X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fappletgui%2FTreePanel.js;h=6c6f089bd2d2b206d65b86cbc2abd6676c065fb7;hp=b1b80fd5370b5a2d9908c6ad67b7bcfa1af77033;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/appletgui/TreePanel.js b/site/j2s/jalview/appletgui/TreePanel.js
index b1b80fd..6c6f089 100644
--- a/site/j2s/jalview/appletgui/TreePanel.js
+++ b/site/j2s/jalview/appletgui/TreePanel.js
@@ -1,261 +1,261 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "java.lang.Thread", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuBar", "$.MenuItem", "$.ScrollPane", "java.awt.BorderLayout"], "jalview.appletgui.TreePanel", ["awt2swing.Frame", "jalview.analysis.NJTree", "jalview.api.analysis.ViewBasedAnalysisI", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.FontChooser", "$.TreeCanvas", "jalview.bin.JalviewLite", "jalview.datamodel.Alignment", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.MessageManager", "java.awt.Color", "$.Font"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.seq = null;
-this.$type = null;
-this.pwtype = null;
-this.start = 0;
-this.end = 0;
-this.treeCanvas = null;
-this.tree = null;
-this.ap = null;
-this.av = null;
-if (!Clazz.isClassDefined ("jalview.appletgui.TreePanel.TreeLoader")) {
-jalview.appletgui.TreePanel.$TreePanel$TreeLoader$ ();
-}
-this.borderLayout1 = null;
-this.scrollPane = null;
-this.jMenuBar1 = null;
-this.jMenu2 = null;
-this.fontSize = null;
-this.bootstrapMenu = null;
-this.distanceMenu = null;
-this.placeholdersMenu = null;
-this.fitToWindow = null;
-this.fileMenu = null;
-this.newickOutput = null;
-this.inputData = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "TreePanel", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener]);
-Clazz.prepareFields (c$, function () {
-this.borderLayout1 =  new java.awt.BorderLayout ();
-this.scrollPane =  new awt2swing.ScrollPane ();
-this.jMenuBar1 =  new awt2swing.MenuBar ();
-this.jMenu2 =  new awt2swing.Menu ();
-this.fontSize =  new awt2swing.MenuItem ();
-this.bootstrapMenu =  new awt2swing.CheckboxMenuItem ();
-this.distanceMenu =  new awt2swing.CheckboxMenuItem ();
-this.placeholdersMenu =  new awt2swing.CheckboxMenuItem ();
-this.fitToWindow =  new awt2swing.CheckboxMenuItem ();
-this.fileMenu =  new awt2swing.Menu ();
-this.newickOutput =  new awt2swing.MenuItem ();
-this.inputData =  new awt2swing.MenuItem ();
-});
-Clazz.defineMethod (c$, "getTree", 
-function () {
-return this.tree;
-});
-Clazz.defineMethod (c$, "finalize", 
-function () {
-this.ap = null;
-this.av = null;
-Clazz.superCall (this, jalview.appletgui.TreePanel, "finalize", []);
-});
-Clazz.makeConstructor (c$, 
-function (ap, type, pwtype) {
-Clazz.superConstructor (this, jalview.appletgui.TreePanel, []);
-try {
-this.jbInit ();
-this.setMenuBar (this.jMenuBar1);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-this.initTreePanel (ap, type, pwtype, null);
-}, "jalview.appletgui.AlignmentPanel,~S,~S");
-Clazz.makeConstructor (c$, 
-function (ap, type, pwtype, newtree) {
-Clazz.superConstructor (this, jalview.appletgui.TreePanel, []);
-try {
-this.jbInit ();
-this.setMenuBar (this.jMenuBar1);
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-this.initTreePanel (ap, type, pwtype, newtree);
-}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile");
-Clazz.defineMethod (c$, "initTreePanel", 
-function (ap, type, pwtype, newTree) {
-this.ap = ap;
-this.av = ap.av;
-this.$type = type;
-this.pwtype = pwtype;
-this.treeCanvas =  new jalview.appletgui.TreeCanvas (ap, this.scrollPane);
-var tl = Clazz.innerTypeInstance (jalview.appletgui.TreePanel.TreeLoader, this, null, newTree);
-tl.start ();
-this.embedMenuIfNeeded (this.treeCanvas);
-this.scrollPane.add (this.treeCanvas, "Center");
-}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile");
-Clazz.defineMethod (c$, "showOriginalData", 
-function () {
-if (this.tree.seqData != null) {
-var gc = '-';
-try {
-gc = this.av.getGapCharacter ();
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-} else {
-throw ex;
-}
-}
-;var alAndColsel = this.tree.seqData.getAlignmentAndColumnSelection (gc);
-if (alAndColsel != null && alAndColsel[0] != null) {
-var al =  new jalview.datamodel.Alignment (alAndColsel[0]);
-var af =  new jalview.appletgui.AlignFrame (al, this.av.applet, "Original Data for Tree", false);
-af.viewport.setHiddenColumns (alAndColsel[1]);
-}} else {
-System.out.println ("Original Tree Data not available");
-}});
-Clazz.overrideMethod (c$, "actionPerformed", 
-function (evt) {
-if (evt.getSource () === this.newickOutput) {
-this.newickOutput_actionPerformed ();
-} else if (evt.getSource () === this.fontSize) {
-this.fontSize_actionPerformed ();
-} else if (evt.getSource () === this.inputData) {
-this.showOriginalData ();
-}}, "java.awt.event.ActionEvent");
-Clazz.overrideMethod (c$, "itemStateChanged", 
-function (evt) {
-if (evt.getSource () === this.fitToWindow) {
-this.treeCanvas.fitToWindow = this.fitToWindow.getState ();
-} else if (evt.getSource () === this.distanceMenu) {
-this.treeCanvas.setShowDistances (this.distanceMenu.getState ());
-} else if (evt.getSource () === this.bootstrapMenu) {
-this.treeCanvas.setShowBootstrap (this.bootstrapMenu.getState ());
-} else if (evt.getSource () === this.placeholdersMenu) {
-this.treeCanvas.setMarkPlaceholders (this.placeholdersMenu.getState ());
-}this.treeCanvas.repaint ();
-}, "java.awt.event.ItemEvent");
-Clazz.defineMethod (c$, "newickOutput_actionPerformed", 
-function () {
-var fout =  new jalview.io.NewickFile (this.tree.getTopNode ());
-var output = fout.print (false, true);
-var cap =  new jalview.appletgui.CutAndPasteTransfer (false, null);
-cap.setText (output);
-var frame =  new awt2swing.Frame ();
-frame.add (cap);
-jalview.bin.JalviewLite.addFrame (frame, this.$type + " " + this.pwtype, 500, 100);
-});
-Clazz.defineMethod (c$, "getTreeFont", 
-function () {
-return this.treeCanvas.$font;
-});
-Clazz.defineMethod (c$, "setTreeFont", 
-function (font) {
-this.treeCanvas.$font = font;
-this.treeCanvas.repaint ();
-}, "java.awt.Font");
-Clazz.defineMethod (c$, "fontSize_actionPerformed", 
-function () {
-if (this.treeCanvas == null) {
-return;
-} new jalview.appletgui.FontChooser (this);
-});
-Clazz.defineMethod (c$, "jbInit", 
- function () {
-this.setLayout (this.borderLayout1);
-this.setBackground (java.awt.Color.white);
-this.setFont ( new java.awt.Font ("Verdana", 0, 12));
-this.jMenu2.setLabel (jalview.util.MessageManager.getString ("action.view"));
-this.fontSize.setLabel (jalview.util.MessageManager.getString ("action.font"));
-this.fontSize.addActionListener (this);
-this.bootstrapMenu.setLabel (jalview.util.MessageManager.getString ("label.show_bootstrap_values"));
-this.bootstrapMenu.addItemListener (this);
-this.distanceMenu.setLabel (jalview.util.MessageManager.getString ("label.show_distances"));
-this.distanceMenu.addItemListener (this);
-this.placeholdersMenu.setLabel (jalview.util.MessageManager.getString ("label.mark_unassociated_leaves"));
-this.placeholdersMenu.addItemListener (this);
-this.fitToWindow.setState (true);
-this.fitToWindow.setLabel (jalview.util.MessageManager.getString ("label.fit_to_window"));
-this.fitToWindow.addItemListener (this);
-this.fileMenu.setLabel (jalview.util.MessageManager.getString ("action.file"));
-this.newickOutput.setLabel (jalview.util.MessageManager.getString ("label.newick_format"));
-this.newickOutput.addActionListener (this);
-this.inputData.setLabel (jalview.util.MessageManager.getString ("label.input_data"));
-this.add (this.scrollPane, "Center");
-this.jMenuBar1.add (this.fileMenu);
-this.jMenuBar1.add (this.jMenu2);
-this.jMenu2.add (this.fitToWindow);
-this.jMenu2.add (this.fontSize);
-this.jMenu2.add (this.distanceMenu);
-this.jMenu2.add (this.bootstrapMenu);
-this.jMenu2.add (this.placeholdersMenu);
-this.fileMenu.add (this.newickOutput);
-this.fileMenu.add (this.inputData);
-this.inputData.addActionListener (this);
-});
-c$.$TreePanel$TreeLoader$ = function () {
-Clazz.pu$h(self.c$);
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-this.newtree = null;
-this.odata = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui.TreePanel, "TreeLoader", Thread);
-Clazz.makeConstructor (c$, 
-function (a) {
-Clazz.superConstructor (this, jalview.appletgui.TreePanel.TreeLoader, []);
-this.newtree = a;
-}, "jalview.io.NewickFile");
-Clazz.overrideMethod (c$, "run", 
-function () {
-if (this.newtree != null) {
-if (this.odata == null) {
-this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.newtree);
-} else {
-this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.odata, this.newtree);
-}} else {
-var a;
-var b;
-var c;
-var d = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup () != null && this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSize () > 1;
-var e = this.b$["jalview.appletgui.TreePanel"].av.getAlignmentView (d);
-if (!d) {
-a = 0;
-b = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getWidth ();
-c = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray ();
-} else {
-a = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getStartRes ();
-b = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getEndRes () + 1;
-c = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSequencesInOrder (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ());
-}var f = jalview.schemes.ResidueProperties.getScoreModel (this.b$["jalview.appletgui.TreePanel"].pwtype);
-if (Clazz.instanceOf (f, jalview.api.analysis.ViewBasedAnalysisI)) {
-try {
-f = f.getClass ().newInstance ();
-(f).configureFromAlignmentView (this.b$["jalview.appletgui.TreePanel"].treeCanvas.ap);
-} catch (q) {
-if (Clazz.exceptionOf (q, Exception)) {
-System.err.println ("Couldn't create a scoremodel instance for " + f.getName ());
-q.printStackTrace ();
-} else {
-throw q;
-}
-}
-this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, f, a, b);
-} else {
-this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, null, a, b);
-}}this.b$["jalview.appletgui.TreePanel"].tree.reCount (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ());
-this.b$["jalview.appletgui.TreePanel"].tree.findHeight (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ());
-this.b$["jalview.appletgui.TreePanel"].treeCanvas.setTree (this.b$["jalview.appletgui.TreePanel"].tree);
-if (this.newtree != null) {
-var a = this.newtree.HasDistances () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeDistances", this.newtree.HasDistances ());
-var b = this.newtree.HasBootstrap () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeBootstraps", this.newtree.HasBootstrap ());
-this.b$["jalview.appletgui.TreePanel"].distanceMenu.setState (a);
-this.b$["jalview.appletgui.TreePanel"].bootstrapMenu.setState (b);
-this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowBootstrap (b);
-this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowDistances (a);
-this.b$["jalview.appletgui.TreePanel"].treeCanvas.setMarkPlaceholders (this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showUnlinkedTreeNodes", false));
-}this.b$["jalview.appletgui.TreePanel"].treeCanvas.repaint ();
-this.b$["jalview.appletgui.TreePanel"].av.setCurrentTree (this.b$["jalview.appletgui.TreePanel"].tree);
-});
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "java.lang.Thread", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuBar", "$.MenuItem", "$.ScrollPane", "java.awt.BorderLayout"], "jalview.appletgui.TreePanel", ["awt2swing.Frame", "jalview.analysis.NJTree", "jalview.api.analysis.ViewBasedAnalysisI", "jalview.appletgui.AlignFrame", "$.CutAndPasteTransfer", "$.FontChooser", "$.TreeCanvas", "jalview.bin.JalviewLite", "jalview.datamodel.Alignment", "jalview.io.NewickFile", "jalview.schemes.ResidueProperties", "jalview.util.MessageManager", "java.awt.Color", "$.Font"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.seq = null;
+this.$type = null;
+this.pwtype = null;
+this.start = 0;
+this.end = 0;
+this.treeCanvas = null;
+this.tree = null;
+this.ap = null;
+this.av = null;
+if (!Clazz.isClassDefined ("jalview.appletgui.TreePanel.TreeLoader")) {
+jalview.appletgui.TreePanel.$TreePanel$TreeLoader$ ();
+}
+this.borderLayout1 = null;
+this.scrollPane = null;
+this.jMenuBar1 = null;
+this.jMenu2 = null;
+this.fontSize = null;
+this.bootstrapMenu = null;
+this.distanceMenu = null;
+this.placeholdersMenu = null;
+this.fitToWindow = null;
+this.fileMenu = null;
+this.newickOutput = null;
+this.inputData = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "TreePanel", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener]);
+Clazz.prepareFields (c$, function () {
+this.borderLayout1 =  new java.awt.BorderLayout ();
+this.scrollPane =  new awt2swing.ScrollPane ();
+this.jMenuBar1 =  new awt2swing.MenuBar ();
+this.jMenu2 =  new awt2swing.Menu ();
+this.fontSize =  new awt2swing.MenuItem ();
+this.bootstrapMenu =  new awt2swing.CheckboxMenuItem ();
+this.distanceMenu =  new awt2swing.CheckboxMenuItem ();
+this.placeholdersMenu =  new awt2swing.CheckboxMenuItem ();
+this.fitToWindow =  new awt2swing.CheckboxMenuItem ();
+this.fileMenu =  new awt2swing.Menu ();
+this.newickOutput =  new awt2swing.MenuItem ();
+this.inputData =  new awt2swing.MenuItem ();
+});
+Clazz.defineMethod (c$, "getTree", 
+function () {
+return this.tree;
+});
+Clazz.defineMethod (c$, "finalize", 
+function () {
+this.ap = null;
+this.av = null;
+Clazz.superCall (this, jalview.appletgui.TreePanel, "finalize", []);
+});
+Clazz.makeConstructor (c$, 
+function (ap, type, pwtype) {
+Clazz.superConstructor (this, jalview.appletgui.TreePanel, []);
+try {
+this.jbInit ();
+this.setMenuBar (this.jMenuBar1);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+this.initTreePanel (ap, type, pwtype, null);
+}, "jalview.appletgui.AlignmentPanel,~S,~S");
+Clazz.makeConstructor (c$, 
+function (ap, type, pwtype, newtree) {
+Clazz.superConstructor (this, jalview.appletgui.TreePanel, []);
+try {
+this.jbInit ();
+this.setMenuBar (this.jMenuBar1);
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+this.initTreePanel (ap, type, pwtype, newtree);
+}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile");
+Clazz.defineMethod (c$, "initTreePanel", 
+function (ap, type, pwtype, newTree) {
+this.ap = ap;
+this.av = ap.av;
+this.$type = type;
+this.pwtype = pwtype;
+this.treeCanvas =  new jalview.appletgui.TreeCanvas (ap, this.scrollPane);
+var tl = Clazz.innerTypeInstance (jalview.appletgui.TreePanel.TreeLoader, this, null, newTree);
+tl.start ();
+this.embedMenuIfNeeded (this.treeCanvas);
+this.scrollPane.add (this.treeCanvas, "Center");
+}, "jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile");
+Clazz.defineMethod (c$, "showOriginalData", 
+function () {
+if (this.tree.seqData != null) {
+var gc = '-';
+try {
+gc = this.av.getGapCharacter ();
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+} else {
+throw ex;
+}
+}
+;var alAndColsel = this.tree.seqData.getAlignmentAndColumnSelection (gc);
+if (alAndColsel != null && alAndColsel[0] != null) {
+var al =  new jalview.datamodel.Alignment (alAndColsel[0]);
+var af =  new jalview.appletgui.AlignFrame (al, this.av.applet, "Original Data for Tree", false);
+af.viewport.setHiddenColumns (alAndColsel[1]);
+}} else {
+System.out.println ("Original Tree Data not available");
+}});
+Clazz.overrideMethod (c$, "actionPerformed", 
+function (evt) {
+if (evt.getSource () === this.newickOutput) {
+this.newickOutput_actionPerformed ();
+} else if (evt.getSource () === this.fontSize) {
+this.fontSize_actionPerformed ();
+} else if (evt.getSource () === this.inputData) {
+this.showOriginalData ();
+}}, "java.awt.event.ActionEvent");
+Clazz.overrideMethod (c$, "itemStateChanged", 
+function (evt) {
+if (evt.getSource () === this.fitToWindow) {
+this.treeCanvas.fitToWindow = this.fitToWindow.getState ();
+} else if (evt.getSource () === this.distanceMenu) {
+this.treeCanvas.setShowDistances (this.distanceMenu.getState ());
+} else if (evt.getSource () === this.bootstrapMenu) {
+this.treeCanvas.setShowBootstrap (this.bootstrapMenu.getState ());
+} else if (evt.getSource () === this.placeholdersMenu) {
+this.treeCanvas.setMarkPlaceholders (this.placeholdersMenu.getState ());
+}this.treeCanvas.repaint ();
+}, "java.awt.event.ItemEvent");
+Clazz.defineMethod (c$, "newickOutput_actionPerformed", 
+function () {
+var fout =  new jalview.io.NewickFile (this.tree.getTopNode ());
+var output = fout.print (false, true);
+var cap =  new jalview.appletgui.CutAndPasteTransfer (false, null);
+cap.setText (output);
+var frame =  new awt2swing.Frame ();
+frame.add (cap);
+jalview.bin.JalviewLite.addFrame (frame, this.$type + " " + this.pwtype, 500, 100);
+});
+Clazz.defineMethod (c$, "getTreeFont", 
+function () {
+return this.treeCanvas.$font;
+});
+Clazz.defineMethod (c$, "setTreeFont", 
+function (font) {
+this.treeCanvas.$font = font;
+this.treeCanvas.repaint ();
+}, "java.awt.Font");
+Clazz.defineMethod (c$, "fontSize_actionPerformed", 
+function () {
+if (this.treeCanvas == null) {
+return;
+} new jalview.appletgui.FontChooser (this);
+});
+Clazz.defineMethod (c$, "jbInit", 
+ function () {
+this.setLayout (this.borderLayout1);
+this.setBackground (java.awt.Color.white);
+this.setFont ( new java.awt.Font ("Verdana", 0, 12));
+this.jMenu2.setLabel (jalview.util.MessageManager.getString ("action.view"));
+this.fontSize.setLabel (jalview.util.MessageManager.getString ("action.font"));
+this.fontSize.addActionListener (this);
+this.bootstrapMenu.setLabel (jalview.util.MessageManager.getString ("label.show_bootstrap_values"));
+this.bootstrapMenu.addItemListener (this);
+this.distanceMenu.setLabel (jalview.util.MessageManager.getString ("label.show_distances"));
+this.distanceMenu.addItemListener (this);
+this.placeholdersMenu.setLabel (jalview.util.MessageManager.getString ("label.mark_unassociated_leaves"));
+this.placeholdersMenu.addItemListener (this);
+this.fitToWindow.setState (true);
+this.fitToWindow.setLabel (jalview.util.MessageManager.getString ("label.fit_to_window"));
+this.fitToWindow.addItemListener (this);
+this.fileMenu.setLabel (jalview.util.MessageManager.getString ("action.file"));
+this.newickOutput.setLabel (jalview.util.MessageManager.getString ("label.newick_format"));
+this.newickOutput.addActionListener (this);
+this.inputData.setLabel (jalview.util.MessageManager.getString ("label.input_data"));
+this.add (this.scrollPane, "Center");
+this.jMenuBar1.add (this.fileMenu);
+this.jMenuBar1.add (this.jMenu2);
+this.jMenu2.add (this.fitToWindow);
+this.jMenu2.add (this.fontSize);
+this.jMenu2.add (this.distanceMenu);
+this.jMenu2.add (this.bootstrapMenu);
+this.jMenu2.add (this.placeholdersMenu);
+this.fileMenu.add (this.newickOutput);
+this.fileMenu.add (this.inputData);
+this.inputData.addActionListener (this);
+});
+c$.$TreePanel$TreeLoader$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.decorateAsClass (function () {
+Clazz.prepareCallback (this, arguments);
+this.newtree = null;
+this.odata = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui.TreePanel, "TreeLoader", Thread);
+Clazz.makeConstructor (c$, 
+function (a) {
+Clazz.superConstructor (this, jalview.appletgui.TreePanel.TreeLoader, []);
+this.newtree = a;
+}, "jalview.io.NewickFile");
+Clazz.overrideMethod (c$, "run", 
+function () {
+if (this.newtree != null) {
+if (this.odata == null) {
+this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.newtree);
+} else {
+this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray (), this.odata, this.newtree);
+}} else {
+var a;
+var b;
+var c;
+var d = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup () != null && this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSize () > 1;
+var e = this.b$["jalview.appletgui.TreePanel"].av.getAlignmentView (d);
+if (!d) {
+a = 0;
+b = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getWidth ();
+c = this.b$["jalview.appletgui.TreePanel"].av.getAlignment ().getSequencesArray ();
+} else {
+a = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getStartRes ();
+b = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getEndRes () + 1;
+c = this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup ().getSequencesInOrder (this.b$["jalview.appletgui.TreePanel"].av.getAlignment ());
+}var f = jalview.schemes.ResidueProperties.getScoreModel (this.b$["jalview.appletgui.TreePanel"].pwtype);
+if (Clazz.instanceOf (f, jalview.api.analysis.ViewBasedAnalysisI)) {
+try {
+f = f.getClass ().newInstance ();
+(f).configureFromAlignmentView (this.b$["jalview.appletgui.TreePanel"].treeCanvas.ap);
+} catch (q) {
+if (Clazz.exceptionOf (q, Exception)) {
+System.err.println ("Couldn't create a scoremodel instance for " + f.getName ());
+q.printStackTrace ();
+} else {
+throw q;
+}
+}
+this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, f, a, b);
+} else {
+this.b$["jalview.appletgui.TreePanel"].tree =  new jalview.analysis.NJTree (c, e, this.b$["jalview.appletgui.TreePanel"].$type, this.b$["jalview.appletgui.TreePanel"].pwtype, null, a, b);
+}}this.b$["jalview.appletgui.TreePanel"].tree.reCount (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ());
+this.b$["jalview.appletgui.TreePanel"].tree.findHeight (this.b$["jalview.appletgui.TreePanel"].tree.getTopNode ());
+this.b$["jalview.appletgui.TreePanel"].treeCanvas.setTree (this.b$["jalview.appletgui.TreePanel"].tree);
+if (this.newtree != null) {
+var a = this.newtree.HasDistances () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeDistances", this.newtree.HasDistances ());
+var b = this.newtree.HasBootstrap () && this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showTreeBootstraps", this.newtree.HasBootstrap ());
+this.b$["jalview.appletgui.TreePanel"].distanceMenu.setState (a);
+this.b$["jalview.appletgui.TreePanel"].bootstrapMenu.setState (b);
+this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowBootstrap (b);
+this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowDistances (a);
+this.b$["jalview.appletgui.TreePanel"].treeCanvas.setMarkPlaceholders (this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter ("showUnlinkedTreeNodes", false));
+}this.b$["jalview.appletgui.TreePanel"].treeCanvas.repaint ();
+this.b$["jalview.appletgui.TreePanel"].av.setCurrentTree (this.b$["jalview.appletgui.TreePanel"].tree);
+});
+c$ = Clazz.p0p ();
+};
+});