-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
-\r
-public class TreePanel\r
- extends GTreePanel\r
-{\r
- SequenceI[] seq;\r
- String type;\r
- String pwtype;\r
- AlignmentPanel ap;\r
- int start;\r
- int end;\r
- TreeCanvas treeCanvas;\r
- NJTree tree;\r
-\r
- public NJTree getTree()\r
- {\r
- return tree;\r
- }\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- * @param e DOCUMENT ME!\r
- */\r
- public TreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e)\r
- {\r
- super();\r
- initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
- }\r
-\r
- /**\r
- * Creates a new TreePanel object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param seqVector DOCUMENT ME!\r
- * @param newtree DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param pwtype DOCUMENT ME!\r
- */\r
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
- String type, String pwtype)\r
- {\r
- super();\r
- initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
- }\r
-\r
-\r
- void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
- String pwtype, int s, int e, NewickFile newTree)\r
- {\r
-\r
- this.type = type;\r
- this.pwtype = pwtype;\r
-\r
- start = s;\r
- end = e;\r
-\r
- seq = new Sequence[seqVector.size()];\r
- for(int i=0; i<seqVector.size(); i++)\r
- seq[i] = (SequenceI)seqVector.elementAt(i);\r
-\r
-\r
- treeCanvas = new TreeCanvas(av, scrollPane);\r
- scrollPane.add(treeCanvas);\r
-\r
-\r
- TreeLoader tl = new TreeLoader(newTree);\r
- tl.start();\r
-\r
- }\r
-\r
- class TreeLoader extends Thread\r
- {\r
- NewickFile newtree;\r
-\r
- public TreeLoader(NewickFile newtree)\r
- {\r
- this.newtree = newtree;\r
- }\r
-\r
- public void run()\r
- {\r
- if(newtree!=null)\r
- tree = new NJTree(seq, newtree);\r
- else\r
- tree = new NJTree(seq, type, pwtype, start, end);\r
-\r
- tree.reCount(tree.getTopNode());\r
- tree.findHeight(tree.getTopNode());\r
- treeCanvas.setTree(tree);\r
- if(newtree!=null)\r
- {\r
- distanceMenu.setState(newtree.HasDistances());\r
- bootstrapMenu.setState(newtree.HasBootstrap());\r
- treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
- treeCanvas.setShowDistances(newtree.HasDistances());\r
- }\r
-\r
-\r
- treeCanvas.repaint();\r
-\r
- }\r
- }\r
-\r
- public String getText(String format)\r
- {\r
- return null;\r
- }\r
-\r
- protected void fitToWindow_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.fitToWindow = fitToWindow.getState();\r
- treeCanvas.repaint();\r
- }\r
-\r
- public void newickOutput_actionPerformed(ActionEvent actionEvent)\r
- {\r
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
- String output = fout.print(false, true);\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
- cap.setText(output);\r
- java.awt.Frame frame = new java.awt.Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);\r
- }\r
-\r
- public java.awt.Font getTreeFont()\r
- {\r
- return treeCanvas.font;\r
- }\r
-\r
- public void setTreeFont(java.awt.Font font)\r
- {\r
- treeCanvas.font = font;\r
- treeCanvas.repaint();\r
- }\r
-\r
- protected void fontSize_actionPerformed(ActionEvent e)\r
- {\r
- if( treeCanvas==null )\r
- return;\r
-\r
- new FontChooser(this);\r
- }\r
-\r
- protected void distanceMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowDistances(distanceMenu.getState());\r
- }\r
-\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
- }\r
-\r
- protected void placeholdersMenu_actionPerformed(ActionEvent e)\r
- {\r
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.event.*;
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class TreePanel extends Frame implements ActionListener, ItemListener
+{
+ SequenceI[] seq;
+ String type;
+ String pwtype;
+ int start;
+ int end;
+ TreeCanvas treeCanvas;
+ NJTree tree;
+ AlignViewport av;
+
+ public NJTree getTree()
+ {
+ return tree;
+ }
+
+ /**
+ * 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(AlignViewport av, String type, String pwtype)
+ {
+ try
+ {
+ jbInit();
+ this.setMenuBar(jMenuBar1);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ initTreePanel(av, 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(AlignViewport av,
+ String type,
+ String pwtype,
+ NewickFile newtree)
+ {
+ try
+ {
+ jbInit();
+ this.setMenuBar(jMenuBar1);
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ initTreePanel(av, type, pwtype, newtree);
+ }
+
+
+ void initTreePanel(AlignViewport av,
+ String type,
+ String pwtype,
+ NewickFile newTree)
+ {
+
+ this.av = av;
+ this.type = type;
+ this.pwtype = pwtype;
+
+ treeCanvas = new TreeCanvas(av, scrollPane);
+ scrollPane.add(treeCanvas);
+
+
+ TreeLoader tl = new TreeLoader(newTree);
+ tl.start();
+
+ }
+
+ 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)
+ {
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+ getGapCharacter());
+
+ 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;
+ jalview.datamodel.AlignmentView odata=null;
+
+ public TreeLoader(NewickFile newtree)
+ {
+ this.newtree = newtree;
+ }
+
+ public void run()
+ {
+ if(newtree!=null)
+ {
+ if (odata == null)
+ tree = new NJTree(av.alignment.getSequencesArray(),
+ newtree);
+ else
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+
+ }
+ else
+ {
+ int start, end;
+ SequenceI [] seqs;
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
+ if(av.getSelectionGroup()==null)
+ {
+ start = 0;
+ end = av.alignment.getWidth();
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes()+1;
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
+
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ }
+
+ tree.reCount(tree.getTopNode());
+ tree.findHeight(tree.getTopNode());
+ treeCanvas.setTree(tree);
+ if(newtree!=null)
+ {
+ distanceMenu.setState(newtree.HasDistances());
+ bootstrapMenu.setState(newtree.HasBootstrap());
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+ treeCanvas.setShowDistances(newtree.HasDistances());
+ }
+
+
+ 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()
+ {
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+ String output = fout.print(false, true);
+ 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, 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 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 {
+ 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