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