X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fappletgui%2FFeatureRenderer.js;h=3d688fde35a442d58e7b89f1a1865a45bd9ef576;hp=05b643c0c8f5118b5c166c5501abfcc53513e3d8;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/appletgui/FeatureRenderer.js b/bin/jalview/appletgui/FeatureRenderer.js
index 05b643c..3d688fd 100644
--- a/bin/jalview/appletgui/FeatureRenderer.js
+++ b/bin/jalview/appletgui/FeatureRenderer.js
@@ -1,272 +1,272 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["awt2swing.Panel", "jalview.renderer.seqfeatures.FeatureRenderer"], "jalview.appletgui.FeatureRenderer", ["awt2swing.Button", "$.Choice", "$.Label", "$.ScrollPane", "$.TextArea", "$.TextField", "jalview.appletgui.FeatureColourChooser", "$.JVDialog", "$.UserDefinedColours", "jalview.datamodel.SearchResults", "jalview.io.FeaturesFile", "jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.Font", "$.GridLayout", "java.awt.event.ActionListener", "$.ItemListener", "$.MouseAdapter", "java.lang.Error"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.featureLinks = null;
-this.featureIndex = 0;
-this.deleteFeature = false;
-this.colourPanel = null;
-if (!Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer.FeatureColourPanel")) {
-jalview.appletgui.FeatureRenderer.$FeatureRenderer$FeatureColourPanel$ ();
-}
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "FeatureRenderer", jalview.renderer.seqfeatures.FeatureRenderer);
-Clazz.makeConstructor (c$, 
-function (av) {
-Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer);
-this.av = av;
-this.setTransparencyAvailable (!System.getProperty ("java.version").startsWith ("1.1"));
-}, "jalview.viewmodel.AlignmentViewport");
-Clazz.defineMethod (c$, "amendFeatures", 
-function (sequences, features, newFeatures, ap) {
-var bigPanel =  new awt2swing.Panel ( new java.awt.BorderLayout ());
-var name =  new awt2swing.TextField (16);
-var source =  new awt2swing.TextField (16);
-var description =  new awt2swing.TextArea (3, 35);
-var start =  new awt2swing.TextField (8);
-var end =  new awt2swing.TextField (8);
-var overlaps;
-var deleteButton =  new awt2swing.Button ("Delete");
-this.deleteFeature = false;
-this.colourPanel = Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer.FeatureColourPanel, this, null);
-this.colourPanel.setSize (110, 15);
-var fr = this;
-var panel =  new awt2swing.Panel ( new java.awt.GridLayout (3, 1));
-this.featureIndex = 0;
-var tmp;
-if (!newFeatures && features.length > 1) {
-panel =  new awt2swing.Panel ( new java.awt.GridLayout (4, 1));
-tmp =  new awt2swing.Panel ();
-tmp.add ( new awt2swing.Label ("Select Feature: "));
-overlaps =  new awt2swing.Choice ();
-for (var i = 0; i < features.length; i++) {
-var item = features[i].getType () + "/" + features[i].getBegin () + "-" + features[i].getEnd ();
-if (features[i].getFeatureGroup () != null) {
-item += " (" + features[i].getFeatureGroup () + ")";
-}overlaps.addItem (item);
-}
-tmp.add (overlaps);
-overlaps.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$1") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$1, this, Clazz.cloneFinals ("overlaps", overlaps, "name", name, "features", features, "description", description, "source", source, "start", start, "end", end, "sequences", sequences, "ap", ap))));
-panel.add (tmp);
-}tmp =  new awt2swing.Panel ();
-panel.add (tmp);
-tmp.add ( new awt2swing.Label ("Name: ", 4));
-tmp.add (name);
-tmp =  new awt2swing.Panel ();
-panel.add (tmp);
-tmp.add ( new awt2swing.Label ("Group: ", 4));
-tmp.add (source);
-tmp =  new awt2swing.Panel ();
-panel.add (tmp);
-tmp.add ( new awt2swing.Label ("Colour: ", 4));
-tmp.add (this.colourPanel);
-bigPanel.add (panel, "North");
-panel =  new awt2swing.Panel ();
-panel.add ( new awt2swing.Label ("Description: ", 4));
-panel.add ( new awt2swing.ScrollPane ().add (description));
-if (!newFeatures) {
-bigPanel.add (panel, "South");
-panel =  new awt2swing.Panel ();
-panel.add ( new awt2swing.Label (" Start:", 4));
-panel.add (start);
-panel.add ( new awt2swing.Label ("  End:", 4));
-panel.add (end);
-bigPanel.add (panel, "Center");
-} else {
-bigPanel.add (panel, "Center");
-}if (jalview.appletgui.FeatureRenderer.lastFeatureAdded == null) {
-if (features[0].type != null) {
-jalview.appletgui.FeatureRenderer.lastFeatureAdded = features[0].type;
-} else {
-jalview.appletgui.FeatureRenderer.lastFeatureAdded = "feature_1";
-}}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded == null) {
-if (features[0].featureGroup != null) {
-jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = features[0].featureGroup;
-} else {
-jalview.appletgui.FeatureRenderer.lastFeatureAdded = "Jalview";
-}}var title = newFeatures ? jalview.util.MessageManager.getString ("label.create_new_sequence_features") : jalview.util.MessageManager.formatMessage ("label.amend_delete_features",  Clazz.newArray (-1, [sequences[0].getName ()]));
-var dialog =  new jalview.appletgui.JVDialog (ap.alignFrame, title, true, 385, 240);
-dialog.setMainPanel (bigPanel);
-if (newFeatures) {
-name.setText (jalview.appletgui.FeatureRenderer.lastFeatureAdded);
-source.setText (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded);
-} else {
-dialog.ok.setLabel (jalview.util.MessageManager.getString ("label.amend"));
-dialog.buttonPanel.add (deleteButton, 1);
-deleteButton.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$2") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$2, this, Clazz.cloneFinals ("dialog", dialog))));
-name.setText (features[0].getType ());
-source.setText (features[0].getFeatureGroup ());
-}start.setText (features[0].getBegin () + "");
-end.setText (features[0].getEnd () + "");
-description.setText (features[0].getDescription ());
-var col = this.getColour (name.getText ());
-if (col == null) {
-col =  new jalview.schemes.UserColourScheme ().createColourFromName (name.getText ());
-}var fcol = this.getFeatureStyle (name.getText ());
-this.colourPanel.updateColor (fcol);
-dialog.setResizable (true);
-this.colourPanel.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$3") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$3, this, Clazz.cloneFinals ("fr", fr, "ap", ap, "name", name, "dialog", dialog))));
-dialog.setVisible (true);
-var ffile =  new jalview.io.FeaturesFile ();
-if (dialog.accept) {
-this.lastSeq = null;
-jalview.appletgui.FeatureRenderer.lastFeatureAdded = name.getText ().trim ();
-jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = source.getText ().trim ();
-jalview.appletgui.FeatureRenderer.lastDescriptionAdded = description.getText ().$replace ('\n', ' ');
-}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null && jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded.length < 1) {
-jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = null;
-}if (!newFeatures) {
-var sf = features[this.featureIndex];
-if (dialog.accept) {
-sf.type = jalview.appletgui.FeatureRenderer.lastFeatureAdded;
-sf.featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded;
-sf.description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded;
-if (!this.colourPanel.isGcol) {
-this.setColour (sf.type, this.colourPanel.getBackground ());
-}try {
-sf.begin = Integer.parseInt (start.getText ());
-sf.end = Integer.parseInt (end.getText ());
-} catch (ex) {
-if (Clazz.exceptionOf (ex, NumberFormatException)) {
-} else {
-throw ex;
-}
-}
-ffile.parseDescriptionHTML (sf, false);
-this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded);
-}if (this.deleteFeature) {
-sequences[0].deleteFeature (sf);
-}} else {
-if (dialog.accept && name.getText ().length > 0) {
-for (var i = 0; i < sequences.length; i++) {
-features[i].type = jalview.appletgui.FeatureRenderer.lastFeatureAdded;
-features[i].featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded;
-features[i].description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded;
-sequences[i].addSequenceFeature (features[i]);
-ffile.parseDescriptionHTML (features[i], false);
-}
-var newColour = this.colourPanel.getBackground ();
-if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null) {
-this.setGroupVisibility (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded, true);
-}this.setColour (jalview.appletgui.FeatureRenderer.lastFeatureAdded, newColour);
-this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded);
-this.findAllFeatures (false);
-} else {
-return false;
-}}if ((this.av).featureSettings != null) {
-(this.av).featureSettings.refreshTable ();
-}ap.paintAlignment (true);
-return true;
-}, "~A,~A,~B,jalview.appletgui.AlignmentPanel");
-c$.$FeatureRenderer$FeatureColourPanel$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-this.label = "";
-this.maxCol = null;
-this.isColourByLabel = false;
-this.isGcol = false;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui.FeatureRenderer, "FeatureColourPanel", awt2swing.Panel);
-Clazz.defineMethod (c$, "updateColor", 
-function (a) {
-var b;
-var c = null;
-var d = null;
-var e = "";
-if (Clazz.instanceOf (a, java.awt.Color)) {
-this.isGcol = false;
-c = a;
-d = null;
-} else if (Clazz.instanceOf (a, jalview.schemes.GraduatedColor)) {
-this.isGcol = true;
-d = a;
-c = null;
-} else {
-throw  new Error (jalview.util.MessageManager.getString ("error.invalid_colour_for_mycheckbox"));
-}if (c != null) {
-this.setBackground (b = c);
-} else {
-if (d.getThreshType () != -1) {
-e += " " + ((d.getThreshType () == 1) ? "(>)" : "(<)");
-}if (this.isColourByLabel = d.isColourByLabel ()) {
-this.setBackground (b = java.awt.Color.white);
-e += " (by Label)";
-} else {
-this.setBackground (b = d.getMinColor ());
-this.maxCol = d.getMaxColor ();
-}}this.label = e;
-this.setBackground (b);
-this.repaint ();
-}, "~O");
-Clazz.makeConstructor (c$, 
-function () {
-Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer.FeatureColourPanel, [null]);
-});
-Clazz.defineMethod (c$, "PaintComponent", 
-function (a) {
-var b = this.getSize ();
-if (this.isGcol) {
-if (this.isColourByLabel) {
-a.setColor (java.awt.Color.white);
-a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height);
-a.setColor (java.awt.Color.black);
-var c =  new java.awt.Font ("Verdana", 0, 10);
-a.setFont (c);
-a.drawString (jalview.util.MessageManager.getString ("label.label"), 0, 0);
-} else {
-a.setColor (this.maxCol);
-a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height);
-}}}, "java.awt.Graphics");
-c$ = Clazz.p0p ();
-};
-c$.$FeatureRenderer$1$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$1", null, java.awt.event.ItemListener);
-Clazz.overrideMethod (c$, "itemStateChanged", 
-function (e) {
-var index = this.f$.overlaps.getSelectedIndex ();
-if (index != -1) {
-this.b$["jalview.appletgui.FeatureRenderer"].featureIndex = index;
-this.f$.name.setText (this.f$.features[index].getType ());
-this.f$.description.setText (this.f$.features[index].getDescription ());
-this.f$.source.setText (this.f$.features[index].getFeatureGroup ());
-this.f$.start.setText (this.f$.features[index].getBegin () + "");
-this.f$.end.setText (this.f$.features[index].getEnd () + "");
-var highlight =  new jalview.datamodel.SearchResults ();
-highlight.addResult (this.f$.sequences[0], this.f$.features[index].getBegin (), this.f$.features[index].getEnd ());
-this.f$.ap.seqPanel.seqCanvas.highlightSearchResults (highlight);
-}var col = this.b$["jalview.appletgui.FeatureRenderer"].getFeatureStyle (this.f$.name.getText ());
-if (col == null) {
-col =  new jalview.schemes.UserColourScheme ().createColourFromName (this.f$.name.getText ());
-}this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.updateColor (col);
-}, "java.awt.event.ItemEvent");
-c$ = Clazz.p0p ();
-};
-c$.$FeatureRenderer$2$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$2", null, java.awt.event.ActionListener);
-Clazz.overrideMethod (c$, "actionPerformed", 
-function (evt) {
-this.b$["jalview.appletgui.FeatureRenderer"].deleteFeature = true;
-this.f$.dialog.setVisible (false);
-}, "java.awt.event.ActionEvent");
-c$ = Clazz.p0p ();
-};
-c$.$FeatureRenderer$3$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$3", java.awt.event.MouseAdapter);
-Clazz.overrideMethod (c$, "mousePressed", 
-function (evt) {
-if (!this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.isGcol) {
- new jalview.appletgui.UserDefinedColours (this.f$.fr, this.f$.ap.alignFrame);
-} else {
-var fcc =  new jalview.appletgui.FeatureColourChooser (this.f$.ap.alignFrame, this.f$.name.getText ());
-this.f$.dialog.transferFocus ();
-}}, "java.awt.event.MouseEvent");
-c$ = Clazz.p0p ();
-};
-Clazz.defineStatics (c$,
-"lastFeatureAdded", null,
-"lastFeatureGroupAdded", null,
-"lastDescriptionAdded", null);
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.Panel", "jalview.renderer.seqfeatures.FeatureRenderer"], "jalview.appletgui.FeatureRenderer", ["awt2swing.Button", "$.Choice", "$.Label", "$.ScrollPane", "$.TextArea", "$.TextField", "jalview.appletgui.FeatureColourChooser", "$.JVDialog", "$.UserDefinedColours", "jalview.datamodel.SearchResults", "jalview.io.FeaturesFile", "jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.MessageManager", "java.awt.BorderLayout", "$.Color", "$.Font", "$.GridLayout", "java.awt.event.ActionListener", "$.ItemListener", "$.MouseAdapter", "java.lang.Error"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.featureLinks = null;
+this.featureIndex = 0;
+this.deleteFeature = false;
+this.colourPanel = null;
+if (!Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer.FeatureColourPanel")) {
+jalview.appletgui.FeatureRenderer.$FeatureRenderer$FeatureColourPanel$ ();
+}
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "FeatureRenderer", jalview.renderer.seqfeatures.FeatureRenderer);
+Clazz.makeConstructor (c$, 
+function (av) {
+Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer);
+this.av = av;
+this.setTransparencyAvailable (!System.getProperty ("java.version").startsWith ("1.1"));
+}, "jalview.viewmodel.AlignmentViewport");
+Clazz.defineMethod (c$, "amendFeatures", 
+function (sequences, features, newFeatures, ap) {
+var bigPanel =  new awt2swing.Panel ( new java.awt.BorderLayout ());
+var name =  new awt2swing.TextField (16);
+var source =  new awt2swing.TextField (16);
+var description =  new awt2swing.TextArea (3, 35);
+var start =  new awt2swing.TextField (8);
+var end =  new awt2swing.TextField (8);
+var overlaps;
+var deleteButton =  new awt2swing.Button ("Delete");
+this.deleteFeature = false;
+this.colourPanel = Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer.FeatureColourPanel, this, null);
+this.colourPanel.setSize (110, 15);
+var fr = this;
+var panel =  new awt2swing.Panel ( new java.awt.GridLayout (3, 1));
+this.featureIndex = 0;
+var tmp;
+if (!newFeatures && features.length > 1) {
+panel =  new awt2swing.Panel ( new java.awt.GridLayout (4, 1));
+tmp =  new awt2swing.Panel ();
+tmp.add ( new awt2swing.Label ("Select Feature: "));
+overlaps =  new awt2swing.Choice ();
+for (var i = 0; i < features.length; i++) {
+var item = features[i].getType () + "/" + features[i].getBegin () + "-" + features[i].getEnd ();
+if (features[i].getFeatureGroup () != null) {
+item += " (" + features[i].getFeatureGroup () + ")";
+}overlaps.addItem (item);
+}
+tmp.add (overlaps);
+overlaps.addItemListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$1") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$1, this, Clazz.cloneFinals ("overlaps", overlaps, "name", name, "features", features, "description", description, "source", source, "start", start, "end", end, "sequences", sequences, "ap", ap))));
+panel.add (tmp);
+}tmp =  new awt2swing.Panel ();
+panel.add (tmp);
+tmp.add ( new awt2swing.Label ("Name: ", 4));
+tmp.add (name);
+tmp =  new awt2swing.Panel ();
+panel.add (tmp);
+tmp.add ( new awt2swing.Label ("Group: ", 4));
+tmp.add (source);
+tmp =  new awt2swing.Panel ();
+panel.add (tmp);
+tmp.add ( new awt2swing.Label ("Colour: ", 4));
+tmp.add (this.colourPanel);
+bigPanel.add (panel, "North");
+panel =  new awt2swing.Panel ();
+panel.add ( new awt2swing.Label ("Description: ", 4));
+panel.add ( new awt2swing.ScrollPane ().add (description));
+if (!newFeatures) {
+bigPanel.add (panel, "South");
+panel =  new awt2swing.Panel ();
+panel.add ( new awt2swing.Label (" Start:", 4));
+panel.add (start);
+panel.add ( new awt2swing.Label ("  End:", 4));
+panel.add (end);
+bigPanel.add (panel, "Center");
+} else {
+bigPanel.add (panel, "Center");
+}if (jalview.appletgui.FeatureRenderer.lastFeatureAdded == null) {
+if (features[0].type != null) {
+jalview.appletgui.FeatureRenderer.lastFeatureAdded = features[0].type;
+} else {
+jalview.appletgui.FeatureRenderer.lastFeatureAdded = "feature_1";
+}}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded == null) {
+if (features[0].featureGroup != null) {
+jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = features[0].featureGroup;
+} else {
+jalview.appletgui.FeatureRenderer.lastFeatureAdded = "Jalview";
+}}var title = newFeatures ? jalview.util.MessageManager.getString ("label.create_new_sequence_features") : jalview.util.MessageManager.formatMessage ("label.amend_delete_features",  Clazz.newArray (-1, [sequences[0].getName ()]));
+var dialog =  new jalview.appletgui.JVDialog (ap.alignFrame, title, true, 385, 240);
+dialog.setMainPanel (bigPanel);
+if (newFeatures) {
+name.setText (jalview.appletgui.FeatureRenderer.lastFeatureAdded);
+source.setText (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded);
+} else {
+dialog.ok.setLabel (jalview.util.MessageManager.getString ("label.amend"));
+dialog.buttonPanel.add (deleteButton, 1);
+deleteButton.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$2") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$2, this, Clazz.cloneFinals ("dialog", dialog))));
+name.setText (features[0].getType ());
+source.setText (features[0].getFeatureGroup ());
+}start.setText (features[0].getBegin () + "");
+end.setText (features[0].getEnd () + "");
+description.setText (features[0].getDescription ());
+var col = this.getColour (name.getText ());
+if (col == null) {
+col =  new jalview.schemes.UserColourScheme ().createColourFromName (name.getText ());
+}var fcol = this.getFeatureStyle (name.getText ());
+this.colourPanel.updateColor (fcol);
+dialog.setResizable (true);
+this.colourPanel.addMouseListener (((Clazz.isClassDefined ("jalview.appletgui.FeatureRenderer$3") ? 0 : jalview.appletgui.FeatureRenderer.$FeatureRenderer$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.FeatureRenderer$3, this, Clazz.cloneFinals ("fr", fr, "ap", ap, "name", name, "dialog", dialog))));
+dialog.setVisible (true);
+var ffile =  new jalview.io.FeaturesFile ();
+if (dialog.accept) {
+this.lastSeq = null;
+jalview.appletgui.FeatureRenderer.lastFeatureAdded = name.getText ().trim ();
+jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = source.getText ().trim ();
+jalview.appletgui.FeatureRenderer.lastDescriptionAdded = description.getText ().$replace ('\n', ' ');
+}if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null && jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded.length < 1) {
+jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded = null;
+}if (!newFeatures) {
+var sf = features[this.featureIndex];
+if (dialog.accept) {
+sf.type = jalview.appletgui.FeatureRenderer.lastFeatureAdded;
+sf.featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded;
+sf.description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded;
+if (!this.colourPanel.isGcol) {
+this.setColour (sf.type, this.colourPanel.getBackground ());
+}try {
+sf.begin = Integer.parseInt (start.getText ());
+sf.end = Integer.parseInt (end.getText ());
+} catch (ex) {
+if (Clazz.exceptionOf (ex, NumberFormatException)) {
+} else {
+throw ex;
+}
+}
+ffile.parseDescriptionHTML (sf, false);
+this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded);
+}if (this.deleteFeature) {
+sequences[0].deleteFeature (sf);
+}} else {
+if (dialog.accept && name.getText ().length > 0) {
+for (var i = 0; i < sequences.length; i++) {
+features[i].type = jalview.appletgui.FeatureRenderer.lastFeatureAdded;
+features[i].featureGroup = jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded;
+features[i].description = jalview.appletgui.FeatureRenderer.lastDescriptionAdded;
+sequences[i].addSequenceFeature (features[i]);
+ffile.parseDescriptionHTML (features[i], false);
+}
+var newColour = this.colourPanel.getBackground ();
+if (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded != null) {
+this.setGroupVisibility (jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded, true);
+}this.setColour (jalview.appletgui.FeatureRenderer.lastFeatureAdded, newColour);
+this.setVisible (jalview.appletgui.FeatureRenderer.lastFeatureAdded);
+this.findAllFeatures (false);
+} else {
+return false;
+}}if ((this.av).featureSettings != null) {
+(this.av).featureSettings.refreshTable ();
+}ap.paintAlignment (true);
+return true;
+}, "~A,~A,~B,jalview.appletgui.AlignmentPanel");
+c$.$FeatureRenderer$FeatureColourPanel$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+this.label = "";
+this.maxCol = null;
+this.isColourByLabel = false;
+this.isGcol = false;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui.FeatureRenderer, "FeatureColourPanel", awt2swing.Panel);
+Clazz.defineMethod (c$, "updateColor", 
+function (a) {
+var b;
+var c = null;
+var d = null;
+var e = "";
+if (Clazz.instanceOf (a, java.awt.Color)) {
+this.isGcol = false;
+c = a;
+d = null;
+} else if (Clazz.instanceOf (a, jalview.schemes.GraduatedColor)) {
+this.isGcol = true;
+d = a;
+c = null;
+} else {
+throw  new Error (jalview.util.MessageManager.getString ("error.invalid_colour_for_mycheckbox"));
+}if (c != null) {
+this.setBackground (b = c);
+} else {
+if (d.getThreshType () != -1) {
+e += " " + ((d.getThreshType () == 1) ? "(>)" : "(<)");
+}if (this.isColourByLabel = d.isColourByLabel ()) {
+this.setBackground (b = java.awt.Color.white);
+e += " (by Label)";
+} else {
+this.setBackground (b = d.getMinColor ());
+this.maxCol = d.getMaxColor ();
+}}this.label = e;
+this.setBackground (b);
+this.repaint ();
+}, "~O");
+Clazz.makeConstructor (c$, 
+function () {
+Clazz.superConstructor (this, jalview.appletgui.FeatureRenderer.FeatureColourPanel, [null]);
+});
+Clazz.defineMethod (c$, "PaintComponent", 
+function (a) {
+var b = this.getSize ();
+if (this.isGcol) {
+if (this.isColourByLabel) {
+a.setColor (java.awt.Color.white);
+a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height);
+a.setColor (java.awt.Color.black);
+var c =  new java.awt.Font ("Verdana", 0, 10);
+a.setFont (c);
+a.drawString (jalview.util.MessageManager.getString ("label.label"), 0, 0);
+} else {
+a.setColor (this.maxCol);
+a.fillRect (Clazz.doubleToInt (b.width / 2), 0, Clazz.doubleToInt (b.width / 2), b.height);
+}}}, "java.awt.Graphics");
+c$ = Clazz.p0p ();
+};
+c$.$FeatureRenderer$1$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$1", null, java.awt.event.ItemListener);
+Clazz.overrideMethod (c$, "itemStateChanged", 
+function (e) {
+var index = this.f$.overlaps.getSelectedIndex ();
+if (index != -1) {
+this.b$["jalview.appletgui.FeatureRenderer"].featureIndex = index;
+this.f$.name.setText (this.f$.features[index].getType ());
+this.f$.description.setText (this.f$.features[index].getDescription ());
+this.f$.source.setText (this.f$.features[index].getFeatureGroup ());
+this.f$.start.setText (this.f$.features[index].getBegin () + "");
+this.f$.end.setText (this.f$.features[index].getEnd () + "");
+var highlight =  new jalview.datamodel.SearchResults ();
+highlight.addResult (this.f$.sequences[0], this.f$.features[index].getBegin (), this.f$.features[index].getEnd ());
+this.f$.ap.seqPanel.seqCanvas.highlightSearchResults (highlight);
+}var col = this.b$["jalview.appletgui.FeatureRenderer"].getFeatureStyle (this.f$.name.getText ());
+if (col == null) {
+col =  new jalview.schemes.UserColourScheme ().createColourFromName (this.f$.name.getText ());
+}this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.updateColor (col);
+}, "java.awt.event.ItemEvent");
+c$ = Clazz.p0p ();
+};
+c$.$FeatureRenderer$2$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$2", null, java.awt.event.ActionListener);
+Clazz.overrideMethod (c$, "actionPerformed", 
+function (evt) {
+this.b$["jalview.appletgui.FeatureRenderer"].deleteFeature = true;
+this.f$.dialog.setVisible (false);
+}, "java.awt.event.ActionEvent");
+c$ = Clazz.p0p ();
+};
+c$.$FeatureRenderer$3$ = function () {
+Clazz.pu$h ();
+c$ = Clazz.declareAnonymous (jalview.appletgui, "FeatureRenderer$3", java.awt.event.MouseAdapter);
+Clazz.overrideMethod (c$, "mousePressed", 
+function (evt) {
+if (!this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.isGcol) {
+ new jalview.appletgui.UserDefinedColours (this.f$.fr, this.f$.ap.alignFrame);
+} else {
+var fcc =  new jalview.appletgui.FeatureColourChooser (this.f$.ap.alignFrame, this.f$.name.getText ());
+this.f$.dialog.transferFocus ();
+}}, "java.awt.event.MouseEvent");
+c$ = Clazz.p0p ();
+};
+Clazz.defineStatics (c$,
+"lastFeatureAdded", null,
+"lastFeatureGroupAdded", null,
+"lastDescriptionAdded", null);
+});