JAL-1807 includes ?j2sdebug flag and DebugJS._(msg)

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

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