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comparison smart_toolShed/SMART/Java/Sav/Smart.java @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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1 /**
2 *
3 * Copyright INRA-URGI 2009-2010
4 *
5 * This software is governed by the CeCILL license under French law and
6 * abiding by the rules of distribution of free software. You can use,
7 * modify and/ or redistribute the software under the terms of the CeCILL
8 * license as circulated by CEA, CNRS and INRIA at the following URL
9 * "http://www.cecill.info".
10 *
11 * As a counterpart to the access to the source code and rights to copy,
12 * modify and redistribute granted by the license, users are provided only
13 * with a limited warranty and the software's author, the holder of the
14 * economic rights, and the successive licensors have only limited
15 * liability.
16 *
17 * In this respect, the user's attention is drawn to the risks associated
18 * with loading, using, modifying and/or developing or reproducing the
19 * software by the user in light of its specific status of free software,
20 * that may mean that it is complicated to manipulate, and that also
21 * therefore means that it is reserved for developers and experienced
22 * professionals having in-depth computer knowledge. Users are therefore
23 * encouraged to load and test the software's suitability as regards their
24 * requirements in conditions enabling the security of their systems and/or
25 * data to be ensured and, more generally, to use and operate it in the
26 * same conditions as regards security.
27 *
28 * The fact that you are presently reading this means that you have had
29 * knowledge of the CeCILL license and that you accept its terms.
30 *
31 */
32 import java.util.*;
33 import java.awt.*;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.io.*;
37 import javax.swing.*;
38 import javax.swing.filechooser.*;
39 import javax.swing.border.*;
40 import javax.swing.SwingUtilities;
41
42
43 public class Smart extends JPanel implements ActionListener {
44
45 String version = "1.0.2";
46
47 JFrame mainFrame;
48 JButton openButton;
49 JButton comparisonGoButton;
50
51 JComboBox formatTypes;
52 JComboBox fileFormats;
53 String[] emptyFormats = {"Choose a type first..."};
54
55 JFrame askFrame;
56 JButton pythonButton;
57 JButton mySqlButton;
58 JButton rButton;
59
60 HashMap <JButton, Program> callingProgram;
61
62 // comparison
63 JList comparisonFile1List;
64 JList comparisonFile2List;
65 JTextField comparisonOutputTextField;
66 JTextField comparisonFiveQueryExtensionTextField;
67 JCheckBox comparisonColinearCheckBox;
68 JCheckBox comparisonAntisenseCheckBox;
69 JCheckBox comparisonInvertCheckBox;
70
71 JList fileList;
72 JTextArea logArea;
73
74 // progress bar
75 JLabel messageField;
76 JProgressBar progressBar;
77 JLabel etaField;
78
79 // process
80 Program currentProgram;
81 Process process;
82 javax.swing.Timer processTimer;
83
84
85 int previousStatus;
86
87 public Smart() {
88 super(new BorderLayout());
89
90 callingProgram = new HashMap <JButton, Program> ();
91
92 previousStatus = -1;
93
94 processTimer = new javax.swing.Timer(1000, this);
95 processTimer.stop();
96
97 // Ask frame buttons
98 pythonButton = new JButton("find...");
99 mySqlButton = new JButton("find...");
100 rButton = new JButton("find...");
101
102 // Get available formats
103 FormatsReader formatReader = new FormatsReader(Global.smartFormatsFileName);
104 if (! formatReader.read()) {
105 System.out.println("Something was wrong while reading file format...");
106 }
107
108 // Get screen size
109 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
110
111 // Log
112 logArea = new JTextArea(512, Global.logAreaSize);
113 logArea.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.22)));
114 logArea.setFont(new Font("Monospaced", logArea.getFont().getStyle(), logArea.getFont().getSize()));
115 JScrollPane logScroll = new JScrollPane(logArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
116 TitledBorder logBorder = BorderFactory.createTitledBorder("Log");
117 logScroll.setBorder(logBorder);
118 logArea.append("Using S-MART " + version + "\n");
119
120 GridLayout horizontalLayout = new GridLayout(1, 0);
121
122 // check configuration
123 this.readConfigurationFile();
124 this.checkConfiguration();
125
126 // Tabs
127 JTabbedPane tabbedPane = new JTabbedPane();
128 tabbedPane.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.75)));
129
130 // File panel
131 JPanel filePanel = new JPanel(false);
132 filePanel.setLayout(new FlowLayout());
133 tabbedPane.add("Files", filePanel);
134
135 // Format sub-panel
136 JPanel formatComboPanel = new JPanel(false);
137 JPanel formatPanel = new JPanel(false);
138 Vector<String> formatTypesString = Global.formats.getFormatTypes();
139 formatPanel.setLayout(horizontalLayout);
140 formatTypesString.insertElementAt("Choose the format type", 0);
141 JLabel formatLabel = new JLabel("Format");
142 formatTypes = new JComboBox(formatTypesString);
143 fileFormats = new JComboBox(emptyFormats);
144 formatLabel.setLabelFor(fileFormats);
145 formatTypes.addActionListener(this);
146 formatComboPanel.add(formatTypes);
147 formatComboPanel.add(fileFormats);
148
149 formatPanel.add(formatLabel);
150 formatPanel.add(formatComboPanel);
151
152 // File chooser sub-panel
153 JPanel fileChooserPanel = new JPanel(false);
154 fileChooserPanel.setLayout(horizontalLayout);
155 JLabel fileLabel = new JLabel("File");
156 openButton = new JButton("Open a File...");
157 openButton.addActionListener(this);
158
159 fileChooserPanel.add(fileLabel);
160 fileChooserPanel.add(openButton);
161
162 // File list sub-panel
163 JPanel existingFilesPanel = new JPanel(false);
164 existingFilesPanel.setLayout(horizontalLayout);
165 existingFilesPanel.setMinimumSize(new Dimension(10000, 10000));
166 JLabel existingFilesLabel = new JLabel("Existing files");
167 Box fileListBox = Box.createHorizontalBox();
168 fileListBox.add(Box.createRigidArea(new Dimension(0, 100)));
169 JList fileList = new JList(Global.fileNames);
170 fileList.setLayoutOrientation(JList.HORIZONTAL_WRAP);
171 fileList.setVisibleRowCount(4);
172 JScrollPane listScroller = new JScrollPane(fileList);
173 fileListBox.add(listScroller);
174
175 existingFilesPanel.add(existingFilesLabel);
176 existingFilesPanel.add(fileListBox);
177
178 // File panel layout
179 Box box = Box.createVerticalBox();
180 box.add(formatPanel);
181 box.add(fileChooserPanel);
182 box.add(existingFilesPanel);
183 filePanel.add(box);
184
185 // Program panels
186 TreeMap < String, JTabbedPane > panels = new TreeMap < String, JTabbedPane >();
187 PythonProgramFinder programFinder = new PythonProgramFinder("Python");
188 String comments = programFinder.findPrograms();
189 if (comments != null) {
190 logArea.append(comments);
191 }
192 for (int i = 0; i < programFinder.getPrograms().size(); i++) {
193 Program program = programFinder.getPrograms().get(i);
194 JPanel programPanel = program.getPanel();
195 String section = program.getSection();
196 JTabbedPane sectionPane = null;
197 if (panels.containsKey(section)) {
198 sectionPane = panels.get(section);
199 }
200 else {
201 sectionPane = new JTabbedPane();
202 tabbedPane.addTab(section, sectionPane);
203 panels.put(section, sectionPane);
204 }
205
206 JScrollPane programScroll = new JScrollPane(programPanel, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
207 sectionPane.addTab(program.getName(), programScroll);
208
209 JButton button = program.getButton();
210 button.addActionListener(this);
211 callingProgram.put(button, program);
212 }
213
214 // Progress bar
215 JPanel progressPanel = new JPanel(new GridLayout(1, 0), false);
216 progressPanel.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.02)));
217 messageField = new JLabel();
218 progressBar = new JProgressBar(0, 100);
219 etaField = new JLabel();
220 messageField.setHorizontalAlignment(JLabel.LEFT);
221 progressBar.setValue(0);
222 etaField.setHorizontalAlignment(JLabel.RIGHT);
223 progressBar.setStringPainted(true);
224 progressPanel.add(messageField);
225 progressPanel.add(progressBar);
226 progressPanel.add(etaField);
227
228 add(tabbedPane, BorderLayout.PAGE_START);
229 add(logScroll, BorderLayout.CENTER);
230 add(progressPanel, BorderLayout.PAGE_END);
231 }
232
233
234 public boolean checkConfiguration() {
235 int status = this.testConfiguration();
236
237 if (status == previousStatus) {
238 logArea.append("S-MART does not seem to work properly... Tried to manage it by myself, unsuccessfully... Check documentation for further explanation...\n");
239 return false;
240 }
241
242 switch (status) {
243 case 0:
244 return true;
245 case 1:
246 logArea.append("S-MART does not seem to work properly... Check documentation for further explanation...\n");
247 break;
248 case 3:
249 this.askWhereIsProgram("python");
250 break;
251 case 4:
252 break;
253 case 5:
254 this.askWhereIsProgram("mySQL");
255 break;
256 case 6:
257 this.askWhereIsProgram("R");
258 break;
259 case 7:
260 logArea.append("Please install 'ColorBrewer' R package...\n");
261 break;
262 default:
263 logArea.append("Weird configuration test status: " + status + "...\n");
264 }
265 previousStatus = status;
266 return true;
267 }
268
269
270 public int testConfiguration() {
271 String[] command = {Global.pythonCommand, "Python" + java.io.File.separator + "testInstall.py"};
272 ProgramLauncher launcher = new ProgramLauncher(command, logArea, messageField, progressBar, etaField);
273 String line;
274 launcher.execute();
275 (new Exception("hello")).printStackTrace();
276 return launcher.getExitValue();
277 }
278
279
280 public void readConfigurationFile() {
281 java.io.File file = new java.io.File(Global.smartConfFileName);
282 String line = null;
283
284 if (! file.exists()) {
285 return;
286 }
287
288 try {
289 BufferedReader reader = new BufferedReader(new FileReader(file));
290
291 while ((line = reader.readLine()) != null) {
292 line = line.trim();
293 if (line.startsWith("python:")) Global.pythonCommand = line.substring("python:".length()).trim();
294 else if (line.startsWith("mysql:")) Global.mysqlCommand = line.substring("mysql:".length()).trim();
295 else if (line.startsWith("r:")) Global.rCommand = line.substring("r:".length()).trim();
296 }
297 reader.close();
298 }
299 catch (FileNotFoundException e) {
300 logArea.append("Configuration file is empty: " + e.getMessage() + "!\n");
301 return;
302 }
303 catch (IOException e) {
304 logArea.append("Weird with configuration file: " + e.getMessage() + "!\n");
305 return;
306 }
307 }
308
309
310 public void askWhereIsProgram(String program) {
311 askFrame = new JFrame("Where is " + program + "?");
312 askFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
313 JLabel label = new JLabel("Where is your " + program + " (or " + program + ".exe) file?");
314 JButton button = null;
315 if ("python".equals(program)) {
316 button = pythonButton;
317 }
318 else if ("mySQL".equals(program)) {
319 button = mySqlButton;
320 }
321 else if ("R".equals(program)) {
322 button = rButton;
323 }
324 else {
325 logArea.append("Problem with the button!\n");
326 }
327 askFrame.getContentPane().add(label, BorderLayout.WEST);
328 askFrame.getContentPane().add(button, BorderLayout.EAST);
329 button.addActionListener(this);
330 askFrame.pack();
331 askFrame.setVisible(true);
332 askFrame.setAlwaysOnTop(true);
333 }
334
335
336 public void actionPerformed(ActionEvent e) {
337
338 // Python command chooser
339 if (e.getSource() == pythonButton) {
340 JFileChooser chooser = new JFileChooser();
341 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
342 Global.pythonCommand = chooser.getSelectedFile().getPath();
343 askFrame.setVisible(false);
344 askFrame.dispose();
345 try {
346 BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
347 out.write("python: " + Global.pythonCommand + "\n");
348 out.close();
349 }
350 catch (IOException exception) {
351 logArea.append("Cannot write configuration file!\n");
352 }
353 }
354 this.checkConfiguration();
355 }
356 // MySQL command chooser
357 else if (e.getSource() == mySqlButton) {
358 JFileChooser chooser = new JFileChooser();
359 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
360 Global.mysqlCommand = chooser.getSelectedFile().getPath();
361 askFrame.setVisible(false);
362 askFrame.dispose();
363 try {
364 BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
365 out.write("mysql: " + Global.mysqlCommand + "\n");
366 out.close();
367 }
368 catch (IOException exception) {
369 logArea.append("Cannot write configuration file!\n");
370 }
371 }
372 this.checkConfiguration();
373 }
374 // R command chooser
375 else if (e.getSource() == rButton) {
376 JFileChooser chooser = new JFileChooser();
377 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
378 Global.rCommand = chooser.getSelectedFile().getPath();
379 askFrame.setVisible(false);
380 askFrame.dispose();
381 try {
382 BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
383 out.write("r: " + Global.rCommand + "\n");
384 out.close();
385 }
386 catch (IOException exception) {
387 logArea.append("Cannot write configuration file!\n");
388 }
389 }
390 this.checkConfiguration();
391 }
392 // Format type
393 else if (e.getSource() == formatTypes) {
394 fileFormats.removeAllItems();
395 Vector < String > selectedFormats = Global.formats.getFormats((String) formatTypes.getSelectedItem()).getFormats();
396 for (int i = 0; i < selectedFormats.size(); i++) {
397 fileFormats.addItem(selectedFormats.get(i));
398 }
399 }
400 // Main file chooser
401 else if (e.getSource() == openButton) {
402 JFileChooser chooser = new JFileChooser();
403 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
404 String fileName = chooser.getSelectedFile().getPath();
405 Global.fileNames.addElement(fileName);
406 Global.files.addFile(fileName, (String) formatTypes.getSelectedItem(), (String) fileFormats.getSelectedItem());
407 }
408 }
409 // Other file choosers
410 else if (Global.otherFilesChooser.containsKey(e.getSource())) {
411 JTextField textField = Global.otherFilesChooser.get(e.getSource());
412 JFileChooser chooser = new JFileChooser();
413 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
414 textField.setText(chooser.getSelectedFile().getPath());
415 }
416 }
417 // Other directories choosers
418 else if (Global.otherDirectoriesChooser.containsKey(e.getSource())) {
419 JTextField textField = Global.otherDirectoriesChooser.get(e.getSource());
420 JFileChooser chooser = new JFileChooser();
421 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
422 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
423 textField.setText(chooser.getSelectedFile().getPath());
424 }
425 }
426 else if (Global.otherFileConcatenationChooser.containsKey(e.getSource())) {
427 JTextField textField = Global.otherDirectoriesChooser.get(e.getSource());
428 JFileChooser chooser = new JFileChooser();
429 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
430 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
431 String text = textField.getText();
432 if ((text == null) || ("".equals(text))) {
433 textField.setText(chooser.getSelectedFile().getPath());
434 }
435 else {
436 textField.setText(text + "," + chooser.getSelectedFile().getPath());
437 }
438 }
439 }
440 // Programs
441 else {
442 currentProgram = callingProgram.get(e.getSource());
443 String comment = currentProgram.checkValues();
444 if (comment != null) {
445 logArea.append(comment);
446 return;
447 }
448 LinkedList <String> command = currentProgram.getCommand();
449 ProgramLauncher launcher = new ProgramLauncher(command, logArea, messageField, progressBar, etaField);
450 launcher.execute();
451 Vector < File > outputFiles = currentProgram.getOutputFiles();
452 for (int i = 0; i < outputFiles.size(); i++) {
453 File file = outputFiles.get(i);
454 if (file.getFormatType().compareToIgnoreCase("other") != 0) {
455 Global.fileNames.addElement(file.getName());
456 Global.files.addFile(file);
457 }
458 }
459 currentProgram = null;
460 }
461 }
462
463
464 private static void createAndShowGUI() {
465 // Create and set up the window.
466 JFrame mainFrame = new JFrame("S-Mart");
467 mainFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
468
469 //Create and set up the content pane.
470 JComponent newContentPane = new Smart();
471 newContentPane.setOpaque(true);
472 mainFrame.setContentPane(newContentPane);
473
474 // Display the window.
475 mainFrame.pack();
476 mainFrame.setVisible(true);
477 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
478 mainFrame.setBounds(0, 0, screenSize.width, screenSize.height);
479 }
480
481
482 public static void main(String[] args) {
483 javax.swing.SwingUtilities.invokeLater(new Runnable() {
484 public void run() {
485 createAndShowGUI();
486 }
487 });
488 }
489 }