001 /*
002 * CRIMSON
003 * Copyright (c) 2006, Stephen Fisher, Susan Davidson, and Junhyong Kim,
004 * University of Pennsylvania.
005 *
006 * This program is free software; you can redistribute it and/or
007 * modify it under the terms of the GNU General Public License as
008 * published by the Free Software Foundation; either version 2 of the
009 * License, or (at your option) any later version.
010 *
011 * This program is distributed in the hope that it will be useful, but
012 * WITHOUT ANY WARRANTY; without even the implied warranty of
013 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
014 * General Public License for more details.
015 *
016 * You should have received a copy of the GNU General Public License
017 * along with this program; if not, write to the Free Software
018 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
019 * 02110-1301 USA.
020 *
021 * @(#)TreeUtils.java
022 */
023
024 package edu.upenn.crimson.gui;
025
026 import edu.upenn.crimson.*;
027 import edu.upenn.crimson.io.*;
028 import java.io.File;
029 import java.util.ArrayList;
030 import java.util.Iterator;
031 import java.awt.*;
032 import java.awt.event.*;
033 import javax.swing.*;
034
035 /**
036 * Static methods used throughout the GUI for Tree objects.
037 *
038 * @author Stephen Fisher
039 * @version $Id: TreeUtils.java,v 1.16 2007/10/09 20:14:16 fisher Exp $
040 */
041
042 public class TreeUtils {
043
044 //--------------------------------------------------------------------------
045 // Miscellaneous Methods
046
047 /** Present a dialog box for selecting a particular Tree. */
048 public static String treeSelector() {
049 // use this to get the return value from ObjectSelectorDialog
050 ArrayList out = new ArrayList();
051 Object[] objects = ObjectHandles.getTrees().toArray();
052 new ObjectSelectorDialog("Tree Selector", objects, out);
053
054 if (out.size() > 0) {
055 return (String) out.get(0);
056 } else {
057 return "";
058 }
059 }
060
061 /**
062 * This will process the NEXUS file selected and then load the
063 * file into the specified database table.
064 */
065 public static void loadTree() {
066 // if no database connection then error
067 if (! Database.isOpen()) {
068 CrimsonUtils.printError("Must open a database before loading a tree.");
069 return;
070 }
071
072 // get file containing tree
073 File file = GUIUtils.openFileChooser("Select NEXUS File", null);
074
075 // no valid file selected
076 if (file == null) return;
077
078 // use filename as tree/partition IDs - without the .nex
079 // extension, if it exists.
080 String name = file.getName();
081 if (name.endsWith(".nex")) name = name.substring(0, name.length()-4);
082 loadTree(file, name, name);
083 }
084
085 public static void loadTree(File file, String treeID, String partitionID) {
086 // if invalid file then try again
087 if (file == null) loadTree();
088
089 // get tree/partition names
090 String[] labels = {" Tree name:", " Partition name:"};
091
092 // use this to get the return value from FieldEditDialog
093 ArrayList textFields = new ArrayList();
094
095 // get the value the user entered
096 JTextField treeTF = new JTextField(20);
097 treeTF.setText(treeID);
098 textFields.add(treeTF);
099 JTextField partitionTF = new JTextField(20);
100 partitionTF.setText(partitionID);
101 textFields.add(partitionTF);
102
103 new FieldEditDialog("Load Tree", labels, textFields);
104
105 // check "exit code" for FieldEditDialog, if false then exit
106 Boolean exitCode = (Boolean) textFields.get(textFields.size()-1);
107 if (! exitCode.booleanValue()) return;
108
109 // get tree/partition names
110 treeID = treeTF.getText().toUpperCase();
111 partitionID = partitionTF.getText().toUpperCase();
112
113 // shouldn't need to test both database and treePool, but
114 // better to be careful
115 if (Trees.dbContains(treeID) || ObjectHandles.containsTree(treeID)) {
116 JOptionPane.showMessageDialog(null,
117 "Tree name already used, please select a different name",
118 "Name Error", JOptionPane.INFORMATION_MESSAGE);
119
120 // rerun the tree/partition ID dialog
121 loadTree(file, treeID, partitionID);
122 return;
123 }
124 if (Partitions.dbContains(partitionID) || ObjectHandles.containsPartition(partitionID)) {
125 JOptionPane.showMessageDialog(null,
126 "Partition name already used, please select a different name",
127 "Name Error", JOptionPane.INFORMATION_MESSAGE);
128
129 // rerun the tree/partition ID dialog
130 loadTree(file, treeID, partitionID);
131 return;
132 }
133
134 // convert any '.' to '_' in treeID since table names can not
135 // contain '.'
136 String origTreeID = treeID;
137 treeID = treeID.replace('.', '_');
138 if (treeID.compareTo(origTreeID) != 0) {
139 CrimsonUtils.printWarning("Tree names can not contain '.' and were converted to '_'.");
140 }
141
142 String msg = "loadTree(\"" + GUIUtils.getFilename(file);
143 msg += "\", \"" + treeID + "\", \"" + partitionID + "\")";
144 Root.runCommand(msg);
145 }
146
147 /**
148 * This will process the NEXUS file selected and then append the
149 * file into the specified database table.
150 */
151 public static void appendTree(String treeID) {
152 // if no database connection then error
153 if (! Database.isOpen()) {
154 CrimsonUtils.printError("Must open a database before appending data to a tree.");
155 return;
156 }
157
158 if (CrimsonUtils.isEmpty(treeID)) {
159 treeID = treeSelector();
160
161 // if the user didn't select a tree, then quit
162 if (CrimsonUtils.isEmpty(treeID)) return;
163 }
164
165 // get file containing tree
166 File file = GUIUtils.openFileChooser("Select NEXUS File", null);
167
168 // no valid file selected
169 if (file == null) return;
170
171 // get tree/partition names
172 String[] labels = {" Tree name:", " Partition name:"};
173
174 // use this to get the return value from FieldEditDialog
175 ArrayList textFields = new ArrayList();
176
177 // get the value the user entered
178 JTextField treeTF = new JTextField(20);
179 treeTF.setText(treeID);
180 treeTF.setEnabled(false);
181 textFields.add(treeTF);
182 JTextField partitionTF = new JTextField(20);
183 // use filename as partition ID, without the .nex extension,
184 // if it exists.
185 String name = file.getName();
186 if (name.endsWith(".nex")) name = name.substring(0, name.length()-4);
187 partitionTF.setText(name);
188 textFields.add(partitionTF);
189
190 new FieldEditDialog("Append Tree", labels, textFields);
191
192 // check "exit code" for FieldEditDialog, if false then exit
193 Boolean exitCode = (Boolean) textFields.get(textFields.size()-1);
194 if (! exitCode.booleanValue()) return;
195
196 // get tree/partition names
197 String partitionID = partitionTF.getText().toUpperCase();
198
199 String msg = "appendTree(\"" + GUIUtils.getFilename(file);
200 msg += "\", \"" + treeID + "\", \"" + partitionID + "\")";
201 Root.runCommand(msg);
202 }
203
204 /** This will export the tree specified by TreeSelector(). */
205 public static void exportTree(String id) {
206 // if no database connection then error
207 if (! Database.isOpen()) {
208 CrimsonUtils.printError("Must open a database before exporting a tree.");
209 return;
210 }
211
212 if (CrimsonUtils.isEmpty(id)) {
213 id = treeSelector();
214
215 // if ID still empty then quit
216 if (CrimsonUtils.isEmpty(id)) return;
217 }
218
219 Tree tree = ObjectHandles.getTree(id);
220 if (tree == null) {
221 CrimsonUtils.printError("Invalid tree: " + id);
222 return;
223 }
224
225 // if no partitions then only export structure, else ask user
226 if (tree.getNumPartitions() == 0) {
227 Root.runCommand("exportStruct(\"" + id + "\")");
228 } else {
229 String msg = "Do you want to include the partition data?\n";
230 msg += "Tree: " + id;
231 Object[] options = {"Structure and Data", "Only Structure", "Cancel"};
232 int flag = JOptionPane.showOptionDialog(null, msg,
233 "Export Tree",
234 JOptionPane.YES_NO_CANCEL_OPTION,
235 JOptionPane.QUESTION_MESSAGE,
236 null,
237 options,
238 options[1]);
239 if (flag == JOptionPane.YES_OPTION) { // include data
240 Root.runCommand("exportTree(\"" + id + "\")");
241 } else if (flag == JOptionPane.NO_OPTION) { // no data
242 Root.runCommand("exportStruct(\"" + id + "\")");
243 }
244 }
245 }
246
247 /** This will delete the tree specified by TreeSelector(). */
248 public static void deleteTree(String id) {
249 if (CrimsonUtils.isEmpty(id)) {
250 id = treeSelector();
251
252 // if ID still empty then quit
253 if (CrimsonUtils.isEmpty(id)) return;
254 }
255
256 id = id.toUpperCase();
257 String queries = "";
258 for (Iterator i = ObjectHandles.queryIterator(); i.hasNext();) {
259 Query query = (Query) i.next();
260 if (id.equals(query.getTreeID())) queries += " Query: " + query.getID() + "\n";
261 }
262
263 String msg = "Are you sure you want to remove this tree?\n";
264 msg += " Tree: " + id;
265
266 if (! CrimsonUtils.isEmpty(queries)) {
267 msg = "Queries exist that reference this tree. These queries will be deleted.\n"
268 + queries + "\n" + msg;
269 }
270
271 Object[] options = {"Delete Tree", "Cancel"};
272 int flag = JOptionPane.showOptionDialog(null, msg,
273 "Delete Confirmation",
274 JOptionPane.YES_NO_OPTION,
275 JOptionPane.QUESTION_MESSAGE,
276 null,
277 options,
278 options[1]);
279 if (flag == JOptionPane.YES_OPTION) { // "Delete"
280 // delete tree
281 Root.runCommand("deleteTree(\"" + id + "\", 1)");
282 }
283 }
284
285 public static boolean isTreeBuilt(Tree tree) {
286 if (tree.isBuilt()) {
287 return true;
288 } else {
289 // if less than 1000 leaves, just build the tree
290 if (tree.getNumLeaves() < 1000) {
291 Root.runCommand("getTree(\"" + tree.getID() + "\").buildTree()");
292 return true;
293 }
294
295 String msg = "The tree structure " + tree.getID() + " needs to be created.\n";
296 msg += "This may take a few minutes for very large trees.\n";
297 msg += "Do you want to continue?\n";
298 Object[] options = {"Ok", "Cancel"};
299 int flag = JOptionPane.showOptionDialog(null, msg,
300 "Build Tree",
301 JOptionPane.YES_NO_OPTION,
302 JOptionPane.QUESTION_MESSAGE,
303 null,
304 options,
305 options[0]);
306 if (flag == JOptionPane.YES_OPTION) { // build tree
307 Root.runCommand("getTree(\"" + tree.getID() + "\").buildTree()");
308 return true;
309 }
310 }
311
312 // user pressed cancel button
313 return false;
314 }
315
316 /** This will view the tree specified by TreeSelector(). */
317 public static void view3DTree(String id) {
318 // don't do anything if WALRUS not loaded
319 if (! CrimsonMain.WALRUS) return;
320
321 // if no database connection then error
322 if (! Database.isOpen()) {
323 CrimsonUtils.printError("Must open a database before viewing a tree.");
324 return;
325 }
326
327 // if no ID, then use treeSelector() to get tree
328 if (CrimsonUtils.isEmpty(id)) {
329 id = treeSelector();
330
331 // if ID still empty then quit
332 if (CrimsonUtils.isEmpty(id)) return;
333 }
334
335 Tree tree = ObjectHandles.getTree(id);
336 // make sure tree exists
337 if (tree == null) {
338 CrimsonUtils.printError("Invalid tree: " + id);
339 return;
340 }
341
342 Root.runCommand("tree2wal(\"" + id + "\")");
343 }
344
345 /** This will display the tree statistics. */
346 public static void statsTree(String id) {
347 // if no database connection then error
348 if (! Database.isOpen()) {
349 CrimsonUtils.printError("Must open a database before viewing tree information.");
350 return;
351 }
352
353 // if no ID, then use treeSelector() to get tree
354 if (CrimsonUtils.isEmpty(id)) {
355 id = treeSelector();
356
357 // if ID still empty then quit
358 if (CrimsonUtils.isEmpty(id)) return;
359 }
360
361 Tree tree = ObjectHandles.getTree(id);
362 // make sure tree exists
363 if (tree == null) {
364 CrimsonUtils.printError("Invalid tree: " + id);
365 return;
366 }
367
368 JOptionPane.showMessageDialog(null, tree.toString(), "Tree Statistics",
369 JOptionPane.INFORMATION_MESSAGE);
370 }
371
372 /** This will display the tree's newick string. */
373 public static void newickTree(String id) {
374 // if no database connection then error
375 if (! Database.isOpen()) {
376 CrimsonUtils.printError("Must open a database before viewing tree information.");
377 return;
378 }
379
380 // if no ID, then use treeSelector() to get tree
381 if (CrimsonUtils.isEmpty(id)) {
382 id = treeSelector();
383
384 // if ID still empty then quit
385 if (CrimsonUtils.isEmpty(id)) return;
386 }
387
388 Tree tree = ObjectHandles.getTree(id);
389 // make sure tree exists
390 if (tree == null) {
391 CrimsonUtils.printError("Invalid tree: " + id);
392 return;
393 }
394
395 new NewickViewer(tree.getNewick());
396 }
397
398 static class NewickViewer extends JFrame {
399 NewickViewer thisFrame;
400
401 public NewickViewer(String newick) {
402 super("Newick Viewer");
403
404 // keep pointer to self so can 'dispose' Frame below
405 thisFrame = this;
406
407 setDefaultCloseOperation(DISPOSE_ON_CLOSE);
408
409 JTextArea text = new JTextArea(20, 110);
410 text.setEditable(false);
411 JScrollPane textSP = new JScrollPane(text);
412 textSP.setBorder(BorderFactory.createLoweredBevelBorder());
413
414 // split into lines of length 100
415 int numLines = newick.length() / 100;
416 for (int i = 0; i < (numLines * 100); i += 100) {
417 text.append(newick.substring(i, i + 100) + "\n");
418 }
419 // print remaining portion of string
420 if ((newick.length() % 100) > 0) {
421 text.append(newick.substring(numLines * 100) + "\n");
422 }
423
424 // setup close button
425 JButton closeB = new JButton("Close Newick Viewer");
426 closeB.addActionListener(new ActionListener() {
427 public void actionPerformed(ActionEvent e) {
428 thisFrame.dispose();
429 }
430 });
431
432 getContentPane().setLayout(new BorderLayout());
433 getContentPane().add(textSP, BorderLayout.CENTER);
434 getContentPane().add(closeB, BorderLayout.SOUTH);
435 pack();
436
437 // set the default window size
438 setSize(800, 900);
439
440 // display the window
441 setVisible(true);
442 }
443 } // NewickViewer
444
445 } // TreeUtils.java