-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import jalview.io.NewickFile;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
-import java.awt.event.*;
-import java.util.*;
-import jalview.io.NewickFile;
-
-
-public class TreePanel extends GTreePanel
-{
- SequenceI[] seq;
- String type;
- String pwtype;
- AlignViewport av;
- int start;
- int end;
- TreeCanvas treeCanvas;
- NJTree tree;
-
- public NJTree getTree()
- {
- return tree;
- }
-
- public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
- {
- super();
-
- this.type = type;
- this.pwtype = pwtype;
-
- start = s;
- end = e;
-
- String longestName = "";
- seq = new Sequence [seqVector.size()];
- for (int i=0;i < seqVector.size();i++)
- {
- seq[i] = (Sequence) seqVector.elementAt(i);
- if(seq[i].getName().length()>longestName.length())
- longestName = seq[i].getName();
- }
-
- tree = new NJTree(seq, type, pwtype, start, end);
-
- treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-
- tree.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
- scrollPane.add(treeCanvas);
-
- }
- public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
- String type, String pwtype)
- {
- super();
- // These are probably only arbitrary strings reflecting source of tree
- this.type = type;
- this.pwtype = pwtype;
-
- start = 0;
- end = seqVector.size();
-
- String longestName = "";
- seq = new Sequence [seqVector.size()];
- for (int i=0;i < seqVector.size();i++)
- {
- seq[i] = (Sequence) seqVector.elementAt(i);
- }
- // 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());
-
- 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.reCount(tree.getTopNode());
- tree.findHeight(tree.getTopNode());
-
- 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);
-
- }
-
-public String getText(String format) {
- return null;
-}
-
- protected void fitToWindow_actionPerformed(ActionEvent e)
- {
- treeCanvas.fitToWindow = fitToWindow.getState();
- repaint();
- }
-
- public void newickOutput_actionPerformed(ActionEvent actionEvent)
- {
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
- String output = fout.print(false, true);
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
- cap.setText(output);
- java.awt.Frame frame = new java.awt.Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
- }
-
-
-
- protected void fontSize_actionPerformed(ActionEvent e)
- {
- /* 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);
-*/
- }
-
- protected void distanceMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setShowDistances(distanceMenu.getState());
- }
-
- protected void bootstrapMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setShowBootstrap(bootstrapMenu.getState());
- }
-
- protected void placeholdersMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
+import java.awt.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+\r
+public class TreePanel extends Frame implements ActionListener, ItemListener\r
+{\r
+ SequenceI[] seq;\r
+ String type;\r
+ String pwtype;\r
+ int start;\r
+ int end;\r
+ TreeCanvas treeCanvas;\r
+ NJTree tree;\r
+ AlignViewport av;\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, String type, String pwtype)\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ initTreePanel(av, type, pwtype, 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,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newtree)\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ initTreePanel(av, type, pwtype, newtree);\r
+ }\r
+\r
+\r
+ void initTreePanel(AlignViewport av,\r
+ String type,\r
+ String pwtype,\r
+ NewickFile newTree)\r
+ {\r
+\r
+ this.av = av;\r
+ this.type = type;\r
+ this.pwtype = pwtype;\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
+ void showOriginalData()\r
+ {\r
+ // decide if av alignment is sufficiently different to original data to warrant a new window to be created\r
+ // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)\r
+ // or create a selection box around columns in alignment view\r
+ // test Alignment(SeqCigar[])\r
+ if(tree.seqData!=null)\r
+ {\r
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.\r
+ getGapCharacter());\r
+\r
+ if (alAndColsel != null && alAndColsel[0] != null)\r
+ {\r
+ Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);\r
+ AlignFrame af = new AlignFrame(al,\r
+ av.applet,\r
+ "Original Data for Tree",\r
+ false);\r
+\r
+ af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);\r
+ }\r
+ }\r
+ else\r
+ System.out.println("Original Tree Data not available");\r
+ }\r
+\r
+ class TreeLoader extends Thread\r
+ {\r
+ NewickFile newtree;\r
+ jalview.datamodel.AlignmentView odata=null;\r
+\r
+ public TreeLoader(NewickFile newtree)\r
+ {\r
+ this.newtree = newtree;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ if(newtree!=null)\r
+ {\r
+ if (odata == null)\r
+ tree = new NJTree(av.alignment.getSequencesArray(),\r
+ newtree);\r
+ else\r
+ tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+\r
+ }\r
+ else\r
+ {\r
+ int start, end;\r
+ SequenceI [] seqs;\r
+ AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);\r
+ if(av.getSelectionGroup()==null)\r
+ {\r
+ start = 0;\r
+ end = av.alignment.getWidth();\r
+ seqs = av.alignment.getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ start = av.getSelectionGroup().getStartRes();\r
+ end = av.getSelectionGroup().getEndRes()+1;\r
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+ }\r
+\r
+ tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+ }\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
+ av.setCurrentTree(tree);\r
+\r
+ }\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if(evt.getSource()==newickOutput)\r
+ newickOutput_actionPerformed();\r
+ else if(evt.getSource()==fontSize)\r
+ fontSize_actionPerformed();\r
+ else if(evt.getSource()==inputData)\r
+ showOriginalData();\r
+ }\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if(evt.getSource()==fitToWindow)\r
+ treeCanvas.fitToWindow = fitToWindow.getState();\r
+\r
+ else if(evt.getSource()==distanceMenu)\r
+ treeCanvas.setShowDistances(distanceMenu.getState());\r
+\r
+ else if(evt.getSource()==bootstrapMenu)\r
+ treeCanvas.setShowBootstrap(bootstrapMenu.getState());\r
+\r
+ else if(evt.getSource()==placeholdersMenu)\r
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
+\r
+ treeCanvas.repaint();\r
+ }\r
+\r
+\r
+ public void newickOutput_actionPerformed()\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, null);\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()\r
+ {\r
+ if( treeCanvas==null )\r
+ return;\r
+\r
+ new FontChooser(this);\r
+ }\r
+\r
+\r
+\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected ScrollPane scrollPane = new ScrollPane();\r
+ MenuBar jMenuBar1 = new MenuBar();\r
+ Menu jMenu2 = new Menu();\r
+ protected MenuItem fontSize = new MenuItem();\r
+ protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
+ Menu fileMenu = new Menu();\r
+ MenuItem newickOutput = new MenuItem();\r
+ MenuItem inputData = new MenuItem();\r
+\r
+ private void jbInit() throws Exception {\r
+ setLayout(borderLayout1);\r
+ this.setBackground(Color.white);\r
+ this.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jMenu2.setLabel("View");\r
+ fontSize.setLabel("Font...");\r
+ fontSize.addActionListener(this);\r
+ bootstrapMenu.setLabel("Show Bootstrap Values");\r
+ bootstrapMenu.addItemListener(this);\r
+ distanceMenu.setLabel("Show Distances");\r
+ distanceMenu.addItemListener(this);\r
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
+ placeholdersMenu.addItemListener(this);\r
+ fitToWindow.setState(true);\r
+ fitToWindow.setLabel("Fit To Window");\r
+ fitToWindow.addItemListener(this);\r
+ fileMenu.setLabel("File");\r
+ newickOutput.setLabel("Newick Format");\r
+ newickOutput.addActionListener(this);\r
+ inputData.setLabel("Input Data...");\r
+\r
+ add(scrollPane, BorderLayout.CENTER);\r
+ jMenuBar1.add(fileMenu);\r
+ jMenuBar1.add(jMenu2);\r
+ jMenu2.add(fitToWindow);\r
+ jMenu2.add(fontSize);\r
+ jMenu2.add(distanceMenu);\r
+ jMenu2.add(bootstrapMenu);\r
+ jMenu2.add(placeholdersMenu);\r
+ fileMenu.add(newickOutput);\r
+ fileMenu.add(inputData);\r
+ inputData.addActionListener(this);\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalview.git / blobdiff