--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Sav/Smart.java	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,489 @@
+/**
+ *
+ * Copyright INRA-URGI 2009-2010
+ * 
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "http://www.cecill.info".
+ * 
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ * 
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ * 
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+import java.util.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.*;
+import javax.swing.*;
+import javax.swing.filechooser.*;
+import javax.swing.border.*;
+import javax.swing.SwingUtilities;
+
+
+public class Smart extends JPanel implements ActionListener {
+
+  String version = "1.0.2";
+
+  JFrame mainFrame;
+  JButton openButton;
+  JButton comparisonGoButton;
+
+  JComboBox formatTypes;
+  JComboBox fileFormats;
+  String[]  emptyFormats = {"Choose a type first..."};
+
+  JFrame  askFrame;
+  JButton pythonButton;
+  JButton mySqlButton;
+  JButton rButton;
+
+  HashMap <JButton, Program> callingProgram;
+
+  // comparison
+  JList comparisonFile1List;
+  JList comparisonFile2List;
+  JTextField comparisonOutputTextField;
+  JTextField comparisonFiveQueryExtensionTextField;
+  JCheckBox comparisonColinearCheckBox;
+  JCheckBox comparisonAntisenseCheckBox;
+  JCheckBox comparisonInvertCheckBox;
+
+  JList        fileList;
+  JTextArea    logArea;
+
+  // progress bar
+  JLabel       messageField;
+  JProgressBar progressBar;
+  JLabel       etaField;
+
+  // process
+  Program           currentProgram;
+  Process           process;
+  javax.swing.Timer processTimer;
+
+
+  int previousStatus;
+
+  public Smart() {
+    super(new BorderLayout());
+
+    callingProgram = new HashMap <JButton, Program> ();
+
+    previousStatus = -1;
+
+    processTimer = new javax.swing.Timer(1000, this);
+    processTimer.stop();
+
+    // Ask frame buttons
+    pythonButton = new JButton("find...");
+    mySqlButton  = new JButton("find...");
+    rButton      = new JButton("find...");
+
+    // Get available formats
+    FormatsReader formatReader = new FormatsReader(Global.smartFormatsFileName);
+    if (! formatReader.read()) {
+      System.out.println("Something was wrong while reading file format...");
+    }
+
+    // Get screen size
+    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+
+    // Log
+    logArea = new JTextArea(512, Global.logAreaSize);
+    logArea.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.22)));
+    logArea.setFont(new Font("Monospaced", logArea.getFont().getStyle(), logArea.getFont().getSize()));
+    JScrollPane logScroll  = new JScrollPane(logArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+    TitledBorder logBorder = BorderFactory.createTitledBorder("Log");
+    logScroll.setBorder(logBorder);
+    logArea.append("Using S-MART " + version + "\n");
+
+    GridLayout horizontalLayout = new GridLayout(1, 0);
+
+    // check configuration
+    this.readConfigurationFile();
+    this.checkConfiguration();
+
+    // Tabs
+    JTabbedPane tabbedPane = new JTabbedPane();
+    tabbedPane.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.75)));
+
+    // File panel
+    JPanel filePanel = new JPanel(false);
+    filePanel.setLayout(new FlowLayout());
+    tabbedPane.add("Files", filePanel);
+
+    // Format sub-panel
+    JPanel         formatComboPanel  = new JPanel(false);
+    JPanel         formatPanel       = new JPanel(false);
+    Vector<String> formatTypesString = Global.formats.getFormatTypes();
+    formatPanel.setLayout(horizontalLayout);
+    formatTypesString.insertElementAt("Choose the format type", 0);
+    JLabel formatLabel = new JLabel("Format");
+    formatTypes        = new JComboBox(formatTypesString);
+    fileFormats        = new JComboBox(emptyFormats);
+    formatLabel.setLabelFor(fileFormats);
+    formatTypes.addActionListener(this);
+    formatComboPanel.add(formatTypes);
+    formatComboPanel.add(fileFormats);
+
+    formatPanel.add(formatLabel);
+    formatPanel.add(formatComboPanel);
+
+    // File chooser sub-panel
+    JPanel fileChooserPanel = new JPanel(false);
+    fileChooserPanel.setLayout(horizontalLayout);
+    JLabel fileLabel = new JLabel("File");
+    openButton = new JButton("Open a File...");
+    openButton.addActionListener(this);
+
+    fileChooserPanel.add(fileLabel);
+    fileChooserPanel.add(openButton);
+
+    // File list sub-panel
+    JPanel existingFilesPanel = new JPanel(false);
+    existingFilesPanel.setLayout(horizontalLayout);
+    existingFilesPanel.setMinimumSize(new Dimension(10000, 10000));
+    JLabel existingFilesLabel = new JLabel("Existing files");
+    Box fileListBox = Box.createHorizontalBox();
+    fileListBox.add(Box.createRigidArea(new Dimension(0, 100)));
+    JList fileList = new JList(Global.fileNames);
+    fileList.setLayoutOrientation(JList.HORIZONTAL_WRAP);
+    fileList.setVisibleRowCount(4);
+    JScrollPane listScroller = new JScrollPane(fileList);
+    fileListBox.add(listScroller);
+
+    existingFilesPanel.add(existingFilesLabel);
+    existingFilesPanel.add(fileListBox);
+
+    // File panel layout
+    Box box = Box.createVerticalBox();
+    box.add(formatPanel);
+    box.add(fileChooserPanel);
+    box.add(existingFilesPanel);
+    filePanel.add(box);
+
+    // Program panels
+    TreeMap < String, JTabbedPane > panels = new TreeMap < String, JTabbedPane >();
+    PythonProgramFinder programFinder = new PythonProgramFinder("Python");
+    String comments = programFinder.findPrograms();
+    if (comments != null) {
+      logArea.append(comments);
+    }
+    for (int i = 0; i < programFinder.getPrograms().size(); i++) {
+      Program program         = programFinder.getPrograms().get(i);
+      JPanel programPanel     = program.getPanel();
+      String section          = program.getSection();
+      JTabbedPane sectionPane = null;
+      if (panels.containsKey(section)) {
+        sectionPane = panels.get(section);
+      }
+      else {
+        sectionPane = new JTabbedPane();
+        tabbedPane.addTab(section, sectionPane);
+        panels.put(section, sectionPane);
+      }
+
+      JScrollPane programScroll  = new JScrollPane(programPanel, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+      sectionPane.addTab(program.getName(), programScroll);
+
+      JButton button  = program.getButton();
+      button.addActionListener(this);
+      callingProgram.put(button, program);
+    }
+
+    // Progress bar
+    JPanel progressPanel = new JPanel(new GridLayout(1, 0), false);
+    progressPanel.setPreferredSize(new Dimension(screenSize.width, (int) (screenSize.height * 0.02)));
+    messageField = new JLabel();
+    progressBar  = new JProgressBar(0, 100);
+    etaField     = new JLabel();
+    messageField.setHorizontalAlignment(JLabel.LEFT);
+    progressBar.setValue(0);
+    etaField.setHorizontalAlignment(JLabel.RIGHT);
+    progressBar.setStringPainted(true);
+    progressPanel.add(messageField);
+    progressPanel.add(progressBar);
+    progressPanel.add(etaField);
+      
+    add(tabbedPane, BorderLayout.PAGE_START);
+    add(logScroll, BorderLayout.CENTER);
+    add(progressPanel, BorderLayout.PAGE_END);
+  }
+
+
+  public boolean checkConfiguration() {
+    int status = this.testConfiguration();
+  
+    if (status == previousStatus) {
+      logArea.append("S-MART does not seem to work properly... Tried to manage it by myself, unsuccessfully... Check documentation for further explanation...\n");
+      return false;
+    }
+
+    switch (status) {
+      case 0:
+        return true;
+      case 1:
+        logArea.append("S-MART does not seem to work properly... Check documentation for further explanation...\n");
+        break;
+      case 3:
+        this.askWhereIsProgram("python");
+        break;
+      case 4:
+        break;
+      case 5:
+        this.askWhereIsProgram("mySQL");
+        break;
+      case 6:
+        this.askWhereIsProgram("R");
+        break;
+      case 7:
+        logArea.append("Please install 'ColorBrewer' R package...\n");
+        break;
+      default:
+        logArea.append("Weird configuration test status: " + status + "...\n");
+    }
+    previousStatus = status;
+    return true;
+  }
+
+
+  public int testConfiguration() {
+    String[]        command  = {Global.pythonCommand, "Python" + java.io.File.separator + "testInstall.py"};
+    ProgramLauncher launcher = new ProgramLauncher(command, logArea, messageField, progressBar, etaField);
+    String          line;
+    launcher.execute();
+    (new Exception("hello")).printStackTrace();
+    return launcher.getExitValue();
+  }
+
+
+  public void readConfigurationFile() {
+    java.io.File   file      = new java.io.File(Global.smartConfFileName);
+    String         line      = null;
+
+    if (! file.exists()) {
+      return;
+    }
+
+    try {
+      BufferedReader reader = new BufferedReader(new FileReader(file));
+
+      while ((line = reader.readLine()) != null) {
+        line = line.trim();
+        if      (line.startsWith("python:")) Global.pythonCommand = line.substring("python:".length()).trim();
+        else if (line.startsWith("mysql:"))  Global.mysqlCommand  = line.substring("mysql:".length()).trim();
+        else if (line.startsWith("r:"))      Global.rCommand      = line.substring("r:".length()).trim();
+      }
+      reader.close();
+    }
+    catch (FileNotFoundException e) {
+      logArea.append("Configuration file is empty: " + e.getMessage() + "!\n");
+      return;
+    }
+    catch (IOException e) {
+      logArea.append("Weird with configuration file: " + e.getMessage() + "!\n");
+      return;
+    }
+  }
+
+
+  public void askWhereIsProgram(String program) {
+    askFrame = new JFrame("Where is " + program + "?");
+    askFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    JLabel label = new JLabel("Where is your " + program + " (or " + program + ".exe) file?");
+    JButton button = null;
+    if ("python".equals(program)) {
+      button = pythonButton;
+    }
+    else if ("mySQL".equals(program)) {
+      button = mySqlButton;
+    }
+    else if ("R".equals(program)) {
+      button = rButton;
+    }
+    else {
+      logArea.append("Problem with the button!\n");
+    }
+    askFrame.getContentPane().add(label, BorderLayout.WEST);
+    askFrame.getContentPane().add(button, BorderLayout.EAST);
+    button.addActionListener(this);
+    askFrame.pack();
+    askFrame.setVisible(true);
+    askFrame.setAlwaysOnTop(true);
+  }
+
+
+  public void actionPerformed(ActionEvent e) {
+
+    // Python command chooser
+    if (e.getSource() == pythonButton) {
+      JFileChooser chooser = new JFileChooser();
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        Global.pythonCommand = chooser.getSelectedFile().getPath();
+        askFrame.setVisible(false);
+        askFrame.dispose();
+        try {
+          BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
+          out.write("python: " + Global.pythonCommand + "\n");
+          out.close();
+        }
+        catch (IOException exception) {
+          logArea.append("Cannot write configuration file!\n");
+        }
+      }
+      this.checkConfiguration();
+    }
+    // MySQL command chooser
+    else if (e.getSource() == mySqlButton) {
+      JFileChooser chooser = new JFileChooser();
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        Global.mysqlCommand = chooser.getSelectedFile().getPath();
+        askFrame.setVisible(false);
+        askFrame.dispose();
+        try {
+          BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
+          out.write("mysql: " + Global.mysqlCommand + "\n");
+          out.close();
+        }
+        catch (IOException exception) {
+          logArea.append("Cannot write configuration file!\n");
+        }
+      }
+      this.checkConfiguration();
+    }
+    // R command chooser
+    else if (e.getSource() == rButton) {
+      JFileChooser chooser = new JFileChooser();
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        Global.rCommand = chooser.getSelectedFile().getPath();
+        askFrame.setVisible(false);
+        askFrame.dispose();
+        try {
+          BufferedWriter out = new BufferedWriter(new FileWriter(Global.smartConfFileName, true));
+          out.write("r: " + Global.rCommand + "\n");
+          out.close();
+        }
+        catch (IOException exception) {
+          logArea.append("Cannot write configuration file!\n");
+        }
+      }
+      this.checkConfiguration();
+    }
+    // Format type
+    else if (e.getSource() == formatTypes) {
+      fileFormats.removeAllItems();
+      Vector < String > selectedFormats = Global.formats.getFormats((String) formatTypes.getSelectedItem()).getFormats();
+      for (int i = 0; i < selectedFormats.size(); i++) {
+        fileFormats.addItem(selectedFormats.get(i));
+      }
+    }
+    // Main file chooser
+    else if (e.getSource() == openButton) {
+      JFileChooser chooser = new JFileChooser();
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        String fileName = chooser.getSelectedFile().getPath();
+        Global.fileNames.addElement(fileName);
+        Global.files.addFile(fileName, (String) formatTypes.getSelectedItem(), (String) fileFormats.getSelectedItem());
+      }
+    }
+    // Other file choosers
+    else if (Global.otherFilesChooser.containsKey(e.getSource())) {
+      JTextField textField = Global.otherFilesChooser.get(e.getSource());
+      JFileChooser chooser = new JFileChooser();
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        textField.setText(chooser.getSelectedFile().getPath());
+      }
+    }
+    // Other directories choosers
+    else if (Global.otherDirectoriesChooser.containsKey(e.getSource())) {
+      JTextField textField = Global.otherDirectoriesChooser.get(e.getSource());
+      JFileChooser chooser = new JFileChooser();
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        textField.setText(chooser.getSelectedFile().getPath());
+      }
+    }
+    else if (Global.otherFileConcatenationChooser.containsKey(e.getSource())) {
+      JTextField textField = Global.otherDirectoriesChooser.get(e.getSource());
+      JFileChooser chooser = new JFileChooser();
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+      if (chooser.showOpenDialog(mainFrame) == JFileChooser.APPROVE_OPTION) {
+        String text = textField.getText();
+        if ((text == null) || ("".equals(text))) {
+          textField.setText(chooser.getSelectedFile().getPath());
+        }
+        else {
+          textField.setText(text + "," + chooser.getSelectedFile().getPath());
+        }
+      }
+    }
+    // Programs
+    else {
+      currentProgram = callingProgram.get(e.getSource());
+      String comment = currentProgram.checkValues();
+      if (comment != null) {
+        logArea.append(comment);
+        return;
+      }
+      LinkedList <String> command = currentProgram.getCommand();
+      ProgramLauncher launcher = new ProgramLauncher(command, logArea, messageField, progressBar, etaField);
+      launcher.execute();
+      Vector < File > outputFiles = currentProgram.getOutputFiles();
+      for (int i = 0; i < outputFiles.size(); i++) {
+        File file = outputFiles.get(i);
+        if (file.getFormatType().compareToIgnoreCase("other") != 0) {
+          Global.fileNames.addElement(file.getName());
+          Global.files.addFile(file);
+        }
+      }
+      currentProgram = null;
+    }
+  }
+
+
+  private static void createAndShowGUI() {
+    // Create and set up the window.
+    JFrame mainFrame = new JFrame("S-Mart");
+    mainFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+    //Create and set up the content pane.
+    JComponent newContentPane = new Smart();
+    newContentPane.setOpaque(true);
+    mainFrame.setContentPane(newContentPane);
+
+    // Display the window.
+    mainFrame.pack();
+    mainFrame.setVisible(true);
+    Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+    mainFrame.setBounds(0, 0, screenSize.width, screenSize.height);
+  }
+
+
+  public static void main(String[] args) {
+    javax.swing.SwingUtilities.invokeLater(new Runnable() {
+      public void run() {
+        createAndShowGUI();
+      }
+    });
+  }
+}