mev-4.0.01/source/org/tigr/microarray/mev/cluster/gui/impl/ease/EASEInitDialog.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2 Copyright @ 1999-2004, The Institute for Genomic Research (TIGR).
2 26 Feb 07 jari 3 All rights reserved.
2 26 Feb 07 jari 4  */
2 26 Feb 07 jari 5 /*
2 26 Feb 07 jari 6  * $RCSfile: EASEInitDialog.java,v $
2 26 Feb 07 jari 7  * $Revision: 1.9 $
2 26 Feb 07 jari 8  * $Date: 2006/02/23 20:59:50 $
2 26 Feb 07 jari 9  * $Author: caliente $
2 26 Feb 07 jari 10  * $State: Exp $
2 26 Feb 07 jari 11  */
2 26 Feb 07 jari 12 /*
2 26 Feb 07 jari 13  * EaseInitDialog.java
2 26 Feb 07 jari 14  *
2 26 Feb 07 jari 15  * Created on August 25, 2003, 11:39 AM
2 26 Feb 07 jari 16  */
2 26 Feb 07 jari 17
2 26 Feb 07 jari 18 package org.tigr.microarray.mev.cluster.gui.impl.ease;
2 26 Feb 07 jari 19
2 26 Feb 07 jari 20 import java.awt.Color;
2 26 Feb 07 jari 21 import java.awt.Component;
2 26 Feb 07 jari 22 import java.awt.Dimension;
2 26 Feb 07 jari 23 import java.awt.Font;
2 26 Feb 07 jari 24 import java.awt.Frame;
2 26 Feb 07 jari 25 import java.awt.GridBagConstraints;
2 26 Feb 07 jari 26 import java.awt.GridBagLayout;
2 26 Feb 07 jari 27 import java.awt.Insets;
2 26 Feb 07 jari 28 import java.awt.Toolkit;
2 26 Feb 07 jari 29 import java.awt.event.ActionEvent;
2 26 Feb 07 jari 30 import java.awt.event.ActionListener;
2 26 Feb 07 jari 31 import java.awt.event.ItemEvent;
2 26 Feb 07 jari 32 import java.awt.event.ItemListener;
2 26 Feb 07 jari 33 import java.awt.event.WindowEvent;
2 26 Feb 07 jari 34 import java.io.File;
2 26 Feb 07 jari 35 import java.util.Vector;
2 26 Feb 07 jari 36
2 26 Feb 07 jari 37 import javax.swing.BorderFactory;
2 26 Feb 07 jari 38 import javax.swing.ButtonGroup;
2 26 Feb 07 jari 39 import javax.swing.DefaultListCellRenderer;
2 26 Feb 07 jari 40 import javax.swing.DefaultListModel;
2 26 Feb 07 jari 41 import javax.swing.JButton;
2 26 Feb 07 jari 42 import javax.swing.JCheckBox;
2 26 Feb 07 jari 43 import javax.swing.JComboBox;
2 26 Feb 07 jari 44 import javax.swing.JFileChooser;
2 26 Feb 07 jari 45 import javax.swing.JFrame;
2 26 Feb 07 jari 46 import javax.swing.JLabel;
2 26 Feb 07 jari 47 import javax.swing.JList;
2 26 Feb 07 jari 48 import javax.swing.JOptionPane;
2 26 Feb 07 jari 49 import javax.swing.JPanel;
2 26 Feb 07 jari 50 import javax.swing.JRadioButton;
2 26 Feb 07 jari 51 import javax.swing.JScrollPane;
2 26 Feb 07 jari 52 import javax.swing.JTabbedPane;
2 26 Feb 07 jari 53 import javax.swing.JTextField;
2 26 Feb 07 jari 54 import javax.swing.JTextPane;
2 26 Feb 07 jari 55 import javax.swing.border.BevelBorder;
2 26 Feb 07 jari 56 import javax.swing.border.EtchedBorder;
2 26 Feb 07 jari 57 import javax.swing.border.TitledBorder;
2 26 Feb 07 jari 58 import javax.swing.event.ListSelectionEvent;
2 26 Feb 07 jari 59 import javax.swing.event.ListSelectionListener;
2 26 Feb 07 jari 60
2 26 Feb 07 jari 61 import org.tigr.microarray.mev.TMEV;
2 26 Feb 07 jari 62 import org.tigr.microarray.mev.cluster.clusterUtil.Cluster;
2 26 Feb 07 jari 63 import org.tigr.microarray.mev.cluster.clusterUtil.ClusterRepository;
2 26 Feb 07 jari 64 import org.tigr.microarray.mev.cluster.gui.helpers.ClusterBrowser;
2 26 Feb 07 jari 65 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.AlgorithmDialog;
2 26 Feb 07 jari 66 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.DialogListener;
2 26 Feb 07 jari 67 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.ParameterPanel;
2 26 Feb 07 jari 68 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.dialogHelpUtil.HelpWindow;
2 26 Feb 07 jari 69
2 26 Feb 07 jari 70 /** Accumulates parameters for execution of
2 26 Feb 07 jari 71  * EASE analysis.
2 26 Feb 07 jari 72  * @author braisted
2 26 Feb 07 jari 73  */
2 26 Feb 07 jari 74 public class EASEInitDialog extends AlgorithmDialog {
2 26 Feb 07 jari 75     
2 26 Feb 07 jari 76     /** Result when dialog is dismissed.
2 26 Feb 07 jari 77      */
2 26 Feb 07 jari 78     private int result = JOptionPane.CANCEL_OPTION;
2 26 Feb 07 jari 79     
2 26 Feb 07 jari 80     ConfigPanel configPanel;
2 26 Feb 07 jari 81     ModePanel modePanel;
2 26 Feb 07 jari 82     PopSelectionPanel popPanel;
2 26 Feb 07 jari 83     ClusterBrowser browser;
2 26 Feb 07 jari 84     EventListener listener;
2 26 Feb 07 jari 85     EaseParameterPanel easeParamPanel;
2 26 Feb 07 jari 86     AlphaPanel alphaPanel;
2 26 Feb 07 jari 87     JTabbedPane tabbedPane;
2 26 Feb 07 jari 88     Font font;
2 26 Feb 07 jari 89     String sep;
2 26 Feb 07 jari 90     Frame parent;
2 26 Feb 07 jari 91     
2 26 Feb 07 jari 92     /** Creates a new instance of EaseInitDialog
2 26 Feb 07 jari 93      * @param parent Parent Frame
2 26 Feb 07 jari 94      * @param repository Cluster repository to construct <CODE>ClusterBrowser</CODE>
2 26 Feb 07 jari 95      * @param annotationLabels Annotation types
2 26 Feb 07 jari 96      */
2 26 Feb 07 jari 97     public EASEInitDialog(Frame parent, ClusterRepository repository, String [] annotationLabels) {
2 26 Feb 07 jari 98         super(parent, "EASE: EASE Annotation Analysis", true);
2 26 Feb 07 jari 99         this.parent = parent;
2 26 Feb 07 jari 100         font = new Font("Dialog", Font.BOLD, 12);
2 26 Feb 07 jari 101         listener = new EventListener();
2 26 Feb 07 jari 102         addWindowListener(listener);
2 26 Feb 07 jari 103         
2 26 Feb 07 jari 104         //Tabbed pane creation
2 26 Feb 07 jari 105         tabbedPane = new JTabbedPane();
2 26 Feb 07 jari 106         
2 26 Feb 07 jari 107         //config panel        
2 26 Feb 07 jari 108         configPanel = new ConfigPanel();        
2 26 Feb 07 jari 109         
2 26 Feb 07 jari 110         JPanel popNClusterPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 111         popNClusterPanel.setBackground(Color.white);
2 26 Feb 07 jari 112         popPanel = new PopSelectionPanel();
2 26 Feb 07 jari 113         browser = new ClusterBrowser(repository);
2 26 Feb 07 jari 114         
2 26 Feb 07 jari 115         popNClusterPanel.add(popPanel, new GridBagConstraints(0,0,1,1,1.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 116         popNClusterPanel.add(browser, new GridBagConstraints(0,1,1,1,1.0,1.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 117         tabbedPane.add("Population and Cluster Selection", popNClusterPanel);
2 26 Feb 07 jari 118         
2 26 Feb 07 jari 119         easeParamPanel = new EaseParameterPanel(annotationLabels);
2 26 Feb 07 jari 120         tabbedPane.add("Annotation Parameters", easeParamPanel);
2 26 Feb 07 jari 121         
2 26 Feb 07 jari 122         alphaPanel = new AlphaPanel();
2 26 Feb 07 jari 123         tabbedPane.add("Statistical Parameters", alphaPanel);
2 26 Feb 07 jari 124         
2 26 Feb 07 jari 125         JPanel parameters = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 126         parameters.setBackground(Color.white);
2 26 Feb 07 jari 127         
2 26 Feb 07 jari 128         //mode panel
2 26 Feb 07 jari 129         modePanel = new ModePanel(!(repository == null || repository.isEmpty()));
2 26 Feb 07 jari 130         
2 26 Feb 07 jari 131         parameters.add(configPanel, new GridBagConstraints(0,0,1,1,1.0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));       
2 26 Feb 07 jari 132         parameters.add(modePanel, new GridBagConstraints(0,1,1,1,1.0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 133         parameters.add(tabbedPane, new GridBagConstraints(0,2,1,1,1.0,1.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 134         
2 26 Feb 07 jari 135         addContent(parameters);
2 26 Feb 07 jari 136         setActionListeners(listener);
2 26 Feb 07 jari 137         
2 26 Feb 07 jari 138         if(repository == null || repository.isEmpty()) {
2 26 Feb 07 jari 139             Component comp = tabbedPane.getComponentAt(0);
2 26 Feb 07 jari 140             JPanel panel = (JPanel)comp;
2 26 Feb 07 jari 141             panel.removeAll();
2 26 Feb 07 jari 142             panel.validate();
2 26 Feb 07 jari 143             panel.setOpaque(false);
2 26 Feb 07 jari 144             panel.add(new JLabel("Empty Cluster Repository"), new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.NORTH, GridBagConstraints.NONE, new Insets(15,0,10,0),0,0));
2 26 Feb 07 jari 145             panel.add(new JLabel("Only Annotation Survey is Enabled"), new GridBagConstraints(0,1,1,1,0,0,GridBagConstraints.NORTH, GridBagConstraints.NONE, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 146             tabbedPane.setSelectedIndex(1);
2 26 Feb 07 jari 147         }
2 26 Feb 07 jari 148         
2 26 Feb 07 jari 149         this.setSize(570,750);
2 26 Feb 07 jari 150     }
2 26 Feb 07 jari 151     
2 26 Feb 07 jari 152         /** Creates a new instance of EaseInitDialog
2 26 Feb 07 jari 153      * @param parent Parent Frame
2 26 Feb 07 jari 154      * @param repository Cluster repository to construct <CODE>ClusterBrowser</CODE>
2 26 Feb 07 jari 155      * @param annotationLabels Annotation types
2 26 Feb 07 jari 156      */
2 26 Feb 07 jari 157     public EASEInitDialog(Frame parent, String [] annotationLabels) {
2 26 Feb 07 jari 158         super(parent, "EASE: EASE Annotation Analysis", true);
2 26 Feb 07 jari 159         this.parent = parent;
2 26 Feb 07 jari 160         font = new Font("Dialog", Font.BOLD, 12);
2 26 Feb 07 jari 161         listener = new EventListener();
2 26 Feb 07 jari 162         addWindowListener(listener);
2 26 Feb 07 jari 163         
2 26 Feb 07 jari 164         //Tabbed pane creation
2 26 Feb 07 jari 165         tabbedPane = new JTabbedPane();
2 26 Feb 07 jari 166         
2 26 Feb 07 jari 167         //config panel        
2 26 Feb 07 jari 168         configPanel = new ConfigPanel();        
2 26 Feb 07 jari 169         
2 26 Feb 07 jari 170         JPanel popNClusterPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 171         popNClusterPanel.setBackground(Color.white);
2 26 Feb 07 jari 172         popPanel = new PopSelectionPanel();
2 26 Feb 07 jari 173        // browser = new ClusterBrowser(repository);
2 26 Feb 07 jari 174         
2 26 Feb 07 jari 175         JPanel emptyClusterPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 176         String text = "<center><b>Note: When running EASE in script mode the cluster<br>";
2 26 Feb 07 jari 177         text += "under analysis is determined by the preceding algorithm<br>";
2 26 Feb 07 jari 178         text += "that feeds source data into EASE.</center>";
2 26 Feb 07 jari 179         JTextPane textArea = new JTextPane();
2 26 Feb 07 jari 180         textArea.setEditable(false);
2 26 Feb 07 jari 181         textArea.setBackground(Color.lightGray);
2 26 Feb 07 jari 182         textArea.setContentType("text/html");
2 26 Feb 07 jari 183         textArea.setText(text);
2 26 Feb 07 jari 184         emptyClusterPanel.add(textArea, new GridBagConstraints(0,0,1,1,0.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 185         
2 26 Feb 07 jari 186         popNClusterPanel.add(popPanel, new GridBagConstraints(0,0,1,1,1.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 187         popNClusterPanel.add(emptyClusterPanel, new GridBagConstraints(0,1,1,1,1.0,1.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 188         tabbedPane.add("Population and Cluster Selection", popNClusterPanel);
2 26 Feb 07 jari 189         
2 26 Feb 07 jari 190         easeParamPanel = new EaseParameterPanel(annotationLabels);
2 26 Feb 07 jari 191         tabbedPane.add("Annotation Parameters", easeParamPanel);
2 26 Feb 07 jari 192         
2 26 Feb 07 jari 193         alphaPanel = new AlphaPanel();
2 26 Feb 07 jari 194         tabbedPane.add("Statistical Parameters", alphaPanel);
2 26 Feb 07 jari 195         
2 26 Feb 07 jari 196         JPanel parameters = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 197         parameters.setBackground(Color.white);
2 26 Feb 07 jari 198             
2 26 Feb 07 jari 199         //mode panel
2 26 Feb 07 jari 200         modePanel = new ModePanel(true);
2 26 Feb 07 jari 201         
2 26 Feb 07 jari 202         parameters.add(configPanel, new GridBagConstraints(0,0,1,1,1.0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));       
2 26 Feb 07 jari 203         parameters.add(modePanel, new GridBagConstraints(0,1,1,1,1.0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 204         parameters.add(tabbedPane, new GridBagConstraints(0,2,1,1,1.0,1.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 205        
2 26 Feb 07 jari 206         addContent(parameters);
2 26 Feb 07 jari 207         setActionListeners(listener);
2 26 Feb 07 jari 208         
2 26 Feb 07 jari 209      /*   if(repository == null || repository.isEmpty()) {
2 26 Feb 07 jari 210             Component comp = tabbedPane.getComponentAt(0);
2 26 Feb 07 jari 211             JPanel panel = (JPanel)comp;
2 26 Feb 07 jari 212             panel.removeAll();
2 26 Feb 07 jari 213             panel.validate();
2 26 Feb 07 jari 214             panel.setOpaque(false);
2 26 Feb 07 jari 215             panel.add(new JLabel("Empty Cluster Repository"), new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.NORTH, GridBagConstraints.NONE, new Insets(15,0,10,0),0,0));
2 26 Feb 07 jari 216             panel.add(new JLabel("Only Annotation Survey is Enabled"), new GridBagConstraints(0,1,1,1,0,0,GridBagConstraints.NORTH, GridBagConstraints.NONE, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 217             tabbedPane.setSelectedIndex(1);
2 26 Feb 07 jari 218         }
2 26 Feb 07 jari 219         */
2 26 Feb 07 jari 220         this.setSize(570,750);
2 26 Feb 07 jari 221     }
2 26 Feb 07 jari 222     
2 26 Feb 07 jari 223     /** Shows the dialog.
2 26 Feb 07 jari 224      * @return  */
2 26 Feb 07 jari 225     public int showModal() {
2 26 Feb 07 jari 226         Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
2 26 Feb 07 jari 227         setLocation((screenSize.width - getSize().width)/2, (screenSize.height - getSize().height)/2);
2 26 Feb 07 jari 228         show();
2 26 Feb 07 jari 229         return result;
2 26 Feb 07 jari 230     }
2 26 Feb 07 jari 231     
2 26 Feb 07 jari 232     /** Resets dialog controls.
2 26 Feb 07 jari 233      */
2 26 Feb 07 jari 234     private void resetControls(){
2 26 Feb 07 jari 235         
2 26 Feb 07 jari 236     }
2 26 Feb 07 jari 237     
2 26 Feb 07 jari 238     /** Indicates if mode is cluster analysis, if not mode is annotation survey.
2 26 Feb 07 jari 239      * @return  */
2 26 Feb 07 jari 240     public boolean isClusterModeSelected(){
2 26 Feb 07 jari 241         return this.modePanel.clusterAnalysisButton.isSelected();
2 26 Feb 07 jari 242     }
2 26 Feb 07 jari 243     
2 26 Feb 07 jari 244     /** Returns the cluster selected for analysis.
2 26 Feb 07 jari 245      * @return  */
2 26 Feb 07 jari 246     public Cluster getSelectedCluster(){
2 26 Feb 07 jari 247         return this.browser.getSelectedCluster();
2 26 Feb 07 jari 248     }
2 26 Feb 07 jari 249     
2 26 Feb 07 jari 250     
2 26 Feb 07 jari 251     public boolean isPopFileModeSelected() {
2 26 Feb 07 jari 252         return popPanel.fileButton.isSelected();
2 26 Feb 07 jari 253     }
2 26 Feb 07 jari 254     
2 26 Feb 07 jari 255     
2 26 Feb 07 jari 256     /** Returns the population fille to load
2 26 Feb 07 jari 257      */
2 26 Feb 07 jari 258     public String getPopulationFileName() {
2 26 Feb 07 jari 259         return this.popPanel.getPopFile();
2 26 Feb 07 jari 260     }
2 26 Feb 07 jari 261     
2 26 Feb 07 jari 262     /** Returns the name of the converter file selected.
2 26 Feb 07 jari 263      * If none selected null is returned.
2 26 Feb 07 jari 264      */
2 26 Feb 07 jari 265     public String getConverterFileName(){
2 26 Feb 07 jari 266         return easeParamPanel.getConverterFileName();
2 26 Feb 07 jari 267     }
2 26 Feb 07 jari 268     
2 26 Feb 07 jari 269     /** Returns the minimum clusters size if trimming result.
2 26 Feb 07 jari 270      */
2 26 Feb 07 jari 271     public int getMinClusterSize() {
2 26 Feb 07 jari 272         String value = easeParamPanel.minClusterSizeField.getText();
2 26 Feb 07 jari 273         try {
2 26 Feb 07 jari 274             int size = Integer.parseInt(value);
2 26 Feb 07 jari 275             return size;
2 26 Feb 07 jari 276         } catch (NumberFormatException e) {
2 26 Feb 07 jari 277             return 0;
2 26 Feb 07 jari 278         }
2 26 Feb 07 jari 279     }
2 26 Feb 07 jari 280     
2 26 Feb 07 jari 281     /** Returns the base file location for EASE file system
2 26 Feb 07 jari 282      */
2 26 Feb 07 jari 283     public String getBaseFileLocation() {
2 26 Feb 07 jari 284         return configPanel.getBaseFileLocation();
2 26 Feb 07 jari 285     }
2 26 Feb 07 jari 286     
2 26 Feb 07 jari 287     /** Returns the annotation key type.
2 26 Feb 07 jari 288      */
2 26 Feb 07 jari 289     public String getAnnotationKeyType(){
2 26 Feb 07 jari 290         return easeParamPanel.getAnnotationKeyType();
2 26 Feb 07 jari 291     }
2 26 Feb 07 jari 292     
2 26 Feb 07 jari 293     
2 26 Feb 07 jari 294     /** Returns a list of file names corresponding to files mapping
2 26 Feb 07 jari 295      * indices to annotation terms (themes).
2 26 Feb 07 jari 296      */
2 26 Feb 07 jari 297     public String [] getAnnToGOFileList(){
2 26 Feb 07 jari 298         return this.easeParamPanel.getAnnToGOFileList();
2 26 Feb 07 jari 299     }
2 26 Feb 07 jari 300     
2 26 Feb 07 jari 301     /** Returns the stat to report.  If true then EaseScore, else Fisher's Exact.
2 26 Feb 07 jari 302      */
2 26 Feb 07 jari 303     public boolean isEaseScoreSelected(){
2 26 Feb 07 jari 304         return (this.alphaPanel.easeBox.isSelected());
2 26 Feb 07 jari 305     }
2 26 Feb 07 jari 306     
2 26 Feb 07 jari 307     /** Returns true if multiplicity corrections are
2 26 Feb 07 jari 308      * selected.
2 26 Feb 07 jari 309      */
2 26 Feb 07 jari 310     public boolean isCorrectPvaluesSelected(){
2 26 Feb 07 jari 311         return (this.isBonferroniSelected() || this.isStepDownBonferroniSelected() || this.isSidakSelected());
2 26 Feb 07 jari 312     }
2 26 Feb 07 jari 313     
2 26 Feb 07 jari 314     /** Returns true if Bonferroni correction is selected.
2 26 Feb 07 jari 315      */
2 26 Feb 07 jari 316     public boolean isBonferroniSelected(){
2 26 Feb 07 jari 317         return alphaPanel.bonferroniBox.isSelected();
2 26 Feb 07 jari 318     }
2 26 Feb 07 jari 319     
2 26 Feb 07 jari 320     /** Returns true if step down Bonferroni is selected.
2 26 Feb 07 jari 321      */
2 26 Feb 07 jari 322     public boolean isStepDownBonferroniSelected(){
2 26 Feb 07 jari 323         return alphaPanel.bonferroniStepBox.isSelected();
2 26 Feb 07 jari 324     }
2 26 Feb 07 jari 325     
2 26 Feb 07 jari 326     /** Returns true is Sidak method correction is selected
2 26 Feb 07 jari 327      */
2 26 Feb 07 jari 328     public boolean isSidakSelected(){
2 26 Feb 07 jari 329         return alphaPanel.sidakBox.isSelected();
2 26 Feb 07 jari 330     }
2 26 Feb 07 jari 331     
2 26 Feb 07 jari 332     /** Returns true if bootstrapping permutations
2 26 Feb 07 jari 333      * are selected.
2 26 Feb 07 jari 334      */
2 26 Feb 07 jari 335     public boolean isPermutationAnalysisSelected(){
2 26 Feb 07 jari 336         return alphaPanel.permBox.isSelected();
2 26 Feb 07 jari 337     }
2 26 Feb 07 jari 338     
2 26 Feb 07 jari 339     /** Returns the number of permutations to perform.
2 26 Feb 07 jari 340      */
2 26 Feb 07 jari 341     public int getPermutationCount(){
2 26 Feb 07 jari 342         return Integer.parseInt(alphaPanel.permField.getText());
2 26 Feb 07 jari 343     }
2 26 Feb 07 jari 344     
2 26 Feb 07 jari 345     /** Returns the trim options as two strings.
2 26 Feb 07 jari 346      * The first string indicates the type of trim
2 26 Feb 07 jari 347      * NO_TRIM, N_TRIM, PERCENT_TRIM.  The second string indicates the value to be applied.
2 26 Feb 07 jari 348      */
2 26 Feb 07 jari 349     public String [] getTrimOptions(){
2 26 Feb 07 jari 350         String [] options = new String[2];
2 26 Feb 07 jari 351         if ( alphaPanel.trimBox.isSelected() ){
2 26 Feb 07 jari 352             if ( alphaPanel.trimPercentBox.isSelected() ){
2 26 Feb 07 jari 353                 options[0] = "PERCENT_TRIM";
2 26 Feb 07 jari 354                 options[1] = alphaPanel.trimPercentField.getText();
2 26 Feb 07 jari 355             } else {
2 26 Feb 07 jari 356                 options[0] = "N_TRIM";
2 26 Feb 07 jari 357                 options[1] = alphaPanel.trimNField.getText();
2 26 Feb 07 jari 358             }
2 26 Feb 07 jari 359         } else {
2 26 Feb 07 jari 360             options[0] = "NO_TRIM";
2 26 Feb 07 jari 361             options[1] = "0";
2 26 Feb 07 jari 362         }
2 26 Feb 07 jari 363         return options;
2 26 Feb 07 jari 364     }
2 26 Feb 07 jari 365     
2 26 Feb 07 jari 366     /** Contains mode controls. (anal. or survey)
2 26 Feb 07 jari 367      */
2 26 Feb 07 jari 368     private class ModePanel extends JPanel {
2 26 Feb 07 jari 369         private JRadioButton clusterAnalysisButton;
2 26 Feb 07 jari 370         private JRadioButton slideSurveyButton;
2 26 Feb 07 jari 371         
2 26 Feb 07 jari 372         /** Constructs a mode panel.
2 26 Feb 07 jari 373          * @param haveClusters
2 26 Feb 07 jari 374          */
2 26 Feb 07 jari 375         public ModePanel(boolean haveClusters){
2 26 Feb 07 jari 376             super(new GridBagLayout());
2 26 Feb 07 jari 377             setLayout(new GridBagLayout());
2 26 Feb 07 jari 378             setBackground(Color.white);
2 26 Feb 07 jari 379             setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Mode Selection", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 380             
2 26 Feb 07 jari 381             ButtonGroup bg = new ButtonGroup();
2 26 Feb 07 jari 382             clusterAnalysisButton = new JRadioButton("Cluster Analysis", haveClusters);
2 26 Feb 07 jari 383             clusterAnalysisButton.setFocusPainted(false);
2 26 Feb 07 jari 384             clusterAnalysisButton.setBackground(Color.white);
2 26 Feb 07 jari 385             clusterAnalysisButton.setHorizontalAlignment(JRadioButton.CENTER);
2 26 Feb 07 jari 386             clusterAnalysisButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 387                 public void actionPerformed(ActionEvent ae) {
2 26 Feb 07 jari 388                     popPanel.setEnableControls(true);
2 26 Feb 07 jari 389                 }
2 26 Feb 07 jari 390             });
2 26 Feb 07 jari 391             bg.add(clusterAnalysisButton);
2 26 Feb 07 jari 392             
2 26 Feb 07 jari 393             slideSurveyButton = new JRadioButton("Annotation Survey");
2 26 Feb 07 jari 394             slideSurveyButton.setToolTipText("Surveys annotation loaded in the CURRENT viewer.");
2 26 Feb 07 jari 395             slideSurveyButton.setFocusPainted(false);
2 26 Feb 07 jari 396             slideSurveyButton.setBackground(Color.white);
2 26 Feb 07 jari 397             slideSurveyButton.setHorizontalAlignment(JRadioButton.CENTER);
2 26 Feb 07 jari 398             slideSurveyButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 399                 public void actionPerformed(ActionEvent ae) {
2 26 Feb 07 jari 400                     popPanel.setEnableControls(false);
2 26 Feb 07 jari 401                 }
2 26 Feb 07 jari 402             });
2 26 Feb 07 jari 403             bg.add(slideSurveyButton);
2 26 Feb 07 jari 404             
2 26 Feb 07 jari 405             if(!haveClusters){
2 26 Feb 07 jari 406                 slideSurveyButton.setSelected(true);
2 26 Feb 07 jari 407                 clusterAnalysisButton.setEnabled(false);
2 26 Feb 07 jari 408             }
2 26 Feb 07 jari 409             
2 26 Feb 07 jari 410             add(clusterAnalysisButton, new GridBagConstraints(0,0,1,1,1.0,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0), 0, 0));
2 26 Feb 07 jari 411             add(slideSurveyButton, new GridBagConstraints(1,0,1,1,1.0,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0), 0, 0));
2 26 Feb 07 jari 412         }
2 26 Feb 07 jari 413     }
2 26 Feb 07 jari 414     
2 26 Feb 07 jari 415     private class PopSelectionPanel extends ParameterPanel {
2 26 Feb 07 jari 416         
2 26 Feb 07 jari 417         JRadioButton fileButton;
2 26 Feb 07 jari 418         JRadioButton dataButton;
2 26 Feb 07 jari 419         JTextField popField;
2 26 Feb 07 jari 420         JButton browseButton;
2 26 Feb 07 jari 421         JLabel fileLabel;
2 26 Feb 07 jari 422         
2 26 Feb 07 jari 423         public PopSelectionPanel() {
2 26 Feb 07 jari 424             super("Population Selection");
2 26 Feb 07 jari 425             setLayout(new GridBagLayout());
2 26 Feb 07 jari 426             
2 26 Feb 07 jari 427             ButtonGroup bg = new ButtonGroup();
2 26 Feb 07 jari 428             fileButton = new JRadioButton("Population from File", true);
2 26 Feb 07 jari 429             fileButton.setBackground(Color.white);
2 26 Feb 07 jari 430             fileButton.setFocusPainted(false);
2 26 Feb 07 jari 431             bg.add(fileButton);
2 26 Feb 07 jari 432             
2 26 Feb 07 jari 433             fileButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 434                 public void actionPerformed(ActionEvent ae) {
2 26 Feb 07 jari 435                     
2 26 Feb 07 jari 436                     browseButton.setEnabled(fileButton.isSelected());
2 26 Feb 07 jari 437                     popField.setEnabled(fileButton.isSelected());
2 26 Feb 07 jari 438                     popField.setBackground(Color.white);
2 26 Feb 07 jari 439                     fileLabel.setEnabled(fileButton.isSelected());
2 26 Feb 07 jari 440                     
2 26 Feb 07 jari 441                 }
2 26 Feb 07 jari 442             });
2 26 Feb 07 jari 443             
2 26 Feb 07 jari 444             dataButton = new JRadioButton("Population from Current Viewer");
2 26 Feb 07 jari 445             dataButton.setBackground(Color.white);
2 26 Feb 07 jari 446             dataButton.setFocusPainted(false);
2 26 Feb 07 jari 447             bg.add(dataButton);
2 26 Feb 07 jari 448             dataButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 449                 public void actionPerformed(ActionEvent ae) {
2 26 Feb 07 jari 450                     browseButton.setEnabled(fileButton.isSelected());
2 26 Feb 07 jari 451                     popField.setEnabled(fileButton.isSelected());
2 26 Feb 07 jari 452                     popField.setBackground(Color.lightGray);
2 26 Feb 07 jari 453                     fileLabel.setEnabled(fileButton.isSelected());
2 26 Feb 07 jari 454                     
2 26 Feb 07 jari 455                 }
2 26 Feb 07 jari 456             });
2 26 Feb 07 jari 457             
2 26 Feb 07 jari 458             browseButton = new JButton("File Browser");
2 26 Feb 07 jari 459             browseButton.setFocusPainted(false);
2 26 Feb 07 jari 460             browseButton.setPreferredSize(new Dimension(150, 25));
2 26 Feb 07 jari 461             browseButton.setSize(150, 25);
2 26 Feb 07 jari 462             browseButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 463                 public void actionPerformed(ActionEvent ae) {
2 26 Feb 07 jari 464                     JFileChooser chooser = new JFileChooser(TMEV.getFile("Data/"));
2 26 Feb 07 jari 465                     chooser.setDialogTitle("Population File Selection");
2 26 Feb 07 jari 466                     chooser.setMultiSelectionEnabled(false);
2 26 Feb 07 jari 467                     if(chooser.showOpenDialog(parent) == JOptionPane.OK_OPTION){
2 26 Feb 07 jari 468                         updatePopField(chooser.getSelectedFile().getPath());
2 26 Feb 07 jari 469                     }
2 26 Feb 07 jari 470                 }
2 26 Feb 07 jari 471             });
2 26 Feb 07 jari 472             
2 26 Feb 07 jari 473             fileLabel = new JLabel("File: ");
2 26 Feb 07 jari 474             popField = new JTextField(25);
2 26 Feb 07 jari 475             
2 26 Feb 07 jari 476             add(fileButton, new GridBagConstraints(0,0,3,1,1,0,GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(10,30,0,0), 0,0));
2 26 Feb 07 jari 477             add(fileLabel, new GridBagConstraints(0,1,1,1,0,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5,30,0,0), 0,0));
2 26 Feb 07 jari 478             add(popField, new GridBagConstraints(1,1,1,1,1,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5,10,0,0), 0,0));
2 26 Feb 07 jari 479             add(browseButton, new GridBagConstraints(2,1,1,1,0,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5,25,0,20), 0,0));
2 26 Feb 07 jari 480             
2 26 Feb 07 jari 481             add(dataButton, new GridBagConstraints(0,2,3,1,1,0,GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(15,30,20,0), 0,0));
2 26 Feb 07 jari 482         }
2 26 Feb 07 jari 483         
2 26 Feb 07 jari 484         private void setEnableControls(boolean enable) {
2 26 Feb 07 jari 485             fileButton.setEnabled(enable);
2 26 Feb 07 jari 486             dataButton.setEnabled(enable);
2 26 Feb 07 jari 487             popField.setEnabled(enable);
2 26 Feb 07 jari 488             browseButton.setEnabled(enable);
2 26 Feb 07 jari 489             fileLabel.setEnabled(enable);
2 26 Feb 07 jari 490             setOpaque(enable);
2 26 Feb 07 jari 491             tabbedPane.setEnabledAt(0, enable);
2 26 Feb 07 jari 492         }
2 26 Feb 07 jari 493         
2 26 Feb 07 jari 494         private void updatePopField(String file) {
2 26 Feb 07 jari 495             this.popField.setText(file);
2 26 Feb 07 jari 496         }
2 26 Feb 07 jari 497         
2 26 Feb 07 jari 498         private String getPopFile() {
2 26 Feb 07 jari 499             return popField.getText();
2 26 Feb 07 jari 500         }        
2 26 Feb 07 jari 501     }
2 26 Feb 07 jari 502     
2 26 Feb 07 jari 503     
2 26 Feb 07 jari 504     
2 26 Feb 07 jari 505     /** Contains annotation parameter controls.
2 26 Feb 07 jari 506      */
2 26 Feb 07 jari 507     private class EaseParameterPanel extends JPanel {
2 26 Feb 07 jari 508         
2 26 Feb 07 jari 509         JTextField converterFileField;
2 26 Feb 07 jari 510         JList fileList;
2 26 Feb 07 jari 511         JButton browserButton;
2 26 Feb 07 jari 512         JTextField minClusterSizeField;
2 26 Feb 07 jari 513         JComboBox fieldNamesBox;
2 26 Feb 07 jari 514         
2 26 Feb 07 jari 515         JList annFileList;
2 26 Feb 07 jari 516         Vector annVector;
2 26 Feb 07 jari 517         JButton removeButton;
2 26 Feb 07 jari 518         JCheckBox useAnnBox;
2 26 Feb 07 jari 519         JLabel fileLabel;
2 26 Feb 07 jari 520         
2 26 Feb 07 jari 521         /** Constructs a new EaseParameterPanel
2 26 Feb 07 jari 522          * @param fieldNames annotation types
2 26 Feb 07 jari 523          */
2 26 Feb 07 jari 524         public EaseParameterPanel(String [] fieldNames) {
2 26 Feb 07 jari 525             //Conversion File Panel
2 26 Feb 07 jari 526             JPanel convPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 527             convPanel.setBackground(Color.white);
2 26 Feb 07 jari 528             convPanel.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Annotation Conversion File", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 529             useAnnBox = new JCheckBox("use annotation converter", false);
2 26 Feb 07 jari 530             useAnnBox.setActionCommand("use-converter-command");
2 26 Feb 07 jari 531             useAnnBox.addActionListener(listener);
2 26 Feb 07 jari 532             useAnnBox.setBackground(Color.white);
2 26 Feb 07 jari 533             useAnnBox.setFocusPainted(false);
2 26 Feb 07 jari 534             
2 26 Feb 07 jari 535             converterFileField = new JTextField(30);
2 26 Feb 07 jari 536             converterFileField.setBorder(BorderFactory.createBevelBorder(BevelBorder.LOWERED, Color.lightGray, Color.gray));
2 26 Feb 07 jari 537             converterFileField.setEnabled(false);
2 26 Feb 07 jari 538             converterFileField.setBackground(Color.lightGray);
2 26 Feb 07 jari 539             
2 26 Feb 07 jari 540             browserButton = new JButton("File Browser");
2 26 Feb 07 jari 541             browserButton.setActionCommand("converter-file-browser-command");
2 26 Feb 07 jari 542             browserButton.setFocusPainted(false);
2 26 Feb 07 jari 543             browserButton.setPreferredSize(new Dimension(150, 25));
2 26 Feb 07 jari 544             browserButton.setSize(150, 25);
2 26 Feb 07 jari 545             browserButton.addActionListener(listener);
2 26 Feb 07 jari 546             browserButton.setEnabled(false);
2 26 Feb 07 jari 547             
2 26 Feb 07 jari 548             fileLabel = new JLabel("File :");
2 26 Feb 07 jari 549             fileLabel.setEnabled(false);
2 26 Feb 07 jari 550             convPanel.add(useAnnBox, new GridBagConstraints(0,0,3,1,0.0,0.0,GridBagConstraints.WEST,GridBagConstraints.BOTH,new Insets(0,15,15,0),0,0));
2 26 Feb 07 jari 551             convPanel.add(fileLabel, new GridBagConstraints(0,1,1,1,0.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,15,15,0),0,0));
2 26 Feb 07 jari 552             convPanel.add(this.browserButton, new GridBagConstraints(0,2,3,1,0.0,0.0,GridBagConstraints.WEST,GridBagConstraints.VERTICAL,new Insets(0,15,0,0),0,0));
2 26 Feb 07 jari 553             convPanel.add(this.converterFileField, new GridBagConstraints(1,1,2,1,0.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,15,15,0),0,0));
2 26 Feb 07 jari 554             
2 26 Feb 07 jari 555             //Annotation file panel
2 26 Feb 07 jari 556             JPanel annPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 557             annPanel.setBackground(Color.white);
2 26 Feb 07 jari 558             annPanel.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Gene Annotation / Gene Ontology Linking Files", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 559             
2 26 Feb 07 jari 560             annVector = new Vector();
2 26 Feb 07 jari 561             annFileList = new JList(new DefaultListModel());
2 26 Feb 07 jari 562             annFileList.setCellRenderer(new ListRenderer());
2 26 Feb 07 jari 563             annFileList.setBorder(BorderFactory.createBevelBorder(BevelBorder.LOWERED));
2 26 Feb 07 jari 564             JScrollPane annPane = new JScrollPane(annFileList);
2 26 Feb 07 jari 565             
2 26 Feb 07 jari 566             JButton  annButton = new JButton("Add Files");
2 26 Feb 07 jari 567             annButton.setActionCommand("ann-file-browser-command");
2 26 Feb 07 jari 568             annButton.addActionListener(listener);
2 26 Feb 07 jari 569             annButton.setFocusPainted(false);
2 26 Feb 07 jari 570             annButton.setPreferredSize(new Dimension(150, 25));
2 26 Feb 07 jari 571             annButton.setSize(150, 25);
2 26 Feb 07 jari 572             
2 26 Feb 07 jari 573             removeButton = new JButton("Remove Selected");
2 26 Feb 07 jari 574             removeButton.setActionCommand("remove-ann-file-command");
2 26 Feb 07 jari 575             removeButton.addActionListener(listener);
2 26 Feb 07 jari 576             removeButton.setFocusPainted(false);
2 26 Feb 07 jari 577             removeButton.setPreferredSize(new Dimension(150, 25));
2 26 Feb 07 jari 578             removeButton.setSize(150, 25);
2 26 Feb 07 jari 579             removeButton.setEnabled(false);
2 26 Feb 07 jari 580             
2 26 Feb 07 jari 581             JPanel fillPanel = new JPanel();
2 26 Feb 07 jari 582             fillPanel.setBackground(Color.white);
2 26 Feb 07 jari 583             annPanel.add(fillPanel, new GridBagConstraints(0,0,1,1,0.0,0.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0), 0,0));
2 26 Feb 07 jari 584             annPanel.add(annButton, new GridBagConstraints(1,0,1,1,0.0,0.0, GridBagConstraints.EAST, GridBagConstraints.VERTICAL, new Insets(0,0,10,5), 0,0));
2 26 Feb 07 jari 585             annPanel.add(removeButton, new GridBagConstraints(2,0,1,1,0.0,0.0, GridBagConstraints.CENTER, GridBagConstraints.VERTICAL, new Insets(0,5,10,0), 0,0));
2 26 Feb 07 jari 586             annPanel.add(new JLabel("Files: "), new GridBagConstraints(0,1,1,1,0.0,0.0, GridBagConstraints.NORTHWEST, GridBagConstraints.NONE, new Insets(0,0,0,0), 0,0));
2 26 Feb 07 jari 587             annPanel.add(annPane, new GridBagConstraints(1,1,2,1,0.0,1.0, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0), 0,0));
2 26 Feb 07 jari 588             
2 26 Feb 07 jari 589             sep = System.getProperty("file.separator");
2 26 Feb 07 jari 590             File file = new File(getBaseFileLocation()+"/Data/Convert/");
2 26 Feb 07 jari 591             String tempPath = file.getPath();
2 26 Feb 07 jari 592             Vector fileVector = new Vector();
2 26 Feb 07 jari 593             fileList = new JList(fileVector);
2 26 Feb 07 jari 594             if(file.exists()){
2 26 Feb 07 jari 595                 String [] listFileNames = file.list();
2 26 Feb 07 jari 596                 for(int i = 0; i < listFileNames.length; i++){
2 26 Feb 07 jari 597                     File tempFile = new File(tempPath+sep+listFileNames[i]);
2 26 Feb 07 jari 598                     if(tempFile.isFile())
2 26 Feb 07 jari 599                         fileVector.add(listFileNames[i]);
2 26 Feb 07 jari 600                 }
2 26 Feb 07 jari 601                 if(fileVector.size() > 0){
2 26 Feb 07 jari 602                     converterFileField.setText(tempPath+sep+((String)fileVector.elementAt(0)));
2 26 Feb 07 jari 603                 }
2 26 Feb 07 jari 604             }
2 26 Feb 07 jari 605             
2 26 Feb 07 jari 606             this.fieldNamesBox = new JComboBox(fieldNames);
2 26 Feb 07 jari 607             this.fieldNamesBox.setEditable(false);
2 26 Feb 07 jari 608             
2 26 Feb 07 jari 609             minClusterSizeField = new JTextField(5);
2 26 Feb 07 jari 610             minClusterSizeField.setText("5");
2 26 Feb 07 jari 611             
2 26 Feb 07 jari 612             JPanel contentPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 613             
2 26 Feb 07 jari 614             JPanel easeFilePanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 615             
2 26 Feb 07 jari 616             this.setLayout(new GridBagLayout());
2 26 Feb 07 jari 617             
2 26 Feb 07 jari 618             JPanel annotKeyPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 619             annotKeyPanel.setBackground(Color.white);
2 26 Feb 07 jari 620             annotKeyPanel.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "MeV Annotation Key  (\"Unique ID\")", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 621             
2 26 Feb 07 jari 622             annotKeyPanel.add(new JLabel("Annotation Key:  "), new GridBagConstraints(0,0,1,1,0.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 623             annotKeyPanel.add(this.fieldNamesBox, new GridBagConstraints(1,0,1,1,0.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 624             
2 26 Feb 07 jari 625             this.add(annotKeyPanel, new GridBagConstraints(0,0,1,1,1.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 626             this.add(convPanel, new GridBagConstraints(0,1,1,1,1.0,0.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 627             this.add(annPanel, new GridBagConstraints(0,2,1,1,1.0,1.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH,new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 628         }
2 26 Feb 07 jari 629         
2 26 Feb 07 jari 630         private void updateFileDirectoryField(){
2 26 Feb 07 jari 631             
2 26 Feb 07 jari 632             File file = new File((String)this.fileList.getSelectedValue());
2 26 Feb 07 jari 633             if(file == null)
2 26 Feb 07 jari 634                 return;
2 26 Feb 07 jari 635             
2 26 Feb 07 jari 636             String tempPath = file.getParent();
2 26 Feb 07 jari 637             int fileIndex = this.fileList.getSelectedIndex();
2 26 Feb 07 jari 638             String fileName = (String)(this.fileList.getModel().getElementAt(this.fileList.getSelectedIndex()));
2 26 Feb 07 jari 639             this.converterFileField.setText(tempPath+sep+fileName);
2 26 Feb 07 jari 640         }
2 26 Feb 07 jari 641         
2 26 Feb 07 jari 642         private void updateAnnFileList(File [] files){
2 26 Feb 07 jari 643             File file;
2 26 Feb 07 jari 644             for(int i = 0; i < files.length; i++){
2 26 Feb 07 jari 645                 file = files[i];
2 26 Feb 07 jari 646                 if(!((DefaultListModel) annFileList.getModel()).contains(file)){
2 26 Feb 07 jari 647                     ((DefaultListModel) annFileList.getModel()).addElement(file);
2 26 Feb 07 jari 648                 }
2 26 Feb 07 jari 649             }
2 26 Feb 07 jari 650             annFileList.validate();
2 26 Feb 07 jari 651         }
2 26 Feb 07 jari 652         
2 26 Feb 07 jari 653         /** Returns the converter file name (or null if none)
2 26 Feb 07 jari 654          */
2 26 Feb 07 jari 655         public String getConverterFileName(){
2 26 Feb 07 jari 656             if(this.useAnnBox.isSelected())
2 26 Feb 07 jari 657                 return converterFileField.getText();
2 26 Feb 07 jari 658             return null;
2 26 Feb 07 jari 659         }
2 26 Feb 07 jari 660         
2 26 Feb 07 jari 661         /** Returns the annotation type string.
2 26 Feb 07 jari 662          */
2 26 Feb 07 jari 663         public String getAnnotationKeyType(){
2 26 Feb 07 jari 664             return (String)this.fieldNamesBox.getSelectedItem();
2 26 Feb 07 jari 665         }
2 26 Feb 07 jari 666         
2 26 Feb 07 jari 667         private class EaseListListener implements ListSelectionListener {
2 26 Feb 07 jari 668             public void valueChanged(ListSelectionEvent listSelectionEvent) {
2 26 Feb 07 jari 669                 updateFileDirectoryField();
2 26 Feb 07 jari 670             }
2 26 Feb 07 jari 671         }
2 26 Feb 07 jari 672         
2 26 Feb 07 jari 673         private void updateConverterFileField(String field){
2 26 Feb 07 jari 674             this.converterFileField.setText(field);
2 26 Feb 07 jari 675         }
2 26 Feb 07 jari 676         
2 26 Feb 07 jari 677         /** Returns the list of annotation-theme mapping files.
2 26 Feb 07 jari 678          */
2 26 Feb 07 jari 679         public String [] getAnnToGOFileList(){
2 26 Feb 07 jari 680             String [] fileNames = new String[((DefaultListModel) annFileList.getModel()).size()];
2 26 Feb 07 jari 681             for(int i = 0; i < fileNames.length; i++){
2 26 Feb 07 jari 682                 fileNames[i] = ((File)(((DefaultListModel)annFileList.getModel()).elementAt(i))).getPath();
2 26 Feb 07 jari 683             }
2 26 Feb 07 jari 684             return fileNames;
2 26 Feb 07 jari 685         }
2 26 Feb 07 jari 686         
2 26 Feb 07 jari 687         public void removeSelectedFiles(){
2 26 Feb 07 jari 688             int [] indices = annFileList.getSelectedIndices();
2 26 Feb 07 jari 689             
2 26 Feb 07 jari 690             for(int i = 0; i < indices.length; i++){
2 26 Feb 07 jari 691                 // annFileList.remove(indices[i]);
2 26 Feb 07 jari 692                 ((DefaultListModel)annFileList.getModel()).removeElementAt(indices[i]);
2 26 Feb 07 jari 693             }
2 26 Feb 07 jari 694             if(annFileList.getModel().getSize() < 1){
2 26 Feb 07 jari 695                 this.removeButton.setEnabled(false);
2 26 Feb 07 jari 696                 okButton.setEnabled(false);
2 26 Feb 07 jari 697             }
2 26 Feb 07 jari 698             annFileList.validate();
2 26 Feb 07 jari 699         }
2 26 Feb 07 jari 700         
2 26 Feb 07 jari 701         private class ListRenderer extends DefaultListCellRenderer {
2 26 Feb 07 jari 702             public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
2 26 Feb 07 jari 703                 super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
2 26 Feb 07 jari 704                 File file = (File) value;
2 26 Feb 07 jari 705                 setText(file.getName());
2 26 Feb 07 jari 706                 return this;
2 26 Feb 07 jari 707             }
2 26 Feb 07 jari 708         }
2 26 Feb 07 jari 709     }
2 26 Feb 07 jari 710     
2 26 Feb 07 jari 711     /** Contains statistical parameter controls.
2 26 Feb 07 jari 712      */
2 26 Feb 07 jari 713     private class AlphaPanel extends JPanel{
2 26 Feb 07 jari 714         
2 26 Feb 07 jari 715         //Stats
2 26 Feb 07 jari 716         private JCheckBox fisherBox;
2 26 Feb 07 jari 717         private JCheckBox easeBox;
2 26 Feb 07 jari 718         //mult. corrections
2 26 Feb 07 jari 719         private JCheckBox bonferroniBox;
2 26 Feb 07 jari 720         private JCheckBox sidakBox;
2 26 Feb 07 jari 721         private JCheckBox bonferroniStepBox;
2 26 Feb 07 jari 722         private JCheckBox permBox;
2 26 Feb 07 jari 723         private JTextField permField;
2 26 Feb 07 jari 724         private JLabel permLabel;
2 26 Feb 07 jari 725         //Trim params
2 26 Feb 07 jari 726         private JCheckBox trimBox;
2 26 Feb 07 jari 727         private JCheckBox trimNBox;
2 26 Feb 07 jari 728         private JLabel trimNLabel;
2 26 Feb 07 jari 729         private JTextField trimNField;
2 26 Feb 07 jari 730         private JCheckBox trimPercentBox;
2 26 Feb 07 jari 731         private JLabel trimPercentLabel;
2 26 Feb 07 jari 732         private JTextField trimPercentField;
2 26 Feb 07 jari 733         
2 26 Feb 07 jari 734         
2 26 Feb 07 jari 735         /** Constucts a new AlphaPanel.
2 26 Feb 07 jari 736          */
2 26 Feb 07 jari 737         public AlphaPanel(){
2 26 Feb 07 jari 738             super(new GridBagLayout());
2 26 Feb 07 jari 739             setBackground(Color.white);
2 26 Feb 07 jari 740             
2 26 Feb 07 jari 741             //STAT PANEL
2 26 Feb 07 jari 742             JPanel statPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 743             statPanel.setBackground(Color.white);
2 26 Feb 07 jari 744             statPanel.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Reported Statistic", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 745             
2 26 Feb 07 jari 746             ButtonGroup bg = new ButtonGroup();
2 26 Feb 07 jari 747             fisherBox = new JCheckBox("Fisher Exact Probability", true);
2 26 Feb 07 jari 748             fisherBox.setBackground(Color.white);
2 26 Feb 07 jari 749             fisherBox.setFocusPainted(false);
2 26 Feb 07 jari 750             bg.add(fisherBox);
2 26 Feb 07 jari 751             
2 26 Feb 07 jari 752             easeBox = new JCheckBox("EASE Score", false);
2 26 Feb 07 jari 753             easeBox.setBackground(Color.white);
2 26 Feb 07 jari 754             easeBox.setFocusPainted(false);
2 26 Feb 07 jari 755             bg.add(easeBox);
2 26 Feb 07 jari 756             
2 26 Feb 07 jari 757             statPanel.add(fisherBox, new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 758             statPanel.add(easeBox, new GridBagConstraints(0,1,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,10,0),0,0));
2 26 Feb 07 jari 759             
2 26 Feb 07 jari 760             
2 26 Feb 07 jari 761             //P-value Correction Panel
2 26 Feb 07 jari 762             JPanel correctionPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 763             correctionPanel.setBackground(Color.white);
2 26 Feb 07 jari 764             correctionPanel.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Multiplicity Corrections", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 765             
2 26 Feb 07 jari 766             bonferroniBox = new JCheckBox("Bonferroni Correction", false);
2 26 Feb 07 jari 767             bonferroniBox.setBackground(Color.white);
2 26 Feb 07 jari 768             bonferroniBox.setFocusPainted(false);
2 26 Feb 07 jari 769             
2 26 Feb 07 jari 770             bonferroniStepBox = new JCheckBox("Bonferroni Step Down Correction", false);
2 26 Feb 07 jari 771             bonferroniStepBox.setBackground(Color.white);
2 26 Feb 07 jari 772             bonferroniStepBox.setFocusPainted(false);
2 26 Feb 07 jari 773             
2 26 Feb 07 jari 774             sidakBox = new JCheckBox("Sidak Method", false);
2 26 Feb 07 jari 775             sidakBox.setBackground(Color.white);
2 26 Feb 07 jari 776             sidakBox.setFocusPainted(false);
2 26 Feb 07 jari 777             
2 26 Feb 07 jari 778             permBox = new JCheckBox("Resampling Probability Analysis", false);
2 26 Feb 07 jari 779             permBox.setActionCommand("permutation-analysis-command");
2 26 Feb 07 jari 780             permBox.setBackground(Color.white);
2 26 Feb 07 jari 781             permBox.setFocusPainted(false);
2 26 Feb 07 jari 782             permBox.addActionListener(listener);
2 26 Feb 07 jari 783             //permBox.setEnabled(false);
2 26 Feb 07 jari 784             
2 26 Feb 07 jari 785             permField = new JTextField("1000", 10);
2 26 Feb 07 jari 786             permField.setBackground(Color.white);
2 26 Feb 07 jari 787             //permField.setEnabled(false);
2 26 Feb 07 jari 788             
2 26 Feb 07 jari 789             permLabel = new JLabel("Number of Permutations");
2 26 Feb 07 jari 790             permLabel.setBackground(Color.white);
2 26 Feb 07 jari 791             //permLabel.setEnabled(false);
2 26 Feb 07 jari 792             
2 26 Feb 07 jari 793             correctionPanel.add(bonferroniBox, new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.WEST,GridBagConstraints.BOTH, new Insets(10,0,0,0),0,0));
2 26 Feb 07 jari 794             correctionPanel.add(sidakBox, new GridBagConstraints(1,0,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(10,0,0,0),0,0));
2 26 Feb 07 jari 795             correctionPanel.add(bonferroniStepBox, new GridBagConstraints(0,1,2,1,0,0,GridBagConstraints.WEST,GridBagConstraints.BOTH, new Insets(0,0,10,0),0,0));
2 26 Feb 07 jari 796             correctionPanel.add(permBox, new GridBagConstraints(0,2,2,1,0,0,GridBagConstraints.WEST,GridBagConstraints.BOTH, new Insets(0,0,5,0),0,0));
2 26 Feb 07 jari 797             correctionPanel.add(permLabel, new GridBagConstraints(0,3,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,15,0),0,0));
2 26 Feb 07 jari 798             correctionPanel.add(permField, new GridBagConstraints(1,3,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.VERTICAL, new Insets(0,0,15,0),0,0));
2 26 Feb 07 jari 799             
2 26 Feb 07 jari 800             //Trim Panel
2 26 Feb 07 jari 801             JPanel trimPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 802             trimPanel.setBackground(Color.white);
2 26 Feb 07 jari 803             trimPanel.setBorder(BorderFactory.createTitledBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), "Trim Parameters", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, font, Color.black));
2 26 Feb 07 jari 804             
2 26 Feb 07 jari 805             trimBox = new JCheckBox("Trim Resulting Groups", false);
2 26 Feb 07 jari 806             trimBox.setActionCommand("trim-result-command");
2 26 Feb 07 jari 807             trimBox.addActionListener(listener);
2 26 Feb 07 jari 808             trimBox.setBackground(Color.white);
2 26 Feb 07 jari 809             trimBox.setHorizontalAlignment(javax.swing.SwingConstants.CENTER);
2 26 Feb 07 jari 810             trimBox.setFocusPainted(false);
2 26 Feb 07 jari 811             
2 26 Feb 07 jari 812             bg = new ButtonGroup();
2 26 Feb 07 jari 813             
2 26 Feb 07 jari 814             trimNBox = new JCheckBox("Select Minimum Hit Number", true);
2 26 Feb 07 jari 815             trimNBox.setActionCommand("trim-result-command");
2 26 Feb 07 jari 816             trimNBox.addActionListener(listener);
2 26 Feb 07 jari 817             trimNBox.setEnabled(false);
2 26 Feb 07 jari 818             trimNBox.setBackground(Color.white);
2 26 Feb 07 jari 819             trimNBox.setFocusPainted(false);
2 26 Feb 07 jari 820             bg.add(trimNBox);
2 26 Feb 07 jari 821             
2 26 Feb 07 jari 822             trimNLabel = new JLabel("Min. Hits");
2 26 Feb 07 jari 823             trimNLabel.setBackground(Color.white);
2 26 Feb 07 jari 824             trimNLabel.setEnabled(false);
2 26 Feb 07 jari 825             
2 26 Feb 07 jari 826             trimNField = new JTextField("5", 10);
2 26 Feb 07 jari 827             trimNField.setEnabled(false);
2 26 Feb 07 jari 828             
2 26 Feb 07 jari 829             trimPercentBox = new JCheckBox("Select Minimum Hit Percentage", false);
2 26 Feb 07 jari 830             trimPercentBox.setActionCommand("trim-result-command");
2 26 Feb 07 jari 831             trimPercentBox.addActionListener(listener);
2 26 Feb 07 jari 832             trimPercentBox.setEnabled(false);
2 26 Feb 07 jari 833             trimPercentBox.setBackground(Color.white);
2 26 Feb 07 jari 834             trimPercentBox.setFocusPainted(false);
2 26 Feb 07 jari 835             bg.add(trimPercentBox);
2 26 Feb 07 jari 836             
2 26 Feb 07 jari 837             trimPercentLabel = new JLabel("Percent Hits");
2 26 Feb 07 jari 838             trimPercentLabel.setBackground(Color.white);
2 26 Feb 07 jari 839             trimPercentLabel.setEnabled(false);
2 26 Feb 07 jari 840             
2 26 Feb 07 jari 841             trimPercentField = new JTextField("5", 10);
2 26 Feb 07 jari 842             trimPercentField.setEnabled(false);
2 26 Feb 07 jari 843             
2 26 Feb 07 jari 844             trimPanel.add(trimBox, new GridBagConstraints(0,0,3,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,20,0),0,0));
2 26 Feb 07 jari 845             
2 26 Feb 07 jari 846             trimPanel.add(trimNBox, new GridBagConstraints(0,1,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 847             trimPanel.add(trimNLabel, new GridBagConstraints(1,1,1,1,0,0,GridBagConstraints.EAST,GridBagConstraints.BOTH, new Insets(0,20,0,15),0,0));
2 26 Feb 07 jari 848             trimPanel.add(trimNField, new GridBagConstraints(2,1,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.NONE, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 849             
2 26 Feb 07 jari 850             trimPanel.add(trimPercentBox, new GridBagConstraints(0,2,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(10,0,0,0),0,0));
2 26 Feb 07 jari 851             trimPanel.add(trimPercentLabel, new GridBagConstraints(1,2,1,1,0,0,GridBagConstraints.EAST,GridBagConstraints.BOTH, new Insets(10,20,0,15),0,0));
2 26 Feb 07 jari 852             trimPanel.add(trimPercentField, new GridBagConstraints(2,2,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.NONE, new Insets(10,0,0,0),0,0));
2 26 Feb 07 jari 853             
2 26 Feb 07 jari 854             //Add panels to main panel
2 26 Feb 07 jari 855             add(statPanel, new GridBagConstraints(0,0,1,1,1.0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 856             add(correctionPanel, new GridBagConstraints(0,1,1,1,1.0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 857             add(trimPanel, new GridBagConstraints(0,2,1,1,1.0,1.0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 858         }
2 26 Feb 07 jari 859         
2 26 Feb 07 jari 860         /** Indicates if permutations are selected.
2 26 Feb 07 jari 861          */
2 26 Feb 07 jari 862         public boolean performPermutations(){
2 26 Feb 07 jari 863             return permBox.isSelected();
2 26 Feb 07 jari 864         }
2 26 Feb 07 jari 865         
2 26 Feb 07 jari 866         public void setEnablePermutations(){
2 26 Feb 07 jari 867             permLabel.setEnabled(permBox.isSelected());
2 26 Feb 07 jari 868             permField.setEnabled(permBox.isSelected());
2 26 Feb 07 jari 869         }
2 26 Feb 07 jari 870         
2 26 Feb 07 jari 871         public void validateTrimOptions(){
2 26 Feb 07 jari 872             if(this.trimBox.isSelected()){
2 26 Feb 07 jari 873                 trimNBox.setEnabled(true);
2 26 Feb 07 jari 874                 trimPercentBox.setEnabled(true);
2 26 Feb 07 jari 875                 
2 26 Feb 07 jari 876                 trimNLabel.setEnabled(trimNBox.isSelected());
2 26 Feb 07 jari 877                 trimNField.setEnabled(trimNBox.isSelected());
2 26 Feb 07 jari 878                 trimPercentLabel.setEnabled(!trimNBox.isSelected());
2 26 Feb 07 jari 879                 trimPercentField.setEnabled(!trimNBox.isSelected());
2 26 Feb 07 jari 880             } else {
2 26 Feb 07 jari 881                 trimNBox.setEnabled(false);
2 26 Feb 07 jari 882                 trimPercentBox.setEnabled(false);
2 26 Feb 07 jari 883                 
2 26 Feb 07 jari 884                 trimNLabel.setEnabled(false);
2 26 Feb 07 jari 885                 trimNField.setEnabled(false);
2 26 Feb 07 jari 886                 trimPercentLabel.setEnabled(false);
2 26 Feb 07 jari 887                 trimPercentField.setEnabled(false);
2 26 Feb 07 jari 888             }
2 26 Feb 07 jari 889         }
2 26 Feb 07 jari 890     }
2 26 Feb 07 jari 891     
2 26 Feb 07 jari 892     private class ConfigPanel extends ParameterPanel {
2 26 Feb 07 jari 893
2 26 Feb 07 jari 894         JTextField defaultFileBaseLocation;
2 26 Feb 07 jari 895         
2 26 Feb 07 jari 896         public ConfigPanel() {
2 26 Feb 07 jari 897             super("File Updates and Configuration");
2 26 Feb 07 jari 898             setLayout(new GridBagLayout());
2 26 Feb 07 jari 899             
2 26 Feb 07 jari 900             JButton updateFilesButton = new JButton("Update EASE File System");
2 26 Feb 07 jari 901             updateFilesButton.setActionCommand("update-files-command");
2 26 Feb 07 jari 902             updateFilesButton.setFocusPainted(false);
2 26 Feb 07 jari 903             updateFilesButton.addActionListener(listener);
2 26 Feb 07 jari 904             updateFilesButton.setToolTipText("<html>Downloads EASE annotation files<br>for a selected species and array type.</html>");
2 26 Feb 07 jari 905             JButton browseFileBaseButton = new JButton("Select EASE File System");
2 26 Feb 07 jari 906             browseFileBaseButton.setActionCommand("select-file-base-command");
2 26 Feb 07 jari 907             browseFileBaseButton.setFocusPainted(false);
2 26 Feb 07 jari 908             browseFileBaseButton.addActionListener(listener);
2 26 Feb 07 jari 909             browseFileBaseButton.setToolTipText("<html>Helps select the EASE annotation file system<br>that corresponds the current species and array type.</html>");
2 26 Feb 07 jari 910             defaultFileBaseLocation = new JTextField(TMEV.getFile("data/ease").getAbsolutePath(), 25);
2 26 Feb 07 jari 911             defaultFileBaseLocation.setEditable(true);
2 26 Feb 07 jari 912             
2 26 Feb 07 jari 913             add(browseFileBaseButton, new GridBagConstraints(0,0,1,1,0,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5,0,5,0), 0, 0));
2 26 Feb 07 jari 914             add(defaultFileBaseLocation,  new GridBagConstraints(1,0,1,1,1,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(5,5,5,0), 0, 0));            
2 26 Feb 07 jari 915             add(updateFilesButton, new GridBagConstraints(0,1,1,1,0,0,GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,5,0), 0, 0));                               
2 26 Feb 07 jari 916         }
2 26 Feb 07 jari 917         
2 26 Feb 07 jari 918         public void selectFileSystem() {
2 26 Feb 07 jari 919             String startDir = defaultFileBaseLocation.getText();
2 26 Feb 07 jari 920             File file = new File(startDir);
2 26 Feb 07 jari 921             if(!file.exists()) {                
2 26 Feb 07 jari 922                 file = TMEV.getFile("data/ease");
2 26 Feb 07 jari 923                 if(file == null) {
2 26 Feb 07 jari 924                     file = new File(System.getProperty("user.dir"));
2 26 Feb 07 jari 925                 }
2 26 Feb 07 jari 926             }
2 26 Feb 07 jari 927             JFileChooser chooser = new JFileChooser(file);
2 26 Feb 07 jari 928             chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
2 26 Feb 07 jari 929             if(chooser.showOpenDialog(EASEInitDialog.this) == JOptionPane.OK_OPTION) {
2 26 Feb 07 jari 930                 defaultFileBaseLocation.setText(chooser.getSelectedFile().getAbsolutePath());
2 26 Feb 07 jari 931             }
2 26 Feb 07 jari 932         }
2 26 Feb 07 jari 933         
2 26 Feb 07 jari 934         public String getBaseFileLocation() {
2 26 Feb 07 jari 935             return defaultFileBaseLocation.getText();
2 26 Feb 07 jari 936         }
2 26 Feb 07 jari 937     }
2 26 Feb 07 jari 938     
2 26 Feb 07 jari 939     /**
2 26 Feb 07 jari 940      * The class to listen to the dialog and check boxes items events.
2 26 Feb 07 jari 941      */
2 26 Feb 07 jari 942     private class EventListener extends DialogListener implements ItemListener {
2 26 Feb 07 jari 943         
2 26 Feb 07 jari 944         public void actionPerformed(ActionEvent e) {
2 26 Feb 07 jari 945             String command = e.getActionCommand();
2 26 Feb 07 jari 946             if (command.equals("use-converter-command")) {
2 26 Feb 07 jari 947                 if(easeParamPanel.useAnnBox.isSelected()){
2 26 Feb 07 jari 948                     easeParamPanel.browserButton.setEnabled(true);
2 26 Feb 07 jari 949                     easeParamPanel.converterFileField.setEnabled(true);
2 26 Feb 07 jari 950                     easeParamPanel.converterFileField.setBackground(Color.white);
2 26 Feb 07 jari 951                     easeParamPanel.fileLabel.setEnabled(true);
2 26 Feb 07 jari 952                 } else {
2 26 Feb 07 jari 953                     easeParamPanel.browserButton.setEnabled(false);
2 26 Feb 07 jari 954                     easeParamPanel.converterFileField.setEnabled(false);
2 26 Feb 07 jari 955                     easeParamPanel.converterFileField.setBackground(Color.lightGray);
2 26 Feb 07 jari 956                     easeParamPanel.fileLabel.setEnabled(false);
2 26 Feb 07 jari 957                 }
2 26 Feb 07 jari 958             } else if (command.equals("converter-file-browser-command")){
2 26 Feb 07 jari 959                 File convertFile = new File(getBaseFileLocation()+"/Data/Convert");
2 26 Feb 07 jari 960                 JFileChooser chooser = new JFileChooser(convertFile);
2 26 Feb 07 jari 961                 chooser.setDialogTitle("Annotation Converter Selection");
2 26 Feb 07 jari 962                 chooser.setMultiSelectionEnabled(false);
2 26 Feb 07 jari 963                 if(chooser.showOpenDialog(parent) == JOptionPane.OK_OPTION){
2 26 Feb 07 jari 964                     easeParamPanel.updateConverterFileField(chooser.getSelectedFile().getPath());
2 26 Feb 07 jari 965                 }
2 26 Feb 07 jari 966                 return;
2 26 Feb 07 jari 967             } else if (command.equals("ann-file-browser-command")){
2 26 Feb 07 jari 968                 
2 26 Feb 07 jari 969                 File classFile = new File(getBaseFileLocation()+"/Data/Class/");
2 26 Feb 07 jari 970                 JFileChooser chooser = new JFileChooser(classFile);
2 26 Feb 07 jari 971                 chooser.setDialogTitle("Annotation --> GO Term, File(s) Selection");
2 26 Feb 07 jari 972                 chooser.setMultiSelectionEnabled(true);
2 26 Feb 07 jari 973                 if(chooser.showOpenDialog(parent) == JOptionPane.OK_OPTION){
2 26 Feb 07 jari 974                     easeParamPanel.updateAnnFileList(chooser.getSelectedFiles());
2 26 Feb 07 jari 975                     easeParamPanel.removeButton.setEnabled(true);
2 26 Feb 07 jari 976                     okButton.setEnabled(true);
2 26 Feb 07 jari 977                 }
2 26 Feb 07 jari 978             } else if (command.equals("remove-ann-file-command")){
2 26 Feb 07 jari 979                 easeParamPanel.removeSelectedFiles();
2 26 Feb 07 jari 980             } else if (command.equals("permutation-analysis-command")){
2 26 Feb 07 jari 981                 alphaPanel.setEnablePermutations();
2 26 Feb 07 jari 982             } else if (command.equals("trim-result-command")){
2 26 Feb 07 jari 983                 alphaPanel.validateTrimOptions();
2 26 Feb 07 jari 984             } else if (command.equals("select-file-base-command")) {
2 26 Feb 07 jari 985                 configPanel.selectFileSystem();
2 26 Feb 07 jari 986             } else if (command.equals("update-files-command")) {
2 26 Feb 07 jari 987                 EASEUpdateManager manager = new EASEUpdateManager((JFrame)parent);
2 26 Feb 07 jari 988                 manager.updateFiles();
2 26 Feb 07 jari 989             } else if (command.equals("ok-command")) {
2 26 Feb 07 jari 990                 result = JOptionPane.OK_OPTION;
2 26 Feb 07 jari 991                 if(isClusterModeSelected() && popPanel.fileButton.isSelected()) {
2 26 Feb 07 jari 992                     String fileName = popPanel.popField.getText();
2 26 Feb 07 jari 993                     if(fileName == null || fileName.equals("") || fileName.equals(" ")) {
2 26 Feb 07 jari 994                         JOptionPane.showMessageDialog(parent, "You have selected to use a population file but have not "+
2 26 Feb 07 jari 995                         "entered a file name.  \nPlease enter a file or use the file browser to select a file.", "EASE Initialization: Missing Parameter", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 996                         tabbedPane.setSelectedIndex(0);
2 26 Feb 07 jari 997                         popPanel.popField.grabFocus();
2 26 Feb 07 jari 998                         popPanel.popField.selectAll();
2 26 Feb 07 jari 999                         popPanel.popField.setCaretPosition(0);
2 26 Feb 07 jari 1000                         return;
2 26 Feb 07 jari 1001                     }
2 26 Feb 07 jari 1002                 }
2 26 Feb 07 jari 1003                 
2 26 Feb 07 jari 1004                 if(getAnnToGOFileList().length == 0) {
2 26 Feb 07 jari 1005                     JOptionPane.showMessageDialog(parent, "You have not selected any gene annotation/gene ontology linking files. \n"+
2 26 Feb 07 jari 1006                     "Please enter files or use the browser to select files.", "EASE Initialization: Missing Parameter", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1007                     tabbedPane.setSelectedIndex(1);
2 26 Feb 07 jari 1008                     easeParamPanel.browserButton.grabFocus();
2 26 Feb 07 jari 1009                     return;
2 26 Feb 07 jari 1010                 }
2 26 Feb 07 jari 1011                 
2 26 Feb 07 jari 1012                 if(easeParamPanel.useAnnBox.isSelected()) {
2 26 Feb 07 jari 1013                     String fileName = easeParamPanel.getConverterFileName();
2 26 Feb 07 jari 1014                     if( fileName == null || fileName.equals("") || fileName.equals(" ") ) {
2 26 Feb 07 jari 1015                         JOptionPane.showMessageDialog(parent, "You have selected to use an annotation conversion file but have not made a file selection.\n" +
2 26 Feb 07 jari 1016                         "Please enter a file name or browse to select a file.", "EASE Initialization: Missing Parameter", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1017                         tabbedPane.setSelectedIndex(1);
2 26 Feb 07 jari 1018                         easeParamPanel.browserButton.grabFocus();
2 26 Feb 07 jari 1019                         return;
2 26 Feb 07 jari 1020                     }
2 26 Feb 07 jari 1021                 }                
2 26 Feb 07 jari 1022                 dispose();
2 26 Feb 07 jari 1023             } else if (command.equals("cancel-command")) {
2 26 Feb 07 jari 1024                 result = JOptionPane.CANCEL_OPTION;
2 26 Feb 07 jari 1025                 dispose();
2 26 Feb 07 jari 1026             } else if (command.equals("reset-command")){
2 26 Feb 07 jari 1027                 resetControls();
2 26 Feb 07 jari 1028                 result = JOptionPane.CANCEL_OPTION;
2 26 Feb 07 jari 1029                 return;
2 26 Feb 07 jari 1030             } else if (command.equals("info-command")){
2 26 Feb 07 jari 1031                 HelpWindow hw = new HelpWindow(EASEInitDialog.this, "EASE Initialization Dialog");
2 26 Feb 07 jari 1032                 result = JOptionPane.CANCEL_OPTION;
2 26 Feb 07 jari 1033                 if(hw.getWindowContent()){
2 26 Feb 07 jari 1034                     hw.setSize(600,600);
2 26 Feb 07 jari 1035                     hw.setLocation();
2 26 Feb 07 jari 1036                     hw.show();
2 26 Feb 07 jari 1037                 }
2 26 Feb 07 jari 1038                 else {
2 26 Feb 07 jari 1039                     hw.setVisible(false);
2 26 Feb 07 jari 1040                     hw.dispose();
2 26 Feb 07 jari 1041                 }
2 26 Feb 07 jari 1042             }
2 26 Feb 07 jari 1043         }
2 26 Feb 07 jari 1044         
2 26 Feb 07 jari 1045         public void itemStateChanged(ItemEvent e) {
2 26 Feb 07 jari 1046             //okButton.setEnabled(genes_box.isSelected() || cluster_box.isSelected());
2 26 Feb 07 jari 1047         }
2 26 Feb 07 jari 1048         
2 26 Feb 07 jari 1049         public void windowClosing(WindowEvent e) {
2 26 Feb 07 jari 1050             result = JOptionPane.CLOSED_OPTION;
2 26 Feb 07 jari 1051             dispose();
2 26 Feb 07 jari 1052         }
2 26 Feb 07 jari 1053     }
2 26 Feb 07 jari 1054     
2 26 Feb 07 jari 1055     public static void main(String [] args) {
2 26 Feb 07 jari 1056         String [] labels = new String [3];
2 26 Feb 07 jari 1057         labels[0] = "TC#";
2 26 Feb 07 jari 1058         labels[1] = "GB#";
2 26 Feb 07 jari 1059         labels[2] = "Role";
2 26 Feb 07 jari 1060
2 26 Feb 07 jari 1061         EASEInitDialog eid = new EASEInitDialog(new JFrame(), labels);
2 26 Feb 07 jari 1062         eid.showModal();
2 26 Feb 07 jari 1063     }
2 26 Feb 07 jari 1064 }

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