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