X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fschemes%2FRNAHelicesColour.js;h=c7d3af2e5563b2b9cc1e79d25c60ef8bdb58e48e;hp=5023c9085c22cbcc7769f17d337d65b19c39ca12;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/schemes/RNAHelicesColour.js b/bin/jalview/schemes/RNAHelicesColour.js
index 5023c90..c7d3af2 100644
--- a/bin/jalview/schemes/RNAHelicesColour.js
+++ b/bin/jalview/schemes/RNAHelicesColour.js
@@ -1,68 +1,68 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.RNAHelicesColour", ["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;
-this.lastrefresh = -1;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "RNAHelicesColour", 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.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]);
-this.annotation = annotation;
-this.refresh ();
-}, "jalview.datamodel.AlignmentAnnotation");
-Clazz.makeConstructor (c$, 
-function (alignment) {
-Clazz.superConstructor (this, jalview.schemes.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]);
-this.alignmentChanged (alignment, null);
-}, "jalview.datamodel.AnnotatedCollectionI");
-Clazz.overrideMethod (c$, "alignmentChanged", 
-function (alignment, hiddenReps) {
-var annotations = alignment.getAlignmentAnnotation ();
-for (var i = 0; i < annotations.length; i++) {
-if (annotations[i].getRNAStruc () != null) {
-this.annotation = annotations[i];
-break;
-}}
-this.refresh ();
-}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
-Clazz.defineMethod (c$, "refresh", 
-function () {
-if (this.annotation != null && ((this.annotation._rnasecstr == null || this.lastrefresh != this.annotation._rnasecstr.hashCode ()) && this.annotation.isValidStruc ())) {
-this.annotation.getRNAStruc ();
-this.lastrefresh = this.annotation._rnasecstr.hashCode ();
-this.numHelix = 0;
-this.positionsToHelix =  new java.util.Hashtable ();
-for (var x = 0; x < this.annotation._rnasecstr.length; x++) {
-this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ());
-this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ());
-if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) {
-this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ());
-}}
-for (var j = 0; j <= this.numHelix; j++) {
-if (!this.helixcolorhash.containsKey (Integer.toString (j))) {
-this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white));
-}}
-}});
-Clazz.defineMethod (c$, "findColour", 
-function (c) {
-return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]];
-}, "~S");
-Clazz.defineMethod (c$, "findColour", 
-function (c, j, seq) {
-this.refresh ();
-var currentColour = java.awt.Color.white;
-var currentHelix = null;
-currentHelix = this.positionsToHelix.get (new Integer (j));
-if (currentHelix != null) {
-currentColour = this.helixcolorhash.get (currentHelix);
-}return currentColour;
-}, "~S,~N,jalview.datamodel.SequenceI");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.RNAHelicesColour", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.helixcolorhash = null;
+this.positionsToHelix = null;
+this.numHelix = 0;
+this.annotation = null;
+this.lastrefresh = -1;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "RNAHelicesColour", 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.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]);
+this.annotation = annotation;
+this.refresh ();
+}, "jalview.datamodel.AlignmentAnnotation");
+Clazz.makeConstructor (c$, 
+function (alignment) {
+Clazz.superConstructor (this, jalview.schemes.RNAHelicesColour, [jalview.schemes.ResidueProperties.nucleotideIndex]);
+this.alignmentChanged (alignment, null);
+}, "jalview.datamodel.AnnotatedCollectionI");
+Clazz.overrideMethod (c$, "alignmentChanged", 
+function (alignment, hiddenReps) {
+var annotations = alignment.getAlignmentAnnotation ();
+for (var i = 0; i < annotations.length; i++) {
+if (annotations[i].getRNAStruc () != null) {
+this.annotation = annotations[i];
+break;
+}}
+this.refresh ();
+}, "jalview.datamodel.AnnotatedCollectionI,java.util.Map");
+Clazz.defineMethod (c$, "refresh", 
+function () {
+if (this.annotation != null && ((this.annotation._rnasecstr == null || this.lastrefresh != this.annotation._rnasecstr.hashCode ()) && this.annotation.isValidStruc ())) {
+this.annotation.getRNAStruc ();
+this.lastrefresh = this.annotation._rnasecstr.hashCode ();
+this.numHelix = 0;
+this.positionsToHelix =  new java.util.Hashtable ();
+for (var x = 0; x < this.annotation._rnasecstr.length; x++) {
+this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ());
+this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ());
+if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) {
+this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ());
+}}
+for (var j = 0; j <= this.numHelix; j++) {
+if (!this.helixcolorhash.containsKey (Integer.toString (j))) {
+this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white));
+}}
+}});
+Clazz.defineMethod (c$, "findColour", 
+function (c) {
+return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]];
+}, "~S");
+Clazz.defineMethod (c$, "findColour", 
+function (c, j, seq) {
+this.refresh ();
+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,jalview.datamodel.SequenceI");
+});