-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) 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
+ AlignViewport av;\r
+ int start;\r
+ int end;\r
+ TreeCanvas treeCanvas;\r
+ NJTree tree;\r
+\r
+ public NJTree getTree()\r
+ {\r
+ return tree;\r
+ }\r
+\r
+ public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+ String pwtype, int s, int e)\r
+ {\r
+ super();\r
+\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
+\r
+ start = s;\r
+ end = e;\r
+\r
+ String longestName = "";\r
+ seq = new Sequence[seqVector.size()];\r
+ for (int i = 0; i < seqVector.size(); i++)\r
+ {\r
+ seq[i] = (Sequence) seqVector.elementAt(i);\r
+ if (seq[i].getName().length() > longestName.length())\r
+ {\r
+ longestName = seq[i].getName();\r
+ }\r
+ }\r
+\r
+ tree = new NJTree(seq, type, pwtype, start, end);\r
+\r
+ treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+ scrollPane.add(treeCanvas);\r
+\r
+ }\r
+\r
+ public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
+ String type, String pwtype)\r
+ {\r
+ super();\r
+ // These are probably only arbitrary strings reflecting source of tree\r
+ this.type = type;\r
+ this.pwtype = pwtype;\r
+\r
+ start = 0;\r
+ end = seqVector.size();\r
+\r
+ String longestName = "";\r
+ seq = new Sequence[seqVector.size()];\r
+ for (int i = 0; i < seqVector.size(); i++)\r
+ {\r
+ seq[i] = (Sequence) seqVector.elementAt(i);\r
+ }\r
+ // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
+ tree = new NJTree(seq, newtree);\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ if (longestName.length() <\r
+ ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().\r
+ length())\r
+ {\r
+ longestName = TreeCanvas.PLACEHOLDER +\r
+ ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).\r
+ getName();\r
+ }\r
+ }\r
+\r
+ tree.reCount(tree.getTopNode());\r
+ tree.findHeight(tree.getTopNode());\r
+\r
+ treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+ treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+ treeCanvas.setShowDistances(newtree.HasDistances());\r
+ distanceMenu.setState(newtree.HasDistances());\r
+ bootstrapMenu.setState(newtree.HasBootstrap());\r
+ if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
+ {\r
+ placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
+ }\r
+ scrollPane.add(treeCanvas);\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
+ 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);\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
+ protected void fontSize_actionPerformed(ActionEvent e)\r
+ {\r
+ /* if( treeCanvas==null )\r
+ return;\r
+\r
+ String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);\r
+\r
+ Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Select font size",\r
+ "Font size",\r
+ JOptionPane.QUESTION_MESSAGE,\r
+ null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
+ ,"Font Size - "+size);\r
+ if(selection!=null)\r
+ {\r
+ fontSize.setText("Font Size - " + selection);\r
+\r
+ int i = Integer.parseInt(selection.toString());\r
+ treeCanvas.setFontSize(i);\r
+ }\r
+ scrollPane.setViewportView(treeCanvas);\r
+ */\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
git://source.jalview.org / jalview.git / blobdiff