--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/ProgramOption.java	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,358 @@
+/**
+ *
+ * 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 ProgramOption {
+  boolean       input;
+  String        identifier;
+  String        type;
+  String        comment;
+  boolean       compulsory;
+  String[]      format;
+  String        formatIdentifier;
+  ProgramOption associatedOption;
+  String        defaultValue;
+  String[]      choices;
+  JComponent    component;
+  JPanel        panel;
+
+
+  public ProgramOption() {
+    this.input            = true;
+    this.identifier       = null;
+    this.type             = null;
+    this.comment          = null;
+    this.compulsory       = false;
+    this.format           = null;
+    this.formatIdentifier = null;
+    this.associatedOption = null;
+    this.defaultValue     = "";
+    this.choices          = null;
+    this.component        = null;
+    this.panel            = null;
+  }
+
+
+  public void setInput(boolean input) {
+    this.input = input;
+  }
+
+
+  public void setIdentifier(String identifier) {
+    this.identifier = identifier;
+  }
+
+
+  public void setType(String type) {
+    this.type = type;
+  }
+
+
+  public void setComment(String comment) {
+    this.comment = comment;
+  }
+
+
+  public void setCompulsory(boolean compulsory) {
+    this.compulsory = compulsory;
+  }
+
+
+  public void setFormat(String[] format) {
+    this.format = format;
+  }
+
+
+  public void setFormat(String format) {
+    this.format    = new String[1];
+    this.format[0] = format;
+  }
+
+
+  public void setFormatIdentifier(String formatIdentifier) {
+    this.formatIdentifier = formatIdentifier;
+  }
+
+
+  public void setAssociatedOption(ProgramOption option) {
+    this.associatedOption = option;
+  }
+
+
+  public void setChoices(String[] choices) {
+    this.choices = new String[choices.length+1];
+    this.choices[0] = "---";
+    for (int i = 0; i < choices.length; i++) {
+      this.choices[i+1] = choices[i];
+    }
+  }
+
+
+  public void setDefault(String defaultValue) {
+    this.defaultValue = defaultValue;
+  }
+
+
+  public boolean isInput() {
+    return this.input;
+  }
+
+
+  public boolean checkSettings() {
+    if (this.identifier == null) {
+      return false;
+    }
+    if (this.type == null) {
+      return false;
+    }
+    if (this.comment == null) {
+      return false;
+    }
+    if (this.comment == null) {
+      return false;
+    }
+    if (("choice".compareToIgnoreCase(this.type) == 0) && (this.choices == null)) {
+      return false;
+    }
+    return true;
+  }
+
+
+  public JPanel getPanel() {
+    if (this.panel != null) {
+      return this.panel;
+    }
+    String comment = this.comment;
+    if (this.compulsory) {
+      comment += " [*]";
+    }
+
+    GridLayout horizontalLayout = new GridLayout(1, 0);
+    this.panel = new JPanel(false);
+    this.panel.setLayout(horizontalLayout);
+    JLabel label = new JLabel(comment);
+
+    if (this.type == null) {
+      System.out.println("Error! Option '" + this.identifier + "' is not set!");
+    }
+
+    if (("int".compareToIgnoreCase(this.type) == 0) || ("float".compareToIgnoreCase(this.type) == 0) || ("string".compareToIgnoreCase(this.type) == 0) || (("file".compareToIgnoreCase(this.type) == 0) && (!this.input))) {
+      this.component = new JTextField();
+      if (this.defaultValue != null) {
+        ((JTextField) this.component).setText(this.defaultValue);
+      }
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      this.panel.add(this.component);
+    }
+    else if ("file".compareToIgnoreCase(this.type) == 0) {
+      this.component = new JComboBox(Global.fileNames);
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      this.panel.add(this.component);
+    }
+    else if ("boolean".compareToIgnoreCase(this.type) == 0) {
+      this.component = new JCheckBox();
+      if ((this.defaultValue != null) && (this.defaultValue.compareToIgnoreCase("true") == 0)) {
+        ((JCheckBox) this.component).setSelected(true);
+      }
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      this.panel.add(this.component);
+    }
+    else if ("format".compareToIgnoreCase(this.type) == 0) {
+      Vector < String > formats = new Vector < String > ();
+      for (String format: this.format) {
+        if (Global.formats.getFormats(format) == null) {
+          System.out.println("Do not know how to handle format '" + format + "'.");
+        }
+        formats.addAll(Global.formats.getFormats(format).getFormats());
+      }
+      this.component = new JComboBox(formats);
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      this.panel.add(this.component);
+    }
+    else if ("files".compareToIgnoreCase(this.type) == 0) {
+      JButton button = new JButton("file...");
+      this.component = new JTextField();
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      this.panel.add(this.component);
+      this.panel.add(button);
+      Global.otherFileConcatenationChooser.put(button, (JTextField) this.component);
+    }
+    else if ("directory".compareToIgnoreCase(this.type) == 0) {
+      JButton button = new JButton("directory...");
+      this.component = new JTextField();
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      JPanel rightPanel = new JPanel(false);
+      rightPanel.setLayout(new BoxLayout(rightPanel, BoxLayout.LINE_AXIS));
+      rightPanel.add(this.component);
+      rightPanel.add(button);
+      this.panel.add(rightPanel);
+      Global.otherDirectoriesChooser.put(button, (JTextField) this.component);
+    }
+    else if ("choice".compareToIgnoreCase(this.type) == 0) {
+      this.component = new JComboBox(this.choices);
+      label.setLabelFor(this.component);
+      this.panel.add(label);
+      this.panel.add(this.component);
+    }
+    else {
+      System.out.println("Do not know how to read type " + this.type);
+    }
+
+    return this.panel;
+  }
+
+
+  public JComponent getComponent() {
+    if (component == null) {
+      this.getPanel();
+    }
+    return this.component;
+  }
+
+
+  private String getValue() {
+    if (("int".equals(this.type)) || ("float".equals(this.type)) || ("string".equals(this.type)) || (("file".equals(this.type)) && (! this.input)) || ("directory".equals(this.type)) || ("files".equals(this.type)))  {
+      String s = ((JTextField) this.component).getText();
+      if ("None".equals(s)) {
+        return "";
+      }
+      return s;
+    }
+    if ("file".equals(this.type)) {
+      return (String) ((JComboBox) this.component).getSelectedItem();
+    }
+    if ("boolean".equals(this.type)) {
+      return ((JCheckBox) this.component).isSelected()? "true": "false";
+    }
+    if ("format".equals(this.type)) {
+      return (String) ((JComboBox) this.component).getSelectedItem();
+    }
+    if ("choice".equals(this.type)) {
+      String s = (String) ((JComboBox) this.component).getSelectedItem();
+      if ("---".equals(s)) {
+        return "";
+      }
+      return s;
+    }
+    System.out.println("Do not know how to get value of '" + this.type + "' (" + this.identifier + ").");
+    return null;
+  }
+
+
+  public String checkValue() {
+    String value = this.getValue();
+    if ((this.compulsory) && ((value == null) || ("".equals(value)))) {
+      return "Option '" + this.comment + "' has no value... Please specify it.\n";
+    }
+    if ("int".equals(this.type)) {
+      if ((value != null) && (! "".equals(value)) && (! "None".equals(value))) {
+        try {
+          int i = Integer.parseInt(value);
+        }
+        catch (NumberFormatException e) {
+          return "Option '" + this.comment + "' should be an integer... Please correct it.\n";
+        }
+      }
+    }
+    else if ("float".equals(this.type)) {
+      if ((value != null) && (! "".equals(value))) {
+        try {
+          float i = Float.parseFloat(value);
+        }
+        catch (NumberFormatException e) {
+          return "Option '" + this.comment + "' should be a float... Please correct it.\n";
+        }
+      }
+    }
+    return null;
+  }
+
+
+  public LinkedList <String> getCommand() {
+    LinkedList <String> list = new LinkedList <String> ();
+
+    if (("int".equals(this.type)) || ("float".equals(this.type)) || ("string".equals(this.type)) || (("file".equals(this.type)) && (! this.input)) || ("format".equals(this.type)) || ("directory".equals(this.type)) || ("files".equals(this.type)) || ("choice".equals(this.type))) {
+      String value = this.getValue();
+      if (value.length() == 0) {
+        return list;
+      }
+      list.add(this.identifier);
+      list.add(value);
+      return list;
+    }
+    if ("file".equals(this.type)) {
+      String fileName = (String) ((JComboBox) this.component).getSelectedItem();
+      if (fileName == null) {
+        return list;
+      }
+      list.add(this.identifier);
+      list.add(this.getValue());
+      return list;
+    }
+    if (("boolean".equals(this.type)) || ("bool".equals(this.type))) {
+      if ("true".equals(this.getValue())) {
+        list.add(this.identifier);
+      }
+      return list;
+    }
+    System.out.println("Cannot get type of option " + this.type + " (" + this.identifier + "): " + this.getValue());
+    return null;
+  }
+
+
+  public File getOutputFile() {
+    if (this.input) return null;
+    String format = "";
+    if (this.format != null) {
+      format = this.format[0];
+    }
+    if (this.associatedOption != null) {
+      format = this.associatedOption.getValue();
+    }
+    return new File(this.getValue(), Global.formats.getFormatType(format), format);
+  }
+}