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1 package edu.unc.genomics;
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2
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3 import java.awt.BorderLayout;
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4 import java.awt.Color;
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5 import java.awt.Component;
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6 import java.awt.Container;
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7 import java.awt.Dimension;
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8 import java.awt.Font;
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9
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10 import javax.swing.JFrame;
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11 import javax.swing.JPanel;
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12
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13 import javax.swing.BorderFactory;
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14 import javax.swing.JComponent;
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15 import javax.swing.JLabel;
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16 import javax.swing.JList;
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17 import javax.swing.JMenuBar;
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18 import javax.swing.JMenu;
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19 import javax.swing.JMenuItem;
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20 import javax.swing.JButton;
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21 import javax.swing.JOptionPane;
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22 import javax.swing.JPopupMenu;
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23 import javax.swing.JScrollPane;
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24 import javax.swing.SwingConstants;
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25
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26 import javax.swing.JProgressBar;
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27 import javax.swing.JSplitPane;
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28 import javax.swing.BoxLayout;
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29 import javax.swing.JTabbedPane;
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30 import javax.swing.JTextPane;
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31
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32 import javax.swing.event.TreeSelectionListener;
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33 import javax.swing.event.TreeSelectionEvent;
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34 import javax.xml.parsers.ParserConfigurationException;
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35
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36 import org.apache.log4j.Logger;
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37 import org.simplericity.macify.eawt.Application;
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38 import org.simplericity.macify.eawt.ApplicationEvent;
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39 import org.simplericity.macify.eawt.ApplicationListener;
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40 import org.simplericity.macify.eawt.DefaultApplication;
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41 import org.xml.sax.SAXException;
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42
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43 import com.beust.jcommander.JCommander;
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44
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45 import java.awt.event.ActionListener;
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46 import java.awt.event.ActionEvent;
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47 import java.io.IOException;
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48
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49 /**
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50 * The main ToolRunner window
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51 * and controller for creating, running, and managing Jobs
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52 *
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53 * @author timpalpant
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54 *
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55 */
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56 public class ToolRunnerFrame extends JFrame implements ApplicationListener {
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57
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58 private static final long serialVersionUID = 6454774196137357898L;
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59 private static final Logger log = Logger.getLogger(ToolRunnerFrame.class);
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60
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61 private final Application application = new DefaultApplication();
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62
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63 private final JPanel contentPane = new JPanel();
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64 private final JSplitPane splitPane = new JSplitPane();
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65 private final JPanel mainPane = new JPanel();
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66 private final JProgressBar progressBar = new JProgressBar();
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67 private final JTabbedPane tabbedPane = new JTabbedPane(SwingConstants.TOP);
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68 private final JobConfigPanel configurationPanel = new JobConfigPanel();
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69 private final JTextPane helpTextPanel = new JTextPane();
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70 private final ToolsTree toolsTree = new ToolsTree();
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71
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72 private final JobQueue queue = new JobQueue();
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73 private final JobQueueManager queueManager = new JobQueueManager(queue);
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74 private final JList<SubmittedJob> queueList = new JList<>(queue);
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75
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76 /**
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77 * Create the frame.
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78 */
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79 public ToolRunnerFrame() {
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80 //application.addPreferencesMenuItem();
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81 //application.setEnabledPreferencesMenu(true);
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82 application.addApplicationListener(this);
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83
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84 // set OS X-specific properties
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85 if (application.isMac()) {
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86 setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
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87 //toolsTree.putClientProperty("Quaqua.Tree.style", "sourceList");
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88 } else {
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89 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
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90 }
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91 setTitle("Genomics Toolkit Tool Runner");
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92 setBounds(100, 100, 1000, 600);
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93
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94 contentPane.setBorder(BorderFactory.createEmptyBorder());
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95 contentPane.setLayout(new BorderLayout(0, 0));
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96 setContentPane(contentPane);
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97
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98 initializeChildren();
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99 initializeMenuBar();
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100 }
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101
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102 private void initializeChildren() {
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103 splitPane.setBorder(BorderFactory.createEmptyBorder());
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104 contentPane.add(splitPane, BorderLayout.CENTER);
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105
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106 initializeQueuePanel();
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107 initializeToolsTree();
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108
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109 mainPane.setLayout(new BorderLayout(0, 0));
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110 mainPane.setBorder(BorderFactory.createLineBorder(Color.LIGHT_GRAY));
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111 mainPane.add(tabbedPane, BorderLayout.CENTER);
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112
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113 JPanel runPanel = new JPanel();
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114 runPanel.setBorder(BorderFactory.createEmptyBorder(0, 5, 0, 0));
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115 runPanel.setLayout(new BoxLayout(runPanel, BoxLayout.X_AXIS));
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116 runPanel.add(progressBar);
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117 JButton btnRun = new JButton("Run");
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118 btnRun.addActionListener(new ActionListener() {
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119 public void actionPerformed(ActionEvent e) {
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120 addJobToQueue();
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121 }
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122 });
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123 runPanel.add(btnRun);
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124 mainPane.add(runPanel, BorderLayout.SOUTH);
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125 splitPane.setRightComponent(mainPane);
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126
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127 initializeConfigurationPanel();
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128 initializeHelpPanel();
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129 }
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130
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131 private void initializeMenuBar() {
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132 JMenuBar menuBar = new JMenuBar();
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133 setJMenuBar(menuBar);
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134
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135 JMenu mnFileMenu = new JMenu("File");
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136 menuBar.add(mnFileMenu);
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137
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138 JMenuItem mntmAssemblyManager = new JMenuItem("Assembly manager");
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139 mntmAssemblyManager.addActionListener(new ActionListener() {
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140 public void actionPerformed(ActionEvent e) {
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141 JMenuItem menuItem = (JMenuItem) e.getSource();
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142 JPopupMenu popupMenu = (JPopupMenu) menuItem.getParent();
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143 Component invoker = popupMenu.getInvoker(); //this is the JMenu (in my code)
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144 JComponent invokerAsJComponent = (JComponent) invoker;
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145 Container topLevel = invokerAsJComponent.getTopLevelAncestor();
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146 AssemblyManagerDialog dialog = new AssemblyManagerDialog((JFrame) topLevel);
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147 //dialog.getRootPane().putClientProperty("Window.style", "small");
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148 dialog.setVisible(true);
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149 }
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150 });
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151 mnFileMenu.add(mntmAssemblyManager);
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152
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153 JMenu mnHelpMenu = new JMenu("Help");
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154 menuBar.add(mnHelpMenu);
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155
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156 JMenuItem mntmHelpContents = new JMenuItem("Help Contents");
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157 mnHelpMenu.add(mntmHelpContents);
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158
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159 if (!application.isMac()) {
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160 JMenuItem mntmAbout = new JMenuItem("About");
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161 mnHelpMenu.add(mntmAbout);
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162 mnHelpMenu.addActionListener(new ActionListener() {
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163 public void actionPerformed(ActionEvent e) {
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164 handleAbout(null);
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165 }
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166 });
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167 }
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168 }
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169
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170 private void initializeQueuePanel() {
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171 JPanel queuePanel = new JPanel();
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172 queuePanel.setLayout(new BoxLayout(queuePanel, BoxLayout.PAGE_AXIS));
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173 queuePanel.setBorder(BorderFactory.createEmptyBorder());
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174 contentPane.add(queuePanel, BorderLayout.EAST);
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175
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176 JLabel queueLabel = new JLabel("Job Queue");
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177 queueLabel.setBorder(BorderFactory.createEmptyBorder(5, 0, 5, 0));
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178 queueLabel.setAlignmentX(JLabel.CENTER_ALIGNMENT);
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179 queuePanel.add(queueLabel);
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180
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181 queueList.setBackground(contentPane.getBackground());
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182 queueList.setCellRenderer(new JobQueueCellRenderer());
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183 JScrollPane queueListScrollPane = new JScrollPane(queueList);
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184 queueListScrollPane.setBorder(BorderFactory.createEmptyBorder());
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185 queueListScrollPane.setBackground(contentPane.getBackground());
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186 queueListScrollPane.setPreferredSize(new Dimension(200, Integer.MAX_VALUE));
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187 queuePanel.add(queueListScrollPane);
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188 }
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189
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190 private void initializeConfigurationPanel() {
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191 JScrollPane configScrollPane = new JScrollPane(configurationPanel);
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192 configScrollPane.setBorder(BorderFactory.createEmptyBorder());
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193 tabbedPane.addTab("Tool Configuration", null, configScrollPane, "Configure tool");
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194 }
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195
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196 private void initializeHelpPanel() {
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197 JPanel helpPanel = new JPanel();
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198 tabbedPane.addTab("Help", null, helpPanel, null);
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199 helpPanel.setLayout(new BorderLayout(0, 0));
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200
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201 helpTextPanel.setEditable(false);
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202 helpTextPanel.setBackground(tabbedPane.getBackground());
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203 Font mono = new Font("Monospaced", helpTextPanel.getFont().getStyle(), helpTextPanel.getFont().getSize());
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204 helpTextPanel.setFont(mono);
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205 JScrollPane helpScrollPane = new JScrollPane(helpTextPanel);
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206 helpScrollPane.setBorder(BorderFactory.createEmptyBorder());
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207 helpPanel.add(helpScrollPane);
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208 }
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209
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210 private void initializeToolsTree() {
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211 try {
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212 ToolsTreeModel model = ToolsTreeModel.loadDefaultConfig();
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213 toolsTree.setModel(model);
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214 } catch (ParserConfigurationException | SAXException | IOException e1) {
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215 log.error("Error loading tool configuration file");
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216 e1.printStackTrace();
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217 System.exit(-1);
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218 } catch (ClassNotFoundException e) {
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219 log.error("Error loading tool: " + e.getMessage());
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220 e.printStackTrace();
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221 System.exit(-1);
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222 }
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223
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224 toolsTree.addTreeSelectionListener(new TreeSelectionListener() {
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225 public void valueChanged(TreeSelectionEvent e) {
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226 changeTool();
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227 }
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228 });
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229
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230 JScrollPane toolsTreeScrollPane = new JScrollPane(toolsTree);
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231 toolsTreeScrollPane.setBorder(BorderFactory.createMatteBorder(0, 0, 0, 1, Color.LIGHT_GRAY));
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232 splitPane.setLeftComponent(toolsTreeScrollPane);
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233 }
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234
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235 /**
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236 * Change the configuration panel to the currently selected tool
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237 * to configure a new Job
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238 */
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239 private void changeTool() {
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240 // Returns the last path element of the selection.
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241 Object node = toolsTree.getLastSelectedPathComponent();
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242 // Nothing is selected
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243 if (node == null) {
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244 return;
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245 }
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246
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247 if (node instanceof ToolsTreeNode) {
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248 ToolsTreeNode toolNode = (ToolsTreeNode) node;
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249 try {
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250 Class<? extends CommandLineTool> tool = toolNode.getClazz();
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251
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252 // Set up the configuration panel to configure this tool
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253 Job job = new Job(tool);
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254 configurationPanel.setJob(job);
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255 // Set the help text to the usage
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256 helpTextPanel.setText(job.getUsageText());
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257 } catch (InstantiationException | IllegalAccessException e) {
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258 log.error("Error initializing Job");
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259 e.printStackTrace();
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260 JOptionPane.showMessageDialog(this, "Error initializing job", "Job Initialization Error", JOptionPane.ERROR_MESSAGE);
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261 }
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262
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263 }
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264 }
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265
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266 private void addJobToQueue() {
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267 Job currentJob = configurationPanel.getJob();
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268 if (currentJob == null) return;
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269
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270 // Validate the required parameters
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271 log.info("Validating parameters for tool");
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272 if (!currentJob.validateArguments()) {
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273 configurationPanel.highlightInvalidArguments();
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274 return;
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275 }
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276
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277 // Add the job to the queue
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278 try {
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279 queueManager.submitJob(currentJob);
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280 configurationPanel.setJob(null);
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281 } catch (JobException e) {
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282 log.error("Error adding Job to queue");
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283 e.printStackTrace();
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284 JOptionPane.showMessageDialog(this, "Error adding job to queue", "Job Queue Error", JOptionPane.ERROR_MESSAGE);
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285 }
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286 }
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287
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288 public void handleAbout(ApplicationEvent event) {
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289 JOptionPane.showMessageDialog(this, "Java Genomics Toolkit v1.0");
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290 if (event != null) {
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291 event.setHandled(true);
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292 }
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293 }
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294
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295 public void handleOpenApplication(ApplicationEvent event) {
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296 // Application was opened
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297 }
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298
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299 public void handleOpenFile(ApplicationEvent event) {
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300 //JOptionPane.showMessageDialog(frmToolRunner, "OS X told us to open " + event.getFilename());
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301 }
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302
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303 public void handlePreferences(ApplicationEvent event) {
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304 //JOptionPane.showMessageDialog(frmToolRunner, "No preferences available");
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305 }
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306
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307 public void handlePrintFile(ApplicationEvent event) {
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308 //JOptionPane.showMessageDialog(frmToolRunner, "OS X told us to print " + event.getFilename());
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309 }
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310
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311 public void handleQuit(ApplicationEvent event) {
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312 boolean confirm = true;
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313 if (queueManager.isRunning()) {
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314 int result = JOptionPane.showConfirmDialog(this, "Jobs are currently running. Are you sure you want to quit?", "Confirm Quit", JOptionPane.OK_CANCEL_OPTION);
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315 confirm = (result == JOptionPane.OK_OPTION);
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316 }
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317
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318 if (confirm) {
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319 dispose();
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320 System.exit(0);
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321 }
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322 }
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323
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324 public void handleReOpenApplication(ApplicationEvent event) {
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325 //JOptionPane.showMessageDialog(frmToolRunner, "OS X told the application was reopened");
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326 setVisible(true);
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327 }
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328 }
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