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