X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fappletgui%2FAnnotationColourChooser.js;fp=site%2Fj2s%2Fjalview%2Fappletgui%2FAnnotationColourChooser.js;h=0e34c10328606b363f956f2ceac379b6679c35df;hp=cd1dff3e992ac37bb49a16020a7116cef3dbcfd7;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/appletgui/AnnotationColourChooser.js b/site/j2s/jalview/appletgui/AnnotationColourChooser.js
index cd1dff3..0e34c10 100644
--- a/site/j2s/jalview/appletgui/AnnotationColourChooser.js
+++ b/site/j2s/jalview/appletgui/AnnotationColourChooser.js
@@ -1,348 +1,348 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Button", "$.Checkbox", "$.Choice", "$.Scrollbar", "$.TextField", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.AnnotationColourChooser", ["awt2swing.Frame", "jalview.appletgui.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.datamodel.GraphLine", "jalview.schemes.AnnotationColourGradient", "$.ColourSchemeI", "jalview.util.MessageManager", "java.awt.Color", "$.Dimension", "$.Font", "java.lang.Error", "$.Float", "java.util.Hashtable", "$.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.frame = null;
-this.av = null;
-this.ap = null;
-this.oldcs = null;
-this.oldgroupColours = null;
-this.currentAnnotation = null;
-this.adjusting = false;
-this.annotations = null;
-this.minColour = null;
-this.maxColour = null;
-this.ok = null;
-this.cancel = null;
-this.defColours = null;
-this.jPanel1 = null;
-this.jPanel2 = null;
-this.threshold = null;
-this.flowLayout1 = null;
-this.jPanel3 = null;
-this.slider = null;
-this.thresholdValue = null;
-this.currentColours = null;
-this.borderLayout1 = null;
-this.thresholdIsMin = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "AnnotationColourChooser", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]);
-Clazz.prepareFields (c$, function () {
-this.annotations =  new awt2swing.Choice ();
-this.minColour =  new awt2swing.Button ();
-this.maxColour =  new awt2swing.Button ();
-this.ok =  new awt2swing.Button ();
-this.cancel =  new awt2swing.Button ();
-this.defColours =  new awt2swing.Button ();
-this.jPanel1 =  new awt2swing.Panel ();
-this.jPanel2 =  new awt2swing.Panel ();
-this.threshold =  new awt2swing.Choice ();
-this.flowLayout1 =  new java.awt.FlowLayout ();
-this.jPanel3 =  new awt2swing.Panel ();
-this.slider =  new awt2swing.Scrollbar (0);
-this.thresholdValue =  new awt2swing.TextField (20);
-this.currentColours =  new awt2swing.Checkbox ();
-this.borderLayout1 =  new java.awt.BorderLayout ();
-this.thresholdIsMin =  new awt2swing.Checkbox ();
-});
-Clazz.makeConstructor (c$, 
-function (av, ap) {
-Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []);
-try {
-this.jbInit ();
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-} else {
-throw ex;
-}
-}
-this.oldcs = av.getGlobalColourScheme ();
-if (av.getAlignment ().getGroups () != null) {
-this.oldgroupColours =  new java.util.Hashtable ();
-for (var sg, $sg = ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.cs != null) {
-this.oldgroupColours.put (sg, sg.cs);
-} else {
-this.oldgroupColours.put (sg, "null");
-}}
-}this.av = av;
-this.ap = ap;
-this.slider.addAdjustmentListener (this);
-this.slider.addMouseListener (this);
-if (av.getAlignment ().getAlignmentAnnotation () == null) {
-return;
-}this.setDefaultMinMax ();
-this.adjusting = true;
-if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) {
-var acg = this.oldcs;
-this.currentColours.setState (acg.isPredefinedColours () || acg.getBaseColour () != null);
-if (!acg.isPredefinedColours () && acg.getBaseColour () == null) {
-this.minColour.setBackground (acg.getMinColour ());
-this.maxColour.setBackground (acg.getMaxColour ());
-}}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++));
-}}
-for (var i = 0; i < list.size (); i++) {
-this.annotations.addItem (list.elementAt (i).toString ());
-}
-this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold"));
-this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold"));
-this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold"));
-if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) {
-var acg = this.oldcs;
-this.annotations.select (acg.getAnnotation ());
-switch (acg.getAboveThreshold ()) {
-case -1:
-this.threshold.select (new Integer (0));
-break;
-case 1:
-this.threshold.select (new Integer (1));
-break;
-case 0:
-this.threshold.select (new Integer (1));
-break;
-default:
-throw  new Error (jalview.util.MessageManager.getString ("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
-}
-this.thresholdIsMin.setState (acg.thresholdIsMinMax);
-this.thresholdValue.setText ("" + acg.getAnnotationThreshold ());
-}this.adjusting = false;
-this.changeColour ();
-this.frame =  new awt2swing.Frame ();
-this.frame.add (this);
-jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.colour_by_annotation"), 560, 175);
-this.validate ();
-}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");
-Clazz.defineMethod (c$, "setDefaultMinMax", 
- function () {
-this.minColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MIN", java.awt.Color.orange));
-this.maxColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MAX", java.awt.Color.red));
-});
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []);
-try {
-this.jbInit ();
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-});
-Clazz.defineMethod (c$, "jbInit", 
- function () {
-this.minColour.setFont ( new java.awt.Font ("Verdana", 0, 11));
-this.minColour.setLabel (jalview.util.MessageManager.getString ("label.min_colour"));
-this.minColour.addActionListener (this);
-this.maxColour.setFont ( new java.awt.Font ("Verdana", 0, 11));
-this.maxColour.setLabel (jalview.util.MessageManager.getString ("label.max_colour"));
-this.maxColour.addActionListener (this);
-this.thresholdIsMin.addItemListener (this);
-this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok"));
-this.ok.addActionListener (this);
-this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel"));
-this.cancel.addActionListener (this);
-this.defColours.setLabel (jalview.util.MessageManager.getString ("action.set_defaults"));
-this.defColours.addActionListener (this);
-this.annotations.addItemListener (this);
-this.thresholdValue.addActionListener (this);
-this.slider.setBackground (java.awt.Color.white);
-this.slider.setPreferredSize ( new java.awt.Dimension (193, 21));
-this.slider.setEnabled (false);
-this.thresholdValue.setPreferredSize ( new java.awt.Dimension (79, 22));
-this.thresholdValue.setEnabled (false);
-this.thresholdValue.setColumns (5);
-this.currentColours.setFont ( new java.awt.Font ("Verdana", 0, 11));
-this.currentColours.setLabel (jalview.util.MessageManager.getString ("label.use_original_colours"));
-this.currentColours.addItemListener (this);
-this.thresholdIsMin.setBackground (java.awt.Color.white);
-this.thresholdIsMin.setLabel (jalview.util.MessageManager.getString ("label.threshold_minmax"));
-this.setLayout (this.borderLayout1);
-this.jPanel1.setBackground (java.awt.Color.white);
-this.jPanel2.setLayout ( new java.awt.FlowLayout ());
-this.jPanel2.setBackground (java.awt.Color.white);
-this.threshold.addItemListener (this);
-this.jPanel3.setLayout ( new java.awt.FlowLayout ());
-this.jPanel3.setBackground (java.awt.Color.white);
-var jPanel4 =  new awt2swing.Panel ();
-jPanel4.setLayout ( new java.awt.BorderLayout ());
-jPanel4.setBackground (java.awt.Color.white);
-this.jPanel1.add (this.ok);
-this.jPanel1.add (this.cancel);
-this.jPanel2.add (this.annotations);
-this.jPanel2.add (this.currentColours);
-this.jPanel2.add (this.minColour);
-this.jPanel2.add (this.maxColour);
-jPanel4.add (this.thresholdIsMin, "West");
-jPanel4.add (this.slider, "Center");
-jPanel4.add (this.thresholdValue, "East");
-var jPanel34 =  new awt2swing.Panel ();
-jPanel34.setLayout ( new java.awt.BorderLayout ());
-jPanel34.setBackground (java.awt.Color.white);
-jPanel34.add (this.jPanel2, "North");
-jPanel34.add (this.threshold, "West");
-this.jPanel3.add (this.defColours);
-jPanel34.add (this.jPanel3, "East");
-jPanel34.add (jPanel4, "South");
-this.add (jPanel34, "Center");
-this.add (this.jPanel1, "South");
-});
-Clazz.overrideMethod (c$, "actionPerformed", 
-function (evt) {
-if (evt.getSource () === this.thresholdValue) {
-try {
-var f =  new Float (this.thresholdValue.getText ()).floatValue ();
-this.slider.setValue (Clazz.floatToInt (f * 1000));
-this.adjustmentValueChanged (null);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, NumberFormatException)) {
-} else {
-throw ex;
-}
-}
-} else if (evt.getSource () === this.minColour) {
-this.minColour_actionPerformed (null);
-} else if (evt.getSource () === this.maxColour) {
-this.maxColour_actionPerformed (null);
-} else if (evt.getSource () === this.defColours) {
-this.defColour_actionPerformed ();
-} else if (evt.getSource () === this.ok) {
-this.changeColour ();
-this.frame.setVisible (false);
-} else if (evt.getSource () === this.cancel) {
-this.reset ();
-this.ap.paintAlignment (true);
-this.frame.setVisible (false);
-} else {
-this.changeColour ();
-}}, "java.awt.event.ActionEvent");
-Clazz.overrideMethod (c$, "itemStateChanged", 
-function (evt) {
-if (evt.getSource () === this.currentColours) {
-if (this.currentColours.getState ()) {
-this.reset ();
-}this.maxColour.setEnabled (!this.currentColours.getState ());
-this.minColour.setEnabled (!this.currentColours.getState ());
-}this.changeColour ();
-}, "java.awt.event.ItemEvent");
-Clazz.overrideMethod (c$, "adjustmentValueChanged", 
-function (evt) {
-if (!this.adjusting) {
-this.thresholdValue.setText ((this.slider.getValue () / 1000) + "");
-if (this.currentColours.getState () && !(Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.AnnotationColourGradient))) {
-this.changeColour ();
-}this.currentAnnotation.threshold.value = this.slider.getValue () / 1000;
-this.ap.paintAlignment (false);
-}}, "java.awt.event.AdjustmentEvent");
-Clazz.defineMethod (c$, "minColour_actionPerformed", 
-function (newCol) {
-if (newCol != null) {
-this.minColour.setBackground (newCol);
-this.minColour.repaint ();
-this.changeColour ();
-} else {
- new jalview.appletgui.UserDefinedColours (this, "Min Colour", this.minColour.getBackground ());
-}}, "java.awt.Color");
-Clazz.defineMethod (c$, "maxColour_actionPerformed", 
-function (newCol) {
-if (newCol != null) {
-this.maxColour.setBackground (newCol);
-this.maxColour.repaint ();
-this.changeColour ();
-} else {
- new jalview.appletgui.UserDefinedColours (this, "Max Colour", this.maxColour.getBackground ());
-}}, "java.awt.Color");
-Clazz.defineMethod (c$, "defColour_actionPerformed", 
-function () {
-this.setDefaultMinMax ();
-this.minColour.repaint ();
-this.maxColour.repaint ();
-this.changeColour ();
-});
-Clazz.defineMethod (c$, "changeColour", 
-function () {
-if (this.adjusting) {
-return;
-}this.currentAnnotation = this.av.getAlignment ().getAlignmentAnnotation ()[this.annotations.getSelectedIndex ()];
-var aboveThreshold = -1;
-if (this.threshold.getSelectedIndex () == 1) {
-aboveThreshold = 1;
-} else if (this.threshold.getSelectedIndex () == 2) {
-aboveThreshold = 0;
-}this.slider.setEnabled (true);
-this.thresholdValue.setEnabled (true);
-this.thresholdIsMin.setEnabled (true);
-if (aboveThreshold == -1) {
-this.slider.setEnabled (false);
-this.thresholdValue.setEnabled (false);
-this.thresholdIsMin.setEnabled (false);
-this.thresholdValue.setText ("");
-} else if (aboveThreshold != -1 && this.currentAnnotation.threshold == null) {
-this.currentAnnotation.setThreshold ( new jalview.datamodel.GraphLine ((this.currentAnnotation.graphMax - this.currentAnnotation.graphMin) / 2, "Threshold", java.awt.Color.black));
-}if (aboveThreshold != -1) {
-this.adjusting = true;
-this.slider.setMinimum (Clazz.floatToInt (this.currentAnnotation.graphMin * 1000));
-this.slider.setMaximum (Clazz.floatToInt (this.currentAnnotation.graphMax * 1000));
-this.slider.setValue (Clazz.floatToInt (this.currentAnnotation.threshold.value * 1000));
-this.thresholdValue.setText (this.currentAnnotation.threshold.value + "");
-this.slider.setEnabled (true);
-this.thresholdValue.setEnabled (true);
-this.adjusting = false;
-}var acg = null;
-if (this.currentColours.getState ()) {
-acg =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.av.getGlobalColourScheme (), aboveThreshold);
-} else {
-acg =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold);
-}if (this.currentAnnotation.graphMin == 0 && this.currentAnnotation.graphMax == 0) {
-acg.setPredefinedColours (true);
-}acg.thresholdIsMinMax = this.thresholdIsMin.getState ();
-this.av.setGlobalColourScheme (acg);
-if (this.av.getAlignment ().getGroups () != null) {
-for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.cs == null) {
-continue;
-}if (this.currentColours.getState ()) {
-sg.cs =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, sg.cs, aboveThreshold);
-} else {
-sg.cs =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold);
-}}
-}this.ap.alignmentChanged ();
-this.ap.paintAlignment (true);
-});
-Clazz.defineMethod (c$, "reset", 
-function () {
-this.av.setGlobalColourScheme (this.oldcs);
-if (this.av.getAlignment ().getGroups () != null) {
-for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-var cs = this.oldgroupColours.get (sg);
-if (Clazz.instanceOf (cs, jalview.schemes.ColourSchemeI)) {
-sg.cs = cs;
-} else {
-sg.cs = null;
-}}
-}this.ap.paintAlignment (true);
-});
-Clazz.overrideMethod (c$, "mouseClicked", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mousePressed", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseReleased", 
-function (evt) {
-this.ap.paintAlignment (true);
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseEntered", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseExited", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.AdjustmentListener", "$.ItemListener", "$.MouseListener", "awt2swing.Button", "$.Checkbox", "$.Choice", "$.Scrollbar", "$.TextField", "java.awt.BorderLayout", "$.FlowLayout"], "jalview.appletgui.AnnotationColourChooser", ["awt2swing.Frame", "jalview.appletgui.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.datamodel.GraphLine", "jalview.schemes.AnnotationColourGradient", "$.ColourSchemeI", "jalview.util.MessageManager", "java.awt.Color", "$.Dimension", "$.Font", "java.lang.Error", "$.Float", "java.util.Hashtable", "$.Vector"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.frame = null;
+this.av = null;
+this.ap = null;
+this.oldcs = null;
+this.oldgroupColours = null;
+this.currentAnnotation = null;
+this.adjusting = false;
+this.annotations = null;
+this.minColour = null;
+this.maxColour = null;
+this.ok = null;
+this.cancel = null;
+this.defColours = null;
+this.jPanel1 = null;
+this.jPanel2 = null;
+this.threshold = null;
+this.flowLayout1 = null;
+this.jPanel3 = null;
+this.slider = null;
+this.thresholdValue = null;
+this.currentColours = null;
+this.borderLayout1 = null;
+this.thresholdIsMin = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "AnnotationColourChooser", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.AdjustmentListener, java.awt.event.ItemListener, java.awt.event.MouseListener]);
+Clazz.prepareFields (c$, function () {
+this.annotations =  new awt2swing.Choice ();
+this.minColour =  new awt2swing.Button ();
+this.maxColour =  new awt2swing.Button ();
+this.ok =  new awt2swing.Button ();
+this.cancel =  new awt2swing.Button ();
+this.defColours =  new awt2swing.Button ();
+this.jPanel1 =  new awt2swing.Panel ();
+this.jPanel2 =  new awt2swing.Panel ();
+this.threshold =  new awt2swing.Choice ();
+this.flowLayout1 =  new java.awt.FlowLayout ();
+this.jPanel3 =  new awt2swing.Panel ();
+this.slider =  new awt2swing.Scrollbar (0);
+this.thresholdValue =  new awt2swing.TextField (20);
+this.currentColours =  new awt2swing.Checkbox ();
+this.borderLayout1 =  new java.awt.BorderLayout ();
+this.thresholdIsMin =  new awt2swing.Checkbox ();
+});
+Clazz.makeConstructor (c$, 
+function (av, ap) {
+Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []);
+try {
+this.jbInit ();
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+} else {
+throw ex;
+}
+}
+this.oldcs = av.getGlobalColourScheme ();
+if (av.getAlignment ().getGroups () != null) {
+this.oldgroupColours =  new java.util.Hashtable ();
+for (var sg, $sg = ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.cs != null) {
+this.oldgroupColours.put (sg, sg.cs);
+} else {
+this.oldgroupColours.put (sg, "null");
+}}
+}this.av = av;
+this.ap = ap;
+this.slider.addAdjustmentListener (this);
+this.slider.addMouseListener (this);
+if (av.getAlignment ().getAlignmentAnnotation () == null) {
+return;
+}this.setDefaultMinMax ();
+this.adjusting = true;
+if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) {
+var acg = this.oldcs;
+this.currentColours.setState (acg.isPredefinedColours () || acg.getBaseColour () != null);
+if (!acg.isPredefinedColours () && acg.getBaseColour () == null) {
+this.minColour.setBackground (acg.getMinColour ());
+this.maxColour.setBackground (acg.getMaxColour ());
+}}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++));
+}}
+for (var i = 0; i < list.size (); i++) {
+this.annotations.addItem (list.elementAt (i).toString ());
+}
+this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_no_thereshold"));
+this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_above_thereshold"));
+this.threshold.addItem (jalview.util.MessageManager.getString ("label.threshold_feature_below_thereshold"));
+if (Clazz.instanceOf (this.oldcs, jalview.schemes.AnnotationColourGradient)) {
+var acg = this.oldcs;
+this.annotations.select (acg.getAnnotation ());
+switch (acg.getAboveThreshold ()) {
+case -1:
+this.threshold.select (new Integer (0));
+break;
+case 1:
+this.threshold.select (new Integer (1));
+break;
+case 0:
+this.threshold.select (new Integer (1));
+break;
+default:
+throw  new Error (jalview.util.MessageManager.getString ("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
+}
+this.thresholdIsMin.setState (acg.thresholdIsMinMax);
+this.thresholdValue.setText ("" + acg.getAnnotationThreshold ());
+}this.adjusting = false;
+this.changeColour ();
+this.frame =  new awt2swing.Frame ();
+this.frame.add (this);
+jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("label.colour_by_annotation"), 560, 175);
+this.validate ();
+}, "jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");
+Clazz.defineMethod (c$, "setDefaultMinMax", 
+ function () {
+this.minColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MIN", java.awt.Color.orange));
+this.maxColour.setBackground (this.av.applet.getDefaultColourParameter ("ANNOTATIONCOLOUR_MAX", java.awt.Color.red));
+});
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.appletgui.AnnotationColourChooser, []);
+try {
+this.jbInit ();
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+});
+Clazz.defineMethod (c$, "jbInit", 
+ function () {
+this.minColour.setFont ( new java.awt.Font ("Verdana", 0, 11));
+this.minColour.setLabel (jalview.util.MessageManager.getString ("label.min_colour"));
+this.minColour.addActionListener (this);
+this.maxColour.setFont ( new java.awt.Font ("Verdana", 0, 11));
+this.maxColour.setLabel (jalview.util.MessageManager.getString ("label.max_colour"));
+this.maxColour.addActionListener (this);
+this.thresholdIsMin.addItemListener (this);
+this.ok.setLabel (jalview.util.MessageManager.getString ("action.ok"));
+this.ok.addActionListener (this);
+this.cancel.setLabel (jalview.util.MessageManager.getString ("action.cancel"));
+this.cancel.addActionListener (this);
+this.defColours.setLabel (jalview.util.MessageManager.getString ("action.set_defaults"));
+this.defColours.addActionListener (this);
+this.annotations.addItemListener (this);
+this.thresholdValue.addActionListener (this);
+this.slider.setBackground (java.awt.Color.white);
+this.slider.setPreferredSize ( new java.awt.Dimension (193, 21));
+this.slider.setEnabled (false);
+this.thresholdValue.setPreferredSize ( new java.awt.Dimension (79, 22));
+this.thresholdValue.setEnabled (false);
+this.thresholdValue.setColumns (5);
+this.currentColours.setFont ( new java.awt.Font ("Verdana", 0, 11));
+this.currentColours.setLabel (jalview.util.MessageManager.getString ("label.use_original_colours"));
+this.currentColours.addItemListener (this);
+this.thresholdIsMin.setBackground (java.awt.Color.white);
+this.thresholdIsMin.setLabel (jalview.util.MessageManager.getString ("label.threshold_minmax"));
+this.setLayout (this.borderLayout1);
+this.jPanel1.setBackground (java.awt.Color.white);
+this.jPanel2.setLayout ( new java.awt.FlowLayout ());
+this.jPanel2.setBackground (java.awt.Color.white);
+this.threshold.addItemListener (this);
+this.jPanel3.setLayout ( new java.awt.FlowLayout ());
+this.jPanel3.setBackground (java.awt.Color.white);
+var jPanel4 =  new awt2swing.Panel ();
+jPanel4.setLayout ( new java.awt.BorderLayout ());
+jPanel4.setBackground (java.awt.Color.white);
+this.jPanel1.add (this.ok);
+this.jPanel1.add (this.cancel);
+this.jPanel2.add (this.annotations);
+this.jPanel2.add (this.currentColours);
+this.jPanel2.add (this.minColour);
+this.jPanel2.add (this.maxColour);
+jPanel4.add (this.thresholdIsMin, "West");
+jPanel4.add (this.slider, "Center");
+jPanel4.add (this.thresholdValue, "East");
+var jPanel34 =  new awt2swing.Panel ();
+jPanel34.setLayout ( new java.awt.BorderLayout ());
+jPanel34.setBackground (java.awt.Color.white);
+jPanel34.add (this.jPanel2, "North");
+jPanel34.add (this.threshold, "West");
+this.jPanel3.add (this.defColours);
+jPanel34.add (this.jPanel3, "East");
+jPanel34.add (jPanel4, "South");
+this.add (jPanel34, "Center");
+this.add (this.jPanel1, "South");
+});
+Clazz.overrideMethod (c$, "actionPerformed", 
+function (evt) {
+if (evt.getSource () === this.thresholdValue) {
+try {
+var f =  new Float (this.thresholdValue.getText ()).floatValue ();
+this.slider.setValue (Clazz.floatToInt (f * 1000));
+this.adjustmentValueChanged (null);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, NumberFormatException)) {
+} else {
+throw ex;
+}
+}
+} else if (evt.getSource () === this.minColour) {
+this.minColour_actionPerformed (null);
+} else if (evt.getSource () === this.maxColour) {
+this.maxColour_actionPerformed (null);
+} else if (evt.getSource () === this.defColours) {
+this.defColour_actionPerformed ();
+} else if (evt.getSource () === this.ok) {
+this.changeColour ();
+this.frame.setVisible (false);
+} else if (evt.getSource () === this.cancel) {
+this.reset ();
+this.ap.paintAlignment (true);
+this.frame.setVisible (false);
+} else {
+this.changeColour ();
+}}, "java.awt.event.ActionEvent");
+Clazz.overrideMethod (c$, "itemStateChanged", 
+function (evt) {
+if (evt.getSource () === this.currentColours) {
+if (this.currentColours.getState ()) {
+this.reset ();
+}this.maxColour.setEnabled (!this.currentColours.getState ());
+this.minColour.setEnabled (!this.currentColours.getState ());
+}this.changeColour ();
+}, "java.awt.event.ItemEvent");
+Clazz.overrideMethod (c$, "adjustmentValueChanged", 
+function (evt) {
+if (!this.adjusting) {
+this.thresholdValue.setText ((this.slider.getValue () / 1000) + "");
+if (this.currentColours.getState () && !(Clazz.instanceOf (this.av.getGlobalColourScheme (), jalview.schemes.AnnotationColourGradient))) {
+this.changeColour ();
+}this.currentAnnotation.threshold.value = this.slider.getValue () / 1000;
+this.ap.paintAlignment (false);
+}}, "java.awt.event.AdjustmentEvent");
+Clazz.defineMethod (c$, "minColour_actionPerformed", 
+function (newCol) {
+if (newCol != null) {
+this.minColour.setBackground (newCol);
+this.minColour.repaint ();
+this.changeColour ();
+} else {
+ new jalview.appletgui.UserDefinedColours (this, "Min Colour", this.minColour.getBackground ());
+}}, "java.awt.Color");
+Clazz.defineMethod (c$, "maxColour_actionPerformed", 
+function (newCol) {
+if (newCol != null) {
+this.maxColour.setBackground (newCol);
+this.maxColour.repaint ();
+this.changeColour ();
+} else {
+ new jalview.appletgui.UserDefinedColours (this, "Max Colour", this.maxColour.getBackground ());
+}}, "java.awt.Color");
+Clazz.defineMethod (c$, "defColour_actionPerformed", 
+function () {
+this.setDefaultMinMax ();
+this.minColour.repaint ();
+this.maxColour.repaint ();
+this.changeColour ();
+});
+Clazz.defineMethod (c$, "changeColour", 
+function () {
+if (this.adjusting) {
+return;
+}this.currentAnnotation = this.av.getAlignment ().getAlignmentAnnotation ()[this.annotations.getSelectedIndex ()];
+var aboveThreshold = -1;
+if (this.threshold.getSelectedIndex () == 1) {
+aboveThreshold = 1;
+} else if (this.threshold.getSelectedIndex () == 2) {
+aboveThreshold = 0;
+}this.slider.setEnabled (true);
+this.thresholdValue.setEnabled (true);
+this.thresholdIsMin.setEnabled (true);
+if (aboveThreshold == -1) {
+this.slider.setEnabled (false);
+this.thresholdValue.setEnabled (false);
+this.thresholdIsMin.setEnabled (false);
+this.thresholdValue.setText ("");
+} else if (aboveThreshold != -1 && this.currentAnnotation.threshold == null) {
+this.currentAnnotation.setThreshold ( new jalview.datamodel.GraphLine ((this.currentAnnotation.graphMax - this.currentAnnotation.graphMin) / 2, "Threshold", java.awt.Color.black));
+}if (aboveThreshold != -1) {
+this.adjusting = true;
+this.slider.setMinimum (Clazz.floatToInt (this.currentAnnotation.graphMin * 1000));
+this.slider.setMaximum (Clazz.floatToInt (this.currentAnnotation.graphMax * 1000));
+this.slider.setValue (Clazz.floatToInt (this.currentAnnotation.threshold.value * 1000));
+this.thresholdValue.setText (this.currentAnnotation.threshold.value + "");
+this.slider.setEnabled (true);
+this.thresholdValue.setEnabled (true);
+this.adjusting = false;
+}var acg = null;
+if (this.currentColours.getState ()) {
+acg =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.av.getGlobalColourScheme (), aboveThreshold);
+} else {
+acg =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold);
+}if (this.currentAnnotation.graphMin == 0 && this.currentAnnotation.graphMax == 0) {
+acg.setPredefinedColours (true);
+}acg.thresholdIsMinMax = this.thresholdIsMin.getState ();
+this.av.setGlobalColourScheme (acg);
+if (this.av.getAlignment ().getGroups () != null) {
+for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.cs == null) {
+continue;
+}if (this.currentColours.getState ()) {
+sg.cs =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, sg.cs, aboveThreshold);
+} else {
+sg.cs =  new jalview.schemes.AnnotationColourGradient (this.currentAnnotation, this.minColour.getBackground (), this.maxColour.getBackground (), aboveThreshold);
+}}
+}this.ap.alignmentChanged ();
+this.ap.paintAlignment (true);
+});
+Clazz.defineMethod (c$, "reset", 
+function () {
+this.av.setGlobalColourScheme (this.oldcs);
+if (this.av.getAlignment ().getGroups () != null) {
+for (var sg, $sg = this.ap.av.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+var cs = this.oldgroupColours.get (sg);
+if (Clazz.instanceOf (cs, jalview.schemes.ColourSchemeI)) {
+sg.cs = cs;
+} else {
+sg.cs = null;
+}}
+}this.ap.paintAlignment (true);
+});
+Clazz.overrideMethod (c$, "mouseClicked", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mousePressed", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseReleased", 
+function (evt) {
+this.ap.paintAlignment (true);
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseEntered", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseExited", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+});