X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2Fappletgui%2FTreePanel.java;fp=unused%2Fappletgui%2FTreePanel.java;h=4bc18a08eb03ec191fece36539dbaba5f2ccd728;hb=6319110ce33faa76ee6cf9832e78faa224510fed;hp=4fa660b4a8a0bbf5ffbf0b4f3e78dc469361d059;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44;p=jalviewjs.git
diff --git a/unused/appletgui/TreePanel.java b/unused/appletgui/TreePanel.java
index 4fa660b..4bc18a0 100644
--- a/unused/appletgui/TreePanel.java
+++ b/unused/appletgui/TreePanel.java
@@ -1,426 +1,426 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see .
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.analysis.NJTree;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.io.NewickFile;
-import jalview.schemes.ResidueProperties;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import javax.swing.JCheckBoxMenuItem;
-import java.awt.Color;
-
-import javax.swing.JFrame;
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.JScrollPane;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-
-public class TreePanel extends EmbmenuFrame implements ActionListener,
- ItemListener
-{
- SequenceI[] seq;
-
- String type;
-
- String pwtype;
-
- int start;
-
- int end;
-
- TreeCanvas treeCanvas;
-
- NJTree tree;
-
- AlignmentPanel ap;
-
- AlignViewport av;
-
- public NJTree getTree()
- {
- return tree;
- }
-
- public void finalize() throws Throwable
- {
- ap = null;
- av = null;
- super.finalize();
- }
-
- /**
- * Creates a new TreePanel object.
- *
- * @param av
- * DOCUMENT ME!
- * @param seqVector
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- * @param pwtype
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
- * @param e
- * DOCUMENT ME!
- */
- public TreePanel(AlignmentPanel ap, String type, String pwtype)
- {
- try
- {
- jbInit();
- this.setJMenuBar(jMenuBar1);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- initTreePanel(ap, type, pwtype, null);
- }
-
- /**
- * Creates a new TreePanel object.
- *
- * @param av
- * DOCUMENT ME!
- * @param seqVector
- * DOCUMENT ME!
- * @param newtree
- * DOCUMENT ME!
- * @param type
- * DOCUMENT ME!
- * @param pwtype
- * DOCUMENT ME!
- */
- public TreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newtree)
- {
- try
- {
- jbInit();
- this.setJMenuBar(jMenuBar1);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
-
- initTreePanel(ap, type, pwtype, newtree);
- }
-
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newTree)
- {
-
- this.ap = ap;
- this.av = ap.av;
- this.type = type;
- this.pwtype = pwtype;
-
- treeCanvas = new TreeCanvas(ap, scrollPane);
- TreeLoader tl = new TreeLoader(newTree);
- tl.start();
- embedMenuIfNeeded(treeCanvas);
- scrollPane.add(treeCanvas, BorderLayout.CENTER);
- }
-
- void showOriginalData()
- {
- // decide if av alignment is sufficiently different to original data to
- // warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions
- // yields unaligned seqs)
- // or create a selection box around columns in alignment view
- // test Alignment(SeqCigar[])
- if (tree.seqData != null)
- {
- char gc = '-';
- try
- {
- // we try to get the associated view's gap character
- // but this may fail if the view was closed...
- gc = av.getGapCharacter();
- } catch (Exception ex)
- {
- }
- ;
- Object[] alAndColsel = tree.seqData
- .getAlignmentAndColumnSelection(gc);
-
- if (alAndColsel != null && alAndColsel[0] != null)
- {
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- AlignFrame af = new AlignFrame(al, av.applet,
- "Original Data for Tree", false);
-
- af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
- }
- }
- else
- {
- System.out.println("Original Tree Data not available");
- }
- }
-
- class TreeLoader extends Thread
- {
- NewickFile newtree;
-
- AlignmentView odata = null;
-
- public TreeLoader(NewickFile newtree)
- {
- this.newtree = newtree;
- }
-
- public void run()
- {
- if (newtree != null)
- {
- if (odata == null)
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
- }
- else
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
- }
-
- }
- else
- {
- int start, end;
- SequenceI[] seqs;
- boolean selview = av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() > 1;
- AlignmentView seqStrings = av.getAlignmentView(selview);
- if (!selview)
- {
- start = 0;
- end = av.getAlignment().getWidth();
- seqs = av.getAlignment().getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
- }
- ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
- if (sm instanceof ViewBasedAnalysisI)
- {
- try
- {
- sm = sm.getClass().newInstance();
- ((ViewBasedAnalysisI) sm)
- .configureFromAlignmentView(treeCanvas.ap);
- } catch (Exception q)
- {
- System.err.println("Couldn't create a scoremodel instance for "
- + sm.getName());
- q.printStackTrace();
- }
- tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
- }
- else
- {
- tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
- end);
- }
- }
-
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- treeCanvas.setTree(tree);
- if (newtree != null)
- {
- // Set default view, paying lip service to any overriding tree view
- // parameter settings
- boolean showDist = newtree.HasDistances()
- && av.applet.getDefaultParameter("showTreeDistances",
- newtree.HasDistances());
- boolean showBoots = newtree.HasBootstrap()
- && av.applet.getDefaultParameter("showTreeBootstraps",
- newtree.HasBootstrap());
- distanceMenu.setSelected(showDist);
- bootstrapMenu.setSelected(showBoots);
- treeCanvas.setShowBootstrap(showBoots);
- treeCanvas.setShowDistances(showDist);
- treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
- "showUnlinkedTreeNodes", false));
- }
-
- treeCanvas.repaint();
-
- av.setCurrentTree(tree);
-
- }
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- if (evt.getSource() == newickOutput)
- {
- newickOutput_actionPerformed();
- }
- else if (evt.getSource() == fontSize)
- {
- fontSize_actionPerformed();
- }
- else if (evt.getSource() == inputData)
- {
- showOriginalData();
- }
- }
-
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt.getSource() == fitToWindow)
- {
- treeCanvas.fitToWindow = fitToWindow.getState();
- }
-
- else if (evt.getSource() == distanceMenu)
- {
- treeCanvas.setShowDistances(distanceMenu.getState());
- }
-
- else if (evt.getSource() == bootstrapMenu)
- {
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());
- }
-
- else if (evt.getSource() == placeholdersMenu)
- {
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
- }
-
- treeCanvas.repaint();
- }
-
- public void newickOutput_actionPerformed()
- {
- NewickFile fout = new NewickFile(tree.getTopNode());
- String output = fout.print(false, true);
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
- cap.setText(output);
- JFrame frame = new JFrame();
- frame.add(cap);
- JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
- }
-
- public java.awt.Font getTreeFont()
- {
- return treeCanvas.font;
- }
-
- public void setTreeFont(java.awt.Font font)
- {
- treeCanvas.font = font;
- treeCanvas.repaint();
- }
-
- protected void fontSize_actionPerformed()
- {
- if (treeCanvas == null)
- {
- return;
- }
-
- new FontChooser(this);
- }
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- protected JScrollPane scrollPane = new JScrollPane();
-
- JMenuBar jMenuBar1 = new JMenuBar();
-
- JMenu jMenu2 = new JMenu();
-
- protected JMenuItem fontSize = new JMenuItem();
-
- protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
-
- JMenu fileMenu = new JMenu();
-
- JMenuItem newickOutput = new JMenuItem();
-
- JMenuItem inputData = new JMenuItem();
-
- private void jbInit() throws Exception
- {
- setLayout(borderLayout1);
- this.setBackground(Color.white);
- this.setFont(new java.awt.Font("Verdana", 0, 12));
- jMenu2.setLabel(MessageManager.getString("action.view"));
- fontSize.setLabel(MessageManager.getString("action.font"));
- fontSize.addActionListener(this);
- bootstrapMenu.setLabel(MessageManager
- .getString("label.show_bootstrap_values"));
- bootstrapMenu.addItemListener(this);
- distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
- distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel(MessageManager
- .getString("label.mark_unassociated_leaves"));
- placeholdersMenu.addItemListener(this);
- fitToWindow.setState(true);
- fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
- fitToWindow.addItemListener(this);
- fileMenu.setLabel(MessageManager.getString("action.file"));
- newickOutput.setLabel(MessageManager.getString("label.newick_format"));
- newickOutput.addActionListener(this);
- inputData.setLabel(MessageManager.getString("label.input_data"));
-
- add(scrollPane, BorderLayout.CENTER);
- jMenuBar1.add(fileMenu);
- jMenuBar1.add(jMenu2);
- jMenu2.add(fitToWindow);
- jMenu2.add(fontSize);
- jMenu2.add(distanceMenu);
- jMenu2.add(bootstrapMenu);
- jMenu2.add(placeholdersMenu);
- fileMenu.add(newickOutput);
- fileMenu.add(inputData);
- inputData.addActionListener(this);
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import javax.swing.JCheckBoxMenuItem;
+import java.awt.Color;
+
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+public class TreePanel extends EmbmenuFrame implements ActionListener,
+ ItemListener
+{
+ SequenceI[] seq;
+
+ String type;
+
+ String pwtype;
+
+ int start;
+
+ int end;
+
+ TreeCanvas treeCanvas;
+
+ NJTree tree;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ public NJTree getTree()
+ {
+ return tree;
+ }
+
+ public void finalize() throws Throwable
+ {
+ ap = null;
+ av = null;
+ super.finalize();
+ }
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ {
+ try
+ {
+ jbInit();
+ this.setJMenuBar(jMenuBar1);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ initTreePanel(ap, type, pwtype, null);
+ }
+
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param newtree
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ */
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newtree)
+ {
+ try
+ {
+ jbInit();
+ this.setJMenuBar(jMenuBar1);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ initTreePanel(ap, type, pwtype, newtree);
+ }
+
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree)
+ {
+
+ this.ap = ap;
+ this.av = ap.av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(ap, scrollPane);
+ TreeLoader tl = new TreeLoader(newTree);
+ tl.start();
+ embedMenuIfNeeded(treeCanvas);
+ scrollPane.add(treeCanvas, BorderLayout.CENTER);
+ }
+
+ void showOriginalData()
+ {
+ // decide if av alignment is sufficiently different to original data to
+ // warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions
+ // yields unaligned seqs)
+ // or create a selection box around columns in alignment view
+ // test Alignment(SeqCigar[])
+ if (tree.seqData != null)
+ {
+ char gc = '-';
+ try
+ {
+ // we try to get the associated view's gap character
+ // but this may fail if the view was closed...
+ gc = av.getGapCharacter();
+ } catch (Exception ex)
+ {
+ }
+ ;
+ Object[] alAndColsel = tree.seqData
+ .getAlignmentAndColumnSelection(gc);
+
+ if (alAndColsel != null && alAndColsel[0] != null)
+ {
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignFrame af = new AlignFrame(al, av.applet,
+ "Original Data for Tree", false);
+
+ af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+ }
+ }
+ else
+ {
+ System.out.println("Original Tree Data not available");
+ }
+ }
+
+ class TreeLoader extends Thread
+ {
+ NewickFile newtree;
+
+ AlignmentView odata = null;
+
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ }
+
+ public void run()
+ {
+ if (newtree != null)
+ {
+ if (odata == null)
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ }
+ else
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
+ newtree);
+ }
+
+ }
+ else
+ {
+ int start, end;
+ SequenceI[] seqs;
+ boolean selview = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 1;
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
+ {
+ start = 0;
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes() + 1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(
+ av.getAlignment());
+ }
+ ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ if (sm instanceof ViewBasedAnalysisI)
+ {
+ try
+ {
+ sm = sm.getClass().newInstance();
+ ((ViewBasedAnalysisI) sm)
+ .configureFromAlignmentView(treeCanvas.ap);
+ } catch (Exception q)
+ {
+ System.err.println("Couldn't create a scoremodel instance for "
+ + sm.getName());
+ q.printStackTrace();
+ }
+ tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ }
+ else
+ {
+ tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+ end);
+ }
+ }
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ if (newtree != null)
+ {
+ // Set default view, paying lip service to any overriding tree view
+ // parameter settings
+ boolean showDist = newtree.HasDistances()
+ && av.applet.getDefaultParameter("showTreeDistances",
+ newtree.HasDistances());
+ boolean showBoots = newtree.HasBootstrap()
+ && av.applet.getDefaultParameter("showTreeBootstraps",
+ newtree.HasBootstrap());
+ distanceMenu.setSelected(showDist);
+ bootstrapMenu.setSelected(showBoots);
+ treeCanvas.setShowBootstrap(showBoots);
+ treeCanvas.setShowDistances(showDist);
+ treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
+ "showUnlinkedTreeNodes", false));
+ }
+
+ treeCanvas.repaint();
+
+ av.setCurrentTree(tree);
+
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == newickOutput)
+ {
+ newickOutput_actionPerformed();
+ }
+ else if (evt.getSource() == fontSize)
+ {
+ fontSize_actionPerformed();
+ }
+ else if (evt.getSource() == inputData)
+ {
+ showOriginalData();
+ }
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == fitToWindow)
+ {
+ treeCanvas.fitToWindow = fitToWindow.getState();
+ }
+
+ else if (evt.getSource() == distanceMenu)
+ {
+ treeCanvas.setShowDistances(distanceMenu.getState());
+ }
+
+ else if (evt.getSource() == bootstrapMenu)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+ }
+
+ else if (evt.getSource() == placeholdersMenu)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+ }
+
+ treeCanvas.repaint();
+ }
+
+ public void newickOutput_actionPerformed()
+ {
+ NewickFile fout = new NewickFile(tree.getTopNode());
+ String output = fout.print(false, true);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
+ cap.setText(output);
+ JFrame frame = new JFrame();
+ frame.add(cap);
+ JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
+ }
+
+ public java.awt.Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
+
+ public void setTreeFont(java.awt.Font font)
+ {
+ treeCanvas.font = font;
+ treeCanvas.repaint();
+ }
+
+ protected void fontSize_actionPerformed()
+ {
+ if (treeCanvas == null)
+ {
+ return;
+ }
+
+ new FontChooser(this);
+ }
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ protected JScrollPane scrollPane = new JScrollPane();
+
+ JMenuBar jMenuBar1 = new JMenuBar();
+
+ JMenu jMenu2 = new JMenu();
+
+ protected JMenuItem fontSize = new JMenuItem();
+
+ protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
+
+ JMenu fileMenu = new JMenu();
+
+ JMenuItem newickOutput = new JMenuItem();
+
+ JMenuItem inputData = new JMenuItem();
+
+ private void jbInit() throws Exception
+ {
+ setLayout(borderLayout1);
+ this.setBackground(Color.white);
+ this.setFont(new java.awt.Font("Verdana", 0, 12));
+ jMenu2.setLabel(MessageManager.getString("action.view"));
+ fontSize.setLabel(MessageManager.getString("action.font"));
+ fontSize.addActionListener(this);
+ bootstrapMenu.setLabel(MessageManager
+ .getString("label.show_bootstrap_values"));
+ bootstrapMenu.addItemListener(this);
+ distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
+ distanceMenu.addItemListener(this);
+ placeholdersMenu.setLabel(MessageManager
+ .getString("label.mark_unassociated_leaves"));
+ placeholdersMenu.addItemListener(this);
+ fitToWindow.setState(true);
+ fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
+ fitToWindow.addItemListener(this);
+ fileMenu.setLabel(MessageManager.getString("action.file"));
+ newickOutput.setLabel(MessageManager.getString("label.newick_format"));
+ newickOutput.addActionListener(this);
+ inputData.setLabel(MessageManager.getString("label.input_data"));
+
+ add(scrollPane, BorderLayout.CENTER);
+ jMenuBar1.add(fileMenu);
+ jMenuBar1.add(jMenu2);
+ jMenu2.add(fitToWindow);
+ jMenu2.add(fontSize);
+ jMenu2.add(distanceMenu);
+ jMenu2.add(bootstrapMenu);
+ jMenu2.add(placeholdersMenu);
+ fileMenu.add(newickOutput);
+ fileMenu.add(inputData);
+ inputData.addActionListener(this);
+ }
+
+}