s_mart: smart_toolShed/SMART/Java/Sav/Smart.java annotate

annotate smart_toolShed/SMART/Java/Sav/Smart.java @ 1:30c5431d8ce4

Uploaded

author	yufei-luo
date	Thu, 17 Jan 2013 11:01:51 -0500
parents	e0f8dcca02ed
children

rev	line source
0 e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	1 /**
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	2 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	3 * Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	4 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	5 * This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	6 * abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	7 * modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	8 * license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	9 * "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	10 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	11 * As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	12 * modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	13 * with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	14 * economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	15 * liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	16 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	17 * In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	18 * with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	19 * software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	20 * that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	21 * therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	22 * professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	23 * encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	24 * requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	25 * data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	26 * same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	27 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	28 * The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	29 * knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	30 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	31 */
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	32 import java.util.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	33 import java.awt.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	34 import java.awt.event.ActionEvent;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	35 import java.awt.event.ActionListener;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	36 import java.io.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	37 import javax.swing.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	38 import javax.swing.filechooser.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	39 import javax.swing.border.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	40 import javax.swing.SwingUtilities;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	41
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	42
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	43 public class Smart extends JPanel implements ActionListener {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	44
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	45 String version = "1.0.2";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	46
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	47 JFrame mainFrame;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	48 JButton openButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	49 JButton comparisonGoButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	50
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	51 JComboBox formatTypes;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	52 JComboBox fileFormats;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	53 String[] emptyFormats = {"Choose a type first..."};
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	54
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	55 JFrame askFrame;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	56 JButton pythonButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	57 JButton mySqlButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	58 JButton rButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	59
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	60 HashMap <JButton, Program> callingProgram;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	61
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	62 // comparison
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	63 JList comparisonFile1List;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	64 JList comparisonFile2List;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	65 JTextField comparisonOutputTextField;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	66 JTextField comparisonFiveQueryExtensionTextField;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	67 JCheckBox comparisonColinearCheckBox;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	68 JCheckBox comparisonAntisenseCheckBox;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	69 JCheckBox comparisonInvertCheckBox;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	70
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	71 JList fileList;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	72 JTextArea logArea;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	73
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	74 // progress bar
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	75 JLabel messageField;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	76 JProgressBar progressBar;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	77 JLabel etaField;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	78
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	79 // process
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	80 Program currentProgram;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	81 Process process;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	82 javax.swing.Timer processTimer;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	83
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	84
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	85 int previousStatus;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	86
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	87 public Smart() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	88 super(new BorderLayout());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	89
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	90 callingProgram = new HashMap <JButton, Program> ();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	91
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	92 previousStatus = -1;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	93
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	94 processTimer = new javax.swing.Timer(1000, this);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	95 processTimer.stop();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	96
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	97 // Ask frame buttons
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	98 pythonButton = new JButton("find...");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	99 mySqlButton = new JButton("find...");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	100 rButton = new JButton("find...");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	101
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	102 // Get available formats
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	103 FormatsReader formatReader = new FormatsReader(Global.smartFormatsFileName);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	104 if (! formatReader.read()) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	105 System.out.println("Something was wrong while reading file format...");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	106 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	107
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	108 // Get screen size
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	109 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	110
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	111 // Log
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	112 logArea = new JTextArea(512, Global.logAreaSize);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	113 logArea.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.22)));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	114 logArea.setFont(new Font("Monospaced", logArea.getFont().getStyle(), logArea.getFont().getSize()));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	115 JScrollPane logScroll = new JScrollPane(logArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	116 TitledBorder logBorder = BorderFactory.createTitledBorder("Log");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	117 logScroll.setBorder(logBorder);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	118 logArea.append("Using S-MART " + version + "\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	119
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	120 GridLayout horizontalLayout = new GridLayout(1, 0);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	121
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	122 // check configuration
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	123 this.readConfigurationFile();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	124 this.checkConfiguration();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	125
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	126 // Tabs
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	127 JTabbedPane tabbedPane = new JTabbedPane();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	128 tabbedPane.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.75)));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	129
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	130 // File panel
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	131 JPanel filePanel = new JPanel(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	132 filePanel.setLayout(new FlowLayout());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	133 tabbedPane.add("Files", filePanel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	134
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	135 // Format sub-panel
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	136 JPanel formatComboPanel = new JPanel(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	137 JPanel formatPanel = new JPanel(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	138 Vector<String> formatTypesString = Global.formats.getFormatTypes();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	139 formatPanel.setLayout(horizontalLayout);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	140 formatTypesString.insertElementAt("Choose the format type", 0);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	141 JLabel formatLabel = new JLabel("Format");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	142 formatTypes = new JComboBox(formatTypesString);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	143 fileFormats = new JComboBox(emptyFormats);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	144 formatLabel.setLabelFor(fileFormats);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	145 formatTypes.addActionListener(this);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	146 formatComboPanel.add(formatTypes);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	147 formatComboPanel.add(fileFormats);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	148
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	149 formatPanel.add(formatLabel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	150 formatPanel.add(formatComboPanel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	151
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	152 // File chooser sub-panel
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	153 JPanel fileChooserPanel = new JPanel(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	154 fileChooserPanel.setLayout(horizontalLayout);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	155 JLabel fileLabel = new JLabel("File");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	156 openButton = new JButton("Open a File...");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	157 openButton.addActionListener(this);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	158
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	159 fileChooserPanel.add(fileLabel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	160 fileChooserPanel.add(openButton);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	161
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	162 // File list sub-panel
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	163 JPanel existingFilesPanel = new JPanel(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	164 existingFilesPanel.setLayout(horizontalLayout);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	165 existingFilesPanel.setMinimumSize(new Dimension(10000, 10000));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	166 JLabel existingFilesLabel = new JLabel("Existing files");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	167 Box fileListBox = Box.createHorizontalBox();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	168 fileListBox.add(Box.createRigidArea(new Dimension(0, 100)));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	169 JList fileList = new JList(Global.fileNames);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	170 fileList.setLayoutOrientation(JList.HORIZONTAL_WRAP);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	171 fileList.setVisibleRowCount(4);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	172 JScrollPane listScroller = new JScrollPane(fileList);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	173 fileListBox.add(listScroller);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	174
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	175 existingFilesPanel.add(existingFilesLabel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	176 existingFilesPanel.add(fileListBox);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	177
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	178 // File panel layout
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	179 Box box = Box.createVerticalBox();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	180 box.add(formatPanel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	181 box.add(fileChooserPanel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	182 box.add(existingFilesPanel);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	183 filePanel.add(box);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	184
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	185 // Program panels
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	186 TreeMap < String, JTabbedPane > panels = new TreeMap < String, JTabbedPane >();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	187 PythonProgramFinder programFinder = new PythonProgramFinder("Python");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	188 String comments = programFinder.findPrograms();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	189 if (comments != null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	190 logArea.append(comments);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	191 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	192 for (int i = 0; i < programFinder.getPrograms().size(); i++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	193 Program program = programFinder.getPrograms().get(i);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	194 JPanel programPanel = program.getPanel();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	195 String section = program.getSection();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	196 JTabbedPane sectionPane = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	197 if (panels.containsKey(section)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	198 sectionPane = panels.get(section);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	199 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	200 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	201 sectionPane = new JTabbedPane();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	202 tabbedPane.addTab(section, sectionPane);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	203 panels.put(section, sectionPane);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	204 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	205
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	206 JScrollPane programScroll = new JScrollPane(programPanel, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	207 sectionPane.addTab(program.getName(), programScroll);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	208
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	209 JButton button = program.getButton();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	210 button.addActionListener(this);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	211 callingProgram.put(button, program);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	212 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	213
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	214 // Progress bar
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	215 JPanel progressPanel = new JPanel(new GridLayout(1, 0), false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	216 progressPanel.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.02)));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	217 messageField = new JLabel();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	218 progressBar = new JProgressBar(0, 100);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	219 etaField = new JLabel();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	220 messageField.setHorizontalAlignment(JLabel.LEFT);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	221 progressBar.setValue(0);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	222 etaField.setHorizontalAlignment(JLabel.RIGHT);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	223 progressBar.setStringPainted(true);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	224 progressPanel.add(messageField);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	225 progressPanel.add(progressBar);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	226 progressPanel.add(etaField);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	227
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	228 add(tabbedPane, BorderLayout.PAGE_START);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	229 add(logScroll, BorderLayout.CENTER);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	230 add(progressPanel, BorderLayout.PAGE_END);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	231 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	232
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	233
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	234 public boolean checkConfiguration() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	235 int status = this.testConfiguration();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	236
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	237 if (status == previousStatus) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	238 logArea.append("S-MART does not seem to work properly... Tried to manage it by myself, unsuccessfully... Check documentation for further explanation...\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	239 return false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	240 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	241
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	242 switch (status) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	243 case 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	244 return true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	245 case 1:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	246 logArea.append("S-MART does not seem to work properly... Check documentation for further explanation...\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	247 break;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	248 case 3:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	249 this.askWhereIsProgram("python");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	250 break;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	251 case 4:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	252 break;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	253 case 5:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	254 this.askWhereIsProgram("mySQL");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	255 break;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	256 case 6:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	257 this.askWhereIsProgram("R");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	258 break;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	259 case 7:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	260 logArea.append("Please install 'ColorBrewer' R package...\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	261 break;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	262 default:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	263 logArea.append("Weird configuration test status: " + status + "...\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	264 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	265 previousStatus = status;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	266 return true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	267 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	268
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	269
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	270 public int testConfiguration() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	271 String[] command = {Global.pythonCommand, "Python" + java.io.File.separator + "testInstall.py"};
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	272 ProgramLauncher launcher = new ProgramLauncher(command, logArea, messageField, progressBar, etaField);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	273 String line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	274 launcher.execute();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	275 (new Exception("hello")).printStackTrace();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	276 return launcher.getExitValue();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	277 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	278
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	279
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	280 public void readConfigurationFile() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	281 java.io.File file = new java.io.File(Global.smartConfFileName);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	282 String line = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	283
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	284 if (! file.exists()) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	285 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	286 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	287
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	288 try {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	289 BufferedReader reader = new BufferedReader(new FileReader(file));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	290
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	291 while ((line = reader.readLine()) != null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	292 line = line.trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	293 if (line.startsWith("python:")) Global.pythonCommand = line.substring("python:".length()).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	294 else if (line.startsWith("mysql:")) Global.mysqlCommand = line.substring("mysql:".length()).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	295 else if (line.startsWith("r:")) Global.rCommand = line.substring("r:".length()).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	296 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	297 reader.close();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	298 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	299 catch (FileNotFoundException e) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	300 logArea.append("Configuration file is empty: " + e.getMessage() + "!\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	301 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	302 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	303 catch (IOException e) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	304 logArea.append("Weird with configuration file: " + e.getMessage() + "!\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	305 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	306 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	307 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	308
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	309
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	310 public void askWhereIsProgram(String program) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	311 askFrame = new JFrame("Where is " + program + "?");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	312 askFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	313 JLabel label = new JLabel("Where is your " + program + " (or " + program + ".exe) file?");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	314 JButton button = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	315 if ("python".equals(program)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	316 button = pythonButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	317 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	318 else if ("mySQL".equals(program)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	319 button = mySqlButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	320 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	321 else if ("R".equals(program)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	322 button = rButton;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	323 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	324 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	325 logArea.append("Problem with the button!\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	326 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	327 askFrame.getContentPane().add(label, BorderLayout.WEST);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	328 askFrame.getContentPane().add(button, BorderLayout.EAST);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	329 button.addActionListener(this);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	330 askFrame.pack();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	331 askFrame.setVisible(true);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	332 askFrame.setAlwaysOnTop(true);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	333 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	334
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	335
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	336 public void actionPerformed(ActionEvent e) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	337
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	338 // Python command chooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	339 if (e.getSource() == pythonButton) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	340 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	341 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	342 Global.pythonCommand = chooser.getSelectedFile().getPath();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	343 askFrame.setVisible(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	344 askFrame.dispose();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	345 try {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	346 BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	347 out.write("python: " + Global.pythonCommand + "\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	348 out.close();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	349 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	350 catch (IOException exception) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	351 logArea.append("Cannot write configuration file!\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	352 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	353 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	354 this.checkConfiguration();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	355 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	356 // MySQL command chooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	357 else if (e.getSource() == mySqlButton) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	358 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	359 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	360 Global.mysqlCommand = chooser.getSelectedFile().getPath();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	361 askFrame.setVisible(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	362 askFrame.dispose();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	363 try {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	364 BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	365 out.write("mysql: " + Global.mysqlCommand + "\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	366 out.close();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	367 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	368 catch (IOException exception) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	369 logArea.append("Cannot write configuration file!\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	370 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	371 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	372 this.checkConfiguration();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	373 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	374 // R command chooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	375 else if (e.getSource() == rButton) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	376 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	377 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	378 Global.rCommand = chooser.getSelectedFile().getPath();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	379 askFrame.setVisible(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	380 askFrame.dispose();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	381 try {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	382 BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	383 out.write("r: " + Global.rCommand + "\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	384 out.close();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	385 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	386 catch (IOException exception) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	387 logArea.append("Cannot write configuration file!\n");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	388 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	389 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	390 this.checkConfiguration();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	391 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	392 // Format type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	393 else if (e.getSource() == formatTypes) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	394 fileFormats.removeAllItems();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	395 Vector < String > selectedFormats = Global.formats.getFormats((String) formatTypes.getSelectedItem()).getFormats();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	396 for (int i = 0; i < selectedFormats.size(); i++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	397 fileFormats.addItem(selectedFormats.get(i));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	398 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	399 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	400 // Main file chooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	401 else if (e.getSource() == openButton) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	402 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	403 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	404 String fileName = chooser.getSelectedFile().getPath();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	405 Global.fileNames.addElement(fileName);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	406 Global.files.addFile(fileName, (String) formatTypes.getSelectedItem(), (String) fileFormats.getSelectedItem());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	407 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	408 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	409 // Other file choosers
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	410 else if (Global.otherFilesChooser.containsKey(e.getSource())) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	411 JTextField textField = Global.otherFilesChooser.get(e.getSource());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	412 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	413 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	414 textField.setText(chooser.getSelectedFile().getPath());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	415 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	416 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	417 // Other directories choosers
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	418 else if (Global.otherDirectoriesChooser.containsKey(e.getSource())) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	419 JTextField textField = Global.otherDirectoriesChooser.get(e.getSource());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	420 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	421 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	422 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	423 textField.setText(chooser.getSelectedFile().getPath());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	424 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	425 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	426 else if (Global.otherFileConcatenationChooser.containsKey(e.getSource())) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	427 JTextField textField = Global.otherDirectoriesChooser.get(e.getSource());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	428 JFileChooser chooser = new JFileChooser();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	429 chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	430 if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	431 String text = textField.getText();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	432 if ((text == null) \|\| ("".equals(text))) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	433 textField.setText(chooser.getSelectedFile().getPath());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	434 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	435 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	436 textField.setText(text + "," + chooser.getSelectedFile().getPath());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	437 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	438 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	439 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	440 // Programs
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	441 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	442 currentProgram = callingProgram.get(e.getSource());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	443 String comment = currentProgram.checkValues();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	444 if (comment != null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	445 logArea.append(comment);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	446 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	447 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	448 LinkedList <String> command = currentProgram.getCommand();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	449 ProgramLauncher launcher = new ProgramLauncher(command, logArea, messageField, progressBar, etaField);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	450 launcher.execute();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	451 Vector < File > outputFiles = currentProgram.getOutputFiles();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	452 for (int i = 0; i < outputFiles.size(); i++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	453 File file = outputFiles.get(i);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	454 if (file.getFormatType().compareToIgnoreCase("other") != 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	455 Global.fileNames.addElement(file.getName());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	456 Global.files.addFile(file);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	457 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	458 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	459 currentProgram = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	460 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	461 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	462
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	463
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	464 private static void createAndShowGUI() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	465 // Create and set up the window.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	466 JFrame mainFrame = new JFrame("S-Mart");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	467 mainFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	468
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	469 //Create and set up the content pane.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	470 JComponent newContentPane = new Smart();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	471 newContentPane.setOpaque(true);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	472 mainFrame.setContentPane(newContentPane);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	473
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	474 // Display the window.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	475 mainFrame.pack();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	476 mainFrame.setVisible(true);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	477 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	478 mainFrame.setBounds(0, 0, screenSize.width, screenSize.height);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	479 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	480
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	481
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	482 public static void main(String[] args) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	483 javax.swing.SwingUtilities.invokeLater(new Runnable() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	484 public void run() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	485 createAndShowGUI();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	486 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	487 });
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	488 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	489 }

Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Sav/Smart.java @ 1:30c5431d8ce4