X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.js;h=0d9cf266f7fcdb1e928ecc217c341714d76d296a;hp=27a0f255f0e6b82bb233eb41b6aa2c859a8e9b9a;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/schemes/RNAHelicesColourChooser.js b/bin/jalview/schemes/RNAHelicesColourChooser.js
index 27a0f25..0d9cf26 100644
--- a/bin/jalview/schemes/RNAHelicesColourChooser.js
+++ b/bin/jalview/schemes/RNAHelicesColourChooser.js
@@ -1,63 +1,63 @@
-Clazz.declarePackage ("jalview.schemes");
-Clazz.load (null, "jalview.schemes.RNAHelicesColourChooser", ["jalview.schemes.RNAHelicesColour", "java.util.Hashtable", "$.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.av = null;
-this.ap = null;
-this.oldcs = null;
-this.oldgroupColours = null;
-this.currentAnnotation = null;
-this.adjusting = false;
-Clazz.instantialize (this, arguments);
-}, jalview.schemes, "RNAHelicesColourChooser");
-Clazz.makeConstructor (c$, 
-function (av, ap) {
-this.oldcs = av.getGlobalColourScheme ();
-if (av.getAlignment ().getGroups () != null) {
-this.oldgroupColours =  new java.util.Hashtable ();
-for (var sg, $sg = ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.cs != null) {
-this.oldgroupColours.put (sg, sg.cs);
-}}
-}this.av = av;
-this.ap = ap;
-if (Clazz.instanceOf (this.oldcs, jalview.schemes.RNAHelicesColour)) {
-var rhc = this.oldcs;
-}this.adjusting = true;
-var list =  new java.util.Vector ();
-var index = 1;
-for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) {
-var label = av.getAlignment ().getAlignmentAnnotation ()[i].label;
-if (!list.contains (label)) list.addElement (label);
- else list.addElement (label + "_" + (index++));
-}
-this.adjusting = false;
-this.changeColour ();
-}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
-Clazz.defineMethod (c$, "changeColour", 
-function () {
-if (this.adjusting) {
-return;
-}var rhc = null;
-rhc =  new jalview.schemes.RNAHelicesColour (this.av.getAlignment ());
-this.av.setGlobalColourScheme (rhc);
-if (this.av.getAlignment ().getGroups () != null) {
-for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.cs == null) {
-continue;
-}sg.cs =  new jalview.schemes.RNAHelicesColour (sg);
-}
-}this.ap.paintAlignment (false);
-});
-Clazz.defineMethod (c$, "reset", 
-function () {
-this.av.setGlobalColourScheme (this.oldcs);
-if (this.av.getAlignment ().getGroups () != null) {
-for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-sg.cs = this.oldgroupColours.get (sg);
-}
-}});
-Clazz.defineMethod (c$, "annotations_actionPerformed", 
-function (e) {
-this.changeColour ();
-}, "java.awt.event.ActionEvent");
-});
+Clazz.declarePackage ("jalview.schemes");
+Clazz.load (null, "jalview.schemes.RNAHelicesColourChooser", ["jalview.schemes.RNAHelicesColour", "java.util.Hashtable", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.av = null;
+this.ap = null;
+this.oldcs = null;
+this.oldgroupColours = null;
+this.currentAnnotation = null;
+this.adjusting = false;
+Clazz.instantialize (this, arguments);
+}, jalview.schemes, "RNAHelicesColourChooser");
+Clazz.makeConstructor (c$, 
+function (av, ap) {
+this.oldcs = av.getGlobalColourScheme ();
+if (av.getAlignment ().getGroups () != null) {
+this.oldgroupColours =  new java.util.Hashtable ();
+for (var sg, $sg = ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.cs != null) {
+this.oldgroupColours.put (sg, sg.cs);
+}}
+}this.av = av;
+this.ap = ap;
+if (Clazz.instanceOf (this.oldcs, jalview.schemes.RNAHelicesColour)) {
+var rhc = this.oldcs;
+}this.adjusting = true;
+var list =  new java.util.Vector ();
+var index = 1;
+for (var i = 0; i < av.getAlignment ().getAlignmentAnnotation ().length; i++) {
+var label = av.getAlignment ().getAlignmentAnnotation ()[i].label;
+if (!list.contains (label)) list.addElement (label);
+ else list.addElement (label + "_" + (index++));
+}
+this.adjusting = false;
+this.changeColour ();
+}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
+Clazz.defineMethod (c$, "changeColour", 
+function () {
+if (this.adjusting) {
+return;
+}var rhc = null;
+rhc =  new jalview.schemes.RNAHelicesColour (this.av.getAlignment ());
+this.av.setGlobalColourScheme (rhc);
+if (this.av.getAlignment ().getGroups () != null) {
+for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.cs == null) {
+continue;
+}sg.cs =  new jalview.schemes.RNAHelicesColour (sg);
+}
+}this.ap.paintAlignment (false);
+});
+Clazz.defineMethod (c$, "reset", 
+function () {
+this.av.setGlobalColourScheme (this.oldcs);
+if (this.av.getAlignment ().getGroups () != null) {
+for (var sg, $sg = this.ap.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+sg.cs = this.oldgroupColours.get (sg);
+}
+}});
+Clazz.defineMethod (c$, "annotations_actionPerformed", 
+function (e) {
+this.changeColour ();
+}, "java.awt.event.ActionEvent");
+});