ b/bin/jalview/schemes/CovariationColourScheme.js
@@ -1,41 +1,41 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.CovariationColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.helixcolorhash = null;
-this.positionsToHelix = null;
-this.numHelix = 0;
-this.annotation = null;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "CovariationColourScheme", jalview.schemes.ResidueColourScheme);
-Clazz.prepareFields (c$, function () {
-this.helixcolorhash =  new java.util.Hashtable ();
-this.positionsToHelix =  new java.util.Hashtable ();
-});
-Clazz.makeConstructor (c$, 
-function (annotation) {
-Clazz.superConstructor (this, jalview.schemes.CovariationColourScheme, []);
-this.annotation = annotation;
-for (var x = 0; x < this.annotation._rnasecstr.length; x++) {
-this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ());
-this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ());
-if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) {
-this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ());
-}}
-for (var j = 0; j <= this.numHelix; j++) {
-this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white));
-}
-}, "jalview.datamodel.AlignmentAnnotation");
-Clazz.defineMethod (c$, "findColour", 
-function (c) {
-return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]];
-}, "~S");
-Clazz.defineMethod (c$, "findColour", 
-function (c, j) {
-var currentColour = java.awt.Color.white;
-var currentHelix = null;
-currentHelix = this.positionsToHelix.get (new Integer (j));
-if (currentHelix != null) {
-currentColour = this.helixcolorhash.get (currentHelix);
-}return currentColour;
-}, "~S,~N");
-});
+Clazz.declarePackage ("jalview.schemes");\r
+Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.CovariationColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.helixcolorhash = null;\r
+this.positionsToHelix = null;\r
+this.numHelix = 0;\r
+this.annotation = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.schemes, "CovariationColourScheme", jalview.schemes.ResidueColourScheme);\r
+Clazz.prepareFields (c$, function () {\r
+this.helixcolorhash =  new java.util.Hashtable ();\r
+this.positionsToHelix =  new java.util.Hashtable ();\r
+});\r
+Clazz.makeConstructor (c$, \r
+function (annotation) {\r
+Clazz.superConstructor (this, jalview.schemes.CovariationColourScheme, []);\r
+this.annotation = annotation;\r
+for (var x = 0; x < this.annotation._rnasecstr.length; x++) {\r
+this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ());\r
+this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ());\r
+if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) {\r
+this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ());\r
+}}\r
+for (var j = 0; j <= this.numHelix; j++) {\r
+this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white));\r
+}\r
+}, "jalview.datamodel.AlignmentAnnotation");\r
+Clazz.defineMethod (c$, "findColour", \r
+function (c) {\r
+return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]];\r
+}, "~S");\r
+Clazz.defineMethod (c$, "findColour", \r
+function (c, j) {\r
+var currentColour = java.awt.Color.white;\r
+var currentHelix = null;\r
+currentHelix = this.positionsToHelix.get (new Integer (j));\r
+if (currentHelix != null) {\r
+currentColour = this.helixcolorhash.get (currentHelix);\r
+}return currentColour;\r
+}, "~S,~N");\r
+});\r