+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ */
package jalview.appletgui;
-import jalview.datamodel.*;
-import jalview.io.NewickFile;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
+import java.awt.*;
import java.awt.event.*;
-import java.util.*;
-import jalview.io.NewickFile;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
-public class TreePanel extends GTreePanel
+public class TreePanel extends EmbmenuFrame implements ActionListener,
+ ItemListener
{
SequenceI[] seq;
+
String type;
+
String pwtype;
- AlignViewport av;
+
int start;
+
int end;
+
TreeCanvas treeCanvas;
+
NJTree tree;
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
public NJTree getTree()
{
return tree;
}
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
+ public void finalize() throws Throwable
{
- super();
+ ap = null;
+ av = null;
+ super.finalize();
+ }
- this.type = type;
- this.pwtype = pwtype;
+ /**
+ * 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.setMenuBar(jMenuBar1);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
- start = s;
- end = e;
+ initTreePanel(ap, type, pwtype, null);
+ }
- String longestName = "";
- seq = new Sequence [seqVector.size()];
- for (int i=0;i < seqVector.size();i++)
+ /**
+ * 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.setMenuBar(jMenuBar1);
+ } catch (Exception e)
{
- seq[i] = (Sequence) seqVector.elementAt(i);
- if(seq[i].getName().length()>longestName.length())
- longestName = seq[i].getName();
+ e.printStackTrace();
}
- tree = new NJTree(seq, type, pwtype, start, end);
+ initTreePanel(ap, type, pwtype, newtree);
+ }
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+ void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newTree)
+ {
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- scrollPane.add(treeCanvas);
+ 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);
}
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
- String type, String pwtype)
+
+ 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
{
- super();
- // These are probably only arbitrary strings reflecting source of tree
- this.type = type;
- this.pwtype = pwtype;
+ System.out.println("Original Tree Data not available");
+ }
+ }
+
+ class TreeLoader extends Thread
+ {
+ NewickFile newtree;
+
+ jalview.datamodel.AlignmentView odata = null;
- start = 0;
- end = seqVector.size();
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ }
- String longestName = "";
- seq = new Sequence [seqVector.size()];
- for (int i=0;i < seqVector.size();i++)
+ public void run()
+ {
+ if (newtree != null)
{
- seq[i] = (Sequence) seqVector.elementAt(i);
+ if (odata == null)
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ }
+ else
+ {
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
+ newtree);
+ }
+
}
- // This constructor matches sequence names to treenodes and sets up the tree layouts.
- tree = new NJTree(seq, newtree);
- // Now have to calculate longest name based on the leaves
- Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
+ 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());
+ }
- for (int i=0;i < leaves.size();i++)
- if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
- longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
+ tree = new NJTree(seqs, seqStrings, type, pwtype, 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.setState(showDist);
+ bootstrapMenu.setState(showBoots);
+ treeCanvas.setShowBootstrap(showBoots);
+ treeCanvas.setShowDistances(showDist);
+ treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
+ "showUnlinkedTreeNodes", false));
+ }
+
+ treeCanvas.repaint();
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());
- treeCanvas.setShowDistances(newtree.HasDistances());
- distanceMenu.setState(newtree.HasDistances());
- bootstrapMenu.setState(newtree.HasBootstrap());
- if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
- placeholdersMenu.setState(treeCanvas.markPlaceholders);
- scrollPane.add(treeCanvas);
+ av.setCurrentTree(tree);
}
+ }
-public String getText(String format) {
- return null;
-}
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == newickOutput)
+ {
+ newickOutput_actionPerformed();
+ }
+ else if (evt.getSource() == fontSize)
+ {
+ fontSize_actionPerformed();
+ }
+ else if (evt.getSource() == inputData)
+ {
+ showOriginalData();
+ }
+ }
- protected void fitToWindow_actionPerformed(ActionEvent e)
+ public void itemStateChanged(ItemEvent evt)
{
- treeCanvas.fitToWindow = fitToWindow.getState();
- repaint();
+ 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(ActionEvent actionEvent)
+ public void newickOutput_actionPerformed()
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
String output = fout.print(false, true);
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
cap.setText(output);
java.awt.Frame frame = new java.awt.Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
+ jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
}
-
-
- protected void fontSize_actionPerformed(ActionEvent e)
+ public java.awt.Font getTreeFont()
{
- /* if( treeCanvas==null )
- return;
-
- String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
-
- Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Select font size",
- "Font size",
- JOptionPane.QUESTION_MESSAGE,
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
- ,"Font Size - "+size);
- if(selection!=null)
- {
- fontSize.setText("Font Size - " + selection);
-
- int i = Integer.parseInt(selection.toString());
- treeCanvas.setFontSize(i);
- }
- scrollPane.setViewportView(treeCanvas);
-*/
+ return treeCanvas.font;
}
- protected void distanceMenu_actionPerformed(ActionEvent e)
+ public void setTreeFont(java.awt.Font font)
{
- treeCanvas.setShowDistances(distanceMenu.getState());
+ treeCanvas.font = font;
+ treeCanvas.repaint();
}
- protected void bootstrapMenu_actionPerformed(ActionEvent e)
+ protected void fontSize_actionPerformed()
{
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+ if (treeCanvas == null)
+ {
+ return;
+ }
+
+ new FontChooser(this);
}
- protected void placeholdersMenu_actionPerformed(ActionEvent e)
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ protected ScrollPane scrollPane = new ScrollPane();
+
+ MenuBar jMenuBar1 = new MenuBar();
+
+ Menu jMenu2 = new Menu();
+
+ protected MenuItem fontSize = new MenuItem();
+
+ protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+
+ Menu fileMenu = new Menu();
+
+ MenuItem newickOutput = new MenuItem();
+
+ MenuItem inputData = new MenuItem();
+
+ private void jbInit() throws Exception
{
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+ setLayout(borderLayout1);
+ this.setBackground(Color.white);
+ this.setFont(new java.awt.Font("Verdana", 0, 12));
+ jMenu2.setLabel("View");
+ fontSize.setLabel("Font...");
+ fontSize.addActionListener(this);
+ bootstrapMenu.setLabel("Show Bootstrap Values");
+ bootstrapMenu.addItemListener(this);
+ distanceMenu.setLabel("Show Distances");
+ distanceMenu.addItemListener(this);
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");
+ placeholdersMenu.addItemListener(this);
+ fitToWindow.setState(true);
+ fitToWindow.setLabel("Fit To Window");
+ fitToWindow.addItemListener(this);
+ fileMenu.setLabel("File");
+ newickOutput.setLabel("Newick Format");
+ newickOutput.addActionListener(this);
+ inputData.setLabel("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);
}
}
git://source.jalview.org / jalview.git / blobdiff