mev-4.0.01/source/org/tigr/microarray/mev/cluster/gui/impl/ttest/TtestInitDialog.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2 Copyright @ 1999-2005, 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: TtestInitDialog.java,v $
2 26 Feb 07 jari 7  * $Revision: 1.11 $
2 26 Feb 07 jari 8  * $Date: 2006/08/11 18:20:48 $
2 26 Feb 07 jari 9  * $Author: eleanorahowe $
2 26 Feb 07 jari 10  * $State: Exp $
2 26 Feb 07 jari 11  */
2 26 Feb 07 jari 12 package org.tigr.microarray.mev.cluster.gui.impl.ttest;
2 26 Feb 07 jari 13 import java.awt.Color;
2 26 Feb 07 jari 14 import java.awt.Component;
2 26 Feb 07 jari 15 import java.awt.Dimension;
2 26 Feb 07 jari 16 import java.awt.Font;
2 26 Feb 07 jari 17 import java.awt.Graphics;
2 26 Feb 07 jari 18 import java.awt.GridBagConstraints;
2 26 Feb 07 jari 19 import java.awt.GridBagLayout;
2 26 Feb 07 jari 20 import java.awt.Insets;
2 26 Feb 07 jari 21 import java.awt.Toolkit;
2 26 Feb 07 jari 22 import java.awt.event.ActionEvent;
2 26 Feb 07 jari 23 import java.awt.event.ActionListener;
2 26 Feb 07 jari 24 import java.io.BufferedReader;
2 26 Feb 07 jari 25 import java.io.File;
2 26 Feb 07 jari 26 import java.io.FileOutputStream;
2 26 Feb 07 jari 27 import java.io.FileReader;
2 26 Feb 07 jari 28 import java.io.PrintWriter;
2 26 Feb 07 jari 29 import java.util.Vector;
2 26 Feb 07 jari 30 import javax.swing.BorderFactory;
2 26 Feb 07 jari 31 import javax.swing.ButtonGroup;
2 26 Feb 07 jari 32 import javax.swing.DefaultListModel;
2 26 Feb 07 jari 33 import javax.swing.JButton;
2 26 Feb 07 jari 34 import javax.swing.JCheckBox;
2 26 Feb 07 jari 35 import javax.swing.JFileChooser;
2 26 Feb 07 jari 36 import javax.swing.JFrame;
2 26 Feb 07 jari 37 import javax.swing.JLabel;
2 26 Feb 07 jari 38 import javax.swing.JList;
2 26 Feb 07 jari 39 import javax.swing.JOptionPane;
2 26 Feb 07 jari 40 import javax.swing.JPanel;
2 26 Feb 07 jari 41 import javax.swing.JRadioButton;
2 26 Feb 07 jari 42 import javax.swing.JScrollPane;
2 26 Feb 07 jari 43 import javax.swing.JSplitPane;
2 26 Feb 07 jari 44 import javax.swing.JTabbedPane;
2 26 Feb 07 jari 45 import javax.swing.JTextField;
2 26 Feb 07 jari 46 import javax.swing.ScrollPaneConstants;
2 26 Feb 07 jari 47 import javax.swing.UIManager;
2 26 Feb 07 jari 48 import javax.swing.border.BevelBorder;
2 26 Feb 07 jari 49 import javax.swing.border.Border;
2 26 Feb 07 jari 50 import javax.swing.border.EtchedBorder;
2 26 Feb 07 jari 51 import javax.swing.border.TitledBorder;
2 26 Feb 07 jari 52 import javax.swing.event.ChangeEvent;
2 26 Feb 07 jari 53 import javax.swing.event.ChangeListener;
2 26 Feb 07 jari 54 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.AlgorithmDialog;
2 26 Feb 07 jari 55 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.HCLSigOnlyPanel;
2 26 Feb 07 jari 56 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.dialogHelpUtil.HelpWindow;
2 26 Feb 07 jari 57 import org.tigr.util.StringSplitter;
2 26 Feb 07 jari 58 /**
2 26 Feb 07 jari 59  *
2 26 Feb 07 jari 60  * @author  nbhagaba
2 26 Feb 07 jari 61  * @version
2 26 Feb 07 jari 62  */
2 26 Feb 07 jari 63 public class TtestInitDialog extends AlgorithmDialog {
2 26 Feb 07 jari 64     
2 26 Feb 07 jari 65     GroupExperimentsPanel gPanel;
2 26 Feb 07 jari 66     OneClassPanel oPanel;
2 26 Feb 07 jari 67     TwoClassPairedMainPanel tcpmPanel;    
2 26 Feb 07 jari 68     PValuePanel pPanel;
2 26 Feb 07 jari 69     SignificancePanel sPanel;
2 26 Feb 07 jari 70     //HCLSelectionPanel hclOpsPanel;
2 26 Feb 07 jari 71     HCLSigOnlyPanel hclOpsPanel;    
2 26 Feb 07 jari 72     Vector exptNames;
2 26 Feb 07 jari 73     JTabbedPane chooseDesignPane;
2 26 Feb 07 jari 74     DfCalcPanel dPanel;
2 26 Feb 07 jari 75     
2 26 Feb 07 jari 76     boolean lotsOfSamples = false;
2 26 Feb 07 jari 77     String lotsOfSamplesWarningText = "                                                Note: You can assign large numbers of samples quickly by using a saved text file.";
2 26 Feb 07 jari 78     
2 26 Feb 07 jari 79     public static final int GROUP_A = 1;
2 26 Feb 07 jari 80     public static final int GROUP_B = 2;
2 26 Feb 07 jari 81     public static final int NEITHER_GROUP = 3;
2 26 Feb 07 jari 82     public static final int JUST_ALPHA = 4;
2 26 Feb 07 jari 83     public static final int STD_BONFERRONI = 5;
2 26 Feb 07 jari 84     public static final int ADJ_BONFERRONI = 6;
2 26 Feb 07 jari 85     public static final int BETWEEN_SUBJECTS = 7;
2 26 Feb 07 jari 86     public static final int ONE_CLASS = 8;
2 26 Feb 07 jari 87     public static final int MAX_T = 9;
2 26 Feb 07 jari 88     public static final int MIN_P = 10;
2 26 Feb 07 jari 89     public static final int PAIRED = 11;   
2 26 Feb 07 jari 90     public static final int FALSE_NUM = 12;
2 26 Feb 07 jari 91     public static final int FALSE_PROP = 13;
2 26 Feb 07 jari 92     
2 26 Feb 07 jari 93     boolean okPressed = false;
2 26 Feb 07 jari 94     boolean permParamOkPressed = false;
2 26 Feb 07 jari 95     private int userNumCombs = 0;
2 26 Feb 07 jari 96     private boolean allCombsUsed = false;
2 26 Feb 07 jari 97     private int allPossCombs;
2 26 Feb 07 jari 98     private Color LABEL_COLOR = UIManager.getColor("Label.foreground");
2 26 Feb 07 jari 99     
2 26 Feb 07 jari 100     
2 26 Feb 07 jari 101     boolean tooMany = false;
2 26 Feb 07 jari 102     int count;
2 26 Feb 07 jari 103    
2 26 Feb 07 jari 104     final int fileLoadMin=20;
2 26 Feb 07 jari 105     /** Creates new TtestInitDialog */
2 26 Feb 07 jari 106     public TtestInitDialog(JFrame parentFrame, boolean modality, Vector exptNames) {
2 26 Feb 07 jari 107         super(parentFrame, "TTEST: T-test", modality);
2 26 Feb 07 jari 108         this.exptNames = exptNames;
2 26 Feb 07 jari 109         setBounds(0, 0, 800, 850);
2 26 Feb 07 jari 110         setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
2 26 Feb 07 jari 111         GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 112         GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 113         constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 114         JPanel pane = new JPanel();
2 26 Feb 07 jari 115         pane.setLayout(gridbag);
2 26 Feb 07 jari 116         
2 26 Feb 07 jari 117         if(exptNames.size()>fileLoadMin){
2 26 Feb 07 jari 118           lotsOfSamples = true;
2 26 Feb 07 jari 119         }
2 26 Feb 07 jari 120         
2 26 Feb 07 jari 121         chooseDesignPane = new JTabbedPane();
2 26 Feb 07 jari 122         sPanel = new SignificancePanel();
2 26 Feb 07 jari 123         pPanel = new PValuePanel();
2 26 Feb 07 jari 124         gPanel = new GroupExperimentsPanel(exptNames);
2 26 Feb 07 jari 125         for (count = 0; count < gPanel.groupARadioButtons.length; count++) {
2 26 Feb 07 jari 126             gPanel.groupARadioButtons[count].addActionListener(new ActionListener() {
2 26 Feb 07 jari 127                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 128                     //if (evt.getSource() == gPanel.groupARadioButtons[count]) {
2 26 Feb 07 jari 129                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 130                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 131                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 132                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 133                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 134                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 135                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 136                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 137                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 138                     pPanel.numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 139                     //}
2 26 Feb 07 jari 140                 }
2 26 Feb 07 jari 141             });
2 26 Feb 07 jari 142        }
2 26 Feb 07 jari 143         for (count = 0; count < gPanel.groupBRadioButtons.length; count++) {
2 26 Feb 07 jari 144             gPanel.groupBRadioButtons[count].addActionListener(new ActionListener() {
2 26 Feb 07 jari 145                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 146                     //if (evt.getSource() == gPanel.groupBRadioButtons[count]) {
2 26 Feb 07 jari 147                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 148                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 149                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 150                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 151                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 152                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 153                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 154                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 155                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 156                     pPanel.numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 157                     //}
2 26 Feb 07 jari 158                 }
2 26 Feb 07 jari 159                 
2 26 Feb 07 jari 160             });
2 26 Feb 07 jari 161         }
2 26 Feb 07 jari 162         
2 26 Feb 07 jari 163         for (count = 0; count < gPanel.neitherGroupRadioButtons.length; count++) {
2 26 Feb 07 jari 164             gPanel.neitherGroupRadioButtons[count].addActionListener(new ActionListener() {
2 26 Feb 07 jari 165                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 166                     //if (evt.getSource() == gPanel.neitherGroupRadioButtons[count]) {
2 26 Feb 07 jari 167                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 168                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 169                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 170                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 171                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 172                     sPanel.minPButton.setEnabled(false);                     
2 26 Feb 07 jari 173                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 174                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 175                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 176                     pPanel.numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 177                     //}
2 26 Feb 07 jari 178                 }
2 26 Feb 07 jari 179                 
2 26 Feb 07 jari 180             });
2 26 Feb 07 jari 181        }
2 26 Feb 07 jari 182         count = 0;
2 26 Feb 07 jari 183         oPanel = new OneClassPanel();
2 26 Feb 07 jari 184         for (int i = 0; i < oPanel.includeExpts.length; i++) {
2 26 Feb 07 jari 185             oPanel.includeExpts[i].addActionListener(new ActionListener() {
2 26 Feb 07 jari 186                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 187                     //if (evt.getSource() == gPanel.neitherGroupRadioButtons[count]) {
2 26 Feb 07 jari 188                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 189                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 190                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 191                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 192                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 193                     sPanel.minPButton.setEnabled(false);                     
2 26 Feb 07 jari 194                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 195                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 196                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 197                     pPanel.numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 198                     //}
2 26 Feb 07 jari 199                 }                
2 26 Feb 07 jari 200             });
2 26 Feb 07 jari 201        }
2 26 Feb 07 jari 202         chooseDesignPane.add("One-class", oPanel);
2 26 Feb 07 jari 203         chooseDesignPane.add("Between subjects", gPanel);
2 26 Feb 07 jari 204         tcpmPanel = new TwoClassPairedMainPanel();
2 26 Feb 07 jari 205         chooseDesignPane.add("Paired", tcpmPanel);        
2 26 Feb 07 jari 206         pPanel.tDistButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 207             public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 208                 sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 209                 sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 210                 sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 211                 sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 212                 sPanel.minPButton.setEnabled(false);  
2 26 Feb 07 jari 213                 sPanel.falseNumButton.setEnabled(false);
2 26 Feb 07 jari 214                 sPanel.falsePropButton.setEnabled(false);
2 26 Feb 07 jari 215                 sPanel.calcFDRPVals.setEnabled(false);
2 26 Feb 07 jari 216                 sPanel.fastFDRButton.setEnabled(false);
2 26 Feb 07 jari 217                 sPanel.slowFDRButton.setEnabled(false);
2 26 Feb 07 jari 218                 sPanel.falseNumField.setEnabled(false);
2 26 Feb 07 jari 219                 sPanel.falsePropField.setEnabled(false);
2 26 Feb 07 jari 220             }
2 26 Feb 07 jari 221         });
2 26 Feb 07 jari 222         pPanel.permutButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 223             public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 224                 if (evt.getSource() == pPanel.permutButton) {                    
2 26 Feb 07 jari 225                     sPanel.maxTButton.setEnabled(true);
2 26 Feb 07 jari 226                     //sPanel.minPButton.setEnabled(true);    // **** ENABLE THIS WHEN MINP MTHOD HAS BEEN DEBUGGED  - 1/12/2004  
2 26 Feb 07 jari 227                     sPanel.falseNumButton.setEnabled(true);
2 26 Feb 07 jari 228                     sPanel.falsePropButton.setEnabled(true);
2 26 Feb 07 jari 229                     //sPanel.calcFDRPVals.setEnabled(true);
2 26 Feb 07 jari 230                     sPanel.fastFDRButton.setEnabled(true);
2 26 Feb 07 jari 231                     //sPanel.slowFDRButton.setEnabled(true);
2 26 Feb 07 jari 232                     sPanel.falseNumField.setEnabled(true);
2 26 Feb 07 jari 233                     sPanel.falsePropField.setEnabled(true); 
2 26 Feb 07 jari 234                     
2 26 Feb 07 jari 235                     if (getTestDesign() == TtestInitDialog.BETWEEN_SUBJECTS) {
2 26 Feb 07 jari 236                         int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 237                         int grpACounter = 0;
2 26 Feb 07 jari 238                         int grpBCounter = 0;
2 26 Feb 07 jari 239                         for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 240                             if (grpAssignments[i] == GROUP_A) {
2 26 Feb 07 jari 241                                 grpACounter++;
2 26 Feb 07 jari 242                             } else if (grpAssignments[i] == GROUP_B) {
2 26 Feb 07 jari 243                                 grpBCounter++;
2 26 Feb 07 jari 244                             }
2 26 Feb 07 jari 245                         }
2 26 Feb 07 jari 246                         if ((grpACounter < 2) || (grpBCounter < 2)) {
2 26 Feb 07 jari 247                             pPanel.numCombsLabel.setForeground(Color.red);
2 26 Feb 07 jari 248                             pPanel.numCombsLabel.setText("Error! Group A and Group B must each contain more than one sample");
2 26 Feb 07 jari 249                             //JOptionPane.showMessageDialog(gPanel, "Group A and Group B must each contain more than one experiment", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 250                         } else {
2 26 Feb 07 jari 251                             int numCombs = 0;
2 26 Feb 07 jari 252                             pPanel.numCombsLabel.setForeground(Color.black);
2 26 Feb 07 jari 253                             pPanel.numCombsLabel.setText("There are too many unique permutations                                  ");
2 26 Feb 07 jari 254                             pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 255                             pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 256                             pPanel.randomGroupsButton.setSelected(true);
2 26 Feb 07 jari 257                             pPanel.timesField.setEnabled(true);
2 26 Feb 07 jari 258                             pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 259                             pPanel.timesField.setText("100");
2 26 Feb 07 jari 260                             //tooMany = true;
2 26 Feb 07 jari 261                             if ((grpACounter + grpBCounter) <= 20) {
2 26 Feb 07 jari 262                                 numCombs = getNumCombs((grpACounter + grpBCounter), grpACounter);
2 26 Feb 07 jari 263                                 pPanel.numCombsLabel.setForeground(Color.black);
2 26 Feb 07 jari 264                                 pPanel.numCombsLabel.setText("There are " + numCombs + " unique permutations                                ");
2 26 Feb 07 jari 265                                 allPossCombs = numCombs;
2 26 Feb 07 jari 266                                 pPanel.allCombsButton.setEnabled(true);
2 26 Feb 07 jari 267                                 pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 268                             }
2 26 Feb 07 jari 269                         }
2 26 Feb 07 jari 270                     } else if (getTestDesign() == TtestInitDialog.ONE_CLASS) {
2 26 Feb 07 jari 271                         pPanel.numCombsLabel.setForeground(Color.black);
2 26 Feb 07 jari 272                         int validNum = getNumValidOneClassExpts();
2 26 Feb 07 jari 273                         if (validNum <= 1) {
2 26 Feb 07 jari 274                             pPanel.numCombsLabel.setForeground(Color.red);
2 26 Feb 07 jari 275                             pPanel.numCombsLabel.setText("Error! Choose at least two samples");
2 26 Feb 07 jari 276                             pPanel.randomGroupsButton.setEnabled(false); 
2 26 Feb 07 jari 277                             pPanel.timesField.setBackground(Color.gray);
2 26 Feb 07 jari 278                             pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 279                         } else if (validNum <= 29) {
2 26 Feb 07 jari 280                             pPanel.numCombsLabel.setText("There are " + (int)Math.pow(2, validNum) + " possible combinations                    ");
2 26 Feb 07 jari 281                             pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 282                             pPanel.allCombsButton.setEnabled(true);
2 26 Feb 07 jari 283                             pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 284                             pPanel.timesField.setEnabled(true);                           
2 26 Feb 07 jari 285                         } else {
2 26 Feb 07 jari 286                             pPanel.numCombsLabel.setText("There are too many unique combinations                                       ");
2 26 Feb 07 jari 287                             pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 288                             pPanel.timesField.setEnabled(true);  
2 26 Feb 07 jari 289                             pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 290                             pPanel.randomGroupsButton.setSelected(true);                            
2 26 Feb 07 jari 291                         }
2 26 Feb 07 jari 292                         //pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 293                         /*
2 26 Feb 07 jari 294                         pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 295                         pPanel.randomGroupsButton.setSelected(true);
2 26 Feb 07 jari 296                         pPanel.timesField.setEnabled(true);
2 26 Feb 07 jari 297                         pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 298                         pPanel.timesField.setText("100");  
2 26 Feb 07 jari 299                          */                    
2 26 Feb 07 jari 300                     }  else if (getTestDesign() == TtestInitDialog.PAIRED) {
2 26 Feb 07 jari 301                         if (tcpmPanel.tcpPanel.pairedListModel.size() < 2) {
2 26 Feb 07 jari 302                             JOptionPane.showMessageDialog(null, "Need at least two pairs of samples!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 303                         } else {
2 26 Feb 07 jari 304                             if (tcpmPanel.tcpPanel.pairedListModel.size() <= 29) {
2 26 Feb 07 jari 305                                 pPanel.numCombsLabel.setText("There are " + (int)(Math.pow(2, tcpmPanel.tcpPanel.pairedListModel.size())) + " possible combinations                    ");
2 26 Feb 07 jari 306                                 pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 307                                 pPanel.allCombsButton.setEnabled(true);
2 26 Feb 07 jari 308                                 pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 309                                 pPanel.timesField.setEnabled(true);
2 26 Feb 07 jari 310                             } else {
2 26 Feb 07 jari 311                                 pPanel.numCombsLabel.setText("There are too many unique combinations                                       ");
2 26 Feb 07 jari 312                                 pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 313                                 pPanel.timesField.setEnabled(true);
2 26 Feb 07 jari 314                                 pPanel.randomGroupsButton.setEnabled(true);
2 26 Feb 07 jari 315                                 pPanel.randomGroupsButton.setSelected(true);                             
2 26 Feb 07 jari 316                             }
2 26 Feb 07 jari 317                         }
2 26 Feb 07 jari 318                     }
2 26 Feb 07 jari 319                 }
2 26 Feb 07 jari 320             }
2 26 Feb 07 jari 321         });
2 26 Feb 07 jari 322         chooseDesignPane.addChangeListener(new ChangeListener() {
2 26 Feb 07 jari 323             public void stateChanged(ChangeEvent e) {
2 26 Feb 07 jari 324                 pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 325                 sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 326                 sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 327                 sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 328                 sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 329                 sPanel.minPButton.setEnabled(false);                
2 26 Feb 07 jari 330                 pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 331                 pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 332                 pPanel.numCombsLabel.setForeground(Color.black);
2 26 Feb 07 jari 333                 pPanel.numCombsLabel.setText(""); 
2 26 Feb 07 jari 334                 pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 335                 if (getTestDesign() == TtestInitDialog.ONE_CLASS) {
2 26 Feb 07 jari 336                     pPanel.numCombsLabel.setForeground(Color.black);
2 26 Feb 07 jari 337                     pPanel.numCombsLabel.setText("");                     
2 26 Feb 07 jari 338                 }
2 26 Feb 07 jari 339             }
2 26 Feb 07 jari 340         });
2 26 Feb 07 jari 341         buildConstraints(constraints, 0, 0, 1, 1, 100, 45);
2 26 Feb 07 jari 342         gridbag.setConstraints(chooseDesignPane, constraints);
2 26 Feb 07 jari 343         pane.add(chooseDesignPane);     
2 26 Feb 07 jari 344         
2 26 Feb 07 jari 345         dPanel = new DfCalcPanel();
2 26 Feb 07 jari 346         buildConstraints(constraints, 0, 1, 1, 1, 0, 5);
2 26 Feb 07 jari 347         gridbag.setConstraints(dPanel, constraints);  
2 26 Feb 07 jari 348         pane.add(dPanel);
2 26 Feb 07 jari 349         
2 26 Feb 07 jari 350         buildConstraints(constraints, 0, 2, 1, 1, 0, 20);
2 26 Feb 07 jari 351         gridbag.setConstraints(pPanel, constraints);
2 26 Feb 07 jari 352         pane.add(pPanel);
2 26 Feb 07 jari 353         
2 26 Feb 07 jari 354         //sPanel = new SignificancePanel();
2 26 Feb 07 jari 355         buildConstraints(constraints, 0, 3, 1, 1, 0, 25);
2 26 Feb 07 jari 356         gridbag.setConstraints(sPanel, constraints);
2 26 Feb 07 jari 357         pane.add(sPanel);
2 26 Feb 07 jari 358         
2 26 Feb 07 jari 359         hclOpsPanel = new HCLSigOnlyPanel();
2 26 Feb 07 jari 360         buildConstraints(constraints, 0, 4, 1, 1, 0, 5);
2 26 Feb 07 jari 361         gridbag.setConstraints(hclOpsPanel, constraints);
2 26 Feb 07 jari 362         
2 26 Feb 07 jari 363         pane.add(hclOpsPanel);
2 26 Feb 07 jari 364         addContent(pane);
2 26 Feb 07 jari 365         
2 26 Feb 07 jari 366         EventListener listener = new EventListener();
2 26 Feb 07 jari 367         setActionListeners(listener);
2 26 Feb 07 jari 368     }
2 26 Feb 07 jari 369     
2 26 Feb 07 jari 370     
2 26 Feb 07 jari 371     public void setVisible(boolean visible) {
2 26 Feb 07 jari 372         Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
2 26 Feb 07 jari 373         setLocation((screenSize.width - getSize().width)/2, (screenSize.height - getSize().height)/2);
2 26 Feb 07 jari 374         
2 26 Feb 07 jari 375         super.setVisible(visible);
2 26 Feb 07 jari 376     }
2 26 Feb 07 jari 377     
2 26 Feb 07 jari 378     void buildConstraints(GridBagConstraints gbc, int gx, int gy,
2 26 Feb 07 jari 379                 int gw, int gh, int wx, int wy) {
2 26 Feb 07 jari 380         gbc.gridx = gx;
2 26 Feb 07 jari 381         gbc.gridy = gy;
2 26 Feb 07 jari 382         gbc.gridwidth = gw;
2 26 Feb 07 jari 383         gbc.gridheight = gh;
2 26 Feb 07 jari 384         gbc.weightx = wx;
2 26 Feb 07 jari 385         gbc.weighty = wy;
2 26 Feb 07 jari 386     }
2 26 Feb 07 jari 387     
2 26 Feb 07 jari 388     class TwoClassPairedMainPanel extends JPanel {
2 26 Feb 07 jari 389         TwoClassPairedPanel tcpPanel;
2 26 Feb 07 jari 390         JButton saveButton, resetButton, loadButton;
2 26 Feb 07 jari 391         GridBagConstraints constraints;
2 26 Feb 07 jari 392         GridBagLayout gridbag;  
2 26 Feb 07 jari 393         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 394         
2 26 Feb 07 jari 395         public TwoClassPairedMainPanel() {
2 26 Feb 07 jari 396             tcpPanel = new TwoClassPairedPanel();
2 26 Feb 07 jari 397             JPanel bottomPanel = new JPanel();
2 26 Feb 07 jari 398             bottomPanel.setBackground(Color.white);
2 26 Feb 07 jari 399             constraints = new GridBagConstraints();
2 26 Feb 07 jari 400             gridbag = new GridBagLayout();   
2 26 Feb 07 jari 401             this.setLayout(gridbag);
2 26 Feb 07 jari 402             
2 26 Feb 07 jari 403             buildConstraints(constraints, 0, 0, 1, 1, 100, 90);
2 26 Feb 07 jari 404             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 405             gridbag.setConstraints(tcpPanel, constraints);
2 26 Feb 07 jari 406             this.add(tcpPanel);
2 26 Feb 07 jari 407             
2 26 Feb 07 jari 408             if(lotsOfSamples){
2 26 Feb 07 jari 409               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 410               lotsOfSamplesWarningLabel.setBackground(Color.gray);
2 26 Feb 07 jari 411               this.add(lotsOfSamplesWarningLabel, new GridBagConstraints(0,1,3,1,0,0,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             GridBagLayout grid1 = new GridBagLayout();
2 26 Feb 07 jari 415             bottomPanel.setLayout(grid1);
2 26 Feb 07 jari 416             
2 26 Feb 07 jari 417             saveButton = new JButton("Save pairings");
2 26 Feb 07 jari 418             
2 26 Feb 07 jari 419             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 420             fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 421             
2 26 Feb 07 jari 422             saveButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 423             public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 424                     int returnVal = fc.showSaveDialog(TwoClassPairedMainPanel.this); 
2 26 Feb 07 jari 425                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 426                         File file = fc.getSelectedFile(); 
2 26 Feb 07 jari 427                         try {
2 26 Feb 07 jari 428                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 429                             for (int i = 0; i < tcpPanel.pairedAExpts.size(); i++) {
2 26 Feb 07 jari 430                                 int currentA = ((Integer)(tcpPanel.pairedAExpts.get(i))).intValue();
2 26 Feb 07 jari 431                                 int currentB = ((Integer)(tcpPanel.pairedBExpts.get(i))).intValue();
2 26 Feb 07 jari 432                                 out.print(currentA);
2 26 Feb 07 jari 433                                 out.print("\t");
2 26 Feb 07 jari 434                                 out.print(currentB);
2 26 Feb 07 jari 435                                 out.print("\t");
2 26 Feb 07 jari 436                                 out.println();
2 26 Feb 07 jari 437                             }
2 26 Feb 07 jari 438                             out.flush();
2 26 Feb 07 jari 439                             out.close();
2 26 Feb 07 jari 440                         } catch (Exception e) {
2 26 Feb 07 jari 441                         }
2 26 Feb 07 jari 442                     } else {
2 26 Feb 07 jari 443                     }
2 26 Feb 07 jari 444                 }
2 26 Feb 07 jari 445             });
2 26 Feb 07 jari 446             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 447             buildConstraints(constraints, 0, 1, 1, 1, 33, 100);
2 26 Feb 07 jari 448             grid1.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 449             bottomPanel.add(saveButton);       
2 26 Feb 07 jari 450             
2 26 Feb 07 jari 451             loadButton = new JButton("Load pairings");
2 26 Feb 07 jari 452            
2 26 Feb 07 jari 453             loadButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 454                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 455                     //tcpPanel.reset();
2 26 Feb 07 jari 456                     int returnVal = fc.showOpenDialog(TwoClassPairedMainPanel.this);  
2 26 Feb 07 jari 457                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 458                         tcpPanel.reset();
2 26 Feb 07 jari 459                         try {
2 26 Feb 07 jari 460                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 461                             BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 462                             String currentLine;  
2 26 Feb 07 jari 463                             while((currentLine = buff.readLine()) != null) {
2 26 Feb 07 jari 464                                 StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 465                                 st.init(currentLine);
2 26 Feb 07 jari 466                                 
2 26 Feb 07 jari 467                                 for (int i = 0; i < 2; i++) {
2 26 Feb 07 jari 468                                     String s = st.nextToken();
2 26 Feb 07 jari 469                                     if (i == 0) {
2 26 Feb 07 jari 470                                         tcpPanel.pairedAExpts.add(new Integer(s));
2 26 Feb 07 jari 471                                     } else if (i == 1) {
2 26 Feb 07 jari 472                                         tcpPanel.pairedBExpts.add(new Integer(s));
2 26 Feb 07 jari 473                                     }
2 26 Feb 07 jari 474                                 }
2 26 Feb 07 jari 475                                 
2 26 Feb 07 jari 476                             }
2 26 Feb 07 jari 477                             buff.close();
2 26 Feb 07 jari 478                             
2 26 Feb 07 jari 479                             for (int i = 0; i < tcpPanel.pairedAExpts.size(); i++) {
2 26 Feb 07 jari 480                                 int currA = ((Integer)(tcpPanel.pairedAExpts.get(i))).intValue();
2 26 Feb 07 jari 481                                 int currB = ((Integer)(tcpPanel.pairedBExpts.get(i))).intValue();
2 26 Feb 07 jari 482                                 String currPair = "A: " + (String)(exptNames.get(currA)) + " - B: " + (String)(exptNames.get(currB));
2 26 Feb 07 jari 483                                 tcpPanel.exptButtons[currA].setEnabled(false);
2 26 Feb 07 jari 484                                 tcpPanel.exptButtons[currB].setEnabled(false); 
2 26 Feb 07 jari 485                                 tcpPanel.pairedListModel.addElement(currPair);
2 26 Feb 07 jari 486                                 
2 26 Feb 07 jari 487                             }
2 26 Feb 07 jari 488                             if (tcpPanel.pairedAExpts.size() > 0) {
2 26 Feb 07 jari 489                                 tcpPanel.removeABPairButton.setEnabled(true);
2 26 Feb 07 jari 490                                 tcpPanel.pairedExptsList.setSelectedIndex(tcpPanel.pairedListModel.size() - 1);
2 26 Feb 07 jari 491                             }                            
2 26 Feb 07 jari 492                             
2 26 Feb 07 jari 493                             pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 494                             sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 495                             sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 496                             sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 497                             sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 498                             sPanel.minPButton.setEnabled(false);
2 26 Feb 07 jari 499                             pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 500                             pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 501                             pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 502                             pPanel.numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 503                             
2 26 Feb 07 jari 504                         } catch (Exception exc) {
2 26 Feb 07 jari 505                             JOptionPane.showMessageDialog(tcpPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 506                         }
2 26 Feb 07 jari 507                     } else {
2 26 Feb 07 jari 508                     }
2 26 Feb 07 jari 509                 }
2 26 Feb 07 jari 510             });
2 26 Feb 07 jari 511            
2 26 Feb 07 jari 512             buildConstraints(constraints, 1, 1, 1, 1, 33, 100);
2 26 Feb 07 jari 513             grid1.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 514             bottomPanel.add(loadButton);     
2 26 Feb 07 jari 515             
2 26 Feb 07 jari 516             resetButton = new JButton("Reset");
2 26 Feb 07 jari 517            
2 26 Feb 07 jari 518             resetButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 519                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 520                     tcpPanel.reset();
2 26 Feb 07 jari 521                     
2 26 Feb 07 jari 522                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 523                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 524                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 525                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 526                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 527                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 528                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 529                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 530                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 531                     pPanel.numCombsLabel.setText("                                                                            ");                    
2 26 Feb 07 jari 532                 }
2 26 Feb 07 jari 533             });
2 26 Feb 07 jari 534             
2 26 Feb 07 jari 535             buildConstraints(constraints, 2, 1, 1, 1, 34, 100);
2 26 Feb 07 jari 536             grid1.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 537             bottomPanel.add(resetButton);    
2 26 Feb 07 jari 538             
2 26 Feb 07 jari 539             
2 26 Feb 07 jari 540             buildConstraints(constraints, 0, 2, 1, 1, 0, 10);
2 26 Feb 07 jari 541             gridbag.setConstraints(bottomPanel, constraints);
2 26 Feb 07 jari 542             this.add(bottomPanel);             
2 26 Feb 07 jari 543         }
2 26 Feb 07 jari 544     }
2 26 Feb 07 jari 545     
2 26 Feb 07 jari 546     class TwoClassPairedPanel extends JPanel {
2 26 Feb 07 jari 547         ExperimentButton[] exptButtons;
2 26 Feb 07 jari 548         GridBagConstraints constraints;
2 26 Feb 07 jari 549         GridBagLayout gridbag;
2 26 Feb 07 jari 550         JTextField currentATextField, currentBTextField;
2 26 Feb 07 jari 551         JButton removeCurrentAButton, removeCurrentBButton, loadABPairButton, removeABPairButton;
2 26 Feb 07 jari 552         PairedExperimentsPanel pairPanel;
2 26 Feb 07 jari 553         JList pairedExptsList;
2 26 Feb 07 jari 554         DefaultListModel pairedListModel;
2 26 Feb 07 jari 555         boolean currentAFilled, currentBFilled;
2 26 Feb 07 jari 556         int currentAExpt, currentBExpt;
2 26 Feb 07 jari 557         int numPanels = 0;
2 26 Feb 07 jari 558         Vector pairedAExpts, pairedBExpts;
2 26 Feb 07 jari 559         
2 26 Feb 07 jari 560         public TwoClassPairedPanel() {
2 26 Feb 07 jari 561             currentAExpt = -1;
2 26 Feb 07 jari 562             currentBExpt = -1;
2 26 Feb 07 jari 563             currentAFilled = false;
2 26 Feb 07 jari 564             currentBFilled = false;
2 26 Feb 07 jari 565             pairedAExpts = new Vector();
2 26 Feb 07 jari 566             pairedBExpts = new Vector();
2 26 Feb 07 jari 567             constraints = new GridBagConstraints();
2 26 Feb 07 jari 568             gridbag = new GridBagLayout();
2 26 Feb 07 jari 569             this.setLayout(gridbag);  
2 26 Feb 07 jari 570             
2 26 Feb 07 jari 571             pairedListModel = new DefaultListModel();
2 26 Feb 07 jari 572             pairedExptsList = new JList(pairedListModel);
2 26 Feb 07 jari 573             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 574             JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 575             
2 26 Feb 07 jari 576             int currPanel = 0;
2 26 Feb 07 jari 577             for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 578                 panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 579             }
2 26 Feb 07 jari 580             exptButtons = new ExperimentButton[exptNames.size()];
2 26 Feb 07 jari 581             
2 26 Feb 07 jari 582             int maxWidth = 0;
2 26 Feb 07 jari 583             int maxNameLength = 0;
2 26 Feb 07 jari 584             
2 26 Feb 07 jari 585             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 586                 exptButtons[i] = new ExperimentButton(i);
2 26 Feb 07 jari 587                 //set current panel
2 26 Feb 07 jari 588                 currPanel = i / 512;
2 26 Feb 07 jari 589                 
2 26 Feb 07 jari 590                 if (exptButtons[i].getPreferredSize().getWidth() > maxWidth) {
2 26 Feb 07 jari 591                     maxWidth = (int)Math.ceil(exptButtons[i].getPreferredSize().getWidth());
2 26 Feb 07 jari 592                 }
2 26 Feb 07 jari 593                 
2 26 Feb 07 jari 594                 String s = (String)(exptNames.get(i));
2 26 Feb 07 jari 595                 int currentNameLength = s.length();
2 26 Feb 07 jari 596                 
2 26 Feb 07 jari 597                 if (currentNameLength > maxNameLength) {
2 26 Feb 07 jari 598                     maxNameLength = currentNameLength;
2 26 Feb 07 jari 599                 }
2 26 Feb 07 jari 600                 buildConstraints(constraints, 0, i%512, 1, 1, 100, 100);
2 26 Feb 07 jari 601                 gridbag.setConstraints(exptButtons[i], constraints);
2 26 Feb 07 jari 602                 panels[currPanel].add(exptButtons[i]);
2 26 Feb 07 jari 603             }
2 26 Feb 07 jari 604             
2 26 Feb 07 jari 605             currentATextField = new JTextField("", maxNameLength + 2);
2 26 Feb 07 jari 606             currentBTextField = new JTextField("", maxNameLength + 2);
2 26 Feb 07 jari 607             
2 26 Feb 07 jari 608             currentATextField.setBackground(Color.white);
2 26 Feb 07 jari 609             currentBTextField.setBackground(Color.white);
2 26 Feb 07 jari 610             currentATextField.setEditable(false);
2 26 Feb 07 jari 611             currentBTextField.setEditable(false);   
2 26 Feb 07 jari 612             JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 613             
2 26 Feb 07 jari 614             for(int i = 0; i < numPanels; i++) {
2 26 Feb 07 jari 615                 bigPanel.add(panels[i] ,new GridBagConstraints(0,i,1,1,1,1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 616             }
2 26 Feb 07 jari 617             
2 26 Feb 07 jari 618             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 619             scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 620             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);            
2 26 Feb 07 jari 621             
2 26 Feb 07 jari 622             buildConstraints(constraints, 0, 0, 1, 1, 40, 100);
2 26 Feb 07 jari 623             constraints.fill =GridBagConstraints.BOTH;
2 26 Feb 07 jari 624             gridbag.setConstraints(scroll, constraints);
2 26 Feb 07 jari 625             this.add(scroll);
2 26 Feb 07 jari 626             
2 26 Feb 07 jari 627             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 628             
2 26 Feb 07 jari 629             JPanel currentSelectionPanel = new JPanel();
2 26 Feb 07 jari 630             GridBagLayout grid2 = new GridBagLayout();
2 26 Feb 07 jari 631             currentSelectionPanel.setLayout(grid2);
2 26 Feb 07 jari 632             removeCurrentAButton = new JButton("< Remove A");
2 26 Feb 07 jari 633             removeCurrentBButton = new JButton("< Remove B");
2 26 Feb 07 jari 634             loadABPairButton = new JButton("   Load Pair >>   ");
2 26 Feb 07 jari 635             removeABPairButton = new JButton("<< Remove Pair");
2 26 Feb 07 jari 636             removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 637             removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 638             loadABPairButton.setEnabled(false); 
2 26 Feb 07 jari 639             removeABPairButton.setEnabled(false);
2 26 Feb 07 jari 640             removeCurrentAButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 641                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 642                     exptButtons[currentAExpt].setEnabled(true);
2 26 Feb 07 jari 643                     currentAExpt = -1;
2 26 Feb 07 jari 644                     currentATextField.setText("");
2 26 Feb 07 jari 645                     currentAFilled = false;
2 26 Feb 07 jari 646                     removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 647                     loadABPairButton.setEnabled(false);
2 26 Feb 07 jari 648                 }
2 26 Feb 07 jari 649             });
2 26 Feb 07 jari 650             
2 26 Feb 07 jari 651             removeCurrentBButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 652                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 653                     exptButtons[currentBExpt].setEnabled(true);
2 26 Feb 07 jari 654                     currentBExpt = -1;
2 26 Feb 07 jari 655                     currentBTextField.setText("");
2 26 Feb 07 jari 656                     currentBFilled = false;
2 26 Feb 07 jari 657                     removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 658                     loadABPairButton.setEnabled(false);                    
2 26 Feb 07 jari 659                 }
2 26 Feb 07 jari 660             });     
2 26 Feb 07 jari 661             
2 26 Feb 07 jari 662             loadABPairButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 663                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 664                     String currentPair = "A: " + (String)(exptNames.get(currentAExpt)) + " - B: " + (String)(exptNames.get(currentBExpt));
2 26 Feb 07 jari 665                     pairedListModel.addElement(currentPair);
2 26 Feb 07 jari 666                     pairedAExpts.add(new Integer(currentAExpt));
2 26 Feb 07 jari 667                     pairedBExpts.add(new Integer(currentBExpt));
2 26 Feb 07 jari 668                     currentAExpt = -1;
2 26 Feb 07 jari 669                     currentBExpt = -1;
2 26 Feb 07 jari 670                     currentATextField.setText("");
2 26 Feb 07 jari 671                     currentBTextField.setText("");
2 26 Feb 07 jari 672                     currentAFilled = false;
2 26 Feb 07 jari 673                     currentBFilled = false;
2 26 Feb 07 jari 674                     removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 675                     removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 676                     loadABPairButton.setEnabled(false); 
2 26 Feb 07 jari 677                     removeABPairButton.setEnabled(true);
2 26 Feb 07 jari 678                     pairedExptsList.setSelectedIndex(pairedListModel.size() - 1);
2 26 Feb 07 jari 679                     
2 26 Feb 07 jari 680                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 681                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 682                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 683                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 684                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 685                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 686                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 687                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 688                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 689                     pPanel.numCombsLabel.setText("                                                                            ");                    
2 26 Feb 07 jari 690                 }
2 26 Feb 07 jari 691             });
2 26 Feb 07 jari 692             
2 26 Feb 07 jari 693             removeABPairButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 694                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 695                     int index = pairedExptsList.getSelectedIndex();
2 26 Feb 07 jari 696                     pairedListModel.removeElementAt(index);
2 26 Feb 07 jari 697                     int removedAIndex = ((Integer)(pairedAExpts.remove(index))).intValue();
2 26 Feb 07 jari 698                     int removedBIndex = ((Integer)(pairedBExpts.remove(index))).intValue();
2 26 Feb 07 jari 699                     exptButtons[removedAIndex].setEnabled(true);
2 26 Feb 07 jari 700                     exptButtons[removedBIndex].setEnabled(true);
2 26 Feb 07 jari 701                     if (pairedListModel.isEmpty()) {
2 26 Feb 07 jari 702                         removeABPairButton.setEnabled(false);
2 26 Feb 07 jari 703                     } else {
2 26 Feb 07 jari 704                         pairedExptsList.setSelectedIndex(pairedListModel.size() - 1);
2 26 Feb 07 jari 705                     }
2 26 Feb 07 jari 706                     
2 26 Feb 07 jari 707                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 708                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 709                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 710                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 711                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 712                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 713                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 714                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 715                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 716                     pPanel.numCombsLabel.setText("                                                                            ");                    
2 26 Feb 07 jari 717                 }
2 26 Feb 07 jari 718             });
2 26 Feb 07 jari 719             JScrollPane currentAScroll = new JScrollPane(currentATextField);
2 26 Feb 07 jari 720             currentAScroll.setMinimumSize(new Dimension(90, 50));
2 26 Feb 07 jari 721             JScrollPane currentBScroll = new JScrollPane(currentBTextField);
2 26 Feb 07 jari 722             currentBScroll.setMinimumSize(new Dimension(90, 50));
2 26 Feb 07 jari 723             
2 26 Feb 07 jari 724             currentAScroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 725             currentAScroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);   
2 26 Feb 07 jari 726             
2 26 Feb 07 jari 727             currentBScroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 728             currentBScroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);            
2 26 Feb 07 jari 729             
2 26 Feb 07 jari 730             buildConstraints(constraints, 0, 0, 1, 1, 20, 50);
2 26 Feb 07 jari 731             grid2.setConstraints(removeCurrentAButton, constraints);
2 26 Feb 07 jari 732             currentSelectionPanel.add(removeCurrentAButton);
2 26 Feb 07 jari 733             
2 26 Feb 07 jari 734             JLabel aLabel = new JLabel(" Current A: ");
2 26 Feb 07 jari 735             buildConstraints(constraints, 1, 0, 1, 1, 20, 0);
2 26 Feb 07 jari 736             grid2.setConstraints(aLabel, constraints);
2 26 Feb 07 jari 737             currentSelectionPanel.add(aLabel);    
2 26 Feb 07 jari 738             
2 26 Feb 07 jari 739             buildConstraints(constraints, 2, 0, 1, 1, 60, 0);
2 26 Feb 07 jari 740             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 741             //constraints.ipady = 100;
2 26 Feb 07 jari 742             grid2.setConstraints(currentAScroll, constraints);
2 26 Feb 07 jari 743             currentSelectionPanel.add(currentAScroll);   
2 26 Feb 07 jari 744             
2 26 Feb 07 jari 745             //constraints.ipady = 0;
2 26 Feb 07 jari 746             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 747             
2 26 Feb 07 jari 748             buildConstraints(constraints, 0, 1, 1, 1, 20, 50);
2 26 Feb 07 jari 749             grid2.setConstraints(removeCurrentBButton, constraints);
2 26 Feb 07 jari 750             currentSelectionPanel.add(removeCurrentBButton);   
2 26 Feb 07 jari 751             
2 26 Feb 07 jari 752             JLabel bLabel = new JLabel("Current B: ");
2 26 Feb 07 jari 753             buildConstraints(constraints, 1, 1, 1, 1, 20, 0);
2 26 Feb 07 jari 754             grid2.setConstraints(bLabel, constraints);
2 26 Feb 07 jari 755             currentSelectionPanel.add(bLabel);  
2 26 Feb 07 jari 756             
2 26 Feb 07 jari 757             buildConstraints(constraints, 2, 1, 1, 1, 60, 0);
2 26 Feb 07 jari 758             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 759             //constraints.ipady = 100;
2 26 Feb 07 jari 760             grid2.setConstraints(currentBScroll, constraints);
2 26 Feb 07 jari 761             currentSelectionPanel.add(currentBScroll);   
2 26 Feb 07 jari 762             
2 26 Feb 07 jari 763             //constraints.ipady = 0;
2 26 Feb 07 jari 764             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 765             
2 26 Feb 07 jari 766             buildConstraints(constraints, 1, 0, 1, 1, 10, 0);
2 26 Feb 07 jari 767             //constraints.fill = GridBagConstraints.HORIZONTAL;
2 26 Feb 07 jari 768             //constraints.ipadx = 200;
2 26 Feb 07 jari 769             gridbag.setConstraints(currentSelectionPanel, constraints);
2 26 Feb 07 jari 770             this.add(currentSelectionPanel);   
2 26 Feb 07 jari 771             
2 26 Feb 07 jari 772             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 773             //constraints.ipadx = 0;
2 26 Feb 07 jari 774             
2 26 Feb 07 jari 775             JPanel pairButtonsPanel = new JPanel();
2 26 Feb 07 jari 776             GridBagLayout grid3 = new GridBagLayout();
2 26 Feb 07 jari 777             pairButtonsPanel.setLayout(grid3);
2 26 Feb 07 jari 778             buildConstraints(constraints, 0, 0, 1, 1, 100, 50);
2 26 Feb 07 jari 779             grid3.setConstraints(loadABPairButton, constraints);
2 26 Feb 07 jari 780             pairButtonsPanel.add(loadABPairButton);
2 26 Feb 07 jari 781             buildConstraints(constraints, 0, 1, 1, 1, 0, 50);
2 26 Feb 07 jari 782             grid3.setConstraints(removeABPairButton, constraints);
2 26 Feb 07 jari 783             pairButtonsPanel.add(removeABPairButton);            
2 26 Feb 07 jari 784             
2 26 Feb 07 jari 785             buildConstraints(constraints, 2, 0, 1, 1, 5, 0);
2 26 Feb 07 jari 786             gridbag.setConstraints(pairButtonsPanel, constraints);
2 26 Feb 07 jari 787             this.add(pairButtonsPanel);  
2 26 Feb 07 jari 788             
2 26 Feb 07 jari 789             buildConstraints(constraints, 3, 0, 1, 1, 45, 0);
2 26 Feb 07 jari 790             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 791             JScrollPane pairScroll = new JScrollPane(pairedExptsList);
2 26 Feb 07 jari 792             pairScroll.setBorder(new TitledBorder("Paired Samples"));
2 26 Feb 07 jari 793             gridbag.setConstraints(pairScroll, constraints);
2 26 Feb 07 jari 794             this.add(pairScroll);              
2 26 Feb 07 jari 795         }
2 26 Feb 07 jari 796         
2 26 Feb 07 jari 797         public void reset() {
2 26 Feb 07 jari 798             for (int i = 0; i < exptButtons.length; i++) {
2 26 Feb 07 jari 799                 exptButtons[i].setEnabled(true);
2 26 Feb 07 jari 800                 currentATextField.setText("");
2 26 Feb 07 jari 801                 currentBTextField.setText("");
2 26 Feb 07 jari 802                 removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 803                 removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 804                 loadABPairButton.setEnabled(false);
2 26 Feb 07 jari 805                 removeABPairButton.setEnabled(false);
2 26 Feb 07 jari 806                 pairedListModel.clear();
2 26 Feb 07 jari 807                 currentAFilled = false;
2 26 Feb 07 jari 808                 currentBFilled = false;
2 26 Feb 07 jari 809                 currentAExpt = -1;
2 26 Feb 07 jari 810                 currentBExpt = -1;
2 26 Feb 07 jari 811                 pairedAExpts.clear();
2 26 Feb 07 jari 812                 pairedBExpts.clear();
2 26 Feb 07 jari 813             }
2 26 Feb 07 jari 814         }
2 26 Feb 07 jari 815         
2 26 Feb 07 jari 816         class ExperimentButton extends JButton {
2 26 Feb 07 jari 817             String s;
2 26 Feb 07 jari 818             int index;
2 26 Feb 07 jari 819             public ExperimentButton(int i) {
2 26 Feb 07 jari 820                 this.index = i;
2 26 Feb 07 jari 821                 s = (String)(exptNames.get(i));
2 26 Feb 07 jari 822                 this.setText(s);
2 26 Feb 07 jari 823                 this.addActionListener(new ActionListener() {
2 26 Feb 07 jari 824                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 825                         if ((currentAFilled)&&(currentBFilled)) {
2 26 Feb 07 jari 826                             JOptionPane.showMessageDialog(null, "Clear at least one current field first!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 827                         } else if (!currentAFilled) {
2 26 Feb 07 jari 828                             currentAExpt = index;
2 26 Feb 07 jari 829                             currentATextField.setText(s);
2 26 Feb 07 jari 830                             currentAFilled = true;
2 26 Feb 07 jari 831                             ExperimentButton.this.setEnabled(false);
2 26 Feb 07 jari 832                             removeCurrentAButton.setEnabled(true);
2 26 Feb 07 jari 833                         } else if (!currentBFilled) {
2 26 Feb 07 jari 834                             currentBExpt = index;
2 26 Feb 07 jari 835                             currentBTextField.setText(s);
2 26 Feb 07 jari 836                             currentBFilled = true;
2 26 Feb 07 jari 837                             ExperimentButton.this.setEnabled(false);
2 26 Feb 07 jari 838                             removeCurrentBButton.setEnabled(true);
2 26 Feb 07 jari 839                         }
2 26 Feb 07 jari 840                         
2 26 Feb 07 jari 841                         if ((currentAFilled) && (currentBFilled)) {
2 26 Feb 07 jari 842                             loadABPairButton.setEnabled(true);
2 26 Feb 07 jari 843                         } else {
2 26 Feb 07 jari 844                             loadABPairButton.setEnabled(false);
2 26 Feb 07 jari 845                         }
2 26 Feb 07 jari 846                     }
2 26 Feb 07 jari 847                 });
2 26 Feb 07 jari 848             }
2 26 Feb 07 jari 849         }
2 26 Feb 07 jari 850        
2 26 Feb 07 jari 851         class PairedExperimentsPanel extends JPanel {
2 26 Feb 07 jari 852             public PairedExperimentsPanel() {
2 26 Feb 07 jari 853                 //this.setBorder(new TitledBorder("Paired Experiments"));
2 26 Feb 07 jari 854             }
2 26 Feb 07 jari 855         }
2 26 Feb 07 jari 856    }    
2 26 Feb 07 jari 857     class OneClassPanel extends JPanel {
2 26 Feb 07 jari 858         JTextField meanField;
2 26 Feb 07 jari 859         JCheckBox[] includeExpts;
2 26 Feb 07 jari 860         int numPanels = 0;
2 26 Feb 07 jari 861         JButton saveButton, loadButton, resetButton;
2 26 Feb 07 jari 862         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 863         
2 26 Feb 07 jari 864         OneClassPanel() {
2 26 Feb 07 jari 865             this.setBackground(Color.white);
2 26 Feb 07 jari 866             JLabel meanLabel = new JLabel("Enter the mean value to be tested against: ");
2 26 Feb 07 jari 867             meanField = new JTextField("0", 7);
2 26 Feb 07 jari 868             includeExpts = new JCheckBox[exptNames.size()];
2 26 Feb 07 jari 869             
2 26 Feb 07 jari 870             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 871             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 872             this.setLayout(gridbag);
2 26 Feb 07 jari 873             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 874              JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 875              
2 26 Feb 07 jari 876              int currPanel = 0;
2 26 Feb 07 jari 877              for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 878                  panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 879              }
2 26 Feb 07 jari 880     
2 26 Feb 07 jari 881             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 882                //set current panel
2 26 Feb 07 jari 883                 currPanel = i / 512;
2 26 Feb 07 jari 884                 //JLabel expLabel = new JLabel((String)(exptNames.get(i)));
2 26 Feb 07 jari 885                 includeExpts[i] = new JCheckBox((String)(exptNames.get(i)), true);
2 26 Feb 07 jari 886                 buildConstraints(constraints, 0, i%512, 1, 1, 100, 100);
2 26 Feb 07 jari 887                 gridbag.setConstraints(includeExpts[i], constraints);
2 26 Feb 07 jari 888                 panels[currPanel].add(includeExpts[i]);
2 26 Feb 07 jari 889             }
2 26 Feb 07 jari 890             JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 891             
2 26 Feb 07 jari 892             for(int i = 0; i < numPanels; i++) {
2 26 Feb 07 jari 893                 bigPanel.add(panels[i] ,new GridBagConstraints(0,i,1,1,1,1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 894             }
2 26 Feb 07 jari 895             
2 26 Feb 07 jari 896             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 897             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 898             
2 26 Feb 07 jari 899             JPanel enterMeanPanel = new JPanel();
2 26 Feb 07 jari 900             GridBagLayout grid2 = new GridBagLayout();
2 26 Feb 07 jari 901             enterMeanPanel.setLayout(grid2);                 
2 26 Feb 07 jari 902             
2 26 Feb 07 jari 903             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 904             buildConstraints(constraints, 0, 0, 1, 1, 50, 100);
2 26 Feb 07 jari 905             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 906             grid2.setConstraints(meanLabel, constraints);
2 26 Feb 07 jari 907             enterMeanPanel.add(meanLabel);
2 26 Feb 07 jari 908             
2 26 Feb 07 jari 909             buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2 26 Feb 07 jari 910             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 911             grid2.setConstraints(meanField, constraints);
2 26 Feb 07 jari 912             enterMeanPanel.add(meanField);    
2 26 Feb 07 jari 913             
2 26 Feb 07 jari 914             JScrollPane scroll2 = new JScrollPane(enterMeanPanel);
2 26 Feb 07 jari 915             
2 26 Feb 07 jari 916             JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, scroll, scroll2);
2 26 Feb 07 jari 917             split.setOneTouchExpandable(true);
2 26 Feb 07 jari 918             split.setDividerLocation(150);
2 26 Feb 07 jari 919           
2 26 Feb 07 jari 920             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 921             buildConstraints(constraints, 0, 0, 1, 1, 100, 80);
2 26 Feb 07 jari 922             gridbag.setConstraints(split, constraints);
2 26 Feb 07 jari 923             this.add(split);  
2 26 Feb 07 jari 924            
2 26 Feb 07 jari 925             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 926             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 927             
2 26 Feb 07 jari 928             if(lotsOfSamples){
2 26 Feb 07 jari 929               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 930               this.add(lotsOfSamplesWarningLabel, 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 931             }
2 26 Feb 07 jari 932             
2 26 Feb 07 jari 933             JPanel lsrPanel = new JPanel();
2 26 Feb 07 jari 934             loadButton = new JButton("Load settings");
2 26 Feb 07 jari 935             saveButton = new JButton("Save settings");
2 26 Feb 07 jari 936             resetButton = new JButton("Reset");
2 26 Feb 07 jari 937             
2 26 Feb 07 jari 938             resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 939                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 940                     for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 941                         includeExpts[i].setSelected(true);
2 26 Feb 07 jari 942                     }
2 26 Feb 07 jari 943                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 944                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 945                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 946                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 947                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 948                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 949                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 950                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 951                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 952                     pPanel.numCombsLabel.setText("                                                                            ");                    
2 26 Feb 07 jari 953                 }
2 26 Feb 07 jari 954             });
2 26 Feb 07 jari 955             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 956             fc.setCurrentDirectory(new File("Data"));  
2 26 Feb 07 jari 957            
2 26 Feb 07 jari 958             saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 959                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 960                     int returnVal = fc.showSaveDialog(OneClassPanel.this);  
2 26 Feb 07 jari 961                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 962                         File file = fc.getSelectedFile();
2 26 Feb 07 jari 963                         try {
2 26 Feb 07 jari 964                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 965                             for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 966                                 if (includeExpts[i].isSelected()) {
2 26 Feb 07 jari 967                                     out.print(1);
2 26 Feb 07 jari 968                                 } else {
2 26 Feb 07 jari 969                                     out.print(0);
2 26 Feb 07 jari 970                                 }
2 26 Feb 07 jari 971                                 if (i < includeExpts.length - 1) {
2 26 Feb 07 jari 972                                     out.print("\t");
2 26 Feb 07 jari 973                                 }
2 26 Feb 07 jari 974                             }
2 26 Feb 07 jari 975                             out.println();
2 26 Feb 07 jari 976                             out.flush();
2 26 Feb 07 jari 977                             out.close();                            
2 26 Feb 07 jari 978                         } catch (Exception e) {
2 26 Feb 07 jari 979                         }
2 26 Feb 07 jari 980                     } else {
2 26 Feb 07 jari 981                     }
2 26 Feb 07 jari 982                 }
2 26 Feb 07 jari 983             });
2 26 Feb 07 jari 984            
2 26 Feb 07 jari 985             loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 986                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 987                     int returnVal = fc.showOpenDialog(OneClassPanel.this);
2 26 Feb 07 jari 988                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 989                         pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 990                         sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 991                         sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 992                         sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 993                         sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 994                         sPanel.minPButton.setEnabled(false);
2 26 Feb 07 jari 995                         pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 996                         pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 997                         pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 998                         pPanel.numCombsLabel.setText("                                                                            ");   
2 26 Feb 07 jari 999                         
2 26 Feb 07 jari 1000                         try {
2 26 Feb 07 jari 1001                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 1002                             BufferedReader buff = new BufferedReader(file);     
2 26 Feb 07 jari 1003                             String line = buff.readLine();
2 26 Feb 07 jari 1004                             //System.out.println(line);
2 26 Feb 07 jari 1005                             StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 1006                             st.init(line);  
2 26 Feb 07 jari 1007                             Vector includeExptsVector = new Vector();
2 26 Feb 07 jari 1008                             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 1009                                 String current = st.nextToken();
2 26 Feb 07 jari 1010                                 includeExptsVector.add(new Integer(current));
2 26 Feb 07 jari 1011                                 //System.out.print(current);
2 26 Feb 07 jari 1012                             }
2 26 Feb 07 jari 1013                             buff.close();
2 26 Feb 07 jari 1014                             if (includeExptsVector.size() != includeExpts.length) {
2 26 Feb 07 jari 1015                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1016                             } else {
2 26 Feb 07 jari 1017                                 for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 1018                                     int currentState = ((Integer)(includeExptsVector.get(i))).intValue();
2 26 Feb 07 jari 1019                                     if (currentState == 0) {
2 26 Feb 07 jari 1020                                         includeExpts[i].setSelected(false);
2 26 Feb 07 jari 1021                                     } else if (currentState == 1) {
2 26 Feb 07 jari 1022                                         includeExpts[i].setSelected(true);
2 26 Feb 07 jari 1023                                     }else {
2 26 Feb 07 jari 1024                                         for (int j = 0; j < includeExpts.length; j++) {
2 26 Feb 07 jari 1025                                             includeExpts[j].setSelected(true);
2 26 Feb 07 jari 1026                                         }
2 26 Feb 07 jari 1027                                         JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1028                                         break;                                        
2 26 Feb 07 jari 1029                                     }
2 26 Feb 07 jari 1030                                 }
2 26 Feb 07 jari 1031                             }
2 26 Feb 07 jari 1032                         } catch (Exception e) {
2 26 Feb 07 jari 1033                             JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE); 
2 26 Feb 07 jari 1034                             
2 26 Feb 07 jari 1035                         }
2 26 Feb 07 jari 1036                     } else {
2 26 Feb 07 jari 1037                     }
2 26 Feb 07 jari 1038                 }
2 26 Feb 07 jari 1039             });
2 26 Feb 07 jari 1040            
2 26 Feb 07 jari 1041             
2 26 Feb 07 jari 1042             GridBagLayout grid3 = new GridBagLayout();
2 26 Feb 07 jari 1043             lsrPanel.setLayout(grid3);
2 26 Feb 07 jari 1044             
2 26 Feb 07 jari 1045             buildConstraints(constraints, 0, 1, 1, 1, 33, 100);
2 26 Feb 07 jari 1046             grid3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 1047             lsrPanel.add(saveButton);
2 26 Feb 07 jari 1048             
2 26 Feb 07 jari 1049             buildConstraints(constraints, 1, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 1050             grid3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 1051             lsrPanel.add(loadButton);            
2 26 Feb 07 jari 1052             
2 26 Feb 07 jari 1053             buildConstraints(constraints, 2, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 1054             grid3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 1055             lsrPanel.add(resetButton);            
2 26 Feb 07 jari 1056             
2 26 Feb 07 jari 1057             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1058             buildConstraints(constraints, 0, 2, 1, 1, 0, 20);
2 26 Feb 07 jari 1059             gridbag.setConstraints(lsrPanel, constraints);
2 26 Feb 07 jari 1060             this.add(lsrPanel);            
2 26 Feb 07 jari 1061         }
2 26 Feb 07 jari 1062         
2 26 Feb 07 jari 1063         
2 26 Feb 07 jari 1064         public void reset() {
2 26 Feb 07 jari 1065             for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 1066                 includeExpts[i].setSelected(true);
2 26 Feb 07 jari 1067             }
2 26 Feb 07 jari 1068             meanField.setText("0");          
2 26 Feb 07 jari 1069         }
2 26 Feb 07 jari 1070     }
2 26 Feb 07 jari 1071    
2 26 Feb 07 jari 1072     class GroupExperimentsPanel extends JPanel {
2 26 Feb 07 jari 1073         JLabel[] expLabels;
2 26 Feb 07 jari 1074         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 1075         int numPanels = 0;
2 26 Feb 07 jari 1076         JRadioButton[] groupARadioButtons, groupBRadioButtons, neitherGroupRadioButtons;
2 26 Feb 07 jari 1077         GroupExperimentsPanel(Vector exptNames) {
2 26 Feb 07 jari 1078             this.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "Group Assignments", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 1079             this.setBackground(Color.white);
2 26 Feb 07 jari 1080             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 1081             expLabels = new JLabel[exptNames.size()];
2 26 Feb 07 jari 1082             groupARadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 1083             groupBRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 1084             neitherGroupRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 1085             ButtonGroup chooseGroup[] = new ButtonGroup[exptNames.size()];
2 26 Feb 07 jari 1086             
2 26 Feb 07 jari 1087             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1088             GridBagLayout gridbag2 = new GridBagLayout();
2 26 Feb 07 jari 1089             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1090             this.setLayout(gridbag2);
2 26 Feb 07 jari 1091             JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 1092             
2 26 Feb 07 jari 1093             int currPanel = 0;
2 26 Feb 07 jari 1094             for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 1095                 panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 1096             }
2 26 Feb 07 jari 1097             
2 26 Feb 07 jari 1098             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 1099                //set current panel
2 26 Feb 07 jari 1100                 currPanel = i / 512;
2 26 Feb 07 jari 1101                 String s1 = (String)(exptNames.get(i));//permut
2 26 Feb 07 jari 1102                 expLabels[i] = new JLabel(s1);
2 26 Feb 07 jari 1103                 expLabels[i].setForeground(Color.black);
2 26 Feb 07 jari 1104                 chooseGroup[i] = new ButtonGroup();
2 26 Feb 07 jari 1105                 groupARadioButtons[i] = new JRadioButton("Group A", true);
2 26 Feb 07 jari 1106                 //      groupARadioButtons[i].setBackground(Color.white);
2 26 Feb 07 jari 1107                 //      groupARadioButtons[i].setForeground(LABEL_COLOR);
2 26 Feb 07 jari 1108              
2 26 Feb 07 jari 1109                 chooseGroup[i].add(groupARadioButtons[i]);
2 26 Feb 07 jari 1110                 groupBRadioButtons[i] = new JRadioButton("Group B", false);
2 26 Feb 07 jari 1111                 //groupBRadioButtons[i].setBackground(Color.white);
2 26 Feb 07 jari 1112                 //groupBRadioButtons[i].setForeground(LABEL_COLOR);
2 26 Feb 07 jari 1113              
2 26 Feb 07 jari 1114                 chooseGroup[i].add(groupBRadioButtons[i]);
2 26 Feb 07 jari 1115                 
2 26 Feb 07 jari 1116                 neitherGroupRadioButtons[i] = new JRadioButton("Neither group", false);
2 26 Feb 07 jari 1117                 // neitherGroupRadioButtons[i].setBackground(Color.white);
2 26 Feb 07 jari 1118                 //neitherGroupRadioButtons[i].setForeground(LABEL_COLOR);
2 26 Feb 07 jari 1119               
2 26 Feb 07 jari 1120                 chooseGroup[i].add(neitherGroupRadioButtons[i]);
2 26 Feb 07 jari 1121                 buildConstraints(constraints, 0, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 1122                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1123                 gridbag.setConstraints(expLabels[i], constraints);
2 26 Feb 07 jari 1124                
2 26 Feb 07 jari 1125                 panels[currPanel].add(expLabels[i]);
2 26 Feb 07 jari 1126                 
2 26 Feb 07 jari 1127                 buildConstraints(constraints, 1, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 1128                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1129                 gridbag.setConstraints(groupARadioButtons[i], constraints);
2 26 Feb 07 jari 1130                 
2 26 Feb 07 jari 1131                 panels[currPanel].add(groupARadioButtons[i]);
2 26 Feb 07 jari 1132                 
2 26 Feb 07 jari 1133                 buildConstraints(constraints, 2, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 1134                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1135                 gridbag.setConstraints(groupBRadioButtons[i], constraints);
2 26 Feb 07 jari 1136               
2 26 Feb 07 jari 1137                 panels[currPanel].add(groupBRadioButtons[i]);
2 26 Feb 07 jari 1138                 
2 26 Feb 07 jari 1139                 buildConstraints(constraints, 3, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 1140                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1141                 gridbag.setConstraints(neitherGroupRadioButtons[i], constraints);
2 26 Feb 07 jari 1142                
2 26 Feb 07 jari 1143                 panels[currPanel].add(neitherGroupRadioButtons[i]);
2 26 Feb 07 jari 1144  
2 26 Feb 07 jari 1145             }
2 26 Feb 07 jari 1146             JPanel bigPanel = new JPanel(new GridBagLayout());           
2 26 Feb 07 jari 1147             for(int i = 0; i < numPanels; i++) {
2 26 Feb 07 jari 1148                 bigPanel.add(panels[i] ,new GridBagConstraints(0,i,1,1,1,1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 1149             }
2 26 Feb 07 jari 1150             
2 26 Feb 07 jari 1151             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 1152             scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1153             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1154             scroll.setBorder(BorderFactory.createLineBorder(Color.black,2));
2 26 Feb 07 jari 1155             
2 26 Feb 07 jari 1156             buildConstraints(constraints, 0, 0, 1, 1, 100, 90);
2 26 Feb 07 jari 1157             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1158             gridbag2.setConstraints(scroll, constraints);
2 26 Feb 07 jari 1159             this.add(scroll);
2 26 Feb 07 jari 1160             
2 26 Feb 07 jari 1161           JLabel label1 = new JLabel("                                                Note: Group A and Group B  MUST each contain more than one sample.");
2 26 Feb 07 jari 1162             buildConstraints(constraints, 0, 1, 1, 1, 0, 5);
2 26 Feb 07 jari 1163             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1164             gridbag2.setConstraints(label1, constraints);
2 26 Feb 07 jari 1165             this.add(label1);
2 26 Feb 07 jari 1166             
2 26 Feb 07 jari 1167             if(lotsOfSamples){
2 26 Feb 07 jari 1168               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 1169               this.add(lotsOfSamplesWarningLabel, new GridBagConstraints(0,2,1,1,0,0,GridBagConstraints.CENTER,GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 1170             }
2 26 Feb 07 jari 1171             
2 26 Feb 07 jari 1172             JPanel panel2 = new JPanel();
2 26 Feb 07 jari 1173             panel2.setBackground(Color.white);
2 26 Feb 07 jari 1174             GridBagLayout gridbag3 = new GridBagLayout();
2 26 Feb 07 jari 1175             panel2.setLayout(gridbag3);
2 26 Feb 07 jari 1176             
2 26 Feb 07 jari 1177             JButton saveButton = new JButton(" Save grouping ");
2 26 Feb 07 jari 1178             saveButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.gray, new Color(185,185,185), Color.darkGray, Color.darkGray));
2 26 Feb 07 jari 1179             saveButton.setFocusPainted(false);
2 26 Feb 07 jari 1180             saveButton.setPreferredSize(new Dimension(100,30));
2 26 Feb 07 jari 1181             JButton loadButton = new JButton(" Load grouping ");
2 26 Feb 07 jari 1182             loadButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.gray, new Color(185,185,185), Color.darkGray, Color.darkGray));
2 26 Feb 07 jari 1183             loadButton.setFocusPainted(false);
2 26 Feb 07 jari 1184             loadButton.setPreferredSize(new Dimension(100,30));
2 26 Feb 07 jari 1185             JButton resetButton = new JButton(" Reset ");
2 26 Feb 07 jari 1186             resetButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.gray, new Color(185,185,185), Color.darkGray, Color.darkGray));
2 26 Feb 07 jari 1187             resetButton.setFocusPainted(false);
2 26 Feb 07 jari 1188             resetButton.setPreferredSize(new Dimension(55,30));
2 26 Feb 07 jari 1189             final int finNum = exptNames.size();
2 26 Feb 07 jari 1190             
2 26 Feb 07 jari 1191             resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1192                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1193                     for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 1194                         groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1195                     }
2 26 Feb 07 jari 1196                  
2 26 Feb 07 jari 1197                     pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 1198                     sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 1199                     sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 1200                     sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 1201                     sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 1202                     sPanel.minPButton.setEnabled(false);                    
2 26 Feb 07 jari 1203                     pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 1204                     pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 1205                     pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 1206                     pPanel.numCombsLabel.setText("                                                                            ");                    
2 26 Feb 07 jari 1207                 }
2 26 Feb 07 jari 1208             });
2 26 Feb 07 jari 1209             
2 26 Feb 07 jari 1210             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 1211             fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 1212             
2 26 Feb 07 jari 1213             saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1214                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1215                     int returnVal = fc.showSaveDialog(GroupExperimentsPanel.this);
2 26 Feb 07 jari 1216                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 1217                         File file = fc.getSelectedFile();
2 26 Feb 07 jari 1218                         try {
2 26 Feb 07 jari 1219                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 1220                             int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 1221                             for (int i = 0; i < groupAssgn.length; i++) {
2 26 Feb 07 jari 1222                                 out.print(groupAssgn[i]);
2 26 Feb 07 jari 1223                                 if (i < groupAssgn.length - 1) {
2 26 Feb 07 jari 1224                                     out.print("\t");
2 26 Feb 07 jari 1225                                 }
2 26 Feb 07 jari 1226                             }
2 26 Feb 07 jari 1227                             out.println();
2 26 Feb 07 jari 1228                             out.flush();
2 26 Feb 07 jari 1229                             out.close();
2 26 Feb 07 jari 1230                         } catch (Exception e) {
2 26 Feb 07 jari 1231                             //e.printStackTrace();
2 26 Feb 07 jari 1232                         }
2 26 Feb 07 jari 1233                         //this is where a real application would save the file.
2 26 Feb 07 jari 1234                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 1235                     } else {
2 26 Feb 07 jari 1236                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 1237                     }
2 26 Feb 07 jari 1238                 }
2 26 Feb 07 jari 1239             });
2 26 Feb 07 jari 1240             
2 26 Feb 07 jari 1241             loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1242                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1243                     int returnVal = fc.showOpenDialog(GroupExperimentsPanel.this);
2 26 Feb 07 jari 1244                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 1245                         try {
2 26 Feb 07 jari 1246                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 1247                             BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 1248                             String line = buff.readLine();
2 26 Feb 07 jari 1249                             //System.out.println(line);
2 26 Feb 07 jari 1250                             StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 1251                             st.init(line);
2 26 Feb 07 jari 1252                             Vector groupsVector = new Vector();
2 26 Feb 07 jari 1253                             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 1254                                 String current = st.nextToken();
2 26 Feb 07 jari 1255                                 groupsVector.add(new Integer(current));
2 26 Feb 07 jari 1256                                 //System.out.print(current);
2 26 Feb 07 jari 1257                             }
2 26 Feb 07 jari 1258                             buff.close();
2 26 Feb 07 jari 1259                             int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 1260                             if (groupsVector.size() != groupAssgn.length) {
2 26 Feb 07 jari 1261                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1262                             } else {
2 26 Feb 07 jari 1263                                 for (int i = 0; i < groupsVector.size(); i++) {
2 26 Feb 07 jari 1264                                     int currentExpt = ((Integer)groupsVector.get(i)).intValue();
2 26 Feb 07 jari 1265                                     if (currentExpt == 1) {
2 26 Feb 07 jari 1266                                         groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1267                                     } else if (currentExpt == 2) {
2 26 Feb 07 jari 1268                                         groupBRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1269                                     } else if (currentExpt == 3) {
2 26 Feb 07 jari 1270                                         neitherGroupRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1271                                     } else {
2 26 Feb 07 jari 1272                                         for (int j = 0; j < finNum; j++) {
2 26 Feb 07 jari 1273                                             groupARadioButtons[j].setSelected(true);
2 26 Feb 07 jari 1274                                         }
2 26 Feb 07 jari 1275                                         JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1276                                         break;
2 26 Feb 07 jari 1277                                     }
2 26 Feb 07 jari 1278                                 }
2 26 Feb 07 jari 1279                             }
2 26 Feb 07 jari 1280                             
2 26 Feb 07 jari 1281                             pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 1282                             sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 1283                             sPanel.maxTButton.setSelected(false);
2 26 Feb 07 jari 1284                             sPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 1285                             sPanel.minPButton.setSelected(false);
2 26 Feb 07 jari 1286                             sPanel.minPButton.setEnabled(false);
2 26 Feb 07 jari 1287                             pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 1288                             pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 1289                             pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 1290                             pPanel.numCombsLabel.setText("                                                                            ");                        
2 26 Feb 07 jari 1291                         
2 26 Feb 07 jari 1292                         } catch (Exception e) {
2 26 Feb 07 jari 1293                             JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1294                             //e.printStackTrace();
2 26 Feb 07 jari 1295                         }
2 26 Feb 07 jari 1296                         
2 26 Feb 07 jari 1297                         //this is where a real application would save the file.
2 26 Feb 07 jari 1298                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 1299                     } else {
2 26 Feb 07 jari 1300                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 1301                     }
2 26 Feb 07 jari 1302                 }
2 26 Feb 07 jari 1303             });
2 26 Feb 07 jari 1304             
2 26 Feb 07 jari 1305             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1306             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1307             constraints.insets = new Insets(0,5,0,5);
2 26 Feb 07 jari 1308             
2 26 Feb 07 jari 1309             buildConstraints(constraints, 0, 1, 1, 1, 33, 100);
2 26 Feb 07 jari 1310             gridbag3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 1311             panel2.add(saveButton);
2 26 Feb 07 jari 1312             
2 26 Feb 07 jari 1313             buildConstraints(constraints, 1, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 1314             gridbag3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 1315             panel2.add(loadButton);
2 26 Feb 07 jari 1316             
2 26 Feb 07 jari 1317             buildConstraints(constraints, 2, 1, 1, 1, 34, 0);
2 26 Feb 07 jari 1318             gridbag3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 1319             panel2.add(resetButton);
2 26 Feb 07 jari 1320             
2 26 Feb 07 jari 1321             buildConstraints(constraints, 0, 3, 1, 1, 0, 5);
2 26 Feb 07 jari 1322             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1323             gridbag2.setConstraints(panel2, constraints);
2 26 Feb 07 jari 1324             this.add(panel2);
2 26 Feb 07 jari 1325             
2 26 Feb 07 jari 1326         }
2 26 Feb 07 jari 1327         public void reset(){
2 26 Feb 07 jari 1328             final int finNum = exptNames.size();
2 26 Feb 07 jari 1329             for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 1330                 groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1331             }
2 26 Feb 07 jari 1332         }
2 26 Feb 07 jari 1333     }
2 26 Feb 07 jari 1334    
2 26 Feb 07 jari 1335     class PValuePanel extends JPanel {
2 26 Feb 07 jari 1336         JRadioButton tDistButton, permutButton, randomGroupsButton, allCombsButton;
2 26 Feb 07 jari 1337         JLabel numCombsLabel;
2 26 Feb 07 jari 1338         JTextField timesField, alphaInputField;
2 26 Feb 07 jari 1339         //JButton permParamButton;
2 26 Feb 07 jari 1340         
2 26 Feb 07 jari 1341         PValuePanel() {
2 26 Feb 07 jari 1342             // this.setBorder(new TitledBorder(new EtchedBorder(), "P-Value parameters"));
2 26 Feb 07 jari 1343             this.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "P-Value Parameters", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 1344             this.setBackground(Color.white);
2 26 Feb 07 jari 1345             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1346             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1347             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1348             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1349             this.setLayout(gridbag);
2 26 Feb 07 jari 1350             
2 26 Feb 07 jari 1351             //permParamButton = new JButton("Permutation parameters");
2 26 Feb 07 jari 1352             //permParamButton.setEnabled(false);
2 26 Feb 07 jari 1353             
2 26 Feb 07 jari 1354             ButtonGroup chooseP = new ButtonGroup();
2 26 Feb 07 jari 1355             
2 26 Feb 07 jari 1356             tDistButton = new JRadioButton("p-values based on t-distribution", true);
2 26 Feb 07 jari 1357             tDistButton.setFocusPainted(false);
2 26 Feb 07 jari 1358             tDistButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1359             tDistButton.setBackground(Color.white);
2 26 Feb 07 jari 1360             /*
2 26 Feb 07 jari 1361             tDistButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1362             public void actionPerformed (ActionEvent evt) {
2 26 Feb 07 jari 1363                     if (evt.getSource() == tDistButton) {
2 26 Feb 07 jari 1364                         permParamButton.setEnabled(false);
2 26 Feb 07 jari 1365                     }
2 26 Feb 07 jari 1366                 }
2 26 Feb 07 jari 1367             });
2 26 Feb 07 jari 1368              */
2 26 Feb 07 jari 1369             chooseP.add(tDistButton);
2 26 Feb 07 jari 1370             
2 26 Feb 07 jari 1371             permutButton = new JRadioButton("p-values based on permutation:  ", false);
2 26 Feb 07 jari 1372             permutButton.setFocusPainted(false);
2 26 Feb 07 jari 1373             permutButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1374             permutButton.setBackground(Color.white);
2 26 Feb 07 jari 1375             /*
2 26 Feb 07 jari 1376             permutButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1377             public void actionPerformed (ActionEvent evt) {
2 26 Feb 07 jari 1378                     if (evt.getSource() == permutButton) {
2 26 Feb 07 jari 1379                 int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 1380                     int grpACounter = 0;
2 26 Feb 07 jari 1381                     int grpBCounter = 0;
2 26 Feb 07 jari 1382                     for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 1383                         if (grpAssignments[i] == GROUP_A) {
2 26 Feb 07 jari 1384                             grpACounter++;
2 26 Feb 07 jari 1385                         } else if (grpAssignments[i] == GROUP_B) {
2 26 Feb 07 jari 1386                             grpBCounter++;
2 26 Feb 07 jari 1387                         }
2 26 Feb 07 jari 1388                     }
2 26 Feb 07 jari 1389                     if ((grpACounter < 2) || (grpBCounter < 2)) {
2 26 Feb 07 jari 1390                         JOptionPane.showMessageDialog(gPanel, "Group A and Group B must each contain more than one experiment", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1391                     } else {
2 26 Feb 07 jari 1392              
2 26 Feb 07 jari 1393                         //if (pPanel.permutButton.isSelected()) {
2 26 Feb 07 jari 1394                             //System.out.println("grpACounter = " + grpACounter + ", grpBCounter = " + grpBCounter);
2 26 Feb 07 jari 1395                             int numCombs = 0;
2 26 Feb 07 jari 1396                             tooMany = true;
2 26 Feb 07 jari 1397                             if ((grpACounter + grpBCounter) <= 20) {
2 26 Feb 07 jari 1398                                 numCombs = getNumCombs((grpACounter + grpBCounter), grpACounter);
2 26 Feb 07 jari 1399                                 tooMany = false;
2 26 Feb 07 jari 1400                             }
2 26 Feb 07 jari 1401                     }
2 26 Feb 07 jari 1402                 }
2 26 Feb 07 jari 1403             });
2 26 Feb 07 jari 1404              */
2 26 Feb 07 jari 1405             
2 26 Feb 07 jari 1406             //permutButton.setEnabled(false);
2 26 Feb 07 jari 1407             chooseP.add(permutButton);
2 26 Feb 07 jari 1408             /*
2 26 Feb 07 jari 1409             buildConstraints(constraints, 0, 0, 1, 1, 0, 20);
2 26 Feb 07 jari 1410             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1411             gridbag.setConstraints(tDistButton, constraints);
2 26 Feb 07 jari 1412             this.add(tDistButton);
2 26 Feb 07 jari 1413              */
2 26 Feb 07 jari 1414             
2 26 Feb 07 jari 1415             /*
2 26 Feb 07 jari 1416             JLabel line1 = new JLabel("___________________________________________________________________________________________________");
2 26 Feb 07 jari 1417             buildConstraints(constraints, 0, 1, 4, 1, 100, 5);
2 26 Feb 07 jari 1418             gridbag.setConstraints(line1, constraints);
2 26 Feb 07 jari 1419             this.add(line1);
2 26 Feb 07 jari 1420              */
2 26 Feb 07 jari 1421             
2 26 Feb 07 jari 1422             
2 26 Feb 07 jari 1423                /*
2 26 Feb 07 jari 1424             buildConstraints(constraints, 0, 2, 1, 1, 0, 15);
2 26 Feb 07 jari 1425             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1426             //constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1427             gridbag.setConstraints(permutButton, constraints);
2 26 Feb 07 jari 1428             this.add(permutButton);
2 26 Feb 07 jari 1429                 */
2 26 Feb 07 jari 1430             
2 26 Feb 07 jari 1431             /*
2 26 Feb 07 jari 1432             buildConstraints(constraints, 1, 1, 1, 1, 0, 0);
2 26 Feb 07 jari 1433             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1434             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1435             gridbag.setConstraints(permParamButton, constraints);
2 26 Feb 07 jari 1436             this.add(permParamButton);
2 26 Feb 07 jari 1437              */
2 26 Feb 07 jari 1438             
2 26 Feb 07 jari 1439             //constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1440             
2 26 Feb 07 jari 1441             numCombsLabel = new JLabel("                                       ");
2 26 Feb 07 jari 1442             numCombsLabel.setOpaque(false);
2 26 Feb 07 jari 1443             /*
2 26 Feb 07 jari 1444             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1445             buildConstraints(constraints, 1, 2, 1, 1, 0, 0);
2 26 Feb 07 jari 1446             gridbag.setConstraints(numCombsLabel, constraints);
2 26 Feb 07 jari 1447             this.add(numCombsLabel);
2 26 Feb 07 jari 1448              */
2 26 Feb 07 jari 1449             
2 26 Feb 07 jari 1450             JPanel panel1 = new JPanel();
2 26 Feb 07 jari 1451             panel1.setBackground(Color.white);
2 26 Feb 07 jari 1452             GridBagLayout grid1 = new GridBagLayout();
2 26 Feb 07 jari 1453             panel1.setLayout(grid1);
2 26 Feb 07 jari 1454             
2 26 Feb 07 jari 1455             buildConstraints(constraints, 0, 0, 1, 1, 30, 50);
2 26 Feb 07 jari 1456             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1457             grid1.setConstraints(tDistButton, constraints);
2 26 Feb 07 jari 1458             panel1.add(tDistButton);
2 26 Feb 07 jari 1459             
2 26 Feb 07 jari 1460             buildConstraints(constraints, 0, 1, 1, 1, 30, 50);
2 26 Feb 07 jari 1461             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1462             grid1.setConstraints(permutButton, constraints);
2 26 Feb 07 jari 1463             panel1.add(permutButton);
2 26 Feb 07 jari 1464             
2 26 Feb 07 jari 1465             buildConstraints(constraints, 1, 1, 1, 1, 70, 0);
2 26 Feb 07 jari 1466             constraints.ipadx = 50;
2 26 Feb 07 jari 1467             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1468             grid1.setConstraints(numCombsLabel, constraints);
2 26 Feb 07 jari 1469             panel1.add(numCombsLabel);
2 26 Feb 07 jari 1470             
2 26 Feb 07 jari 1471             constraints.ipadx = 100;
2 26 Feb 07 jari 1472             //constraints.ipady = 100;
2 26 Feb 07 jari 1473             
2 26 Feb 07 jari 1474             buildConstraints(constraints, 0, 0, 1, 1, 100, 20);
2 26 Feb 07 jari 1475             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1476             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1477             gridbag.setConstraints(panel1, constraints);
2 26 Feb 07 jari 1478             this.add(panel1);
2 26 Feb 07 jari 1479             
2 26 Feb 07 jari 1480             //DONE UPTO HERE -- 9/18/02
2 26 Feb 07 jari 1481             
2 26 Feb 07 jari 1482             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1483             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1484             constraints.ipadx = 0;
2 26 Feb 07 jari 1485             constraints.ipady = 0;
2 26 Feb 07 jari 1486             
2 26 Feb 07 jari 1487             JPanel panel2 = new JPanel();
2 26 Feb 07 jari 1488             panel2.setBackground(Color.white);
2 26 Feb 07 jari 1489             GridBagLayout grid2 = new GridBagLayout();
2 26 Feb 07 jari 1490             panel2.setLayout(grid2);
2 26 Feb 07 jari 1491             panel2.setBorder(new EtchedBorder());
2 26 Feb 07 jari 1492             
2 26 Feb 07 jari 1493             
2 26 Feb 07 jari 1494             randomGroupsButton = new JRadioButton("Randomly group samples ", true);
2 26 Feb 07 jari 1495             randomGroupsButton.setFocusPainted(false);
2 26 Feb 07 jari 1496             randomGroupsButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1497             randomGroupsButton.setBackground(Color.white);
2 26 Feb 07 jari 1498             randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 1499             
2 26 Feb 07 jari 1500             allCombsButton = new JRadioButton("Use all permutations                 ", false);
2 26 Feb 07 jari 1501             allCombsButton.setFocusPainted(false);
2 26 Feb 07 jari 1502             allCombsButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1503             allCombsButton.setBackground(Color.white);
2 26 Feb 07 jari 1504             allCombsButton.setEnabled(false);
2 26 Feb 07 jari 1505             
2 26 Feb 07 jari 1506             
2 26 Feb 07 jari 1507             ButtonGroup chooseAllOrRandom = new ButtonGroup();
2 26 Feb 07 jari 1508             
2 26 Feb 07 jari 1509             buildConstraints(constraints, 0, 0, 1, 1, 60, 50);
2 26 Feb 07 jari 1510             grid2.setConstraints(randomGroupsButton, constraints);
2 26 Feb 07 jari 1511             panel2.add(randomGroupsButton);
2 26 Feb 07 jari 1512             
2 26 Feb 07 jari 1513             timesField = new JTextField("100", 7);
2 26 Feb 07 jari 1514             timesField.setEnabled(false);
2 26 Feb 07 jari 1515             buildConstraints(constraints, 1, 0, 1, 1, 20, 0);
2 26 Feb 07 jari 1516             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1517             grid2.setConstraints(timesField, constraints);
2 26 Feb 07 jari 1518             panel2.add(timesField);
2 26 Feb 07 jari 1519             
2 26 Feb 07 jari 1520             JLabel timesLabel = new JLabel("times");
2 26 Feb 07 jari 1521             timesLabel.setOpaque(false);
2 26 Feb 07 jari 1522             buildConstraints(constraints, 2, 0, 1, 1, 20, 0);
2 26 Feb 07 jari 1523             grid2.setConstraints(timesLabel, constraints);
2 26 Feb 07 jari 1524             panel2.add(timesLabel);
2 26 Feb 07 jari 1525             
2 26 Feb 07 jari 1526             buildConstraints(constraints, 0, 1, 1, 1, 60, 0);
2 26 Feb 07 jari 1527             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1528             grid2.setConstraints(allCombsButton, constraints);
2 26 Feb 07 jari 1529             panel2.add(allCombsButton);
2 26 Feb 07 jari 1530             
2 26 Feb 07 jari 1531             chooseAllOrRandom.add(randomGroupsButton);
2 26 Feb 07 jari 1532             chooseAllOrRandom.add(allCombsButton);
2 26 Feb 07 jari 1533             
2 26 Feb 07 jari 1534             allCombsButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1535                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1536                     if (evt.getSource() == allCombsButton) {
2 26 Feb 07 jari 1537                         timesField.setText("");
2 26 Feb 07 jari 1538                         timesField.setBackground(Color.gray);
2 26 Feb 07 jari 1539                         timesField.setEnabled(false);
2 26 Feb 07 jari 1540                     }
2 26 Feb 07 jari 1541                 }
2 26 Feb 07 jari 1542             });
2 26 Feb 07 jari 1543             
2 26 Feb 07 jari 1544             randomGroupsButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1545                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1546                     if (evt.getSource() == randomGroupsButton) {
2 26 Feb 07 jari 1547                         timesField.setText("100");
2 26 Feb 07 jari 1548                         timesField.setBackground(Color.white);
2 26 Feb 07 jari 1549                         timesField.setEnabled(true);
2 26 Feb 07 jari 1550                     }
2 26 Feb 07 jari 1551                 }
2 26 Feb 07 jari 1552             });
2 26 Feb 07 jari 1553             
2 26 Feb 07 jari 1554             tDistButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1555                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1556                     if (evt.getSource() ==tDistButton) {
2 26 Feb 07 jari 1557                         randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 1558                         allCombsButton.setEnabled(false);
2 26 Feb 07 jari 1559                         timesField.setEnabled(false);
2 26 Feb 07 jari 1560                         numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 1561                     }
2 26 Feb 07 jari 1562                 }
2 26 Feb 07 jari 1563             });
2 26 Feb 07 jari 1564             
2 26 Feb 07 jari 1565             buildConstraints(constraints, 0, 1, 1, 1, 100, 60);
2 26 Feb 07 jari 1566             constraints.anchor = GridBagConstraints.NORTH;
2 26 Feb 07 jari 1567             constraints.fill = GridBagConstraints.VERTICAL;
2 26 Feb 07 jari 1568             gridbag.setConstraints(panel2, constraints);
2 26 Feb 07 jari 1569             this.add(panel2);
2 26 Feb 07 jari 1570             /*
2 26 Feb 07 jari 1571             JLabel line2 = new JLabel("___________________________________________________________________________________________________");
2 26 Feb 07 jari 1572             buildConstraints(constraints, 0, 5, 4, 1, 100, 5);
2 26 Feb 07 jari 1573             gridbag.setConstraints(line2, constraints);
2 26 Feb 07 jari 1574             this.add(line2);
2 26 Feb 07 jari 1575              */
2 26 Feb 07 jari 1576             
2 26 Feb 07 jari 1577             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1578             
2 26 Feb 07 jari 1579             JPanel panel3 = new JPanel();
2 26 Feb 07 jari 1580             panel3.setBackground(Color.white);
2 26 Feb 07 jari 1581             GridBagLayout grid3 = new GridBagLayout();
2 26 Feb 07 jari 1582             panel3.setLayout(grid3);
2 26 Feb 07 jari 1583             
2 26 Feb 07 jari 1584             JLabel alphaLabel = new JLabel("Overall alpha (critical p-value):                   ");
2 26 Feb 07 jari 1585             alphaLabel.setOpaque(false);
2 26 Feb 07 jari 1586             buildConstraints(constraints, 0, 0, 1, 1, 75, 100);
2 26 Feb 07 jari 1587             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1588             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1589             grid3.setConstraints(alphaLabel, constraints);
2 26 Feb 07 jari 1590             panel3.add(alphaLabel);
2 26 Feb 07 jari 1591             
2 26 Feb 07 jari 1592             alphaInputField = new JTextField("0.01", 7);
2 26 Feb 07 jari 1593             buildConstraints(constraints, 1, 0, 1, 1, 25, 0);
2 26 Feb 07 jari 1594             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1595             grid3.setConstraints(alphaInputField, constraints);
2 26 Feb 07 jari 1596             panel3.add(alphaInputField);
2 26 Feb 07 jari 1597             
2 26 Feb 07 jari 1598             buildConstraints(constraints, 0, 2, 1, 1, 0, 20);
2 26 Feb 07 jari 1599             gridbag.setConstraints(panel3, constraints);
2 26 Feb 07 jari 1600             this.add(panel3);
2 26 Feb 07 jari 1601             
2 26 Feb 07 jari 1602             /*
2 26 Feb 07 jari 1603             JButton pButton = new JButton("pValuePanel");
2 26 Feb 07 jari 1604             buildConstraints(constraints, 0, 0, 1, 1, 100, 100);
2 26 Feb 07 jari 1605             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1606             gridbag.setConstraints(pButton, constraints);
2 26 Feb 07 jari 1607             this.add(pButton);
2 26 Feb 07 jari 1608              */        
2 26 Feb 07 jari 1609         }
2 26 Feb 07 jari 1610     }
2 26 Feb 07 jari 1611     
2 26 Feb 07 jari 1612     class SignificancePanel extends JPanel {
2 26 Feb 07 jari 1613         JRadioButton minPButton, maxTButton, justAlphaButton, stdBonfButton, adjBonfButton, falseNumButton, falsePropButton, fastFDRButton, slowFDRButton;
2 26 Feb 07 jari 1614         JTextField falseNumField, falsePropField;
2 26 Feb 07 jari 1615         JCheckBox calcFDRPVals;
2 26 Feb 07 jari 1616         SignificancePanel() {
2 26 Feb 07 jari 1617             //      this.setBorder(new TitledBorder(new EtchedBorder(), "Significance based on: "));
2 26 Feb 07 jari 1618             this.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "p-value / false discovery corrections", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 1619             this.setBackground(Color.white);
2 26 Feb 07 jari 1620             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1621             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1622             this.setLayout(gridbag);
2 26 Feb 07 jari 1623             
2 26 Feb 07 jari 1624             /*
2 26 Feb 07 jari 1625             JLabel sigLabel = new JLabel("Significance based on: ");
2 26 Feb 07 jari 1626             buildConstraints(constraints, 0, 0, 3, 1, 0, 50);
2 26 Feb 07 jari 1627             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1628             gridbag.setConstraints(sigLabel, constraints);
2 26 Feb 07 jari 1629             this.add(sigLabel);
2 26 Feb 07 jari 1630              */
2 26 Feb 07 jari 1631             
2 26 Feb 07 jari 1632             ButtonGroup sigGroup = new ButtonGroup();
2 26 Feb 07 jari 1633             
2 26 Feb 07 jari 1634             justAlphaButton = new JRadioButton("just alpha (no correction)", true);
2 26 Feb 07 jari 1635             justAlphaButton.setFocusPainted(false);
2 26 Feb 07 jari 1636             justAlphaButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1637             justAlphaButton.setBackground(Color.white);
2 26 Feb 07 jari 1638             sigGroup.add(justAlphaButton);
2 26 Feb 07 jari 1639             
2 26 Feb 07 jari 1640             stdBonfButton = new JRadioButton("standard Bonferroni correction", false);
2 26 Feb 07 jari 1641             stdBonfButton.setFocusPainted(false);
2 26 Feb 07 jari 1642             stdBonfButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1643             stdBonfButton.setBackground(Color.white);
2 26 Feb 07 jari 1644             sigGroup.add(stdBonfButton);
2 26 Feb 07 jari 1645             
2 26 Feb 07 jari 1646             adjBonfButton = new JRadioButton("adjusted Bonferroni correction", false);
2 26 Feb 07 jari 1647             adjBonfButton.setFocusPainted(false);
2 26 Feb 07 jari 1648             adjBonfButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1649             adjBonfButton.setBackground(Color.white);
2 26 Feb 07 jari 1650             sigGroup.add(adjBonfButton);
2 26 Feb 07 jari 1651             
2 26 Feb 07 jari 1652             minPButton = new JRadioButton("minP", false);
2 26 Feb 07 jari 1653             minPButton.setEnabled(false);
2 26 Feb 07 jari 1654             minPButton.setFocusPainted(false);
2 26 Feb 07 jari 1655             minPButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1656             minPButton.setBackground(Color.white);
2 26 Feb 07 jari 1657             sigGroup.add(minPButton);            
2 26 Feb 07 jari 1658             
2 26 Feb 07 jari 1659             maxTButton = new JRadioButton("maxT", false);
2 26 Feb 07 jari 1660             maxTButton.setEnabled(false);
2 26 Feb 07 jari 1661             maxTButton.setFocusPainted(false);
2 26 Feb 07 jari 1662             maxTButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1663             maxTButton.setBackground(Color.white);
2 26 Feb 07 jari 1664             sigGroup.add(maxTButton);            
2 26 Feb 07 jari 1665             
2 26 Feb 07 jari 1666             falseNumButton = new JRadioButton("EITHER, The number of false significant genes should not exceed", false);
2 26 Feb 07 jari 1667             falseNumButton.setEnabled(false);
2 26 Feb 07 jari 1668             //falseNumButton.setEnabled(false);
2 26 Feb 07 jari 1669             falseNumButton.setFocusPainted(false);
2 26 Feb 07 jari 1670             falseNumButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1671             falseNumButton.setBackground(Color.white);
2 26 Feb 07 jari 1672             sigGroup.add(falseNumButton);            
2 26 Feb 07 jari 1673             
2 26 Feb 07 jari 1674             falsePropButton = new JRadioButton("OR, The proportion of false significant genes should not exceed", false);
2 26 Feb 07 jari 1675             falsePropButton.setEnabled(false);
2 26 Feb 07 jari 1676             //falsePropButton.setEnabled(false);
2 26 Feb 07 jari 1677             falsePropButton.setFocusPainted(false);
2 26 Feb 07 jari 1678             falsePropButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1679             falsePropButton.setBackground(Color.white);
2 26 Feb 07 jari 1680             sigGroup.add(falsePropButton);            
2 26 Feb 07 jari 1681             
2 26 Feb 07 jari 1682             falseNumField = new JTextField(10);
2 26 Feb 07 jari 1683             falseNumField.setText("10");
2 26 Feb 07 jari 1684             falseNumField.setEnabled(false);
2 26 Feb 07 jari 1685             falsePropField = new JTextField(10);
2 26 Feb 07 jari 1686             falsePropField.setText("0.05");
2 26 Feb 07 jari 1687             falsePropField.setEnabled(false);
2 26 Feb 07 jari 1688             calcFDRPVals = new JCheckBox("Calculate adjusted p values for false discovery control", false);
2 26 Feb 07 jari 1689             calcFDRPVals.setEnabled(false);
2 26 Feb 07 jari 1690             calcFDRPVals.setBackground(Color.white);
2 26 Feb 07 jari 1691             
2 26 Feb 07 jari 1692             buildConstraints(constraints, 0, 0, 1, 1, 33, 33);
2 26 Feb 07 jari 1693             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1694             gridbag.setConstraints(justAlphaButton, constraints);
2 26 Feb 07 jari 1695             this.add(justAlphaButton);
2 26 Feb 07 jari 1696             
2 26 Feb 07 jari 1697             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 1698             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1699             gridbag.setConstraints(stdBonfButton, constraints);
2 26 Feb 07 jari 1700             this.add(stdBonfButton);
2 26 Feb 07 jari 1701             
2 26 Feb 07 jari 1702             buildConstraints(constraints, 2, 0, 1, 1, 34, 0);
2 26 Feb 07 jari 1703             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1704             gridbag.setConstraints(adjBonfButton, constraints);
2 26 Feb 07 jari 1705             this.add(adjBonfButton);
2 26 Feb 07 jari 1706             
2 26 Feb 07 jari 1707             JPanel westfallYoungPanel = new JPanel();
2 26 Feb 07 jari 1708             westfallYoungPanel.setBackground(Color.white);
2 26 Feb 07 jari 1709             westfallYoungPanel.setBorder(new EtchedBorder());
2 26 Feb 07 jari 1710             GridBagLayout grid2 = new GridBagLayout(); 
2 26 Feb 07 jari 1711             westfallYoungPanel.setLayout(grid2);
2 26 Feb 07 jari 1712  
2 26 Feb 07 jari 1713             JLabel stepDownLabel = new JLabel("Step-down Westfall and Young methods (for permutations only): ");
2 26 Feb 07 jari 1714             buildConstraints(constraints, 0, 0, 1, 1, 34, 100);
2 26 Feb 07 jari 1715             //buildConstraints(constraints, 0, 1, 1, 1, 34, 50);
2 26 Feb 07 jari 1716             ////constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1717             //constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1718             //gridbag.setConstraints(stepDownLabel, constraints);
2 26 Feb 07 jari 1719             grid2.setConstraints(stepDownLabel, constraints);
2 26 Feb 07 jari 1720             //this.add(stepDownLabel);  
2 26 Feb 07 jari 1721             westfallYoungPanel.add(stepDownLabel);
2 26 Feb 07 jari 1722             
2 26 Feb 07 jari 1723             //buildConstraints(constraints, 1, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 1724             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 1725             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1726             //constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1727             //gridbag.setConstraints(minPButton, constraints);
2 26 Feb 07 jari 1728             grid2.setConstraints(minPButton, constraints);
2 26 Feb 07 jari 1729             //this.add(minPButton); 
2 26 Feb 07 jari 1730             westfallYoungPanel.add(minPButton);
2 26 Feb 07 jari 1731             
2 26 Feb 07 jari 1732             
2 26 Feb 07 jari 1733             //buildConstraints(constraints, 2, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 1734             buildConstraints(constraints, 2, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 1735             ////constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1736             //constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1737             //gridbag.setConstraints(maxTButton, constraints);
2 26 Feb 07 jari 1738             grid2.setConstraints(maxTButton, constraints);
2 26 Feb 07 jari 1739             //this.add(maxTButton);  
2 26 Feb 07 jari 1740             westfallYoungPanel.add(maxTButton);
2 26 Feb 07 jari 1741             
2 26 Feb 07 jari 1742             buildConstraints(constraints, 0, 1, 3, 1, 100, 33);
2 26 Feb 07 jari 1743             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1744             gridbag.setConstraints(westfallYoungPanel, constraints);
2 26 Feb 07 jari 1745             this.add(westfallYoungPanel);
2 26 Feb 07 jari 1746             
2 26 Feb 07 jari 1747             ButtonGroup fastOrSlow = new ButtonGroup();
2 26 Feb 07 jari 1748             fastFDRButton = new JRadioButton("Fast approximation (but possibly conservative)", true);
2 26 Feb 07 jari 1749             fastFDRButton.setSelected(true);
2 26 Feb 07 jari 1750             fastFDRButton.setEnabled(false);
2 26 Feb 07 jari 1751             fastFDRButton.setBackground(Color.white);
2 26 Feb 07 jari 1752             fastOrSlow.add(fastFDRButton);
2 26 Feb 07 jari 1753             slowFDRButton = new JRadioButton("Complete computation (possibly slow)");
2 26 Feb 07 jari 1754             slowFDRButton.setEnabled(false);
2 26 Feb 07 jari 1755             slowFDRButton.setBackground(Color.white);
2 26 Feb 07 jari 1756             fastOrSlow.add(slowFDRButton);
2 26 Feb 07 jari 1757             
2 26 Feb 07 jari 1758             JPanel FDRPanel = new JPanel();
2 26 Feb 07 jari 1759             FDRPanel.setBackground(Color.white);
2 26 Feb 07 jari 1760             FDRPanel.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "False discovery control (permutations only)", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 1761             GridBagLayout grid3 = new GridBagLayout(); 
2 26 Feb 07 jari 1762             FDRPanel.setLayout(grid3); 
2 26 Feb 07 jari 1763             
2 26 Feb 07 jari 1764             JLabel FDRLabel = new JLabel("With confidence of [1 - alpha] : ");            
2 26 Feb 07 jari 1765             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1766             buildConstraints(constraints, 0, 0, 2, 1, 100, 20);
2 26 Feb 07 jari 1767             grid3.setConstraints(FDRLabel, constraints);
2 26 Feb 07 jari 1768             FDRPanel.add(FDRLabel);
2 26 Feb 07 jari 1769             
2 26 Feb 07 jari 1770             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1771             
2 26 Feb 07 jari 1772             buildConstraints(constraints, 0, 1, 1, 1, 50, 20);
2 26 Feb 07 jari 1773             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1774             grid3.setConstraints(falseNumButton, constraints);
2 26 Feb 07 jari 1775             FDRPanel.add(falseNumButton);       
2 26 Feb 07 jari 1776             
2 26 Feb 07 jari 1777             buildConstraints(constraints, 1, 1, 1, 1, 50, 0);
2 26 Feb 07 jari 1778             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1779             grid3.setConstraints(falseNumField, constraints);
2 26 Feb 07 jari 1780             FDRPanel.add(falseNumField);    
2 26 Feb 07 jari 1781             
2 26 Feb 07 jari 1782             buildConstraints(constraints, 0, 2, 1, 1, 50, 20);
2 26 Feb 07 jari 1783             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1784             grid3.setConstraints(falsePropButton, constraints);
2 26 Feb 07 jari 1785             FDRPanel.add(falsePropButton);    
2 26 Feb 07 jari 1786             
2 26 Feb 07 jari 1787             buildConstraints(constraints, 1, 2, 1, 1, 50, 0);
2 26 Feb 07 jari 1788             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1789             grid3.setConstraints(falsePropField, constraints);
2 26 Feb 07 jari 1790             FDRPanel.add(falsePropField);    
2 26 Feb 07 jari 1791             
2 26 Feb 07 jari 1792             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1793             
2 26 Feb 07 jari 1794             buildConstraints(constraints, 0, 3, 1, 1, 50, 20);
2 26 Feb 07 jari 1795             grid3.setConstraints(fastFDRButton, constraints);
2 26 Feb 07 jari 1796             FDRPanel.add(fastFDRButton);    
2 26 Feb 07 jari 1797             
2 26 Feb 07 jari 1798             buildConstraints(constraints, 1, 3, 1, 1, 50, 0);
2 26 Feb 07 jari 1799             grid3.setConstraints(slowFDRButton, constraints);
2 26 Feb 07 jari 1800             FDRPanel.add(slowFDRButton);              
2 26 Feb 07 jari 1801             
2 26 Feb 07 jari 1802             buildConstraints(constraints, 0, 4, 2, 1, 100, 20);
2 26 Feb 07 jari 1803             grid3.setConstraints(calcFDRPVals, constraints);
2 26 Feb 07 jari 1804             FDRPanel.add(calcFDRPVals);     
2 26 Feb 07 jari 1805             
2 26 Feb 07 jari 1806             buildConstraints(constraints, 0, 2, 3, 1, 100, 34);
2 26 Feb 07 jari 1807             constraints.fill = GridBagConstraints.HORIZONTAL;
2 26 Feb 07 jari 1808             gridbag.setConstraints(FDRPanel, constraints);
2 26 Feb 07 jari 1809             this.add(FDRPanel); 
2 26 Feb 07 jari 1810             
2 26 Feb 07 jari 1811             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1812             /*
2 26 Feb 07 jari 1813             JButton sButton = new JButton("significancePanel");
2 26 Feb 07 jari 1814             buildConstraints(constraints, 0, 0, 1, 1, 100, 100);
2 26 Feb 07 jari 1815             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1816             gridbag.setConstraints(sButton, constraints);
2 26 Feb 07 jari 1817             this.add(sButton);
2 26 Feb 07 jari 1818              */
2 26 Feb 07 jari 1819             
2 26 Feb 07 jari 1820         }
2 26 Feb 07 jari 1821     }
2 26 Feb 07 jari 1822     
2 26 Feb 07 jari 1823     class OkCancelPanel extends JPanel {
2 26 Feb 07 jari 1824         JButton okButton, cancelButton;
2 26 Feb 07 jari 1825         JCheckBox drawTreesBox;
2 26 Feb 07 jari 1826         OkCancelPanel() {
2 26 Feb 07 jari 1827             this.setBorder(new TitledBorder(new EtchedBorder(), "General"));
2 26 Feb 07 jari 1828             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1829             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1830             this.setLayout(gridbag);
2 26 Feb 07 jari 1831             
2 26 Feb 07 jari 1832             drawTreesBox = new JCheckBox("Draw hierarchical trees", false);
2 26 Feb 07 jari 1833             buildConstraints(constraints, 0, 0, 2, 1, 100, 50);
2 26 Feb 07 jari 1834             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1835             gridbag.setConstraints(drawTreesBox, constraints);
2 26 Feb 07 jari 1836             this.add(drawTreesBox);
2 26 Feb 07 jari 1837             
2 26 Feb 07 jari 1838             okButton = new JButton("OK");
2 26 Feb 07 jari 1839             buildConstraints(constraints, 0, 1, 1, 1, 50, 50);
2 26 Feb 07 jari 1840             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1841             gridbag.setConstraints(okButton, constraints);
2 26 Feb 07 jari 1842             this.add(okButton);
2 26 Feb 07 jari 1843             
2 26 Feb 07 jari 1844             cancelButton = new JButton("Cancel");
2 26 Feb 07 jari 1845             buildConstraints(constraints, 1, 1, 1, 1, 50, 0);
2 26 Feb 07 jari 1846             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1847             gridbag.setConstraints(cancelButton, constraints);
2 26 Feb 07 jari 1848             this.add(cancelButton);
2 26 Feb 07 jari 1849             
2 26 Feb 07 jari 1850             /*
2 26 Feb 07 jari 1851             JButton oButton = new JButton("OkCancelPanel");
2 26 Feb 07 jari 1852             buildConstraints(constraints, 0, 0, 1, 1, 100, 100);
2 26 Feb 07 jari 1853             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1854             gridbag.setConstraints(oButton, constraints);
2 26 Feb 07 jari 1855             this.add(oButton);
2 26 Feb 07 jari 1856              */
2 26 Feb 07 jari 1857         }
2 26 Feb 07 jari 1858     }
2 26 Feb 07 jari 1859     
2 26 Feb 07 jari 1860     class DfCalcPanel extends JPanel {
2 26 Feb 07 jari 1861         JRadioButton welchButton, eqVarButton;
2 26 Feb 07 jari 1862         DfCalcPanel() {
2 26 Feb 07 jari 1863             this.setBorder(new TitledBorder(new EtchedBorder(), "Variance assumption (for between subjects t-test only)"));  
2 26 Feb 07 jari 1864             this.setBackground(Color.white);
2 26 Feb 07 jari 1865             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1866             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1867             this.setLayout(gridbag);
2 26 Feb 07 jari 1868             
2 26 Feb 07 jari 1869             welchButton = new JRadioButton("Welch approximation (unequal group variances)", true);
2 26 Feb 07 jari 1870             welchButton.setBackground(Color.white);
2 26 Feb 07 jari 1871             eqVarButton = new JRadioButton("Assume equal group variances", false);
2 26 Feb 07 jari 1872             eqVarButton.setBackground(Color.white);
2 26 Feb 07 jari 1873             
2 26 Feb 07 jari 1874             ButtonGroup group = new ButtonGroup();
2 26 Feb 07 jari 1875             group.add(welchButton);
2 26 Feb 07 jari 1876             group.add(eqVarButton);
2 26 Feb 07 jari 1877             
2 26 Feb 07 jari 1878             buildConstraints(constraints, 0, 0, 1, 1, 50, 100);
2 26 Feb 07 jari 1879             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1880             gridbag.setConstraints(welchButton, constraints);
2 26 Feb 07 jari 1881             this.add(welchButton);    
2 26 Feb 07 jari 1882             
2 26 Feb 07 jari 1883             buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2 26 Feb 07 jari 1884             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1885             gridbag.setConstraints(eqVarButton, constraints);
2 26 Feb 07 jari 1886             this.add(eqVarButton);            
2 26 Feb 07 jari 1887         }
2 26 Feb 07 jari 1888         
2 26 Feb 07 jari 1889         public void reset() {
2 26 Feb 07 jari 1890             welchButton.setSelected(true);
2 26 Feb 07 jari 1891         }
2 26 Feb 07 jari 1892     }
2 26 Feb 07 jari 1893     
2 26 Feb 07 jari 1894     private long factorial(int n) {
2 26 Feb 07 jari 1895         if ((n==1) || (n == 0)) {
2 26 Feb 07 jari 1896             return 1;
2 26 Feb 07 jari 1897         }
2 26 Feb 07 jari 1898         else {
2 26 Feb 07 jari 1899             return factorial(n-1) * n;
2 26 Feb 07 jari 1900         }
2 26 Feb 07 jari 1901     }
2 26 Feb 07 jari 1902     
2 26 Feb 07 jari 1903     private int getNumCombs(int n, int k) { // nCk
2 26 Feb 07 jari 1904         
2 26 Feb 07 jari 1905         /*
2 26 Feb 07 jari 1906         System.out.println("n = " + n);
2 26 Feb 07 jari 1907         System.out.println("k = " + k);
2 26 Feb 07 jari 1908         System.out.println("Numerator: factorial(n) = " + factorial(n));
2 26 Feb 07 jari 1909         System.out.println("factorial(k) = " + factorial(k));
2 26 Feb 07 jari 1910         System.out.println("factorial(n-k) = " + factorial(n-k));
2 26 Feb 07 jari 1911          */
2 26 Feb 07 jari 1912         return Math.round(factorial(n)/(factorial(k)*factorial(n-k)));
2 26 Feb 07 jari 1913     }
2 26 Feb 07 jari 1914     
2 26 Feb 07 jari 1915     
2 26 Feb 07 jari 1916     public boolean isOkPressed() {
2 26 Feb 07 jari 1917         return okPressed;
2 26 Feb 07 jari 1918     }
2 26 Feb 07 jari 1919     
2 26 Feb 07 jari 1920     public boolean isDrawTrees() {
2 26 Feb 07 jari 1921         return hclOpsPanel.isHCLSelected();
2 26 Feb 07 jari 1922     }
2 26 Feb 07 jari 1923     
2 26 Feb 07 jari 1924     public boolean drawSigTreesOnly() {
2 26 Feb 07 jari 1925         return hclOpsPanel.drawSigTreesOnly();
2 26 Feb 07 jari 1926     }
2 26 Feb 07 jari 1927     
2 26 Feb 07 jari 1928     public int getTestDesign() {
2 26 Feb 07 jari 1929         int design = -1;
2 26 Feb 07 jari 1930         if (chooseDesignPane.getSelectedIndex() == 0) {
2 26 Feb 07 jari 1931             design = TtestInitDialog.ONE_CLASS;
2 26 Feb 07 jari 1932         } else if (chooseDesignPane.getSelectedIndex() == 1){
2 26 Feb 07 jari 1933             design = TtestInitDialog.BETWEEN_SUBJECTS;
2 26 Feb 07 jari 1934         } else if (chooseDesignPane.getSelectedIndex() == 2) {
2 26 Feb 07 jari 1935             design = TtestInitDialog.PAIRED;
2 26 Feb 07 jari 1936         }
2 26 Feb 07 jari 1937         return design;
2 26 Feb 07 jari 1938     }
2 26 Feb 07 jari 1939     
2 26 Feb 07 jari 1940     public int[] getGroupAssignments() {
2 26 Feb 07 jari 1941         int[] groupAssignments = new int[exptNames.size()];
2 26 Feb 07 jari 1942         for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 1943             if (gPanel.groupARadioButtons[i].isSelected()) {
2 26 Feb 07 jari 1944                 groupAssignments[i] = GROUP_A;
2 26 Feb 07 jari 1945             } else if (gPanel.groupBRadioButtons[i].isSelected()) {
2 26 Feb 07 jari 1946                 groupAssignments[i] = GROUP_B;
2 26 Feb 07 jari 1947             } else {
2 26 Feb 07 jari 1948                 groupAssignments[i] = NEITHER_GROUP;
2 26 Feb 07 jari 1949             }
2 26 Feb 07 jari 1950         }
2 26 Feb 07 jari 1951         
2 26 Feb 07 jari 1952         return groupAssignments;
2 26 Feb 07 jari 1953     }
2 26 Feb 07 jari 1954     
2 26 Feb 07 jari 1955     public boolean isPermut() {
2 26 Feb 07 jari 1956         return pPanel.permutButton.isSelected();
2 26 Feb 07 jari 1957     }
2 26 Feb 07 jari 1958     
2 26 Feb 07 jari 1959     public int getUserNumCombs() {
2 26 Feb 07 jari 1960         String s1 = pPanel.timesField.getText();
2 26 Feb 07 jari 1961         int num = 0;
2 26 Feb 07 jari 1962         if (!useAllCombs()) {
2 26 Feb 07 jari 1963             num = Integer.parseInt(s1);
2 26 Feb 07 jari 1964         } else {
2 26 Feb 07 jari 1965             if (getTestDesign() == TtestInitDialog.BETWEEN_SUBJECTS) {
2 26 Feb 07 jari 1966                 num = allPossCombs;
2 26 Feb 07 jari 1967             } else if (getTestDesign() == TtestInitDialog.ONE_CLASS) {
2 26 Feb 07 jari 1968                 num = (int)Math.pow(2, getNumValidOneClassExpts());
2 26 Feb 07 jari 1969             } else if (getTestDesign() == TtestInitDialog.PAIRED) {
2 26 Feb 07 jari 1970                 num = (int)(Math.pow(2, tcpmPanel.tcpPanel.pairedListModel.size()));
2 26 Feb 07 jari 1971             }
2 26 Feb 07 jari 1972         }
2 26 Feb 07 jari 1973         return num;
2 26 Feb 07 jari 1974     }
2 26 Feb 07 jari 1975     
2 26 Feb 07 jari 1976     public double getAlphaValue() {
2 26 Feb 07 jari 1977         String s1 = pPanel.alphaInputField.getText();
2 26 Feb 07 jari 1978         
2 26 Feb 07 jari 1979         return Double.parseDouble(s1);
2 26 Feb 07 jari 1980     }
2 26 Feb 07 jari 1981     
2 26 Feb 07 jari 1982     public int[] getOneClassAssignments() {
2 26 Feb 07 jari 1983         int[] oneClassAssignments = new int[oPanel.includeExpts.length];
2 26 Feb 07 jari 1984        
2 26 Feb 07 jari 1985         for (int i = 0; i < oneClassAssignments.length; i++) {
2 26 Feb 07 jari 1986             if (oPanel.includeExpts[i].isSelected()) {
2 26 Feb 07 jari 1987                 oneClassAssignments[i] = 1;
2 26 Feb 07 jari 1988             } else {
2 26 Feb 07 jari 1989                 oneClassAssignments[i] = 0;
2 26 Feb 07 jari 1990             }
2 26 Feb 07 jari 1991         }
2 26 Feb 07 jari 1992         
2 26 Feb 07 jari 1993         return oneClassAssignments;
2 26 Feb 07 jari 1994     }
2 26 Feb 07 jari 1995     
2 26 Feb 07 jari 1996     public int getNumValidOneClassExpts() {
2 26 Feb 07 jari 1997         int validNum = 0;
2 26 Feb 07 jari 1998         int[] oca = getOneClassAssignments();
2 26 Feb 07 jari 1999         
2 26 Feb 07 jari 2000         for (int i =0; i < oca.length; i++) {
2 26 Feb 07 jari 2001             if (oca[i] == 1) {
2 26 Feb 07 jari 2002                 validNum++;
2 26 Feb 07 jari 2003             }
2 26 Feb 07 jari 2004         }
2 26 Feb 07 jari 2005         
2 26 Feb 07 jari 2006         return validNum;
2 26 Feb 07 jari 2007     }
2 26 Feb 07 jari 2008     
2 26 Feb 07 jari 2009     public double getOneClassMean() {
2 26 Feb 07 jari 2010         return Double.parseDouble(oPanel.meanField.getText());
2 26 Feb 07 jari 2011     }
2 26 Feb 07 jari 2012     
2 26 Feb 07 jari 2013     public int getFalseNum() {
2 26 Feb 07 jari 2014         return Integer.parseInt(sPanel.falseNumField.getText());
2 26 Feb 07 jari 2015     }
2 26 Feb 07 jari 2016     
2 26 Feb 07 jari 2017     public double getFalseProp() {
2 26 Feb 07 jari 2018         return Double.parseDouble(sPanel.falsePropField.getText());
2 26 Feb 07 jari 2019     }
2 26 Feb 07 jari 2020     
2 26 Feb 07 jari 2021     public boolean validateAlpha(String alpha){
2 26 Feb 07 jari 2022         float a;
2 26 Feb 07 jari 2023         try{
2 26 Feb 07 jari 2024             a = Float.parseFloat(alpha);
2 26 Feb 07 jari 2025         } catch (NumberFormatException e){
2 26 Feb 07 jari 2026             JOptionPane.showMessageDialog(TtestInitDialog.this, "Alpha value is not a valid input value.", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2027             pPanel.alphaInputField.requestFocus();
2 26 Feb 07 jari 2028             pPanel.alphaInputField.selectAll();
2 26 Feb 07 jari 2029             return false;
2 26 Feb 07 jari 2030         }
2 26 Feb 07 jari 2031         if(a <= 0 || a >= 1){
2 26 Feb 07 jari 2032             JOptionPane.showMessageDialog(TtestInitDialog.this, "Alpha value must be > 0 and < 1.0", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2033             pPanel.alphaInputField.requestFocus();
2 26 Feb 07 jari 2034             pPanel.alphaInputField.selectAll();
2 26 Feb 07 jari 2035             return false;
2 26 Feb 07 jari 2036         }
2 26 Feb 07 jari 2037         return true;
2 26 Feb 07 jari 2038     }
2 26 Feb 07 jari 2039     
2 26 Feb 07 jari 2040     public boolean validateFalseNum() {
2 26 Feb 07 jari 2041         int a;
2 26 Feb 07 jari 2042         try {
2 26 Feb 07 jari 2043             String falseNum = sPanel.falseNumField.getText();
2 26 Feb 07 jari 2044             a = Integer.parseInt(falseNum);
2 26 Feb 07 jari 2045         } catch (NumberFormatException e) {
2 26 Feb 07 jari 2046             JOptionPane.showMessageDialog(TtestInitDialog.this, "False number must be an integer >= 0", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2047             sPanel.falseNumField.requestFocus();
2 26 Feb 07 jari 2048             sPanel.falseNumField.selectAll();
2 26 Feb 07 jari 2049             return false;
2 26 Feb 07 jari 2050         }
2 26 Feb 07 jari 2051         if (a < 0) {
2 26 Feb 07 jari 2052             JOptionPane.showMessageDialog(TtestInitDialog.this, "False number must be an integer >= 0", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2053             sPanel.falseNumField.requestFocus();
2 26 Feb 07 jari 2054             sPanel.falseNumField.selectAll();
2 26 Feb 07 jari 2055             return false;          
2 26 Feb 07 jari 2056         }
2 26 Feb 07 jari 2057         return true;
2 26 Feb 07 jari 2058     }
2 26 Feb 07 jari 2059     
2 26 Feb 07 jari 2060     public boolean validateFalseProp() {
2 26 Feb 07 jari 2061         float a;
2 26 Feb 07 jari 2062         try {
2 26 Feb 07 jari 2063             String falseProp = sPanel.falsePropField.getText();
2 26 Feb 07 jari 2064             a = Float.parseFloat(falseProp);
2 26 Feb 07 jari 2065         } catch (NumberFormatException e) {
2 26 Feb 07 jari 2066             JOptionPane.showMessageDialog(TtestInitDialog.this, "False proportion must be between 0 and 1", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2067             sPanel.falsePropField.requestFocus();
2 26 Feb 07 jari 2068             sPanel.falsePropField.selectAll();
2 26 Feb 07 jari 2069             return false;
2 26 Feb 07 jari 2070         }
2 26 Feb 07 jari 2071         if ((a <= 0) || (a > 1)) {
2 26 Feb 07 jari 2072             JOptionPane.showMessageDialog(TtestInitDialog.this, "False proportion must be between 0 and 1", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2073             sPanel.falsePropField.requestFocus();
2 26 Feb 07 jari 2074             sPanel.falsePropField.selectAll();
2 26 Feb 07 jari 2075             return false;          
2 26 Feb 07 jari 2076         }
2 26 Feb 07 jari 2077         return true;
2 26 Feb 07 jari 2078     }    
2 26 Feb 07 jari 2079     
2 26 Feb 07 jari 2080     public boolean validatePermutations(String n){
2 26 Feb 07 jari 2081         int i;
2 26 Feb 07 jari 2082         try {
2 26 Feb 07 jari 2083             i = Integer.parseInt(n);
2 26 Feb 07 jari 2084         } catch (NumberFormatException e){
2 26 Feb 07 jari 2085             JOptionPane.showMessageDialog(TtestInitDialog.this, "Number of Permutations is not a valid input value.", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2086             pPanel.timesField.requestFocus();
2 26 Feb 07 jari 2087             pPanel.timesField.selectAll();
2 26 Feb 07 jari 2088             return false;
2 26 Feb 07 jari 2089         }
2 26 Feb 07 jari 2090         if(i <= 0){
2 26 Feb 07 jari 2091             JOptionPane.showMessageDialog(TtestInitDialog.this, "Number of Permutations must be > 0", "Input Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2092             pPanel.timesField.requestFocus();
2 26 Feb 07 jari 2093             pPanel.timesField.selectAll();
2 26 Feb 07 jari 2094             return false;
2 26 Feb 07 jari 2095         }
2 26 Feb 07 jari 2096         return true;
2 26 Feb 07 jari 2097     }
2 26 Feb 07 jari 2098     
2 26 Feb 07 jari 2099     
2 26 Feb 07 jari 2100     public class EventListener implements ActionListener{
2 26 Feb 07 jari 2101         
2 26 Feb 07 jari 2102         public void actionPerformed(ActionEvent ae){
2 26 Feb 07 jari 2103             
2 26 Feb 07 jari 2104             String command = ae.getActionCommand();
2 26 Feb 07 jari 2105             
2 26 Feb 07 jari 2106             if(command.equals("ok-command")){
2 26 Feb 07 jari 2107                 if (getTestDesign() == TtestInitDialog.BETWEEN_SUBJECTS) {
2 26 Feb 07 jari 2108                     int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 2109                     int grpACounter = 0;
2 26 Feb 07 jari 2110                     int grpBCounter = 0;
2 26 Feb 07 jari 2111                     for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2112                         if (grpAssignments[i] == GROUP_A) {
2 26 Feb 07 jari 2113                             grpACounter++;
2 26 Feb 07 jari 2114                         } else if (grpAssignments[i] == GROUP_B) {
2 26 Feb 07 jari 2115                             grpBCounter++;
2 26 Feb 07 jari 2116                         }
2 26 Feb 07 jari 2117                     }
2 26 Feb 07 jari 2118                     if ((grpACounter < 2) || (grpBCounter < 2)) {
2 26 Feb 07 jari 2119                         JOptionPane.showMessageDialog(gPanel, "Group A and Group B must each contain more than one sample", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2120                     } else {
2 26 Feb 07 jari 2121                         String alpha = pPanel.alphaInputField.getText();
2 26 Feb 07 jari 2122                         float a;
2 26 Feb 07 jari 2123                         if(pPanel.permutButton.isSelected() && pPanel.randomGroupsButton.isSelected()){
2 26 Feb 07 jari 2124                             String iter = pPanel.timesField.getText();
2 26 Feb 07 jari 2125                             if(!validatePermutations(iter)){
2 26 Feb 07 jari 2126                                 okPressed = false;
2 26 Feb 07 jari 2127                                 return;                            
2 26 Feb 07 jari 2128                             }
2 26 Feb 07 jari 2129                         }                    
2 26 Feb 07 jari 2130                         if(!validateAlpha(alpha)){
2 26 Feb 07 jari 2131                         okPressed = false;
2 26 Feb 07 jari 2132                             return;
2 26 Feb 07 jari 2133                         } 
2 26 Feb 07 jari 2134                         if (sPanel.falseNumButton.isSelected()) {                           
2 26 Feb 07 jari 2135                             if (!validateFalseNum()) {
2 26 Feb 07 jari 2136                                 okPressed = false; 
2 26 Feb 07 jari 2137                                 return;
2 26 Feb 07 jari 2138                             }
2 26 Feb 07 jari 2139                         }
2 26 Feb 07 jari 2140                         if (sPanel.falsePropButton.isSelected()) {
2 26 Feb 07 jari 2141                             if (!validateFalseProp()) {
2 26 Feb 07 jari 2142                                 okPressed = false;
2 26 Feb 07 jari 2143                                 return;
2 26 Feb 07 jari 2144                             }
2 26 Feb 07 jari 2145                         }
2 26 Feb 07 jari 2146                         okPressed = true;
2 26 Feb 07 jari 2147                         hide();
2 26 Feb 07 jari 2148                         dispose();
2 26 Feb 07 jari 2149                     }
2 26 Feb 07 jari 2150                 } else if (getTestDesign() == TtestInitDialog.ONE_CLASS) {
2 26 Feb 07 jari 2151                     try {
2 26 Feb 07 jari 2152                         float mean = Float.parseFloat(oPanel.meanField.getText());
2 26 Feb 07 jari 2153                     } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2154                         JOptionPane.showMessageDialog(oPanel, "Invalid value entered for mean", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2155                         okPressed = false;
2 26 Feb 07 jari 2156                         return;
2 26 Feb 07 jari 2157                     }
2 26 Feb 07 jari 2158                     
2 26 Feb 07 jari 2159                     if (getNumValidOneClassExpts() < 2) {
2 26 Feb 07 jari 2160                         JOptionPane.showMessageDialog(oPanel, "Select at least two samples", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2161                         okPressed = false;
2 26 Feb 07 jari 2162                         return;      
2 26 Feb 07 jari 2163                     }
2 26 Feb 07 jari 2164                     
2 26 Feb 07 jari 2165                     String alpha = pPanel.alphaInputField.getText();
2 26 Feb 07 jari 2166                     
2 26 Feb 07 jari 2167                     float a;
2 26 Feb 07 jari 2168                     if(pPanel.permutButton.isSelected() && pPanel.randomGroupsButton.isSelected()){
2 26 Feb 07 jari 2169                         String iter = pPanel.timesField.getText();
2 26 Feb 07 jari 2170                         if(!validatePermutations(iter)){
2 26 Feb 07 jari 2171                             okPressed = false;
2 26 Feb 07 jari 2172                             return;
2 26 Feb 07 jari 2173                         }
2 26 Feb 07 jari 2174                     }
2 26 Feb 07 jari 2175                     if(!validateAlpha(alpha)){
2 26 Feb 07 jari 2176                         okPressed = false;
2 26 Feb 07 jari 2177                         return;
2 26 Feb 07 jari 2178                     } 
2 26 Feb 07 jari 2179                     
2 26 Feb 07 jari 2180                     if (sPanel.falseNumButton.isSelected()) {
2 26 Feb 07 jari 2181                         if (!validateFalseNum()) {
2 26 Feb 07 jari 2182                             okPressed = false;
2 26 Feb 07 jari 2183                             return;
2 26 Feb 07 jari 2184                         }
2 26 Feb 07 jari 2185                     }
2 26 Feb 07 jari 2186                     if (sPanel.falsePropButton.isSelected()) {
2 26 Feb 07 jari 2187                         if (!validateFalseProp()) {
2 26 Feb 07 jari 2188                             okPressed = false;
2 26 Feb 07 jari 2189                             return;
2 26 Feb 07 jari 2190                         }
2 26 Feb 07 jari 2191                     }                   
2 26 Feb 07 jari 2192                     okPressed = true;
2 26 Feb 07 jari 2193                     hide();
2 26 Feb 07 jari 2194                     dispose();                    
2 26 Feb 07 jari 2195                 } else if (getTestDesign() == TtestInitDialog.PAIRED) {
2 26 Feb 07 jari 2196                     if (tcpmPanel.tcpPanel.pairedListModel.size() < 2) {
2 26 Feb 07 jari 2197                         JOptionPane.showMessageDialog(null, "Need at least two pairs of samples!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2198                     } else {
2 26 Feb 07 jari 2199                         if (tcpmPanel.tcpPanel.pairedListModel.size() <= 29) {
2 26 Feb 07 jari 2200                             int numCombs = getUserNumCombs();
2 26 Feb 07 jari 2201                             int numUniquePerms = (int)(Math.pow(2, tcpmPanel.tcpPanel.pairedListModel.size()));
2 26 Feb 07 jari 2202                             //SAMAllPermsDialog sapDialog = new SAMAllPermsDialog(SAMGUI.SAMFrame, true, numUniquePerms, numCombs);
2 26 Feb 07 jari 2203                             //sapDialog.setVisible(true);
2 26 Feb 07 jari 2204                            //allUniquePermsUsed = sapDialog.useAllPerms();                            
2 26 Feb 07 jari 2205                         }
2 26 Feb 07 jari 2206                         
2 26 Feb 07 jari 2207                     
2 26 Feb 07 jari 2208                     String alpha = pPanel.alphaInputField.getText();
2 26 Feb 07 jari 2209                     
2 26 Feb 07 jari 2210                     float a;
2 26 Feb 07 jari 2211                     if(pPanel.permutButton.isSelected() && pPanel.randomGroupsButton.isSelected()){
2 26 Feb 07 jari 2212                         String iter = pPanel.timesField.getText();
2 26 Feb 07 jari 2213                         if(!validatePermutations(iter)){
2 26 Feb 07 jari 2214                             okPressed = false;
2 26 Feb 07 jari 2215                             return;
2 26 Feb 07 jari 2216                         }
2 26 Feb 07 jari 2217                     }
2 26 Feb 07 jari 2218                     if(!validateAlpha(alpha)){
2 26 Feb 07 jari 2219                         okPressed = false;
2 26 Feb 07 jari 2220                         return;
2 26 Feb 07 jari 2221                     }    
2 26 Feb 07 jari 2222                     
2 26 Feb 07 jari 2223                     if (sPanel.falseNumButton.isSelected()) {
2 26 Feb 07 jari 2224                         if (!validateFalseNum()) {
2 26 Feb 07 jari 2225                             okPressed = false;
2 26 Feb 07 jari 2226                             return;
2 26 Feb 07 jari 2227                         }
2 26 Feb 07 jari 2228                     }
2 26 Feb 07 jari 2229                     if (sPanel.falsePropButton.isSelected()) {
2 26 Feb 07 jari 2230                         if (!validateFalseProp()) {
2 26 Feb 07 jari 2231                             okPressed = false;
2 26 Feb 07 jari 2232                             return;
2 26 Feb 07 jari 2233                         }
2 26 Feb 07 jari 2234                     }                    
2 26 Feb 07 jari 2235                         
2 26 Feb 07 jari 2236                     okPressed = true;
2 26 Feb 07 jari 2237                     javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2238                     dispose();
2 26 Feb 07 jari 2239                     }
2 26 Feb 07 jari 2240                     
2 26 Feb 07 jari 2241                 }
2 26 Feb 07 jari 2242             } else if(command.equals("reset-command")){
2 26 Feb 07 jari 2243                 if (getTestDesign() == TtestInitDialog.BETWEEN_SUBJECTS) {
2 26 Feb 07 jari 2244                     gPanel.reset();
2 26 Feb 07 jari 2245                 } else if (getTestDesign() == TtestInitDialog.ONE_CLASS) {
2 26 Feb 07 jari 2246                     oPanel.reset();
2 26 Feb 07 jari 2247                 } else if (getTestDesign() == TtestInitDialog.PAIRED) {
2 26 Feb 07 jari 2248                     tcpmPanel.tcpPanel.reset();
2 26 Feb 07 jari 2249                 }
2 26 Feb 07 jari 2250                 pPanel.tDistButton.setSelected(true);
2 26 Feb 07 jari 2251                 pPanel.randomGroupsButton.setEnabled(false);
2 26 Feb 07 jari 2252                 pPanel.allCombsButton.setEnabled(false);
2 26 Feb 07 jari 2253                 pPanel.timesField.setEnabled(false);
2 26 Feb 07 jari 2254                 pPanel.timesField.setBackground(Color.white);
2 26 Feb 07 jari 2255                 pPanel.timesField.setText("100");
2 26 Feb 07 jari 2256                 pPanel.numCombsLabel.setText("                                                                            ");
2 26 Feb 07 jari 2257                 pPanel.alphaInputField.setText("0.01");
2 26 Feb 07 jari 2258                 sPanel.justAlphaButton.setSelected(true);
2 26 Feb 07 jari 2259                 sPanel.falseNumField.setText("10");
2 26 Feb 07 jari 2260                 sPanel.falsePropField.setText("0.05");
2 26 Feb 07 jari 2261                 hclOpsPanel.setHCLSelected(false);
2 26 Feb 07 jari 2262                 dPanel.reset();
2 26 Feb 07 jari 2263             } else if(command.equals("cancel-command")){
2 26 Feb 07 jari 2264                 okPressed = false;
2 26 Feb 07 jari 2265                 setVisible(false);
2 26 Feb 07 jari 2266                 dispose();
2 26 Feb 07 jari 2267             } else if(command.equals("info-command")){
2 26 Feb 07 jari 2268                 HelpWindow helpWindow = new HelpWindow(TtestInitDialog.this, "TTEST Initialization Dialog");
2 26 Feb 07 jari 2269                 if(helpWindow.getWindowContent()){
2 26 Feb 07 jari 2270                     helpWindow.setSize(450, 600);
2 26 Feb 07 jari 2271                     helpWindow.setLocation();
2 26 Feb 07 jari 2272                     helpWindow.show();
2 26 Feb 07 jari 2273                 } else{
2 26 Feb 07 jari 2274                     helpWindow.dispose();
2 26 Feb 07 jari 2275                 }
2 26 Feb 07 jari 2276             }
2 26 Feb 07 jari 2277         }
2 26 Feb 07 jari 2278     }
2 26 Feb 07 jari 2279     
2 26 Feb 07 jari 2280     
2 26 Feb 07 jari 2281     public Vector getPairedAExpts() {
2 26 Feb 07 jari 2282         return tcpmPanel.tcpPanel.pairedAExpts;
2 26 Feb 07 jari 2283     }
2 26 Feb 07 jari 2284     
2 26 Feb 07 jari 2285     public Vector getPairedBExpts() {
2 26 Feb 07 jari 2286         return tcpmPanel.tcpPanel.pairedBExpts;
2 26 Feb 07 jari 2287     }    
2 26 Feb 07 jari 2288     
2 26 Feb 07 jari 2289     public int getSignificanceMethod() {
2 26 Feb 07 jari 2290         if (sPanel.justAlphaButton.isSelected()) {
2 26 Feb 07 jari 2291             return TtestInitDialog.JUST_ALPHA;
2 26 Feb 07 jari 2292         } else if (sPanel.stdBonfButton.isSelected()) {
2 26 Feb 07 jari 2293             return TtestInitDialog.STD_BONFERRONI;
2 26 Feb 07 jari 2294         } else if (sPanel.adjBonfButton.isSelected()){
2 26 Feb 07 jari 2295             return TtestInitDialog.ADJ_BONFERRONI;
2 26 Feb 07 jari 2296         } else if (sPanel.maxTButton.isSelected()) {
2 26 Feb 07 jari 2297             return TtestInitDialog.MAX_T;
2 26 Feb 07 jari 2298         } else if (sPanel.minPButton.isSelected()){
2 26 Feb 07 jari 2299             return TtestInitDialog.MIN_P;
2 26 Feb 07 jari 2300         } else if (sPanel.falseNumButton.isSelected()) {
2 26 Feb 07 jari 2301             return TtestInitDialog.FALSE_NUM;
2 26 Feb 07 jari 2302         } else if (sPanel.falsePropButton.isSelected()) {
2 26 Feb 07 jari 2303             return TtestInitDialog.FALSE_PROP;
2 26 Feb 07 jari 2304         } else {
2 26 Feb 07 jari 2305             return -1;
2 26 Feb 07 jari 2306         }
2 26 Feb 07 jari 2307     }
2 26 Feb 07 jari 2308     
2 26 Feb 07 jari 2309     public boolean calculateFDRPVals() {
2 26 Feb 07 jari 2310         return sPanel.calcFDRPVals.isSelected();
2 26 Feb 07 jari 2311     }
2 26 Feb 07 jari 2312     
2 26 Feb 07 jari 2313     public boolean doFastFDRApprox() {
2 26 Feb 07 jari 2314         return sPanel.fastFDRButton.isSelected();
2 26 Feb 07 jari 2315     }
2 26 Feb 07 jari 2316     
2 26 Feb 07 jari 2317     public boolean useWelchDf() {
2 26 Feb 07 jari 2318         return dPanel.welchButton.isSelected();
2 26 Feb 07 jari 2319     }
2 26 Feb 07 jari 2320     
2 26 Feb 07 jari 2321     public boolean useAllCombs() {
2 26 Feb 07 jari 2322         return pPanel.allCombsButton.isSelected();
2 26 Feb 07 jari 2323     }
2 26 Feb 07 jari 2324     
2 26 Feb 07 jari 2325     public static void main(String[] args) {
2 26 Feb 07 jari 2326         JFrame dummyFrame = new JFrame();
2 26 Feb 07 jari 2327         Vector nameVector = new Vector();
2 26 Feb 07 jari 2328         
2 26 Feb 07 jari 2329         for (int i = 0; i < 10; i++) {
2 26 Feb 07 jari 2330             nameVector.add("Exp " + i);
2 26 Feb 07 jari 2331         }
2 26 Feb 07 jari 2332         TtestInitDialog  tDialog= new TtestInitDialog(dummyFrame, true, nameVector);
2 26 Feb 07 jari 2333         for (int i = 0; i < 50; i++) {
2 26 Feb 07 jari 2334             System.out.println("2^" + i + " = " + (int)Math.pow(2, i));
2 26 Feb 07 jari 2335         }
2 26 Feb 07 jari 2336         
2 26 Feb 07 jari 2337         tDialog.setVisible(true);
2 26 Feb 07 jari 2338         
2 26 Feb 07 jari 2339         System.exit(0);
2 26 Feb 07 jari 2340     }    
2 26 Feb 07 jari 2341 }

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