mev-4.0.01/source/org/tigr/microarray/mev/cluster/gui/impl/sam/SAMInitDialog.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2 Copyright @ 1999-2003, 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  * SAMInitDialog.java
2 26 Feb 07 jari 7  *
2 26 Feb 07 jari 8  * Created on November 7, 2002, 2:06 PM
2 26 Feb 07 jari 9  */
2 26 Feb 07 jari 10 package org.tigr.microarray.mev.cluster.gui.impl.sam;
2 26 Feb 07 jari 11
2 26 Feb 07 jari 12 import java.awt.Color;
2 26 Feb 07 jari 13 import java.awt.Dimension;
2 26 Feb 07 jari 14 import java.awt.Font;
2 26 Feb 07 jari 15 import java.awt.GridBagConstraints;
2 26 Feb 07 jari 16 import java.awt.GridBagLayout;
2 26 Feb 07 jari 17 import java.awt.Insets;
2 26 Feb 07 jari 18 import java.awt.Toolkit;
2 26 Feb 07 jari 19 import java.awt.event.ActionEvent;
2 26 Feb 07 jari 20 import java.awt.event.ActionListener;
2 26 Feb 07 jari 21 import java.awt.event.ItemEvent;
2 26 Feb 07 jari 22 import java.awt.event.ItemListener;
2 26 Feb 07 jari 23 import java.awt.event.WindowAdapter;
2 26 Feb 07 jari 24 import java.awt.event.WindowEvent;
2 26 Feb 07 jari 25 import java.io.BufferedReader;
2 26 Feb 07 jari 26 import java.io.File;
2 26 Feb 07 jari 27 import java.io.FileOutputStream;
2 26 Feb 07 jari 28 import java.io.FileReader;
2 26 Feb 07 jari 29 import java.io.PrintWriter;
2 26 Feb 07 jari 30 import java.util.Vector;
2 26 Feb 07 jari 31 import javax.swing.BorderFactory;
2 26 Feb 07 jari 32 import javax.swing.ButtonGroup;
2 26 Feb 07 jari 33 import javax.swing.DefaultListModel;
2 26 Feb 07 jari 34 import javax.swing.ImageIcon;
2 26 Feb 07 jari 35 import javax.swing.JButton;
2 26 Feb 07 jari 36 import javax.swing.JCheckBox;
2 26 Feb 07 jari 37 import javax.swing.JComboBox;
2 26 Feb 07 jari 38 import javax.swing.JFileChooser;
2 26 Feb 07 jari 39 import javax.swing.JFrame;
2 26 Feb 07 jari 40 import javax.swing.JLabel;
2 26 Feb 07 jari 41 import javax.swing.JList;
2 26 Feb 07 jari 42 import javax.swing.JOptionPane;
2 26 Feb 07 jari 43 import javax.swing.JPanel;
2 26 Feb 07 jari 44 import javax.swing.JRadioButton;
2 26 Feb 07 jari 45 import javax.swing.JScrollPane;
2 26 Feb 07 jari 46 import javax.swing.JSplitPane;
2 26 Feb 07 jari 47 import javax.swing.JTabbedPane;
2 26 Feb 07 jari 48 import javax.swing.JTextField;
2 26 Feb 07 jari 49 import javax.swing.ScrollPaneConstants;
2 26 Feb 07 jari 50 import javax.swing.UIManager;
2 26 Feb 07 jari 51 import javax.swing.border.BevelBorder;
2 26 Feb 07 jari 52 import javax.swing.border.EtchedBorder;
2 26 Feb 07 jari 53 import javax.swing.border.TitledBorder;
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 SAMInitDialog extends AlgorithmDialog {
2 26 Feb 07 jari 64  
2 26 Feb 07 jari 65     ImageIcon forwardImage, backImage; 
2 26 Feb 07 jari 66     JTabbedPane tabPane;
2 26 Feb 07 jari 67     GroupExperimentsPanel gPanel;
2 26 Feb 07 jari 68     TwoClassPairedMainPanel tcpmPanel;
2 26 Feb 07 jari 69     MultiClassPanel mPanel;
2 26 Feb 07 jari 70     CensoredSurvivalPanel csPanel;
2 26 Feb 07 jari 71     OneClassPanel oneCPanel;
2 26 Feb 07 jari 72     S0AndQValueCalcPanel sqPanel;
2 26 Feb 07 jari 73     PermutationsPanel pPanel;
2 26 Feb 07 jari 74     ImputationPanel iPanel;
2 26 Feb 07 jari 75     OKCancelPanel oPanel;
2 26 Feb 07 jari 76     final int fileLoadMin=20;
2 26 Feb 07 jari 77     boolean okPressed = false, allUniquePermsUsed = false;
2 26 Feb 07 jari 78     Vector exptNames;
2 26 Feb 07 jari 79     int numGenes, numUniquePerms;
2 26 Feb 07 jari 80     HCLSigOnlyPanel hclOpsPanel;
2 26 Feb 07 jari 81     boolean lotsOfSamples = false;
2 26 Feb 07 jari 82     String lotsOfSamplesWarningText = "                                                Note: You can assign large numbers of samples quickly by using a saved text file.";
2 26 Feb 07 jari 83     
2 26 Feb 07 jari 84     
2 26 Feb 07 jari 85     public static final int GROUP_A = 1;
2 26 Feb 07 jari 86     public static final int GROUP_B = 2;
2 26 Feb 07 jari 87     public static final int NEITHER_GROUP = 3;
2 26 Feb 07 jari 88     
2 26 Feb 07 jari 89     public static final int TWO_CLASS_UNPAIRED = 4;
2 26 Feb 07 jari 90     public static final int TWO_CLASS_PAIRED = 5;
2 26 Feb 07 jari 91     public static final int MULTI_CLASS = 6;
2 26 Feb 07 jari 92     public static final int CENSORED_SURVIVAL = 7;
2 26 Feb 07 jari 93     public static final int ONE_CLASS = 8;    
2 26 Feb 07 jari 94     
2 26 Feb 07 jari 95     /** Creates new SAMInitDialog */
2 26 Feb 07 jari 96     public SAMInitDialog(JFrame parentFrame, boolean modality, Vector exptNames, int numGenes) {
2 26 Feb 07 jari 97         
2 26 Feb 07 jari 98         super(parentFrame, "SAM Initialization", modality);
2 26 Feb 07 jari 99         //this.parentFrame = parentFrame;
2 26 Feb 07 jari 100         this.exptNames = exptNames;
2 26 Feb 07 jari 101         this.numGenes = numGenes;
2 26 Feb 07 jari 102         this.numUniquePerms = 0;
2 26 Feb 07 jari 103         setBounds(0, 0, 700, 800);
2 26 Feb 07 jari 104         setBackground(Color.white);
2 26 Feb 07 jari 105         setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
2 26 Feb 07 jari 106         
2 26 Feb 07 jari 107         if(exptNames.size()>fileLoadMin){
2 26 Feb 07 jari 108           lotsOfSamples = true;
2 26 Feb 07 jari 109         }
2 26 Feb 07 jari 110         
2 26 Feb 07 jari 111         forwardImage = new ImageIcon(Toolkit.getDefaultToolkit().getImage(this.getClass().getClassLoader().getResource("org/tigr/images/Forward24.gif")));        
2 26 Feb 07 jari 112         backImage = new ImageIcon(Toolkit.getDefaultToolkit().getImage(this.getClass().getClassLoader().getResource("org/tigr/images/Back24.gif")));        
2 26 Feb 07 jari 113         GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 114         GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 115         constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 116         
2 26 Feb 07 jari 117         JPanel pane = new JPanel();
2 26 Feb 07 jari 118         pane.setLayout(gridbag);
2 26 Feb 07 jari 119         
2 26 Feb 07 jari 120         javax.swing.UIManager.put("TabbedPane.selected", Color.white);
2 26 Feb 07 jari 121         tabPane = new JTabbedPane();
2 26 Feb 07 jari 122         gPanel = new GroupExperimentsPanel(exptNames);
2 26 Feb 07 jari 123         
2 26 Feb 07 jari 124         tabPane.add("Two-class unpaired", gPanel);
2 26 Feb 07 jari 125         tcpmPanel = new TwoClassPairedMainPanel();
2 26 Feb 07 jari 126         tabPane.add("Two-class paired", tcpmPanel);
2 26 Feb 07 jari 127         mPanel = new MultiClassPanel(/*exptNames*/);
2 26 Feb 07 jari 128         tabPane.add("Multi-class", mPanel);
2 26 Feb 07 jari 129         
2 26 Feb 07 jari 130         csPanel = new CensoredSurvivalPanel(exptNames);
2 26 Feb 07 jari 131         tabPane.add("Censored survival", csPanel);
2 26 Feb 07 jari 132         oneCPanel = new OneClassPanel();
2 26 Feb 07 jari 133         tabPane.add("One-Class", oneCPanel);
2 26 Feb 07 jari 134    
2 26 Feb 07 jari 135         buildConstraints(constraints, 0, 0, 1, 1, 100, 75);
2 26 Feb 07 jari 136         
2 26 Feb 07 jari 137         gridbag.setConstraints(tabPane, constraints);
2 26 Feb 07 jari 138         
2 26 Feb 07 jari 139         pane.add(tabPane);
2 26 Feb 07 jari 140         
2 26 Feb 07 jari 141         pPanel = new PermutationsPanel();
2 26 Feb 07 jari 142         buildConstraints(constraints, 0, 1, 1, 1, 0, 5);
2 26 Feb 07 jari 143         gridbag.setConstraints(pPanel, constraints);
2 26 Feb 07 jari 144         pane.add(pPanel);
2 26 Feb 07 jari 145         sqPanel = new S0AndQValueCalcPanel();
2 26 Feb 07 jari 146         buildConstraints(constraints, 0, 2, 1, 1, 0, 10);
2 26 Feb 07 jari 147         gridbag.setConstraints(sqPanel, constraints);
2 26 Feb 07 jari 148         pane.add(sqPanel);        
2 26 Feb 07 jari 149   
2 26 Feb 07 jari 150         iPanel = new ImputationPanel();
2 26 Feb 07 jari 151         buildConstraints(constraints, 0, 3, 1, 1, 0, 5);
2 26 Feb 07 jari 152         gridbag.setConstraints(iPanel, constraints);
2 26 Feb 07 jari 153         pane.add(iPanel);
2 26 Feb 07 jari 154         
2 26 Feb 07 jari 155         hclOpsPanel = new HCLSigOnlyPanel();
2 26 Feb 07 jari 156         buildConstraints(constraints, 0, 4, 1, 1, 0, 5);
2 26 Feb 07 jari 157         gridbag.setConstraints(hclOpsPanel, constraints);
2 26 Feb 07 jari 158         pane.add(hclOpsPanel);
2 26 Feb 07 jari 159         
2 26 Feb 07 jari 160         addContent(pane);
2 26 Feb 07 jari 161         EventListener listener = new EventListener();
2 26 Feb 07 jari 162         setActionListeners(listener);
2 26 Feb 07 jari 163         this.addWindowListener(listener);
2 26 Feb 07 jari 164     }
2 26 Feb 07 jari 165     
2 26 Feb 07 jari 166     public void setVisible(boolean visible) {
2 26 Feb 07 jari 167         Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
2 26 Feb 07 jari 168         setLocation((screenSize.width - getSize().width)/2, (screenSize.height - getSize().height)/2);
2 26 Feb 07 jari 169         
2 26 Feb 07 jari 170         super.setVisible(visible);
2 26 Feb 07 jari 171         
2 26 Feb 07 jari 172         if (visible) {
2 26 Feb 07 jari 173             //bPanel.okButton.requestFocus(); //UNCOMMMENT THIS LATER
2 26 Feb 07 jari 174         }
2 26 Feb 07 jari 175     }
2 26 Feb 07 jari 176     
2 26 Feb 07 jari 177     void buildConstraints(GridBagConstraints gbc, int gx, int gy,
2 26 Feb 07 jari 178     int gw, int gh, int wx, int wy) {
2 26 Feb 07 jari 179         
2 26 Feb 07 jari 180         gbc.gridx = gx;
2 26 Feb 07 jari 181         gbc.gridy = gy;
2 26 Feb 07 jari 182         gbc.gridwidth = gw;
2 26 Feb 07 jari 183         gbc.gridheight = gh;
2 26 Feb 07 jari 184         gbc.weightx = wx;
2 26 Feb 07 jari 185         gbc.weighty = wy;
2 26 Feb 07 jari 186     }
2 26 Feb 07 jari 187     public boolean isOkPressed() {
2 26 Feb 07 jari 188         return okPressed;
2 26 Feb 07 jari 189     }
2 26 Feb 07 jari 190     
2 26 Feb 07 jari 191     public boolean isSaveMatrix() {
2 26 Feb 07 jari 192         return iPanel.saveMatrixChkBox.isSelected();
2 26 Feb 07 jari 193     }
2 26 Feb 07 jari 194     
2 26 Feb 07 jari 195     class GroupExperimentsPanel extends JPanel {
2 26 Feb 07 jari 196         JLabel[] expLabels;
2 26 Feb 07 jari 197         int numPanels = 0;
2 26 Feb 07 jari 198         JRadioButton[] groupARadioButtons, groupBRadioButtons, neitherGroupRadioButtons;
2 26 Feb 07 jari 199         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 200      
2 26 Feb 07 jari 201        GroupExperimentsPanel(Vector exptNames) {
2 26 Feb 07 jari 202             this.setBorder(new TitledBorder(new EtchedBorder(), "Group Assignments", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 203             setBackground(Color.white);
2 26 Feb 07 jari 204             JPanel panel1 = new JPanel();
2 26 Feb 07 jari 205             expLabels = new JLabel[exptNames.size()];
2 26 Feb 07 jari 206             groupARadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 207             groupBRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 208             neitherGroupRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 209             ButtonGroup chooseGroup[] = new ButtonGroup[exptNames.size()];
2 26 Feb 07 jari 210             
2 26 Feb 07 jari 211             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 212             GridBagLayout gridbag2 = new GridBagLayout();
2 26 Feb 07 jari 213             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 214             this.setLayout(gridbag2);
2 26 Feb 07 jari 215             panel1.setLayout(gridbag);
2 26 Feb 07 jari 216             
2 26 Feb 07 jari 217             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 218             JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 219             
2 26 Feb 07 jari 220             int currPanel = 0;
2 26 Feb 07 jari 221             for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 222                 panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 223             }
2 26 Feb 07 jari 224             
2 26 Feb 07 jari 225             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 226                 String s1 = (String)(exptNames.get(i));
2 26 Feb 07 jari 227                 expLabels[i] = new JLabel(s1);
2 26 Feb 07 jari 228                 chooseGroup[i] = new ButtonGroup();
2 26 Feb 07 jari 229                 groupARadioButtons[i] = new JRadioButton("Group A", true);
2 26 Feb 07 jari 230                 chooseGroup[i].add(groupARadioButtons[i]);
2 26 Feb 07 jari 231                 groupBRadioButtons[i] = new JRadioButton("Group B", false);
2 26 Feb 07 jari 232                 chooseGroup[i].add(groupBRadioButtons[i]);
2 26 Feb 07 jari 233                 neitherGroupRadioButtons[i] = new JRadioButton("Neither group", false);
2 26 Feb 07 jari 234                 chooseGroup[i].add(neitherGroupRadioButtons[i]);
2 26 Feb 07 jari 235  
2 26 Feb 07 jari 236 //              set current panel
2 26 Feb 07 jari 237                 currPanel = i / 512;
2 26 Feb 07 jari 238                 
2 26 Feb 07 jari 239                 buildConstraints(constraints, 0, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 240                 gridbag.setConstraints(expLabels[i], constraints);
2 26 Feb 07 jari 241                 panels[currPanel].add(expLabels[i]);
2 26 Feb 07 jari 242                 
2 26 Feb 07 jari 243                 buildConstraints(constraints, 1, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 244                 gridbag.setConstraints(groupARadioButtons[i], constraints);
2 26 Feb 07 jari 245                 panels[currPanel].add(groupARadioButtons[i]);
2 26 Feb 07 jari 246                 
2 26 Feb 07 jari 247                 buildConstraints(constraints, 2, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 248                 gridbag.setConstraints(groupBRadioButtons[i], constraints);
2 26 Feb 07 jari 249                 panels[currPanel].add(groupBRadioButtons[i]);
2 26 Feb 07 jari 250                 buildConstraints(constraints, 3, i%512, 1, 1, 25, 100);
2 26 Feb 07 jari 251                 gridbag.setConstraints(neitherGroupRadioButtons[i], constraints);
2 26 Feb 07 jari 252                 panels[currPanel].add(neitherGroupRadioButtons[i]);                                
2 26 Feb 07 jari 253             }
2 26 Feb 07 jari 254             
2 26 Feb 07 jari 255             JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 256             
2 26 Feb 07 jari 257             for(int i = 0; i < numPanels; i++) {
2 26 Feb 07 jari 258                 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 259             }
2 26 Feb 07 jari 260             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 261             scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 262             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 263             
2 26 Feb 07 jari 264             buildConstraints(constraints, 0, 0, 1, 1, 100, 90);
2 26 Feb 07 jari 265             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 266             gridbag2.setConstraints(scroll, constraints);
2 26 Feb 07 jari 267             this.add(scroll);
2 26 Feb 07 jari 268             
2 26 Feb 07 jari 269             JLabel label1 = new JLabel("Note: Group A and Group B  MUST each contain more than one sample.");
2 26 Feb 07 jari 270             label1.setHorizontalAlignment(JLabel.CENTER);
2 26 Feb 07 jari 271             buildConstraints(constraints, 0, 1, 1, 1, 0, 5);
2 26 Feb 07 jari 272             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 273             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 274             gridbag2.setConstraints(label1, constraints);
2 26 Feb 07 jari 275             this.add(label1);
2 26 Feb 07 jari 276             if(lotsOfSamples){
2 26 Feb 07 jari 277               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 278               lotsOfSamplesWarningLabel.setBackground(Color.gray);
2 26 Feb 07 jari 279               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 280             }
2 26 Feb 07 jari 281             
2 26 Feb 07 jari 282             JPanel panel2 = new JPanel();
2 26 Feb 07 jari 283             panel2.setBackground(Color.white);
2 26 Feb 07 jari 284             GridBagLayout gridbag3 = new GridBagLayout();
2 26 Feb 07 jari 285             panel2.setLayout(gridbag3);
2 26 Feb 07 jari 286             
2 26 Feb 07 jari 287             JButton saveButton = new JButton("  Save grouping  ");
2 26 Feb 07 jari 288             saveButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 289             saveButton.setSize(180,30);
2 26 Feb 07 jari 290             saveButton.setPreferredSize(new Dimension(180,30));
2 26 Feb 07 jari 291             JButton loadButton = new JButton("  Load grouping  ");
2 26 Feb 07 jari 292             loadButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 293             loadButton.setPreferredSize(new Dimension(180,30));
2 26 Feb 07 jari 294             loadButton.setSize(180,30);
2 26 Feb 07 jari 295             JButton resetButton = new JButton("  Reset  ");
2 26 Feb 07 jari 296             resetButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 297             resetButton.setSize(180,30);
2 26 Feb 07 jari 298             resetButton.setPreferredSize(new Dimension(180,30));
2 26 Feb 07 jari 299             final int finNum = exptNames.size();
2 26 Feb 07 jari 300             
2 26 Feb 07 jari 301             resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 302                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 303                     for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 304                         groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 305                     }
2 26 Feb 07 jari 306                 }
2 26 Feb 07 jari 307             });
2 26 Feb 07 jari 308             
2 26 Feb 07 jari 309             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 310             fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 311             
2 26 Feb 07 jari 312             saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 313                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 314                     int returnVal = fc.showSaveDialog(GroupExperimentsPanel.this);
2 26 Feb 07 jari 315                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 316                         File file = fc.getSelectedFile();
2 26 Feb 07 jari 317                         try {
2 26 Feb 07 jari 318                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 319                             int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 320                             for (int i = 0; i < groupAssgn.length; i++) {
2 26 Feb 07 jari 321                                 out.print(groupAssgn[i]);
2 26 Feb 07 jari 322                                 if (i < groupAssgn.length - 1) {
2 26 Feb 07 jari 323                                     out.print("\t");
2 26 Feb 07 jari 324                                 }
2 26 Feb 07 jari 325                             }
2 26 Feb 07 jari 326                             out.println();
2 26 Feb 07 jari 327                             out.flush();
2 26 Feb 07 jari 328                             out.close();
2 26 Feb 07 jari 329                         } catch (Exception e) {
2 26 Feb 07 jari 330                             //e.printStackTrace();
2 26 Feb 07 jari 331                         }
2 26 Feb 07 jari 332                         //this is where a real application would save the file.
2 26 Feb 07 jari 333                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 334                     } else {
2 26 Feb 07 jari 335                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 336                     }
2 26 Feb 07 jari 337                 }
2 26 Feb 07 jari 338             });
2 26 Feb 07 jari 339             
2 26 Feb 07 jari 340             loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 341                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 342                     int returnVal = fc.showOpenDialog(GroupExperimentsPanel.this);
2 26 Feb 07 jari 343                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 344                         try {
2 26 Feb 07 jari 345                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 346                             BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 347                             String line = buff.readLine();
2 26 Feb 07 jari 348                             //System.out.println(line);
2 26 Feb 07 jari 349                             StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 350                             st.init(line);
2 26 Feb 07 jari 351                             Vector groupsVector = new Vector();
2 26 Feb 07 jari 352                             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 353                                 String current = st.nextToken();
2 26 Feb 07 jari 354                                 groupsVector.add(new Integer(current));
2 26 Feb 07 jari 355                                 //System.out.print(current);
2 26 Feb 07 jari 356                             }
2 26 Feb 07 jari 357                             buff.close();
2 26 Feb 07 jari 358                             int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 359                             if (groupsVector.size() != groupAssgn.length) {
2 26 Feb 07 jari 360                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 361                             } else {
2 26 Feb 07 jari 362                                 for (int i = 0; i < groupsVector.size(); i++) {
2 26 Feb 07 jari 363                                     int currentExpt = ((Integer)groupsVector.get(i)).intValue();
2 26 Feb 07 jari 364                                     if (currentExpt == 1) {
2 26 Feb 07 jari 365                                         groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 366                                     } else if (currentExpt == 2) {
2 26 Feb 07 jari 367                                         groupBRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 368                                     } else if (currentExpt == 3) {
2 26 Feb 07 jari 369                                         neitherGroupRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 370                                     } else {
2 26 Feb 07 jari 371                                         for (int j = 0; j < finNum; j++) {
2 26 Feb 07 jari 372                                             groupARadioButtons[j].setSelected(true);
2 26 Feb 07 jari 373                                         }
2 26 Feb 07 jari 374                                         JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 375                                         break;
2 26 Feb 07 jari 376                                     }
2 26 Feb 07 jari 377                                 }
2 26 Feb 07 jari 378                             }
2 26 Feb 07 jari 379                         } catch (Exception e) {
2 26 Feb 07 jari 380                             JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 381                             //e.printStackTrace();
2 26 Feb 07 jari 382                         }
2 26 Feb 07 jari 383                         
2 26 Feb 07 jari 384                         //this is where a real application would save the file.
2 26 Feb 07 jari 385                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 386                     } else {
2 26 Feb 07 jari 387                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 388                     }
2 26 Feb 07 jari 389                 }
2 26 Feb 07 jari 390             });
2 26 Feb 07 jari 391             
2 26 Feb 07 jari 392             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 393             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 394             constraints.insets = new Insets(5,5,5,5);
2 26 Feb 07 jari 395             buildConstraints(constraints, 0, 0, 1, 1, 33, 10);
2 26 Feb 07 jari 396             gridbag3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 397             panel2.add(saveButton);
2 26 Feb 07 jari 398             
2 26 Feb 07 jari 399             buildConstraints(constraints, 1, 0, 1, 1, 33, 10);
2 26 Feb 07 jari 400             gridbag3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 401             panel2.add(loadButton);
2 26 Feb 07 jari 402             
2 26 Feb 07 jari 403             buildConstraints(constraints, 2, 0, 1, 1, 33, 10);
2 26 Feb 07 jari 404             gridbag3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 405             panel2.add(resetButton);
2 26 Feb 07 jari 406             
2 26 Feb 07 jari 407             constraints.insets = new Insets(0,0,0,0);
2 26 Feb 07 jari 408             buildConstraints(constraints, 0, 3, 1, 1, 0, 5);
2 26 Feb 07 jari 409             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 410             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 411             gridbag2.setConstraints(panel2, constraints);
2 26 Feb 07 jari 412             this.add(panel2);           
2 26 Feb 07 jari 413         }
2 26 Feb 07 jari 414         /*
2 26 Feb 07 jari 415          *  Resets group selections
2 26 Feb 07 jari 416          */
2 26 Feb 07 jari 417         private void reset(){
2 26 Feb 07 jari 418             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 419                 groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 420             }
2 26 Feb 07 jari 421         }
2 26 Feb 07 jari 422         
2 26 Feb 07 jari 423         
2 26 Feb 07 jari 424     }
2 26 Feb 07 jari 425     
2 26 Feb 07 jari 426     class CensoredSurvivalPanel extends JPanel {
2 26 Feb 07 jari 427         ExptTimeField[] fields;
2 26 Feb 07 jari 428         int numPanels = 0;
2 26 Feb 07 jari 429         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 430         
2 26 Feb 07 jari 431         CensoredSurvivalPanel(Vector exptNames) {
2 26 Feb 07 jari 432             this.setBorder(new TitledBorder(new EtchedBorder(), "Time / State Assignments", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 433             setBackground(Color.white);
2 26 Feb 07 jari 434            // JPanel panel1 = new JPanel();
2 26 Feb 07 jari 435             fields = new ExptTimeField[exptNames.size()];
2 26 Feb 07 jari 436             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 437             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 438             GridBagLayout gridbag2 = new GridBagLayout();
2 26 Feb 07 jari 439             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 440             this.setLayout(gridbag2);
2 26 Feb 07 jari 441            // panel1.setLayout(gridbag);
2 26 Feb 07 jari 442             JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 443             
2 26 Feb 07 jari 444             int currPanel = 0;
2 26 Feb 07 jari 445             for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 446                 panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 447             }
2 26 Feb 07 jari 448             
2 26 Feb 07 jari 449             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 450                 String s1 = (String)(exptNames.get(i));
2 26 Feb 07 jari 451                 fields[i] = new ExptTimeField(s1);
2 26 Feb 07 jari 452 //              set current panel
2 26 Feb 07 jari 453                 currPanel = i / 512;
2 26 Feb 07 jari 454             
2 26 Feb 07 jari 455                 buildConstraints(constraints, 0, i%512, 1, 1, 20, 100);
2 26 Feb 07 jari 456                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 457                 gridbag.setConstraints(fields[i].inAnalysisCheckBox, constraints);
2 26 Feb 07 jari 458                
2 26 Feb 07 jari 459                 panels[currPanel].add(fields[i].inAnalysisCheckBox);
2 26 Feb 07 jari 460                 
2 26 Feb 07 jari 461                 buildConstraints(constraints, 1, i%512, 1, 1, 20, 100);
2 26 Feb 07 jari 462                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 463                 gridbag.setConstraints(fields[i].expLabel, constraints);
2 26 Feb 07 jari 464                 
2 26 Feb 07 jari 465                 panels[currPanel].add(fields[i].expLabel);
2 26 Feb 07 jari 466                 
2 26 Feb 07 jari 467                 
2 26 Feb 07 jari 468                 buildConstraints(constraints, 2, i%512, 1, 1, 20, 100);
2 26 Feb 07 jari 469                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 470                 constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 471                 gridbag.setConstraints(fields[i].timeLabel, constraints);
2 26 Feb 07 jari 472                
2 26 Feb 07 jari 473                 panels[currPanel].add(fields[i].timeLabel);
2 26 Feb 07 jari 474                 
2 26 Feb 07 jari 475                 buildConstraints(constraints, 3, i%512, 1, 1, 20, 100);
2 26 Feb 07 jari 476                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 477                 constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 478                 gridbag.setConstraints(fields[i].timeInputField, constraints);
2 26 Feb 07 jari 479                 
2 26 Feb 07 jari 480                 panels[currPanel].add(fields[i].timeInputField);
2 26 Feb 07 jari 481                 
2 26 Feb 07 jari 482                 constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 483                 buildConstraints(constraints, 4, i%512, 1, 1, 20, 100);
2 26 Feb 07 jari 484                 gridbag.setConstraints(fields[i].censoredRadioButton, constraints);
2 26 Feb 07 jari 485                 panels[currPanel].add(fields[i].censoredRadioButton);
2 26 Feb 07 jari 486                 
2 26 Feb 07 jari 487                 buildConstraints(constraints, 5, i%512, 1, 1, 20, 100);
2 26 Feb 07 jari 488                 gridbag.setConstraints(fields[i].deadRadioButton, constraints);
2 26 Feb 07 jari 489  
2 26 Feb 07 jari 490                 panels[currPanel].add(fields[i].deadRadioButton);
2 26 Feb 07 jari 491                 
2 26 Feb 07 jari 492             }
2 26 Feb 07 jari 493             
2 26 Feb 07 jari 494             JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 495             
2 26 Feb 07 jari 496             for(int i = 0; i < numPanels; i++) {
2 26 Feb 07 jari 497                 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 498             }
2 26 Feb 07 jari 499             
2 26 Feb 07 jari 500             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 501             scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 502             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 503             
2 26 Feb 07 jari 504             buildConstraints(constraints, 0, 0, 1, 1, 100, 90);
2 26 Feb 07 jari 505             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 506             gridbag2.setConstraints(scroll, constraints);
2 26 Feb 07 jari 507             this.add(scroll);
2 26 Feb 07 jari 508             if(lotsOfSamples){
2 26 Feb 07 jari 509               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 510               lotsOfSamplesWarningLabel.setBackground(Color.gray);
2 26 Feb 07 jari 511               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 512             }
2 26 Feb 07 jari 513            
2 26 Feb 07 jari 514             JPanel panel2 = new JPanel();
2 26 Feb 07 jari 515             GridBagLayout gridbag3 = new GridBagLayout();
2 26 Feb 07 jari 516             panel2.setLayout(gridbag3);
2 26 Feb 07 jari 517             panel2.setBackground(Color.white);
2 26 Feb 07 jari 518             JButton saveButton = new JButton("  Save settings  ");
2 26 Feb 07 jari 519             saveButton.setFocusPainted(false);
2 26 Feb 07 jari 520             saveButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 521             JButton loadButton = new JButton("  Load settings  ");
2 26 Feb 07 jari 522             loadButton.setFocusPainted(false);
2 26 Feb 07 jari 523             loadButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 524             JButton resetButton = new JButton("  Reset  ");
2 26 Feb 07 jari 525             resetButton.setFocusPainted(false);
2 26 Feb 07 jari 526             resetButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 527             
2 26 Feb 07 jari 528             final int finNum = exptNames.size();
2 26 Feb 07 jari 529             
2 26 Feb 07 jari 530             resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 531                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 532                     for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 533                         fields[i].inAnalysisCheckBox.setSelected(true);
2 26 Feb 07 jari 534                         fields[i].timeInputField.setText("0.0");
2 26 Feb 07 jari 535                         fields[i].censoredRadioButton.setSelected(true);
2 26 Feb 07 jari 536                     }
2 26 Feb 07 jari 537                 }
2 26 Feb 07 jari 538             });
2 26 Feb 07 jari 539             
2 26 Feb 07 jari 540             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 541             fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 542             
2 26 Feb 07 jari 543             saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 544                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 545                     int returnVal = fc.showSaveDialog(CensoredSurvivalPanel.this);
2 26 Feb 07 jari 546                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 547                         File file = fc.getSelectedFile();
2 26 Feb 07 jari 548                         try {
2 26 Feb 07 jari 549                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 550                             //int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 551                             for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 552                                 if (fields[i].inAnalysisCheckBox.isSelected()) {
2 26 Feb 07 jari 553                                     out.print(1);
2 26 Feb 07 jari 554                                     out.print("\t");
2 26 Feb 07 jari 555                                     if (fields[i].timeInputField.getText() == "") {
2 26 Feb 07 jari 556                                         out.print("0.0");
2 26 Feb 07 jari 557                                     } else {
2 26 Feb 07 jari 558                                         out.print(fields[i].timeInputField.getText());
2 26 Feb 07 jari 559                                     }
2 26 Feb 07 jari 560                                     out.print("\t");
2 26 Feb 07 jari 561                                     if (fields[i].censoredRadioButton.isSelected()) {
2 26 Feb 07 jari 562                                         out.print(1);
2 26 Feb 07 jari 563                                     } else {
2 26 Feb 07 jari 564                                         out.print(0);
2 26 Feb 07 jari 565                                     }
2 26 Feb 07 jari 566                                     //DONE UP TO HERE 3/20/03
2 26 Feb 07 jari 567                                 } else {
2 26 Feb 07 jari 568                                     out.print(0);
2 26 Feb 07 jari 569                                 }
2 26 Feb 07 jari 570                                 out.println();
2 26 Feb 07 jari 571                             }
2 26 Feb 07 jari 572                             //out.println();
2 26 Feb 07 jari 573                             out.flush();
2 26 Feb 07 jari 574                             out.close();
2 26 Feb 07 jari 575                         } catch (Exception e) {
2 26 Feb 07 jari 576                             //e.printStackTrace();
2 26 Feb 07 jari 577                         }
2 26 Feb 07 jari 578                         //this is where a real application would save the file.
2 26 Feb 07 jari 579                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 580                     } else {
2 26 Feb 07 jari 581                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 582                     }
2 26 Feb 07 jari 583                 }
2 26 Feb 07 jari 584             });
2 26 Feb 07 jari 585             
2 26 Feb 07 jari 586             loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 587                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 588                     int returnVal = fc.showOpenDialog(CensoredSurvivalPanel.this);
2 26 Feb 07 jari 589                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 590                         try {
2 26 Feb 07 jari 591                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 592                             BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 593                             String currentLine;
2 26 Feb 07 jari 594                             Vector inputVector = new Vector();
2 26 Feb 07 jari 595                             //System.out.println(line);
2 26 Feb 07 jari 596                             //StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 597                             while((currentLine = buff.readLine()) != null) {
2 26 Feb 07 jari 598                                 inputVector.add(currentLine);
2 26 Feb 07 jari 599                             }
2 26 Feb 07 jari 600                             buff.close();
2 26 Feb 07 jari 601                             for (int i = 0; i < inputVector.size(); i++) {
2 26 Feb 07 jari 602                                 double[] currentSettings = getCurrentSettings((String)inputVector.get(i));
2 26 Feb 07 jari 603                                 if (currentSettings[0] == 0) {
2 26 Feb 07 jari 604                                     fields[i].inAnalysisCheckBox.setSelected(false);
2 26 Feb 07 jari 605                                 } else if (currentSettings[0] == 1) {
2 26 Feb 07 jari 606                                     fields[i].inAnalysisCheckBox.setSelected(true);
2 26 Feb 07 jari 607                                     fields[i].timeInputField.setText("" + currentSettings[1]);
2 26 Feb 07 jari 608                                     if (currentSettings[2] == 0) {
2 26 Feb 07 jari 609                                         fields[i].deadRadioButton.setSelected(true);
2 26 Feb 07 jari 610                                     } else if (currentSettings[2] == 1) {
2 26 Feb 07 jari 611                                         fields[i].censoredRadioButton.setSelected(true);
2 26 Feb 07 jari 612                                     } else {
2 26 Feb 07 jari 613                                         for (int k = 0; k < finNum; k++) {
2 26 Feb 07 jari 614                                             fields[k].inAnalysisCheckBox.setSelected(false);
2 26 Feb 07 jari 615                                         }
2 26 Feb 07 jari 616                                         JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 617                                         break;
2 26 Feb 07 jari 618                                     }
2 26 Feb 07 jari 619                                 } else { // if currentSettings[0] != 0 or 1
2 26 Feb 07 jari 620                                     for (int k = 0; k < finNum; k++) {
2 26 Feb 07 jari 621                                         fields[k].inAnalysisCheckBox.setSelected(false);
2 26 Feb 07 jari 622                                     }
2 26 Feb 07 jari 623                                     JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 624                                     break;
2 26 Feb 07 jari 625                                 }
2 26 Feb 07 jari 626                             }
2 26 Feb 07 jari 627                             
2 26 Feb 07 jari 628                         } catch (Exception e) {
2 26 Feb 07 jari 629                             for (int k = 0; k < finNum; k++) {
2 26 Feb 07 jari 630                                 fields[k].inAnalysisCheckBox.setSelected(false);
2 26 Feb 07 jari 631                             }
2 26 Feb 07 jari 632                             JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 633                             //e.printStackTrace();
2 26 Feb 07 jari 634                         }
2 26 Feb 07 jari 635                         
2 26 Feb 07 jari 636                         //this is where a real application would save the file.
2 26 Feb 07 jari 637                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 638                     } else {
2 26 Feb 07 jari 639                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 640                     }
2 26 Feb 07 jari 641                 }
2 26 Feb 07 jari 642             });
2 26 Feb 07 jari 643            
2 26 Feb 07 jari 644             
2 26 Feb 07 jari 645             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 646             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 647             constraints.insets = new Insets(5,5,5,5);
2 26 Feb 07 jari 648             buildConstraints(constraints, 0, 0, 1, 1, 33, 100);
2 26 Feb 07 jari 649             gridbag3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 650             panel2.add(saveButton);
2 26 Feb 07 jari 651             
2 26 Feb 07 jari 652             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 653             gridbag3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 654             panel2.add(loadButton);
2 26 Feb 07 jari 655             
2 26 Feb 07 jari 656             buildConstraints(constraints, 2, 0, 1, 1, 34, 0);
2 26 Feb 07 jari 657             gridbag3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 658             panel2.add(resetButton);
2 26 Feb 07 jari 659             constraints.insets = new Insets(0,0,0,0);
2 26 Feb 07 jari 660             buildConstraints(constraints, 0, 2, 1, 1, 0, 10);
2 26 Feb 07 jari 661             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 662             gridbag2.setConstraints(panel2, constraints);
2 26 Feb 07 jari 663             this.add(panel2);
2 26 Feb 07 jari 664         }
2 26 Feb 07 jari 665         
2 26 Feb 07 jari 666         /*
2 26 Feb 07 jari 667          *  Resets valuse to default values
2 26 Feb 07 jari 668          */
2 26 Feb 07 jari 669         private void reset(){
2 26 Feb 07 jari 670             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 671                 fields[i].inAnalysisCheckBox.setSelected(true);
2 26 Feb 07 jari 672                 fields[i].timeInputField.setText("0.0");
2 26 Feb 07 jari 673                 fields[i].censoredRadioButton.setSelected(true);
2 26 Feb 07 jari 674             }
2 26 Feb 07 jari 675         }
2 26 Feb 07 jari 676         
2 26 Feb 07 jari 677         /*
2 26 Feb 07 jari 678         private void addAnalysisCheckBoxListener(JCheckBox inAnalysisCheckBox, JLabel expLabel, JTextField timeInputField, JRadioButton censoredRadioButton, JRadioButton deadRadioButton, JLabel timeLabel) {
2 26 Feb 07 jari 679             inAnalysisCheckBox.addItemListener(new ItemListener() {
2 26 Feb 07 jari 680                 public void itemStateChanged(ItemEvent e) {
2 26 Feb 07 jari 681                     if (e.getStateChange() == ItemEvent.DESELECTED) {
2 26 Feb 07 jari 682                         expLabel.setEnabled(false);
2 26 Feb 07 jari 683                         timeLabel.setEnabled(false);
2 26 Feb 07 jari 684                         timeInputField.setBackground(Color.darkGray);
2 26 Feb 07 jari 685                         timeInputField.setEnabled(false);
2 26 Feb 07 jari 686                         censoredRadioButton.setEnabled(false);
2 26 Feb 07 jari 687                         deadRadioButton.setEnabled(false);
2 26 Feb 07 jari 688          
2 26 Feb 07 jari 689                     }
2 26 Feb 07 jari 690          
2 26 Feb 07 jari 691                     if (e.getStateChange() == ItemEvent.SELECTED) {
2 26 Feb 07 jari 692                         expLabel.setEnabled(true);
2 26 Feb 07 jari 693                         timeLabel.setEnabled(false);
2 26 Feb 07 jari 694                         timeInputField.setBackground(Color.white);
2 26 Feb 07 jari 695                         timeInputField.setEnabled(true);
2 26 Feb 07 jari 696                         censoredRadioButton.setEnabled(true);
2 26 Feb 07 jari 697                         deadRadioButton.setEnabled(true);
2 26 Feb 07 jari 698                     }
2 26 Feb 07 jari 699          
2 26 Feb 07 jari 700                 }
2 26 Feb 07 jari 701             });
2 26 Feb 07 jari 702         }
2 26 Feb 07 jari 703          */
2 26 Feb 07 jari 704         
2 26 Feb 07 jari 705         private class ExptTimeField {
2 26 Feb 07 jari 706             JCheckBox inAnalysisCheckBox;
2 26 Feb 07 jari 707             JLabel expLabel, timeLabel;
2 26 Feb 07 jari 708             JTextField timeInputField;
2 26 Feb 07 jari 709             JRadioButton censoredRadioButton, deadRadioButton;
2 26 Feb 07 jari 710             public ExptTimeField(String exptName) {
2 26 Feb 07 jari 711                 inAnalysisCheckBox = new JCheckBox("", true);
2 26 Feb 07 jari 712                 expLabel = new JLabel(exptName);
2 26 Feb 07 jari 713                 timeLabel = new JLabel("Time: ");
2 26 Feb 07 jari 714                 timeInputField = new JTextField("0.0", 7);
2 26 Feb 07 jari 715                 censoredRadioButton = new JRadioButton("Censored", true);
2 26 Feb 07 jari 716                 deadRadioButton = new JRadioButton("Dead", false);
2 26 Feb 07 jari 717                 ButtonGroup chooseGroup = new ButtonGroup();
2 26 Feb 07 jari 718                 chooseGroup.add(censoredRadioButton);
2 26 Feb 07 jari 719                 chooseGroup.add(deadRadioButton);
2 26 Feb 07 jari 720                 inAnalysisCheckBox.addItemListener(new ItemListener() {
2 26 Feb 07 jari 721                     public void itemStateChanged(ItemEvent e) {
2 26 Feb 07 jari 722                         if (e.getStateChange() == ItemEvent.DESELECTED) {
2 26 Feb 07 jari 723                             expLabel.setEnabled(false);
2 26 Feb 07 jari 724                             timeLabel.setEnabled(false);
2 26 Feb 07 jari 725                             timeInputField.setText("");
2 26 Feb 07 jari 726                             timeInputField.setBackground(Color.darkGray);
2 26 Feb 07 jari 727                             timeInputField.setEnabled(false);
2 26 Feb 07 jari 728                             censoredRadioButton.setEnabled(false);
2 26 Feb 07 jari 729                             deadRadioButton.setEnabled(false);
2 26 Feb 07 jari 730                             
2 26 Feb 07 jari 731                         }
2 26 Feb 07 jari 732                         
2 26 Feb 07 jari 733                         if (e.getStateChange() == ItemEvent.SELECTED) {
2 26 Feb 07 jari 734                             expLabel.setEnabled(true);
2 26 Feb 07 jari 735                             timeLabel.setEnabled(true);
2 26 Feb 07 jari 736                             timeInputField.setText("0.0");
2 26 Feb 07 jari 737                             timeInputField.setBackground(Color.white);
2 26 Feb 07 jari 738                             timeInputField.setEnabled(true);
2 26 Feb 07 jari 739                             censoredRadioButton.setEnabled(true);
2 26 Feb 07 jari 740                             deadRadioButton.setEnabled(true);
2 26 Feb 07 jari 741                         }
2 26 Feb 07 jari 742                         
2 26 Feb 07 jari 743                     }
2 26 Feb 07 jari 744                 });
2 26 Feb 07 jari 745             }
2 26 Feb 07 jari 746             
2 26 Feb 07 jari 747         }
2 26 Feb 07 jari 748         
2 26 Feb 07 jari 749         private double[] getCurrentSettings(String currentLine) {
2 26 Feb 07 jari 750             double[] currentSettings;
2 26 Feb 07 jari 751             Vector currentVector = new Vector();
2 26 Feb 07 jari 752             StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 753             st.init(currentLine);
2 26 Feb 07 jari 754             
2 26 Feb 07 jari 755             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 756                 String current = st.nextToken();
2 26 Feb 07 jari 757                 currentVector.add(new Double(current));
2 26 Feb 07 jari 758             }
2 26 Feb 07 jari 759             
2 26 Feb 07 jari 760             currentSettings = new double[currentVector.size()];
2 26 Feb 07 jari 761             for (int i = 0; i < currentSettings.length; i++) {
2 26 Feb 07 jari 762                 currentSettings[i] = ((Double)currentVector.get(i)).doubleValue();
2 26 Feb 07 jari 763             }
2 26 Feb 07 jari 764             
2 26 Feb 07 jari 765             return currentSettings;
2 26 Feb 07 jari 766             
2 26 Feb 07 jari 767         }
2 26 Feb 07 jari 768         
2 26 Feb 07 jari 769         
2 26 Feb 07 jari 770     }
2 26 Feb 07 jari 771     
2 26 Feb 07 jari 772     class OneClassPanel extends JPanel {
2 26 Feb 07 jari 773         JTextField meanField;
2 26 Feb 07 jari 774         JCheckBox[] includeExpts;
2 26 Feb 07 jari 775         int numPanels = 0;
2 26 Feb 07 jari 776         JButton saveButton, loadButton, resetButton;
2 26 Feb 07 jari 777         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 778         
2 26 Feb 07 jari 779         OneClassPanel() {
2 26 Feb 07 jari 780             this.setBackground(Color.white);
2 26 Feb 07 jari 781             JLabel meanLabel = new JLabel("Enter the mean value to be tested against: ");
2 26 Feb 07 jari 782             meanField = new JTextField("0", 7);
2 26 Feb 07 jari 783             includeExpts = new JCheckBox[exptNames.size()];
2 26 Feb 07 jari 784             
2 26 Feb 07 jari 785             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 786             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 787             this.setLayout(gridbag);
2 26 Feb 07 jari 788             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 789             JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 790             
2 26 Feb 07 jari 791             int currPanel = 0;
2 26 Feb 07 jari 792             for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 793                 panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 794             }
2 26 Feb 07 jari 795             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 796                 //set current panel
2 26 Feb 07 jari 797                 currPanel = i / 512;
2 26 Feb 07 jari 798                 
2 26 Feb 07 jari 799                 includeExpts[i] = new JCheckBox((String)(exptNames.get(i)), true);
2 26 Feb 07 jari 800                 buildConstraints(constraints, 0, i%512, 1, 1, 100, 100);
2 26 Feb 07 jari 801                 gridbag.setConstraints(includeExpts[i], constraints);
2 26 Feb 07 jari 802            
2 26 Feb 07 jari 803                 panels[currPanel].add(includeExpts[i]);
2 26 Feb 07 jari 804             }
2 26 Feb 07 jari 805             JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 806             
2 26 Feb 07 jari 807             for(int i = 0; i < numPanels; i++) {
2 26 Feb 07 jari 808                 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 809             }
2 26 Feb 07 jari 810             
2 26 Feb 07 jari 811             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 812             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 813             
2 26 Feb 07 jari 814             JPanel enterMeanPanel = new JPanel();
2 26 Feb 07 jari 815             GridBagLayout grid2 = new GridBagLayout();
2 26 Feb 07 jari 816             enterMeanPanel.setLayout(grid2);        
2 26 Feb 07 jari 817             
2 26 Feb 07 jari 818             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 819             buildConstraints(constraints, 0, 0, 1, 1, 50, 100);
2 26 Feb 07 jari 820             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 821             grid2.setConstraints(meanLabel, constraints);
2 26 Feb 07 jari 822             enterMeanPanel.add(meanLabel);
2 26 Feb 07 jari 823             
2 26 Feb 07 jari 824             buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2 26 Feb 07 jari 825             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 826             grid2.setConstraints(meanField, constraints);
2 26 Feb 07 jari 827             enterMeanPanel.add(meanField);    
2 26 Feb 07 jari 828             
2 26 Feb 07 jari 829             JScrollPane scroll2 = new JScrollPane(enterMeanPanel);
2 26 Feb 07 jari 830             
2 26 Feb 07 jari 831             JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, scroll, scroll2);
2 26 Feb 07 jari 832             split.setOneTouchExpandable(true);
2 26 Feb 07 jari 833             split.setDividerLocation(150);
2 26 Feb 07 jari 834            
2 26 Feb 07 jari 835             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 836             buildConstraints(constraints, 0, 0, 1, 1, 100, 80);
2 26 Feb 07 jari 837             gridbag.setConstraints(split, constraints);
2 26 Feb 07 jari 838             this.add(split);  
2 26 Feb 07 jari 839             if(lotsOfSamples){
2 26 Feb 07 jari 840               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 841               lotsOfSamplesWarningLabel.setBackground(Color.gray);
2 26 Feb 07 jari 842               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 843             }
2 26 Feb 07 jari 844             
2 26 Feb 07 jari 845             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 846             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 847             
2 26 Feb 07 jari 848             JPanel lsrPanel = new JPanel();
2 26 Feb 07 jari 849             loadButton = new JButton("Load settings");
2 26 Feb 07 jari 850             saveButton = new JButton("Save settings");
2 26 Feb 07 jari 851             resetButton = new JButton("Reset");
2 26 Feb 07 jari 852             
2 26 Feb 07 jari 853             resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 854                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 855                     for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 856                         includeExpts[i].setSelected(true);
2 26 Feb 07 jari 857                     }
2 26 Feb 07 jari 858                 }
2 26 Feb 07 jari 859             });
2 26 Feb 07 jari 860             
2 26 Feb 07 jari 861             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 862             fc.setCurrentDirectory(new File("Data"));  
2 26 Feb 07 jari 863             
2 26 Feb 07 jari 864             saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 865                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 866                     int returnVal = fc.showSaveDialog(OneClassPanel.this);  
2 26 Feb 07 jari 867                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 868                         File file = fc.getSelectedFile();
2 26 Feb 07 jari 869                         try {
2 26 Feb 07 jari 870                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 871                             for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 872                                 if (includeExpts[i].isSelected()) {
2 26 Feb 07 jari 873                                     out.print(1);
2 26 Feb 07 jari 874                                 } else {
2 26 Feb 07 jari 875                                     out.print(0);
2 26 Feb 07 jari 876                                 }
2 26 Feb 07 jari 877                                 if (i < includeExpts.length - 1) {
2 26 Feb 07 jari 878                                     out.print("\t");
2 26 Feb 07 jari 879                                 }
2 26 Feb 07 jari 880                             }
2 26 Feb 07 jari 881                             out.println();
2 26 Feb 07 jari 882                             out.flush();
2 26 Feb 07 jari 883                             out.close();                            
2 26 Feb 07 jari 884                         } catch (Exception e) {
2 26 Feb 07 jari 885                         }
2 26 Feb 07 jari 886                     } else {
2 26 Feb 07 jari 887                     }
2 26 Feb 07 jari 888                 }
2 26 Feb 07 jari 889             });
2 26 Feb 07 jari 890             
2 26 Feb 07 jari 891             loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 892                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 893                     int returnVal = fc.showOpenDialog(OneClassPanel.this);
2 26 Feb 07 jari 894                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 895                         try {
2 26 Feb 07 jari 896                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 897                             BufferedReader buff = new BufferedReader(file);     
2 26 Feb 07 jari 898                             String line = buff.readLine();
2 26 Feb 07 jari 899                             //System.out.println(line);
2 26 Feb 07 jari 900                             StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 901                             st.init(line);  
2 26 Feb 07 jari 902                             Vector includeExptsVector = new Vector();
2 26 Feb 07 jari 903                             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 904                                 String current = st.nextToken();
2 26 Feb 07 jari 905                                 includeExptsVector.add(new Integer(current));
2 26 Feb 07 jari 906                                 //System.out.print(current);
2 26 Feb 07 jari 907                             }
2 26 Feb 07 jari 908                             buff.close();
2 26 Feb 07 jari 909                             if (includeExptsVector.size() != includeExpts.length) {
2 26 Feb 07 jari 910                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 911                             } else {
2 26 Feb 07 jari 912                                 for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 913                                     int currentState = ((Integer)(includeExptsVector.get(i))).intValue();
2 26 Feb 07 jari 914                                     if (currentState == 0) {
2 26 Feb 07 jari 915                                         includeExpts[i].setSelected(false);
2 26 Feb 07 jari 916                                     } else if (currentState == 1) {
2 26 Feb 07 jari 917                                         includeExpts[i].setSelected(true);
2 26 Feb 07 jari 918                                     }else {
2 26 Feb 07 jari 919                                         for (int j = 0; j < includeExpts.length; j++) {
2 26 Feb 07 jari 920                                             includeExpts[j].setSelected(true);
2 26 Feb 07 jari 921                                         }
2 26 Feb 07 jari 922                                         JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 923                                         break;                                        
2 26 Feb 07 jari 924                                     }
2 26 Feb 07 jari 925                                 }
2 26 Feb 07 jari 926                             }
2 26 Feb 07 jari 927                         } catch (Exception e) {
2 26 Feb 07 jari 928                             JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE); 
2 26 Feb 07 jari 929                             
2 26 Feb 07 jari 930                         }
2 26 Feb 07 jari 931                     } else {
2 26 Feb 07 jari 932                     }
2 26 Feb 07 jari 933                 }
2 26 Feb 07 jari 934             });
2 26 Feb 07 jari 935             
2 26 Feb 07 jari 936             
2 26 Feb 07 jari 937             GridBagLayout grid3 = new GridBagLayout();
2 26 Feb 07 jari 938             lsrPanel.setLayout(grid3);
2 26 Feb 07 jari 939             
2 26 Feb 07 jari 940             buildConstraints(constraints, 0, 0, 1, 1, 33, 100);
2 26 Feb 07 jari 941             grid3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 942             lsrPanel.add(saveButton);
2 26 Feb 07 jari 943             
2 26 Feb 07 jari 944             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 945             grid3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 946             lsrPanel.add(loadButton);            
2 26 Feb 07 jari 947             
2 26 Feb 07 jari 948             buildConstraints(constraints, 2, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 949             grid3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 950             lsrPanel.add(resetButton);            
2 26 Feb 07 jari 951             
2 26 Feb 07 jari 952             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 953             buildConstraints(constraints, 0, 2, 1, 1, 0, 20);
2 26 Feb 07 jari 954             gridbag.setConstraints(lsrPanel, constraints);
2 26 Feb 07 jari 955             this.add(lsrPanel);            
2 26 Feb 07 jari 956         }
2 26 Feb 07 jari 957         
2 26 Feb 07 jari 958         
2 26 Feb 07 jari 959         public void reset() {
2 26 Feb 07 jari 960             for (int i = 0; i < includeExpts.length; i++) {
2 26 Feb 07 jari 961                 includeExpts[i].setSelected(true);
2 26 Feb 07 jari 962             }
2 26 Feb 07 jari 963             meanField.setText("0");
2 26 Feb 07 jari 964         }
2 26 Feb 07 jari 965     }    
2 26 Feb 07 jari 966     
2 26 Feb 07 jari 967     class TwoClassPairedMainPanel extends JPanel {
2 26 Feb 07 jari 968         TwoClassPairedPanel tcpPanel;
2 26 Feb 07 jari 969         JButton saveButton, resetButton, loadButton;
2 26 Feb 07 jari 970         GridBagConstraints constraints;
2 26 Feb 07 jari 971         GridBagLayout gridbag;  
2 26 Feb 07 jari 972         int dummy=0;
2 26 Feb 07 jari 973         JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 974         
2 26 Feb 07 jari 975         public TwoClassPairedMainPanel() {
2 26 Feb 07 jari 976           //if(exptNames.size()<11)
2 26 Feb 07 jari 977             tcpPanel = new TwoClassPairedPanel();
2 26 Feb 07 jari 978           //else
2 26 Feb 07 jari 979             //tcpPanel = new TwoClassPairedPanel(dummy);
2 26 Feb 07 jari 980             JPanel bottomPanel = new JPanel();
2 26 Feb 07 jari 981             bottomPanel.setBackground(Color.white);
2 26 Feb 07 jari 982             constraints = new GridBagConstraints();
2 26 Feb 07 jari 983             gridbag = new GridBagLayout();   
2 26 Feb 07 jari 984             this.setLayout(gridbag);
2 26 Feb 07 jari 985             
2 26 Feb 07 jari 986             buildConstraints(constraints, 0, 0, 1, 1, 100, 90);
2 26 Feb 07 jari 987             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 988             gridbag.setConstraints(tcpPanel, constraints);
2 26 Feb 07 jari 989             this.add(tcpPanel);
2 26 Feb 07 jari 990             if(lotsOfSamples){
2 26 Feb 07 jari 991               lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 992               lotsOfSamplesWarningLabel.setBackground(Color.gray);
2 26 Feb 07 jari 993               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 994             }
2 26 Feb 07 jari 995             
2 26 Feb 07 jari 996             GridBagLayout grid1 = new GridBagLayout();
2 26 Feb 07 jari 997             bottomPanel.setLayout(grid1);
2 26 Feb 07 jari 998             
2 26 Feb 07 jari 999             saveButton = new JButton("Save pairings");
2 26 Feb 07 jari 1000             
2 26 Feb 07 jari 1001             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 1002             fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 1003             
2 26 Feb 07 jari 1004             saveButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1005                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1006                     int returnVal = fc.showSaveDialog(TwoClassPairedMainPanel.this); 
2 26 Feb 07 jari 1007                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 1008                         File file = fc.getSelectedFile(); 
2 26 Feb 07 jari 1009                         try {
2 26 Feb 07 jari 1010                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 1011                             for (int i = 0; i < tcpPanel.pairedAExpts.size(); i++) {
2 26 Feb 07 jari 1012                                 int currentA = ((Integer)(tcpPanel.pairedAExpts.get(i))).intValue();
2 26 Feb 07 jari 1013                                 int currentB = ((Integer)(tcpPanel.pairedBExpts.get(i))).intValue();
2 26 Feb 07 jari 1014                                 out.print(currentA);
2 26 Feb 07 jari 1015                                 out.print("\t");
2 26 Feb 07 jari 1016                                 out.print(currentB);
2 26 Feb 07 jari 1017                                 out.print("\t");
2 26 Feb 07 jari 1018                                 out.println();
2 26 Feb 07 jari 1019                             }
2 26 Feb 07 jari 1020                             out.flush();
2 26 Feb 07 jari 1021                             out.close();
2 26 Feb 07 jari 1022                         } catch (Exception e) {
2 26 Feb 07 jari 1023                         }
2 26 Feb 07 jari 1024                     } else {
2 26 Feb 07 jari 1025                     }
2 26 Feb 07 jari 1026                 }
2 26 Feb 07 jari 1027             });
2 26 Feb 07 jari 1028             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1029             buildConstraints(constraints, 0, 0, 1, 1, 33, 100);
2 26 Feb 07 jari 1030             grid1.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 1031             bottomPanel.add(saveButton);       
2 26 Feb 07 jari 1032             
2 26 Feb 07 jari 1033             loadButton = new JButton("Load pairings");
2 26 Feb 07 jari 1034             
2 26 Feb 07 jari 1035             loadButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1036                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1037                     tcpPanel.reset();
2 26 Feb 07 jari 1038                     int returnVal = fc.showOpenDialog(TwoClassPairedMainPanel.this);  
2 26 Feb 07 jari 1039                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 1040                         try {
2 26 Feb 07 jari 1041                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 1042                             BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 1043                             String currentLine;  
2 26 Feb 07 jari 1044                             while((currentLine = buff.readLine()) != null) {
2 26 Feb 07 jari 1045                                 StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 1046                                 st.init(currentLine);
2 26 Feb 07 jari 1047                                 
2 26 Feb 07 jari 1048                                 for (int i = 0; i < 2; i++) {
2 26 Feb 07 jari 1049                                     String s = st.nextToken();
2 26 Feb 07 jari 1050                                     if (i == 0) {
2 26 Feb 07 jari 1051                                         tcpPanel.pairedAExpts.add(new Integer(s));
2 26 Feb 07 jari 1052                                     } else if (i == 1) {
2 26 Feb 07 jari 1053                                         tcpPanel.pairedBExpts.add(new Integer(s));
2 26 Feb 07 jari 1054                                     }
2 26 Feb 07 jari 1055                                 }
2 26 Feb 07 jari 1056                                 
2 26 Feb 07 jari 1057                             }
2 26 Feb 07 jari 1058                             buff.close();
2 26 Feb 07 jari 1059                             
2 26 Feb 07 jari 1060                             for (int i = 0; i < tcpPanel.pairedAExpts.size(); i++) {
2 26 Feb 07 jari 1061                                 int currA = ((Integer)(tcpPanel.pairedAExpts.get(i))).intValue();
2 26 Feb 07 jari 1062                                 int currB = ((Integer)(tcpPanel.pairedBExpts.get(i))).intValue();
2 26 Feb 07 jari 1063                                 String currPair = "A: " + (String)(exptNames.get(currA)) + " - B: " + (String)(exptNames.get(currB));
2 26 Feb 07 jari 1064                               //  tcpPanel.exptButtons[currA].setEnabled(false);
2 26 Feb 07 jari 1065                                // tcpPanel.exptButtons[currB].setEnabled(false); 
2 26 Feb 07 jari 1066                                 tcpPanel.pairedListModel.addElement(currPair);
2 26 Feb 07 jari 1067                                 
2 26 Feb 07 jari 1068                             }
2 26 Feb 07 jari 1069                             
2 26 Feb 07 jari 1070                             if (tcpPanel.pairedAExpts.size() > 0) {
2 26 Feb 07 jari 1071                                 tcpPanel.removeABPairButton.setEnabled(true);
2 26 Feb 07 jari 1072                                 tcpPanel.pairedExptsList.setSelectedIndex(tcpPanel.pairedListModel.size() - 1);
2 26 Feb 07 jari 1073                             }
2 26 Feb 07 jari 1074                             
2 26 Feb 07 jari 1075                         } catch (Exception exc) {
2 26 Feb 07 jari 1076                             JOptionPane.showMessageDialog(tcpPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);                            
2 26 Feb 07 jari 1077                         }
2 26 Feb 07 jari 1078                     } else {
2 26 Feb 07 jari 1079                     }
2 26 Feb 07 jari 1080                 }
2 26 Feb 07 jari 1081             });
2 26 Feb 07 jari 1082             
2 26 Feb 07 jari 1083             buildConstraints(constraints, 1, 0, 1, 1, 33, 100);
2 26 Feb 07 jari 1084             grid1.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 1085             bottomPanel.add(loadButton);     
2 26 Feb 07 jari 1086             
2 26 Feb 07 jari 1087             resetButton = new JButton("Reset");
2 26 Feb 07 jari 1088             
2 26 Feb 07 jari 1089             resetButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1090                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1091                     tcpPanel.reset();
2 26 Feb 07 jari 1092                 }
2 26 Feb 07 jari 1093             });
2 26 Feb 07 jari 1094             
2 26 Feb 07 jari 1095             buildConstraints(constraints, 2, 0, 1, 1, 34, 100);
2 26 Feb 07 jari 1096             grid1.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 1097             bottomPanel.add(resetButton);    
2 26 Feb 07 jari 1098             
2 26 Feb 07 jari 1099             buildConstraints(constraints, 0, 2, 1, 1, 0, 10);
2 26 Feb 07 jari 1100             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1101             gridbag.setConstraints(bottomPanel, constraints);
2 26 Feb 07 jari 1102             this.add(bottomPanel);             
2 26 Feb 07 jari 1103         }
2 26 Feb 07 jari 1104     }
2 26 Feb 07 jari 1105     
2 26 Feb 07 jari 1106     class TwoClassPairedPanel extends JPanel {
2 26 Feb 07 jari 1107         ExperimentButton[] exptButtons;
2 26 Feb 07 jari 1108         GridBagConstraints constraints;
2 26 Feb 07 jari 1109         GridBagLayout gridbag;
2 26 Feb 07 jari 1110         JTextField currentATextField, currentBTextField;
2 26 Feb 07 jari 1111         JButton removeCurrentAButton, removeCurrentBButton, loadABPairButton, removeABPairButton;
2 26 Feb 07 jari 1112         PairedExperimentsPanel pairPanel;
2 26 Feb 07 jari 1113         JList pairedExptsList;
2 26 Feb 07 jari 1114         DefaultListModel pairedListModel;
2 26 Feb 07 jari 1115         boolean currentAFilled, currentBFilled;
2 26 Feb 07 jari 1116         int currentAExpt, currentBExpt;
2 26 Feb 07 jari 1117         Vector pairedAExpts, pairedBExpts;
2 26 Feb 07 jari 1118       
2 26 Feb 07 jari 1119         public TwoClassPairedPanel() {
2 26 Feb 07 jari 1120             currentAExpt = -1;
2 26 Feb 07 jari 1121             currentBExpt = -1;
2 26 Feb 07 jari 1122             int numPanels = 0;
2 26 Feb 07 jari 1123             currentAFilled = false;
2 26 Feb 07 jari 1124             currentBFilled = false;
2 26 Feb 07 jari 1125             pairedAExpts = new Vector();
2 26 Feb 07 jari 1126             pairedBExpts = new Vector();
2 26 Feb 07 jari 1127             constraints = new GridBagConstraints();
2 26 Feb 07 jari 1128             gridbag = new GridBagLayout();
2 26 Feb 07 jari 1129             //this.setBackground(Color.white);
2 26 Feb 07 jari 1130             this.setLayout(gridbag);  
2 26 Feb 07 jari 1131             /*
2 26 Feb 07 jari 1132             currentATextField = new JTextField("", 10);
2 26 Feb 07 jari 1133             currentBTextField = new JTextField("", 10);
2 26 Feb 07 jari 1134             currentATextField.setBackground(Color.white);
2 26 Feb 07 jari 1135             currentBTextField.setBackground(Color.white);
2 26 Feb 07 jari 1136             currentATextField.setEditable(false);
2 26 Feb 07 jari 1137             currentBTextField.setEditable(false);   
2 26 Feb 07 jari 1138              */      
2 26 Feb 07 jari 1139             
2 26 Feb 07 jari 1140             pairedListModel = new DefaultListModel();
2 26 Feb 07 jari 1141             pairedExptsList = new JList(pairedListModel);
2 26 Feb 07 jari 1142             
2 26 Feb 07 jari 1143             /*JPanel exptNamesPanel = new JPanel();
2 26 Feb 07 jari 1144             GridBagLayout grid1 = new GridBagLayout();
2 26 Feb 07 jari 1145             exptNamesPanel.setLayout(grid1);
2 26 Feb 07 jari 1146            */
2 26 Feb 07 jari 1147             exptButtons = new ExperimentButton[exptNames.size()];
2 26 Feb 07 jari 1148             
2 26 Feb 07 jari 1149             //wwang add for fixing 512 problem
2 26 Feb 07 jari 1150             numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 1151             JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 1152             
2 26 Feb 07 jari 1153             int currPanel = 0;
2 26 Feb 07 jari 1154             for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 1155                 panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 1156             }
2 26 Feb 07 jari 1157             
2 26 Feb 07 jari 1158             int maxWidth = 0,i=0;
2 26 Feb 07 jari 1159             int maxNameLength = 0;
2 26 Feb 07 jari 1160            
2 26 Feb 07 jari 1161             for ( i = 0; i <exptNames.size() ; i++) {
2 26 Feb 07 jari 1162                 //String s = (String)(exptNames.get(i));
2 26 Feb 07 jari 1163                 exptButtons[i] = new ExperimentButton(i);
2 26 Feb 07 jari 1164                 
2 26 Feb 07 jari 1165                 if (exptButtons[i].getPreferredSize().getWidth() > maxWidth) {
2 26 Feb 07 jari 1166                     maxWidth = (int)Math.ceil(exptButtons[i].getPreferredSize().getWidth());
2 26 Feb 07 jari 1167                 }
2 26 Feb 07 jari 1168                 
2 26 Feb 07 jari 1169                 String s = (String)(exptNames.get(i));
2 26 Feb 07 jari 1170                 int currentNameLength = s.length();
2 26 Feb 07 jari 1171                 
2 26 Feb 07 jari 1172                 if (currentNameLength > maxNameLength) {
2 26 Feb 07 jari 1173                     maxNameLength = currentNameLength;
2 26 Feb 07 jari 1174                 }
2 26 Feb 07 jari 1175                 
2 26 Feb 07 jari 1176 //              set current panel
2 26 Feb 07 jari 1177                 currPanel = i / 512;
2 26 Feb 07 jari 1178  
2 26 Feb 07 jari 1179                 buildConstraints(constraints, 0, i%512, 1, 1, 100, 100);
2 26 Feb 07 jari 1180                 gridbag.setConstraints(exptButtons[i], constraints);
2 26 Feb 07 jari 1181                 panels[currPanel].add(exptButtons[i]);
2 26 Feb 07 jari 1182                // if(i<maxButton)
2 26 Feb 07 jari 1183                // exptNamesPanel.add(exptButtons[i]);
2 26 Feb 07 jari 1184             }
2 26 Feb 07 jari 1185             
2 26 Feb 07 jari 1186             currentATextField = new JTextField("", maxNameLength + 2);
2 26 Feb 07 jari 1187             currentBTextField = new JTextField("", maxNameLength + 2);
2 26 Feb 07 jari 1188             //currentATextField.setSize(maxWidth + 5, 80);
2 26 Feb 07 jari 1189             //currentBTextField.setSize(maxWidth + 5, 80);
2 26 Feb 07 jari 1190             //currentATextField.setPreferredSize(new Dimension(maxWidth + 5, 80));
2 26 Feb 07 jari 1191             //currentBTextField.setPreferredSize(new Dimension(maxWidth + 5, 80));
2 26 Feb 07 jari 1192             
2 26 Feb 07 jari 1193             currentATextField.setBackground(Color.white);
2 26 Feb 07 jari 1194             currentBTextField.setBackground(Color.white);
2 26 Feb 07 jari 1195             currentATextField.setEditable(false);
2 26 Feb 07 jari 1196             currentBTextField.setEditable(false);   
2 26 Feb 07 jari 1197             
2 26 Feb 07 jari 1198             JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 1199             
2 26 Feb 07 jari 1200             for(int m = 0; m < numPanels; m++) {
2 26 Feb 07 jari 1201                 bigPanel.add(panels[m] ,new GridBagConstraints(0,m,1,1,1,1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 1202             }
2 26 Feb 07 jari 1203             JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 1204             scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1205             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);            
2 26 Feb 07 jari 1206             
2 26 Feb 07 jari 1207             buildConstraints(constraints, 0, 0, 1, 1, 40, 100);
2 26 Feb 07 jari 1208             constraints.fill =GridBagConstraints.BOTH;
2 26 Feb 07 jari 1209             gridbag.setConstraints(scroll, constraints);
2 26 Feb 07 jari 1210             this.add(scroll);
2 26 Feb 07 jari 1211             
2 26 Feb 07 jari 1212             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1213             
2 26 Feb 07 jari 1214             JPanel currentSelectionPanel = new JPanel();
2 26 Feb 07 jari 1215             GridBagLayout grid2 = new GridBagLayout();
2 26 Feb 07 jari 1216             currentSelectionPanel.setLayout(grid2);
2 26 Feb 07 jari 1217             removeCurrentAButton = new JButton("< Remove A");
2 26 Feb 07 jari 1218             removeCurrentBButton = new JButton("< Remove B");
2 26 Feb 07 jari 1219             loadABPairButton = new JButton("   Load Pair >>   ");
2 26 Feb 07 jari 1220             removeABPairButton = new JButton("<< Remove Pair");
2 26 Feb 07 jari 1221             removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 1222             removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 1223             loadABPairButton.setEnabled(false); 
2 26 Feb 07 jari 1224             removeABPairButton.setEnabled(false);
2 26 Feb 07 jari 1225             removeCurrentAButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1226                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1227                     exptButtons[currentAExpt].setEnabled(true);
2 26 Feb 07 jari 1228                     currentAExpt = -1;
2 26 Feb 07 jari 1229                     currentATextField.setText("");
2 26 Feb 07 jari 1230                     currentAFilled = false;
2 26 Feb 07 jari 1231                     removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 1232                     loadABPairButton.setEnabled(false);
2 26 Feb 07 jari 1233                 }
2 26 Feb 07 jari 1234             });
2 26 Feb 07 jari 1235             
2 26 Feb 07 jari 1236             removeCurrentBButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1237                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1238                     exptButtons[currentBExpt].setEnabled(true);
2 26 Feb 07 jari 1239                     currentBExpt = -1;
2 26 Feb 07 jari 1240                     currentBTextField.setText("");
2 26 Feb 07 jari 1241                     currentBFilled = false;
2 26 Feb 07 jari 1242                     removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 1243                     loadABPairButton.setEnabled(false);                    
2 26 Feb 07 jari 1244                 }
2 26 Feb 07 jari 1245             });     
2 26 Feb 07 jari 1246             
2 26 Feb 07 jari 1247             loadABPairButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1248                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1249                     String currentPair = "A: " + (String)(exptNames.get(currentAExpt)) + " - B: " + (String)(exptNames.get(currentBExpt));
2 26 Feb 07 jari 1250                     pairedListModel.addElement(currentPair);
2 26 Feb 07 jari 1251                     pairedAExpts.add(new Integer(currentAExpt));
2 26 Feb 07 jari 1252                     pairedBExpts.add(new Integer(currentBExpt));
2 26 Feb 07 jari 1253                     currentAExpt = -1;
2 26 Feb 07 jari 1254                     currentBExpt = -1;
2 26 Feb 07 jari 1255                     currentATextField.setText("");
2 26 Feb 07 jari 1256                     currentBTextField.setText("");
2 26 Feb 07 jari 1257                     currentAFilled = false;
2 26 Feb 07 jari 1258                     currentBFilled = false;
2 26 Feb 07 jari 1259                     removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 1260                     removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 1261                     loadABPairButton.setEnabled(false); 
2 26 Feb 07 jari 1262                     removeABPairButton.setEnabled(true);
2 26 Feb 07 jari 1263                     pairedExptsList.setSelectedIndex(pairedListModel.size() - 1);
2 26 Feb 07 jari 1264                 }
2 26 Feb 07 jari 1265             });
2 26 Feb 07 jari 1266             
2 26 Feb 07 jari 1267             removeABPairButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1268                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1269                     int index = pairedExptsList.getSelectedIndex();
2 26 Feb 07 jari 1270                     pairedListModel.removeElementAt(index);
2 26 Feb 07 jari 1271                     int removedAIndex = ((Integer)(pairedAExpts.remove(index))).intValue();
2 26 Feb 07 jari 1272                     int removedBIndex = ((Integer)(pairedBExpts.remove(index))).intValue();
2 26 Feb 07 jari 1273                     exptButtons[removedAIndex].setEnabled(true);
2 26 Feb 07 jari 1274                     exptButtons[removedBIndex].setEnabled(true);
2 26 Feb 07 jari 1275                     if (pairedListModel.isEmpty()) {
2 26 Feb 07 jari 1276                         removeABPairButton.setEnabled(false);
2 26 Feb 07 jari 1277                     } else {
2 26 Feb 07 jari 1278                         pairedExptsList.setSelectedIndex(pairedListModel.size() - 1);
2 26 Feb 07 jari 1279                     }
2 26 Feb 07 jari 1280                 }
2 26 Feb 07 jari 1281             });
2 26 Feb 07 jari 1282
2 26 Feb 07 jari 1283             JScrollPane currentAScroll = new JScrollPane(currentATextField);
2 26 Feb 07 jari 1284             currentAScroll.setMinimumSize(new Dimension(90, 50));
2 26 Feb 07 jari 1285             JScrollPane currentBScroll = new JScrollPane(currentBTextField);
2 26 Feb 07 jari 1286             currentBScroll.setMinimumSize(new Dimension(90, 50));
2 26 Feb 07 jari 1287             
2 26 Feb 07 jari 1288             currentAScroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1289             currentAScroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);   
2 26 Feb 07 jari 1290             
2 26 Feb 07 jari 1291             currentBScroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1292             currentBScroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);            
2 26 Feb 07 jari 1293             
2 26 Feb 07 jari 1294             buildConstraints(constraints, 0, 0, 1, 1, 20, 50);
2 26 Feb 07 jari 1295             grid2.setConstraints(removeCurrentAButton, constraints);
2 26 Feb 07 jari 1296             currentSelectionPanel.add(removeCurrentAButton);
2 26 Feb 07 jari 1297             
2 26 Feb 07 jari 1298             JLabel aLabel = new JLabel(" Current A: ");
2 26 Feb 07 jari 1299             buildConstraints(constraints, 1, 0, 1, 1, 20, 0);
2 26 Feb 07 jari 1300             grid2.setConstraints(aLabel, constraints);
2 26 Feb 07 jari 1301             currentSelectionPanel.add(aLabel);    
2 26 Feb 07 jari 1302             
2 26 Feb 07 jari 1303             buildConstraints(constraints, 2, 0, 1, 1, 60, 0);
2 26 Feb 07 jari 1304             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1305             //constraints.ipady = 100;
2 26 Feb 07 jari 1306             grid2.setConstraints(currentAScroll, constraints);
2 26 Feb 07 jari 1307             currentSelectionPanel.add(currentAScroll);   
2 26 Feb 07 jari 1308             
2 26 Feb 07 jari 1309             //constraints.ipady = 0;
2 26 Feb 07 jari 1310             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1311             
2 26 Feb 07 jari 1312             buildConstraints(constraints, 0, 1, 1, 1, 20, 50);
2 26 Feb 07 jari 1313             grid2.setConstraints(removeCurrentBButton, constraints);
2 26 Feb 07 jari 1314             currentSelectionPanel.add(removeCurrentBButton);   
2 26 Feb 07 jari 1315             
2 26 Feb 07 jari 1316             JLabel bLabel = new JLabel("Current B: ");
2 26 Feb 07 jari 1317             buildConstraints(constraints, 1, 1, 1, 1, 20, 0);
2 26 Feb 07 jari 1318             grid2.setConstraints(bLabel, constraints);
2 26 Feb 07 jari 1319             currentSelectionPanel.add(bLabel);  
2 26 Feb 07 jari 1320             
2 26 Feb 07 jari 1321             buildConstraints(constraints, 2, 1, 1, 1, 60, 0);
2 26 Feb 07 jari 1322             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1323             //constraints.ipady = 100;
2 26 Feb 07 jari 1324             grid2.setConstraints(currentBScroll, constraints);
2 26 Feb 07 jari 1325             currentSelectionPanel.add(currentBScroll);   
2 26 Feb 07 jari 1326             
2 26 Feb 07 jari 1327             //constraints.ipady = 0;
2 26 Feb 07 jari 1328             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1329             
2 26 Feb 07 jari 1330             buildConstraints(constraints, 1, 0, 1, 1, 10, 0);
2 26 Feb 07 jari 1331             //constraints.fill = GridBagConstraints.HORIZONTAL;
2 26 Feb 07 jari 1332             //constraints.ipadx = 200;
2 26 Feb 07 jari 1333             gridbag.setConstraints(currentSelectionPanel, constraints);
2 26 Feb 07 jari 1334             this.add(currentSelectionPanel);   
2 26 Feb 07 jari 1335             
2 26 Feb 07 jari 1336             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1337             //constraints.ipadx = 0;
2 26 Feb 07 jari 1338             
2 26 Feb 07 jari 1339             JPanel pairButtonsPanel = new JPanel();
2 26 Feb 07 jari 1340             GridBagLayout grid3 = new GridBagLayout();
2 26 Feb 07 jari 1341             pairButtonsPanel.setLayout(grid3);
2 26 Feb 07 jari 1342
2 26 Feb 07 jari 1343             buildConstraints(constraints, 0, 0, 1, 1, 100, 50);
2 26 Feb 07 jari 1344             grid3.setConstraints(loadABPairButton, constraints);
2 26 Feb 07 jari 1345             pairButtonsPanel.add(loadABPairButton);
2 26 Feb 07 jari 1346
2 26 Feb 07 jari 1347             buildConstraints(constraints, 0, 1, 1, 1, 0, 50);
2 26 Feb 07 jari 1348             grid3.setConstraints(removeABPairButton, constraints);
2 26 Feb 07 jari 1349             pairButtonsPanel.add(removeABPairButton);            
2 26 Feb 07 jari 1350             
2 26 Feb 07 jari 1351             buildConstraints(constraints, 2, 0, 1, 1, 5, 0);
2 26 Feb 07 jari 1352             gridbag.setConstraints(pairButtonsPanel, constraints);
2 26 Feb 07 jari 1353             this.add(pairButtonsPanel);  
2 26 Feb 07 jari 1354             
2 26 Feb 07 jari 1355             //pairPanel = new PairedExperimentsPanel();
2 26 Feb 07 jari 1356             buildConstraints(constraints, 3, 0, 1, 1, 45, 0);
2 26 Feb 07 jari 1357             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1358             JScrollPane pairScroll = new JScrollPane(pairedExptsList);
2 26 Feb 07 jari 1359             pairScroll.setBorder(new TitledBorder("Paired Samples"));
2 26 Feb 07 jari 1360             gridbag.setConstraints(pairScroll, constraints);
2 26 Feb 07 jari 1361             this.add(pairScroll);              
2 26 Feb 07 jari 1362             
2 26 Feb 07 jari 1363         }
2 26 Feb 07 jari 1364         
2 26 Feb 07 jari 1365      
2 26 Feb 07 jari 1366         public void reset() {
2 26 Feb 07 jari 1367           
2 26 Feb 07 jari 1368             for (int i = 0; i < exptButtons.length; i++) {
2 26 Feb 07 jari 1369                 exptButtons[i].setEnabled(true);
2 26 Feb 07 jari 1370                 currentATextField.setText("");
2 26 Feb 07 jari 1371                 currentBTextField.setText("");
2 26 Feb 07 jari 1372                 removeCurrentAButton.setEnabled(false);
2 26 Feb 07 jari 1373                 removeCurrentBButton.setEnabled(false);
2 26 Feb 07 jari 1374                 loadABPairButton.setEnabled(false);
2 26 Feb 07 jari 1375                 removeABPairButton.setEnabled(false);
2 26 Feb 07 jari 1376                 pairedListModel.clear();
2 26 Feb 07 jari 1377                 currentAFilled = false;
2 26 Feb 07 jari 1378                 currentBFilled = false;
2 26 Feb 07 jari 1379                 currentAExpt = -1;
2 26 Feb 07 jari 1380                 currentBExpt = -1;
2 26 Feb 07 jari 1381                 pairedAExpts.clear();
2 26 Feb 07 jari 1382                 pairedBExpts.clear();
2 26 Feb 07 jari 1383             }
2 26 Feb 07 jari 1384         }
2 26 Feb 07 jari 1385         
2 26 Feb 07 jari 1386         class ExperimentButton extends JButton {
2 26 Feb 07 jari 1387             String s;
2 26 Feb 07 jari 1388             int index;
2 26 Feb 07 jari 1389             public ExperimentButton(int i) {
2 26 Feb 07 jari 1390                 this.index = i;
2 26 Feb 07 jari 1391                 s = (String)(exptNames.get(i));
2 26 Feb 07 jari 1392                 this.setText(s);
2 26 Feb 07 jari 1393                 this.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1394                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1395                         if ((currentAFilled)&&(currentBFilled)) {
2 26 Feb 07 jari 1396                             JOptionPane.showMessageDialog(null, "Clear at least one current field first!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 1397                         } else if (!currentAFilled) {
2 26 Feb 07 jari 1398                             currentAExpt = index;
2 26 Feb 07 jari 1399                             currentATextField.setText(s);
2 26 Feb 07 jari 1400                             currentAFilled = true;
2 26 Feb 07 jari 1401                             ExperimentButton.this.setEnabled(false);
2 26 Feb 07 jari 1402                             removeCurrentAButton.setEnabled(true);
2 26 Feb 07 jari 1403                         } else if (!currentBFilled) {
2 26 Feb 07 jari 1404                             currentBExpt = index;
2 26 Feb 07 jari 1405                             currentBTextField.setText(s);
2 26 Feb 07 jari 1406                             currentBFilled = true;
2 26 Feb 07 jari 1407                             ExperimentButton.this.setEnabled(false);
2 26 Feb 07 jari 1408                             removeCurrentBButton.setEnabled(true);
2 26 Feb 07 jari 1409                         }
2 26 Feb 07 jari 1410                         
2 26 Feb 07 jari 1411                         if ((currentAFilled) && (currentBFilled)) {
2 26 Feb 07 jari 1412                             loadABPairButton.setEnabled(true);
2 26 Feb 07 jari 1413                         } else {
2 26 Feb 07 jari 1414                             loadABPairButton.setEnabled(false);
2 26 Feb 07 jari 1415                         }
2 26 Feb 07 jari 1416                     }
2 26 Feb 07 jari 1417                 });
2 26 Feb 07 jari 1418             }
2 26 Feb 07 jari 1419         }
2 26 Feb 07 jari 1420         
2 26 Feb 07 jari 1421         class PairedExperimentsPanel extends JPanel {
2 26 Feb 07 jari 1422             public PairedExperimentsPanel() {
2 26 Feb 07 jari 1423                 //this.setBorder(new TitledBorder("Paired Experiments"));
2 26 Feb 07 jari 1424             }
2 26 Feb 07 jari 1425         }
2 26 Feb 07 jari 1426     }
2 26 Feb 07 jari 1427     
2 26 Feb 07 jari 1428     
2 26 Feb 07 jari 1429     class MultiClassPanel extends JPanel {
2 26 Feb 07 jari 1430         NumGroupsPanel ngPanel;
2 26 Feb 07 jari 1431         GridBagConstraints constraints;
2 26 Feb 07 jari 1432         GridBagLayout gridbag;
2 26 Feb 07 jari 1433         JPanel dummyPanel;
2 26 Feb 07 jari 1434         MultiGroupExperimentsPanel mulgPanel;
2 26 Feb 07 jari 1435         int numGroups;
2 26 Feb 07 jari 1436         //Vector exptNames;        
2 26 Feb 07 jari 1437         
2 26 Feb 07 jari 1438         public MultiClassPanel(/*Vector exptNames*/) {
2 26 Feb 07 jari 1439             constraints = new GridBagConstraints();
2 26 Feb 07 jari 1440             gridbag = new GridBagLayout();
2 26 Feb 07 jari 1441             this.setBackground(Color.white);
2 26 Feb 07 jari 1442             //this.exptNames = exptNames;
2 26 Feb 07 jari 1443             this.setLayout(gridbag);
2 26 Feb 07 jari 1444             ngPanel = new NumGroupsPanel();
2 26 Feb 07 jari 1445             
2 26 Feb 07 jari 1446             buildConstraints(constraints, 0, 0, 1, 1, 100, 10);
2 26 Feb 07 jari 1447             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1448             gridbag.setConstraints(ngPanel, constraints);
2 26 Feb 07 jari 1449             ngPanel.okButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1450                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1451                     ngPanel.okPressed = true;
2 26 Feb 07 jari 1452                     try {
2 26 Feb 07 jari 1453                         numGroups = Integer.parseInt(ngPanel.numGroupsField.getText());
2 26 Feb 07 jari 1454                         if (numGroups <= 2) {
2 26 Feb 07 jari 1455                             JOptionPane.showMessageDialog(null, "Please enter a positive integer >= 2!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 1456                         } else {
2 26 Feb 07 jari 1457                             mulgPanel = new MultiGroupExperimentsPanel(exptNames, numGroups);
2 26 Feb 07 jari 1458                             buildConstraints(constraints, 0, 1, 1, 1, 0, 90);
2 26 Feb 07 jari 1459                             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1460                             gridbag.setConstraints(mulgPanel, constraints);
2 26 Feb 07 jari 1461                             //dummyButton.setVisible(true);
2 26 Feb 07 jari 1462                             MultiClassPanel.this.remove(dummyPanel);
2 26 Feb 07 jari 1463                             MultiClassPanel.this.add(mulgPanel);
2 26 Feb 07 jari 1464                             //MultiClassPanel.this.add(dummyButton);
2 26 Feb 07 jari 1465                             MultiClassPanel.this.validate();
2 26 Feb 07 jari 1466                             ngPanel.okButton.setEnabled(false);
2 26 Feb 07 jari 1467                             ngPanel.numGroupsField.setEnabled(false);
2 26 Feb 07 jari 1468                         }
2 26 Feb 07 jari 1469                        
2 26 Feb 07 jari 1470                     } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 1471                         JOptionPane.showMessageDialog(null, "Please enter a positive integer >= 2!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 1472                     }
2 26 Feb 07 jari 1473                 }
2 26 Feb 07 jari 1474             });
2 26 Feb 07 jari 1475             this.add(ngPanel);
2 26 Feb 07 jari 1476             
2 26 Feb 07 jari 1477             
2 26 Feb 07 jari 1478             buildConstraints(constraints, 0, 1, 1, 1, 0, 90);
2 26 Feb 07 jari 1479             dummyPanel = new JPanel();
2 26 Feb 07 jari 1480             dummyPanel.setBackground(Color.white);
2 26 Feb 07 jari 1481             gridbag.setConstraints(dummyPanel, constraints);
2 26 Feb 07 jari 1482             this.add(dummyPanel);
2 26 Feb 07 jari 1483         }
2 26 Feb 07 jari 1484         
2 26 Feb 07 jari 1485         
2 26 Feb 07 jari 1486         class NumGroupsPanel extends JPanel {
2 26 Feb 07 jari 1487             JTextField numGroupsField;
2 26 Feb 07 jari 1488             JButton okButton;
2 26 Feb 07 jari 1489             boolean okPressed = false;
2 26 Feb 07 jari 1490             
2 26 Feb 07 jari 1491             public NumGroupsPanel() {
2 26 Feb 07 jari 1492                 //super(parentFrame, "Multiclass design: number of groups", modality);
2 26 Feb 07 jari 1493                 //setBounds(0, 0, 350, 150);
2 26 Feb 07 jari 1494                 //setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
2 26 Feb 07 jari 1495                 setBackground(Color.white);
2 26 Feb 07 jari 1496                 GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1497                 GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1498                 
2 26 Feb 07 jari 1499                 //JPanel pane = new JPanel();
2 26 Feb 07 jari 1500                 this.setLayout(gridbag);
2 26 Feb 07 jari 1501                 
2 26 Feb 07 jari 1502                 JLabel numGroupsLabel = new JLabel("Number of groups ");
2 26 Feb 07 jari 1503                 buildConstraints(constraints, 0, 0, 1, 1, 30, 100);
2 26 Feb 07 jari 1504                 constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1505                 gridbag.setConstraints(numGroupsLabel, constraints);
2 26 Feb 07 jari 1506                 this.add(numGroupsLabel);
2 26 Feb 07 jari 1507                 
2 26 Feb 07 jari 1508                 numGroupsField = new JTextField("", 7);
2 26 Feb 07 jari 1509                 constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1510                 buildConstraints(constraints, 1, 0, 1, 1, 30, 0);
2 26 Feb 07 jari 1511                 gridbag.setConstraints(numGroupsField, constraints);
2 26 Feb 07 jari 1512                 this.add(numGroupsField);
2 26 Feb 07 jari 1513                 
2 26 Feb 07 jari 1514                 okButton = new JButton("OK");
2 26 Feb 07 jari 1515                 buildConstraints(constraints, 2, 0, 1, 1, 40, 0);
2 26 Feb 07 jari 1516                 gridbag.setConstraints(okButton, constraints);
2 26 Feb 07 jari 1517                 /*
2 26 Feb 07 jari 1518                 okButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1519                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1520                         okPressed = true;
2 26 Feb 07 jari 1521                         //dispose();
2 26 Feb 07 jari 1522                     }
2 26 Feb 07 jari 1523                 });
2 26 Feb 07 jari 1524                  */
2 26 Feb 07 jari 1525                 this.add(okButton);
2 26 Feb 07 jari 1526                 /*
2 26 Feb 07 jari 1527                 cancelButton = new JButton("Cancel");
2 26 Feb 07 jari 1528                 buildConstraints(constraints, 1, 1, 1, 1, 0, 0);
2 26 Feb 07 jari 1529                 gridbag.setConstraints(cancelButton, constraints);
2 26 Feb 07 jari 1530                 cancelButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1531                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1532                         okPressed = false;
2 26 Feb 07 jari 1533                         dispose();
2 26 Feb 07 jari 1534                     }
2 26 Feb 07 jari 1535                 });
2 26 Feb 07 jari 1536                 pane.add(cancelButton);
2 26 Feb 07 jari 1537                  */
2 26 Feb 07 jari 1538                 
2 26 Feb 07 jari 1539                 //setContentPane(pane);
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             
2 26 Feb 07 jari 1545             public void setVisible(boolean visible) {
2 26 Feb 07 jari 1546                 //Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
2 26 Feb 07 jari 1547                 setLocation((MultiClassPanel.this.getWidth() - getSize().width)/2, (MultiClassPanel.this.getHeight() - getSize().height)/2);
2 26 Feb 07 jari 1548                 
2 26 Feb 07 jari 1549                 super.setVisible(visible);
2 26 Feb 07 jari 1550                 
2 26 Feb 07 jari 1551                 if (visible) {
2 26 Feb 07 jari 1552                     //bPanel.okButton.requestFocus(); //UNCOMMMENT THIS LATER
2 26 Feb 07 jari 1553                 }
2 26 Feb 07 jari 1554             }
2 26 Feb 07 jari 1555             
2 26 Feb 07 jari 1556             public boolean isOkPressed() {
2 26 Feb 07 jari 1557                 return okPressed;
2 26 Feb 07 jari 1558             }
2 26 Feb 07 jari 1559             
2 26 Feb 07 jari 1560         }
2 26 Feb 07 jari 1561         
2 26 Feb 07 jari 1562         class MultiGroupExperimentsPanel extends JPanel {
2 26 Feb 07 jari 1563             JLabel[] expLabels;
2 26 Feb 07 jari 1564             JRadioButton[][] exptGroupRadioButtons;
2 26 Feb 07 jari 1565             JRadioButton[] notInGroupRadioButtons;
2 26 Feb 07 jari 1566             int numPanels = 0;
2 26 Feb 07 jari 1567             JLabel lotsOfSamplesWarningLabel;
2 26 Feb 07 jari 1568             MultiGroupExperimentsPanel(Vector exptNames, int numGroups) {
2 26 Feb 07 jari 1569                 this.setBorder(new TitledBorder(new EtchedBorder(), "Group Assignments"));
2 26 Feb 07 jari 1570                 setBackground(Color.white);
2 26 Feb 07 jari 1571                // JPanel panel1 = new JPanel();
2 26 Feb 07 jari 1572                 expLabels = new JLabel[exptNames.size()];
2 26 Feb 07 jari 1573                 
2 26 Feb 07 jari 1574                 exptGroupRadioButtons = new JRadioButton[numGroups][exptNames.size()];
2 26 Feb 07 jari 1575                 notInGroupRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 1576                 ButtonGroup chooseGroup[] = new ButtonGroup[exptNames.size()];
2 26 Feb 07 jari 1577                 
2 26 Feb 07 jari 1578                 GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1579                 GridBagLayout gridbag2 = new GridBagLayout();
2 26 Feb 07 jari 1580                 GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1581                 this.setLayout(gridbag2);
2 26 Feb 07 jari 1582                 //wwang fix 512 problem
2 26 Feb 07 jari 1583                 numPanels = exptNames.size()/512 + 1;
2 26 Feb 07 jari 1584                 JPanel [] panels = new JPanel[numPanels];
2 26 Feb 07 jari 1585                 int currPanel = 0;
2 26 Feb 07 jari 1586                 for(int i = 0; i < panels.length; i++) {
2 26 Feb 07 jari 1587                     panels[i] = new JPanel(gridbag);
2 26 Feb 07 jari 1588                 }
2 26 Feb 07 jari 1589        
2 26 Feb 07 jari 1590                 for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 1591                     String s1 = (String)(exptNames.get(i));
2 26 Feb 07 jari 1592                     expLabels[i] = new JLabel(s1);
2 26 Feb 07 jari 1593                     chooseGroup[i] = new ButtonGroup();
2 26 Feb 07 jari 1594                     for (int j = 0; j < numGroups; j++) {
2 26 Feb 07 jari 1595                         exptGroupRadioButtons[j][i] = new JRadioButton("Group " + (j + 1) + "     ", j == 0? true: false);
2 26 Feb 07 jari 1596                         chooseGroup[i].add(exptGroupRadioButtons[j][i]);
2 26 Feb 07 jari 1597                     }
2 26 Feb 07 jari 1598                     //set current panel
2 26 Feb 07 jari 1599                     currPanel = i / 512;
2 26 Feb 07 jari 1600                      
2 26 Feb 07 jari 1601                     notInGroupRadioButtons[i] = new JRadioButton("Not in groups", false);
2 26 Feb 07 jari 1602                     chooseGroup[i].add(notInGroupRadioButtons[i]);
2 26 Feb 07 jari 1603  
2 26 Feb 07 jari 1604                     for (int j = 0; j < numGroups; j++) {
2 26 Feb 07 jari 1605                         buildConstraints(constraints, j, i%512, 1, 1, 100, 100);
2 26 Feb 07 jari 1606                         //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1607                         gridbag.setConstraints(exptGroupRadioButtons[j][i], constraints);
2 26 Feb 07 jari 1608                         panels[currPanel].add(exptGroupRadioButtons[j][i]);
2 26 Feb 07 jari 1609                     }
2 26 Feb 07 jari 1610                     
2 26 Feb 07 jari 1611                     buildConstraints(constraints, (numGroups + 1), i%512, 1, 1, 100, 100);
2 26 Feb 07 jari 1612                     //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1613                     gridbag.setConstraints(notInGroupRadioButtons[i], constraints);
2 26 Feb 07 jari 1614                     panels[currPanel].add(notInGroupRadioButtons[i]);
2 26 Feb 07 jari 1615  
2 26 Feb 07 jari 1616                 }
2 26 Feb 07 jari 1617                 
2 26 Feb 07 jari 1618                 int maxLabelWidth = 0;
2 26 Feb 07 jari 1619                 
2 26 Feb 07 jari 1620                 for (int j= 0; j < expLabels.length; j++) {
2 26 Feb 07 jari 1621                     if (expLabels[j].getPreferredSize().getWidth() > maxLabelWidth) {
2 26 Feb 07 jari 1622                         maxLabelWidth = (int)Math.ceil(expLabels[j].getPreferredSize().getWidth());
2 26 Feb 07 jari 1623                     }
2 26 Feb 07 jari 1624                 }
2 26 Feb 07 jari 1625                 
2 26 Feb 07 jari 1626                 JPanel bigPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 1627                 
2 26 Feb 07 jari 1628                 for(int m = 0; m< numPanels; m++) {
2 26 Feb 07 jari 1629                     bigPanel.add(panels[m] ,new GridBagConstraints(0,m,1,1,1,1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0));
2 26 Feb 07 jari 1630                 }
2 26 Feb 07 jari 1631                 JScrollPane scroll = new JScrollPane(bigPanel);
2 26 Feb 07 jari 1632                 scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1633                 scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 1634                 
2 26 Feb 07 jari 1635                 //add by wwang
2 26 Feb 07 jari 1636                 JPanel [] exptNameHeaderPanels = new JPanel[this.numPanels];
2 26 Feb 07 jari 1637                 GridBagLayout exptHeaderGridbag = new GridBagLayout();
2 26 Feb 07 jari 1638                 
2 26 Feb 07 jari 1639                 for(int i = 0; i< exptNameHeaderPanels.length; i++) {
2 26 Feb 07 jari 1640                     exptNameHeaderPanels[i] = new JPanel();
2 26 Feb 07 jari 1641                     exptNameHeaderPanels[i].setSize(50, panels[i].getPreferredSize().height);
2 26 Feb 07 jari 1642                     exptNameHeaderPanels[i].setPreferredSize(new Dimension(maxLabelWidth + 10, panels[i].getPreferredSize().height));
2 26 Feb 07 jari 1643                     exptNameHeaderPanels[i].setLayout(exptHeaderGridbag);
2 26 Feb 07 jari 1644                 }
2 26 Feb 07 jari 1645  
2 26 Feb 07 jari 1646                 //need to possibly add to additional panels if number of exp. excedes 512
2 26 Feb 07 jari 1647                 for (int m = 0; m < expLabels.length; m++) {
2 26 Feb 07 jari 1648                     currPanel = m/512;
2 26 Feb 07 jari 1649                     buildConstraints(constraints, 0, m%512, 1, 1, 100, 100);
2 26 Feb 07 jari 1650                     constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1651                     exptHeaderGridbag.setConstraints(expLabels[m], constraints);
2 26 Feb 07 jari 1652                     exptNameHeaderPanels[currPanel].add(expLabels[m]);
2 26 Feb 07 jari 1653                 }
2 26 Feb 07 jari 1654
2 26 Feb 07 jari 1655                JPanel headerPanel = new JPanel(new GridBagLayout());
2 26 Feb 07 jari 1656                 for(int k = 0; k < exptNameHeaderPanels.length; k++) {
2 26 Feb 07 jari 1657                     headerPanel.add(exptNameHeaderPanels[k], new GridBagConstraints(0,k,1,1,1,1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets(0,0,0,0),0,0)); 
2 26 Feb 07 jari 1658                 }
2 26 Feb 07 jari 1659                 
2 26 Feb 07 jari 1660                 scroll.setRowHeaderView(headerPanel);
2 26 Feb 07 jari 1661                 
2 26 Feb 07 jari 1662                 buildConstraints(constraints, 0, 0, 1, 1, 100, 90);
2 26 Feb 07 jari 1663                 constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1664                 gridbag2.setConstraints(scroll, constraints);
2 26 Feb 07 jari 1665                 this.add(scroll);
2 26 Feb 07 jari 1666                
2 26 Feb 07 jari 1667                 JLabel label1 = new JLabel("Note: Each group MUST each contain more than one sample.");
2 26 Feb 07 jari 1668                 label1.setHorizontalAlignment(JLabel.CENTER);
2 26 Feb 07 jari 1669                 buildConstraints(constraints, 0, 1, 1, 1, 0, 5);
2 26 Feb 07 jari 1670                 constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1671                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 1672                 gridbag2.setConstraints(label1, constraints);
2 26 Feb 07 jari 1673                 this.add(label1);
2 26 Feb 07 jari 1674                 
2 26 Feb 07 jari 1675                 if(lotsOfSamples){
2 26 Feb 07 jari 1676                   lotsOfSamplesWarningLabel = new JLabel(lotsOfSamplesWarningText);
2 26 Feb 07 jari 1677                   lotsOfSamplesWarningLabel.setBackground(Color.gray);
2 26 Feb 07 jari 1678                   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 1679                 }
2 26 Feb 07 jari 1680                 
2 26 Feb 07 jari 1681                 JPanel panel2 = new JPanel();
2 26 Feb 07 jari 1682                 GridBagLayout gridbag3 = new GridBagLayout();
2 26 Feb 07 jari 1683                 panel2.setLayout(gridbag3);
2 26 Feb 07 jari 1684                 panel2.setBackground(Color.white);
2 26 Feb 07 jari 1685                 JButton saveButton = new JButton("  Save settings  ");
2 26 Feb 07 jari 1686                 saveButton.setFocusPainted(false);
2 26 Feb 07 jari 1687                 saveButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 1688                 JButton loadButton = new JButton("  Load settings  ");
2 26 Feb 07 jari 1689                 loadButton.setFocusPainted(false);
2 26 Feb 07 jari 1690                 loadButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 1691                 JButton resetButton = new JButton("  Reset  ");
2 26 Feb 07 jari 1692                 resetButton.setFocusPainted(false);
2 26 Feb 07 jari 1693                 resetButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 1694                 
2 26 Feb 07 jari 1695               
2 26 Feb 07 jari 1696                final int finNum = exptNames.size();
2 26 Feb 07 jari 1697                
2 26 Feb 07 jari 1698                 resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1699                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1700                         for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 1701                             exptGroupRadioButtons[0][i].setSelected(true);
2 26 Feb 07 jari 1702                         }
2 26 Feb 07 jari 1703                     }
2 26 Feb 07 jari 1704                 });
2 26 Feb 07 jari 1705                
2 26 Feb 07 jari 1706                 final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 1707                 fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 1708                
2 26 Feb 07 jari 1709                 saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1710                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1711                         int returnVal = fc.showSaveDialog(MultiGroupExperimentsPanel.this);
2 26 Feb 07 jari 1712                         if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 1713                             File file = fc.getSelectedFile();
2 26 Feb 07 jari 1714                             try {
2 26 Feb 07 jari 1715                                 PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 1716                                 int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 1717                                 for (int i = 0; i < groupAssgn.length; i++) {
2 26 Feb 07 jari 1718                                     out.print(groupAssgn[i]);
2 26 Feb 07 jari 1719                                     if (i < groupAssgn.length - 1) {
2 26 Feb 07 jari 1720                                         out.print("\t");
2 26 Feb 07 jari 1721                                     }
2 26 Feb 07 jari 1722                                 }
2 26 Feb 07 jari 1723                                 out.println();
2 26 Feb 07 jari 1724                                 out.flush();
2 26 Feb 07 jari 1725                                 out.close();
2 26 Feb 07 jari 1726                             } catch (Exception e) {
2 26 Feb 07 jari 1727                                 //e.printStackTrace();
2 26 Feb 07 jari 1728                             }
2 26 Feb 07 jari 1729                             //this is where a real application would save the file.
2 26 Feb 07 jari 1730                             //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 1731                         } else {
2 26 Feb 07 jari 1732                             //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 1733                         }
2 26 Feb 07 jari 1734                     }
2 26 Feb 07 jari 1735                 });
2 26 Feb 07 jari 1736                
2 26 Feb 07 jari 1737                
2 26 Feb 07 jari 1738                 //NEED TO REWORK THIS FOR MULTICLASS
2 26 Feb 07 jari 1739                
2 26 Feb 07 jari 1740                 loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 1741                     public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1742                         int returnVal = fc.showOpenDialog(MultiGroupExperimentsPanel.this);
2 26 Feb 07 jari 1743                         if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 1744                             try {
2 26 Feb 07 jari 1745                                 FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 1746                                 BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 1747                                 String line = buff.readLine();
2 26 Feb 07 jari 1748                                 //System.out.println(line);
2 26 Feb 07 jari 1749                                 StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 1750                                 st.init(line);
2 26 Feb 07 jari 1751                                 Vector groupsVector = new Vector();
2 26 Feb 07 jari 1752                                 while (st.hasMoreTokens()) {
2 26 Feb 07 jari 1753                                     String current = st.nextToken();
2 26 Feb 07 jari 1754                                     groupsVector.add(new Integer(current));
2 26 Feb 07 jari 1755                                     //System.out.print(current);
2 26 Feb 07 jari 1756                                 }
2 26 Feb 07 jari 1757                                 buff.close();
2 26 Feb 07 jari 1758                                 int[] groupAssgn = getGroupAssignments();
2 26 Feb 07 jari 1759                                 if (groupsVector.size() != groupAssgn.length) {
2 26 Feb 07 jari 1760                                     JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1761                                 } else {
2 26 Feb 07 jari 1762                                     for (int i = 0; i < groupsVector.size(); i++) {
2 26 Feb 07 jari 1763                                         int currentGroup = ((Integer)groupsVector.get(i)).intValue();
2 26 Feb 07 jari 1764                                         if (currentGroup != 0) {
2 26 Feb 07 jari 1765                                             exptGroupRadioButtons[currentGroup - 1][i].setSelected(true);
2 26 Feb 07 jari 1766                                         } else {
2 26 Feb 07 jari 1767                                             notInGroupRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1768                                         }
2 26 Feb 07 jari 1769                                             /*
2 26 Feb 07 jari 1770                                             if (currentExpt == 1) {
2 26 Feb 07 jari 1771                                                 groupARadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1772                                             } else if (currentExpt == 2) {
2 26 Feb 07 jari 1773                                                 groupBRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1774                                             } else if (currentExpt == 3) {
2 26 Feb 07 jari 1775                                                 neitherGroupRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 1776                                             } else {
2 26 Feb 07 jari 1777                                                 for (int j = 0; j < finNum; j++) {
2 26 Feb 07 jari 1778                                                     groupARadioButtons[j].setSelected(true);
2 26 Feb 07 jari 1779                                                 }
2 26 Feb 07 jari 1780                                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1781                                                 break;
2 26 Feb 07 jari 1782                                             }
2 26 Feb 07 jari 1783                                              */
2 26 Feb 07 jari 1784                                     }
2 26 Feb 07 jari 1785                                 }
2 26 Feb 07 jari 1786                             } catch (Exception e) {
2 26 Feb 07 jari 1787                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 1788                                 for (int i = 0; i < finNum; i++) {
2 26 Feb 07 jari 1789                                     exptGroupRadioButtons[0][i].setSelected(true);
2 26 Feb 07 jari 1790                                 }
2 26 Feb 07 jari 1791                                 //e.printStackTrace();
2 26 Feb 07 jari 1792                             }
2 26 Feb 07 jari 1793                             
2 26 Feb 07 jari 1794                             //this is where a real application would save the file.
2 26 Feb 07 jari 1795                             //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 1796                         } else {
2 26 Feb 07 jari 1797                             //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 1798                         }
2 26 Feb 07 jari 1799                     }
2 26 Feb 07 jari 1800                 });
2 26 Feb 07 jari 1801                 //
2 26 Feb 07 jari 1802                 
2 26 Feb 07 jari 1803                 
2 26 Feb 07 jari 1804                 constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1805                 constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 1806                 constraints.insets = new Insets(5,5,5,5);
2 26 Feb 07 jari 1807                 buildConstraints(constraints, 0, 0, 1, 1, 33, 100);
2 26 Feb 07 jari 1808                 gridbag3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 1809                 panel2.add(saveButton);
2 26 Feb 07 jari 1810                 
2 26 Feb 07 jari 1811                 buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 1812                 gridbag3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 1813                 panel2.add(loadButton);
2 26 Feb 07 jari 1814                 
2 26 Feb 07 jari 1815                 buildConstraints(constraints, 2, 0, 1, 1, 34, 0);
2 26 Feb 07 jari 1816                 gridbag3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 1817                 panel2.add(resetButton);
2 26 Feb 07 jari 1818                 constraints.insets = new Insets(0,0,0,0);
2 26 Feb 07 jari 1819                 buildConstraints(constraints, 0, 3, 1, 1, 0, 5);
2 26 Feb 07 jari 1820                 constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 1821                 gridbag2.setConstraints(panel2, constraints);
2 26 Feb 07 jari 1822                 this.add(panel2);
2 26 Feb 07 jari 1823       
2 26 Feb 07 jari 1824                 
2 26 Feb 07 jari 1825             }
2 26 Feb 07 jari 1826             
2 26 Feb 07 jari 1827             /**
2 26 Feb 07 jari 1828              *  resets group assignments
2 26 Feb 07 jari 1829              */
2 26 Feb 07 jari 1830             private void reset(){
2 26 Feb 07 jari 1831                 for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 1832                     exptGroupRadioButtons[0][i].setSelected(true);
2 26 Feb 07 jari 1833                 }
2 26 Feb 07 jari 1834             }
2 26 Feb 07 jari 1835         }
2 26 Feb 07 jari 1836         private void reset(){
2 26 Feb 07 jari 1837             mulgPanel.reset();
2 26 Feb 07 jari 1838         }
2 26 Feb 07 jari 1839     }
2 26 Feb 07 jari 1840     
2 26 Feb 07 jari 1841     class PermutationsPanel extends JPanel {
2 26 Feb 07 jari 1842         //JLabel permsInfoLabel;
2 26 Feb 07 jari 1843         //JRadioButton useAllPermsButton, numPermsButton;
2 26 Feb 07 jari 1844         JLabel numPermsLabel;
2 26 Feb 07 jari 1845         JTextField numPermsInputField;
2 26 Feb 07 jari 1846         PermutationsPanel() {
2 26 Feb 07 jari 1847             this.setBorder(new TitledBorder(new EtchedBorder(), "Number of permutations", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 1848             setBackground(Color.white);
2 26 Feb 07 jari 1849             numPermsLabel = new JLabel("Enter number of permutations:   ");
2 26 Feb 07 jari 1850             numPermsInputField = new JTextField("100", 7);
2 26 Feb 07 jari 1851             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1852             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1853             this.setLayout(gridbag);
2 26 Feb 07 jari 1854             
2 26 Feb 07 jari 1855             buildConstraints(constraints, 0, 0, 1, 1, 50, 100);
2 26 Feb 07 jari 1856             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1857             gridbag.setConstraints(numPermsLabel, constraints);
2 26 Feb 07 jari 1858             this.add(numPermsLabel);
2 26 Feb 07 jari 1859             
2 26 Feb 07 jari 1860             buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2 26 Feb 07 jari 1861             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1862             gridbag.setConstraints(numPermsInputField, constraints);
2 26 Feb 07 jari 1863             this.add(numPermsInputField);
2 26 Feb 07 jari 1864            
2 26 Feb 07 jari 1865         }
2 26 Feb 07 jari 1866         
2 26 Feb 07 jari 1867         public void reset(){
2 26 Feb 07 jari 1868             this.numPermsInputField.setText("100");
2 26 Feb 07 jari 1869         }
2 26 Feb 07 jari 1870         
2 26 Feb 07 jari 1871     }
2 26 Feb 07 jari 1872     
2 26 Feb 07 jari 1873     class S0AndQValueCalcPanel extends JPanel {
2 26 Feb 07 jari 1874         JComboBox s0SelectBox;
2 26 Feb 07 jari 1875         JTextField s0EntryField;
2 26 Feb 07 jari 1876         JRadioButton s0SelectButton, s0EntryButton, qYesButton, qNoButton;
2 26 Feb 07 jari 1877         
2 26 Feb 07 jari 1878         S0AndQValueCalcPanel() {
2 26 Feb 07 jari 1879             this.setBorder(new TitledBorder(new EtchedBorder(), "S0 and Q Value parameters", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));            
2 26 Feb 07 jari 1880             String[] s0SelectOptions = {"Tusher et al. method", "5th percentile", "50th percentile", "90th percentile", "Minimum S Value"};
2 26 Feb 07 jari 1881             setBackground(Color.white);
2 26 Feb 07 jari 1882             s0SelectBox = new JComboBox(s0SelectOptions);
2 26 Feb 07 jari 1883             //s0SelectBox.setBackground(Color.white);
2 26 Feb 07 jari 1884             s0SelectButton = new JRadioButton("Select S0 using", true);
2 26 Feb 07 jari 1885             s0SelectButton.setBackground(Color.white);
2 26 Feb 07 jari 1886             s0EntryButton = new JRadioButton(" OR Enter s0 percentile (0-100)", false);
2 26 Feb 07 jari 1887             s0EntryButton.setBackground(Color.white);
2 26 Feb 07 jari 1888             s0EntryField = new JTextField("", 7);
2 26 Feb 07 jari 1889             s0EntryField.setEnabled(false);
2 26 Feb 07 jari 1890             s0EntryField.setBackground(Color.darkGray);         
2 26 Feb 07 jari 1891             ButtonGroup s0Group = new ButtonGroup();
2 26 Feb 07 jari 1892             s0SelectButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1893                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1894                     s0SelectBox.setEnabled(true);
2 26 Feb 07 jari 1895                     s0EntryField.setText("");
2 26 Feb 07 jari 1896                     s0EntryField.setEnabled(false);
2 26 Feb 07 jari 1897                     s0EntryField.setBackground(Color.darkGray);
2 26 Feb 07 jari 1898                 }
2 26 Feb 07 jari 1899             });
2 26 Feb 07 jari 1900             s0EntryButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1901                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1902                     s0EntryField.setText("10");
2 26 Feb 07 jari 1903                     s0EntryField.setEnabled(true);
2 26 Feb 07 jari 1904                     s0EntryField.setBackground(Color.white);
2 26 Feb 07 jari 1905                     s0SelectBox.setEnabled(false);
2 26 Feb 07 jari 1906                 }
2 26 Feb 07 jari 1907             });            
2 26 Feb 07 jari 1908             s0Group.add(s0SelectButton);
2 26 Feb 07 jari 1909             s0Group.add(s0EntryButton);
2 26 Feb 07 jari 1910             
2 26 Feb 07 jari 1911             qYesButton = new JRadioButton("Yes (slow!)", false);
2 26 Feb 07 jari 1912             qYesButton.setBackground(Color.white);
2 26 Feb 07 jari 1913             qNoButton = new JRadioButton("No (quick)", true);
2 26 Feb 07 jari 1914             qNoButton.setBackground(Color.white);
2 26 Feb 07 jari 1915             ButtonGroup qGroup = new ButtonGroup();
2 26 Feb 07 jari 1916             qGroup.add(qYesButton);
2 26 Feb 07 jari 1917             qGroup.add(qNoButton);
2 26 Feb 07 jari 1918             
2 26 Feb 07 jari 1919             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 1920             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 1921             this.setLayout(gridbag);
2 26 Feb 07 jari 1922
2 26 Feb 07 jari 1923             buildConstraints(constraints, 0, 0, 1, 1, 25, 50);
2 26 Feb 07 jari 1924             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1925             gridbag.setConstraints(s0SelectButton, constraints);
2 26 Feb 07 jari 1926             this.add(s0SelectButton);            
2 26 Feb 07 jari 1927             
2 26 Feb 07 jari 1928             buildConstraints(constraints, 1, 0, 1, 1, 25, 0);
2 26 Feb 07 jari 1929             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1930             gridbag.setConstraints(s0SelectBox, constraints);
2 26 Feb 07 jari 1931             this.add(s0SelectBox);  
2 26 Feb 07 jari 1932             
2 26 Feb 07 jari 1933             buildConstraints(constraints, 2, 0, 1, 1, 25, 0);
2 26 Feb 07 jari 1934             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1935             gridbag.setConstraints(s0EntryButton, constraints);
2 26 Feb 07 jari 1936             this.add(s0EntryButton);   
2 26 Feb 07 jari 1937             
2 26 Feb 07 jari 1938             
2 26 Feb 07 jari 1939             buildConstraints(constraints, 3, 0, 1, 1, 25, 0);
2 26 Feb 07 jari 1940             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1941             gridbag.setConstraints(s0EntryField, constraints);
2 26 Feb 07 jari 1942             this.add(s0EntryField);   
2 26 Feb 07 jari 1943             
2 26 Feb 07 jari 1944             JLabel qLabel = new JLabel("Calculate q-values?  ");
2 26 Feb 07 jari 1945             buildConstraints(constraints, 0, 1, 1, 1, 10, 50);
2 26 Feb 07 jari 1946             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1947             gridbag.setConstraints(qLabel, constraints);
2 26 Feb 07 jari 1948             this.add(qLabel);   
2 26 Feb 07 jari 1949             
2 26 Feb 07 jari 1950             buildConstraints(constraints, 1, 1, 1, 1, 10, 0);
2 26 Feb 07 jari 1951             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 1952             gridbag.setConstraints(qNoButton, constraints);
2 26 Feb 07 jari 1953             this.add(qNoButton);
2 26 Feb 07 jari 1954             
2 26 Feb 07 jari 1955             buildConstraints(constraints, 2, 1, 2, 1, 80, 0);
2 26 Feb 07 jari 1956             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 1957             gridbag.setConstraints(qYesButton, constraints);
2 26 Feb 07 jari 1958             this.add(qYesButton);             
2 26 Feb 07 jari 1959             
2 26 Feb 07 jari 1960         }
2 26 Feb 07 jari 1961         
2 26 Feb 07 jari 1962         public void reset() {
2 26 Feb 07 jari 1963             s0SelectButton.setSelected(true);
2 26 Feb 07 jari 1964             s0SelectBox.setEnabled(true);
2 26 Feb 07 jari 1965             s0SelectBox.setSelectedIndex(0);
2 26 Feb 07 jari 1966             s0EntryField.setText("");
2 26 Feb 07 jari 1967             s0EntryField.setBackground(Color.darkGray);
2 26 Feb 07 jari 1968             s0EntryField.setEnabled(false);
2 26 Feb 07 jari 1969             qNoButton.setSelected(true);
2 26 Feb 07 jari 1970         }
2 26 Feb 07 jari 1971     }
2 26 Feb 07 jari 1972     
2 26 Feb 07 jari 1973     class ImputationPanel extends JPanel {
2 26 Feb 07 jari 1974         JRadioButton kNearestButton, rowAverageButton;
2 26 Feb 07 jari 1975         JTextField numNeighborsField;
2 26 Feb 07 jari 1976         JLabel numNeighborsLabel;
2 26 Feb 07 jari 1977         String numNeighborsText;
2 26 Feb 07 jari 1978         JCheckBox saveMatrixChkBox;
2 26 Feb 07 jari 1979         ImputationPanel() {
2 26 Feb 07 jari 1980             //           this.setBorder(new TitledBorder(new EtchedBorder(), "Imputation Engine"));
2 26 Feb 07 jari 1981             this.setBorder(new TitledBorder(new EtchedBorder(), "Imputation Engine", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 1982             setBackground(Color.white);
2 26 Feb 07 jari 1983             numNeighborsText = "10";
2 26 Feb 07 jari 1984             if (numGenes < 10) {
2 26 Feb 07 jari 1985                 numNeighborsText = Integer.toString(numGenes);
2 26 Feb 07 jari 1986             }
2 26 Feb 07 jari 1987             numNeighborsField = new JTextField(numNeighborsText, 7);
2 26 Feb 07 jari 1988             numNeighborsLabel = new JLabel("Number of neighbors:       ");
2 26 Feb 07 jari 1989             kNearestButton = new JRadioButton("K-nearest neighbors imputer", true);
2 26 Feb 07 jari 1990             kNearestButton.setBackground(Color.white);
2 26 Feb 07 jari 1991             kNearestButton.setFocusPainted(false);
2 26 Feb 07 jari 1992             kNearestButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1993             rowAverageButton = new JRadioButton("Row average imputer              ", false);
2 26 Feb 07 jari 1994             rowAverageButton.setBackground(Color.white);
2 26 Feb 07 jari 1995             rowAverageButton.setFocusPainted(false);
2 26 Feb 07 jari 1996             rowAverageButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 1997             kNearestButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 1998                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 1999                     numNeighborsLabel.setEnabled(true);
2 26 Feb 07 jari 2000                     numNeighborsField.setEnabled(true);
2 26 Feb 07 jari 2001                     numNeighborsField.setBackground(Color.white);
2 26 Feb 07 jari 2002                     numNeighborsField.setText(numNeighborsText);
2 26 Feb 07 jari 2003                 }
2 26 Feb 07 jari 2004             });
2 26 Feb 07 jari 2005             
2 26 Feb 07 jari 2006             rowAverageButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 2007                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 2008                     numNeighborsLabel.setEnabled(false);
2 26 Feb 07 jari 2009                     numNeighborsField.setEnabled(false);
2 26 Feb 07 jari 2010                     numNeighborsField.setBackground(Color.gray);
2 26 Feb 07 jari 2011                     numNeighborsField.setText("");
2 26 Feb 07 jari 2012                 }
2 26 Feb 07 jari 2013             });
2 26 Feb 07 jari 2014             ButtonGroup chooseKOrRowAvg = new ButtonGroup();
2 26 Feb 07 jari 2015             chooseKOrRowAvg.add(kNearestButton);
2 26 Feb 07 jari 2016             chooseKOrRowAvg.add(rowAverageButton);
2 26 Feb 07 jari 2017             
2 26 Feb 07 jari 2018             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 2019             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 2020             this.setLayout(gridbag);
2 26 Feb 07 jari 2021             
2 26 Feb 07 jari 2022             //buildConstraints(constraints, 0, 0, 1, 1, 100, 25);
2 26 Feb 07 jari 2023             buildConstraints(constraints, 0, 0, 1, 1, 40, 50);
2 26 Feb 07 jari 2024             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 2025             gridbag.setConstraints(kNearestButton, constraints);
2 26 Feb 07 jari 2026             this.add(kNearestButton);
2 26 Feb 07 jari 2027             
2 26 Feb 07 jari 2028             
2 26 Feb 07 jari 2029             
2 26 Feb 07 jari 2030             buildConstraints(constraints, 1, 0, 1, 1, 30, 0);
2 26 Feb 07 jari 2031             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 2032             gridbag.setConstraints(numNeighborsLabel, constraints);
2 26 Feb 07 jari 2033             this.add(numNeighborsLabel);
2 26 Feb 07 jari 2034             
2 26 Feb 07 jari 2035             
2 26 Feb 07 jari 2036             buildConstraints(constraints, 2, 0, 1, 1, 30, 0);
2 26 Feb 07 jari 2037             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 2038             gridbag.setConstraints(numNeighborsField, constraints);
2 26 Feb 07 jari 2039             this.add(numNeighborsField);
2 26 Feb 07 jari 2040             
2 26 Feb 07 jari 2041             buildConstraints(constraints, 0, 1, 1, 1, 0, 50);
2 26 Feb 07 jari 2042             constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 2043             gridbag.setConstraints(rowAverageButton, constraints);
2 26 Feb 07 jari 2044             this.add(rowAverageButton);
2 26 Feb 07 jari 2045             
2 26 Feb 07 jari 2046             buildConstraints(constraints, 1, 1, 1, 1, 0, 50);
2 26 Feb 07 jari 2047             //  constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 2048             JPanel dummy = new JPanel();
2 26 Feb 07 jari 2049             dummy.setBackground(Color.white);
2 26 Feb 07 jari 2050             gridbag.setConstraints(dummy, constraints);
2 26 Feb 07 jari 2051             this.add(dummy);
2 26 Feb 07 jari 2052             
2 26 Feb 07 jari 2053             buildConstraints(constraints, 2, 1, 1, 1, 0, 50);
2 26 Feb 07 jari 2054             //  constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 2055             gridbag.setConstraints(dummy, constraints);
2 26 Feb 07 jari 2056             this.add(dummy);
2 26 Feb 07 jari 2057             
2 26 Feb 07 jari 2058             
2 26 Feb 07 jari 2059             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 2060             buildConstraints(constraints, 0, 2, 3, 1, 0, 50);
2 26 Feb 07 jari 2061             saveMatrixChkBox = new JCheckBox("Save Imputed Matrix", false);
2 26 Feb 07 jari 2062             saveMatrixChkBox.setBackground(Color.white);
2 26 Feb 07 jari 2063             saveMatrixChkBox.setFocusPainted(false);
2 26 Feb 07 jari 2064             saveMatrixChkBox.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 2065             gridbag.setConstraints(saveMatrixChkBox, constraints);
2 26 Feb 07 jari 2066             this.add(saveMatrixChkBox);
2 26 Feb 07 jari 2067         }
2 26 Feb 07 jari 2068         
2 26 Feb 07 jari 2069         private void reset(){
2 26 Feb 07 jari 2070             this.numNeighborsField.setText(this.numNeighborsText);
2 26 Feb 07 jari 2071             this.numNeighborsField.setBackground(Color.white);
2 26 Feb 07 jari 2072             this.numNeighborsField.setEnabled(true);
2 26 Feb 07 jari 2073             this.kNearestButton.setSelected(true);
2 26 Feb 07 jari 2074             this.saveMatrixChkBox.setSelected(false);
2 26 Feb 07 jari 2075         }
2 26 Feb 07 jari 2076     }
2 26 Feb 07 jari 2077     
2 26 Feb 07 jari 2078     
2 26 Feb 07 jari 2079     class OKCancelPanel extends JPanel {
2 26 Feb 07 jari 2080         JButton okButton, cancelButton;
2 26 Feb 07 jari 2081         JCheckBox drawTreesBox;
2 26 Feb 07 jari 2082         
2 26 Feb 07 jari 2083         OKCancelPanel() {
2 26 Feb 07 jari 2084             okButton = new JButton("OK");
2 26 Feb 07 jari 2085             cancelButton = new JButton("Cancel");
2 26 Feb 07 jari 2086             drawTreesBox = new JCheckBox("Draw Hierarchical Trees");
2 26 Feb 07 jari 2087             
2 26 Feb 07 jari 2088             okButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 2089                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 2090                     if (getStudyDesign() == SAMInitDialog.TWO_CLASS_UNPAIRED) {
2 26 Feb 07 jari 2091                         // if (evt.getSource() == okButton) {
2 26 Feb 07 jari 2092                         int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 2093                         int grpACounter = 0;
2 26 Feb 07 jari 2094                         int grpBCounter = 0;
2 26 Feb 07 jari 2095                         for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2096                             if (grpAssignments[i] == GROUP_A) {
2 26 Feb 07 jari 2097                                 grpACounter++;
2 26 Feb 07 jari 2098                             } else if (grpAssignments[i] == GROUP_B) {
2 26 Feb 07 jari 2099                                 grpBCounter++;
2 26 Feb 07 jari 2100                             }
2 26 Feb 07 jari 2101                         }
2 26 Feb 07 jari 2102                         if ((grpACounter < 2) || (grpBCounter < 2)) {
2 26 Feb 07 jari 2103                             JOptionPane.showMessageDialog(null, "Group A and Group B must contain more than one sample", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2104                         } /*else if ((Integer.parseInt(iPanel.numNeighborsField.getText()) > numGenes) || (Integer.parseInt(iPanel.numNeighborsField.getText()) <= 0)) {
2 26 Feb 07 jari 2105                             JOptionPane.showMessageDialog(null, "Number of neighbors must be  > 0, and <= the total number of genes", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2106                         } else if (Integer.parseInt(pPanel.numPermsInputField.getText()) < 0) {
2 26 Feb 07 jari 2107                             JOptionPane.showMessageDialog(null, "Number of permutations must be > 0", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2108                         } */else {
2 26 Feb 07 jari 2109                             try {
2 26 Feb 07 jari 2110                                 int numCombs = 0;
2 26 Feb 07 jari 2111                                 //if (!useAllCombs()) {
2 26 Feb 07 jari 2112                                 numCombs = getUserNumCombs();
2 26 Feb 07 jari 2113                                 //}
2 26 Feb 07 jari 2114                                 int numNeibs = 0;
2 26 Feb 07 jari 2115                                 if (useKNearest()) {
2 26 Feb 07 jari 2116                                     numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2117                                 }
2 26 Feb 07 jari 2118                                 okPressed = true;
2 26 Feb 07 jari 2119                                 dispose();
2 26 Feb 07 jari 2120                             } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2121                                 JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2122                             }
2 26 Feb 07 jari 2123                             
2 26 Feb 07 jari 2124                             //okPressed = true;
2 26 Feb 07 jari 2125                             //hide();
2 26 Feb 07 jari 2126                             //dispose();
2 26 Feb 07 jari 2127                         }
2 26 Feb 07 jari 2128                         // }
2 26 Feb 07 jari 2129                     } else if (getStudyDesign() == SAMInitDialog.MULTI_CLASS) {
2 26 Feb 07 jari 2130                         boolean tooFew = false;
2 26 Feb 07 jari 2131                         int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 2132                         int numGroups = getMultiClassNumGroups();
2 26 Feb 07 jari 2133                         int[] groupSize = new int[numGroups];
2 26 Feb 07 jari 2134                         
2 26 Feb 07 jari 2135                         for (int i = 0; i < groupSize.length; i++) {
2 26 Feb 07 jari 2136                             groupSize[i] = 0;
2 26 Feb 07 jari 2137                         }
2 26 Feb 07 jari 2138                         
2 26 Feb 07 jari 2139                         for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2140                             int currentGroup = grpAssignments[i];
2 26 Feb 07 jari 2141                             if (currentGroup != 0) {
2 26 Feb 07 jari 2142                                 groupSize[currentGroup - 1]++;
2 26 Feb 07 jari 2143                             }
2 26 Feb 07 jari 2144                         }
2 26 Feb 07 jari 2145                         
2 26 Feb 07 jari 2146                         /*
2 26 Feb 07 jari 2147                         for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2148                             System.out.println("grpAssignments[" + i + "] = "  + grpAssignments[i]);
2 26 Feb 07 jari 2149                         }
2 26 Feb 07 jari 2150                          
2 26 Feb 07 jari 2151                         for (int i = 0; i < groupSize.length; i++) {
2 26 Feb 07 jari 2152                             System.out.println("groupSize[" + i + "] = " + groupSize[i] + " (group " + (i +1) + ")");
2 26 Feb 07 jari 2153                         }
2 26 Feb 07 jari 2154                          */
2 26 Feb 07 jari 2155                         
2 26 Feb 07 jari 2156                         for (int i = 0; i < groupSize.length; i++) {
2 26 Feb 07 jari 2157                             if (groupSize[i] <= 1) {
2 26 Feb 07 jari 2158                                 JOptionPane.showMessageDialog(null, "Each group must contain more than one sample.", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2159                                 tooFew = true;
2 26 Feb 07 jari 2160                                 break;
2 26 Feb 07 jari 2161                             }
2 26 Feb 07 jari 2162                         }
2 26 Feb 07 jari 2163                         
2 26 Feb 07 jari 2164                         if (!tooFew) {
2 26 Feb 07 jari 2165                             try {
2 26 Feb 07 jari 2166                                 int numCombs = 0;
2 26 Feb 07 jari 2167                                 //if (!useAllCombs()) {
2 26 Feb 07 jari 2168                                 numCombs = getUserNumCombs();
2 26 Feb 07 jari 2169                                 //}
2 26 Feb 07 jari 2170                                 int numNeibs = 0;
2 26 Feb 07 jari 2171                                 if (useKNearest()) {
2 26 Feb 07 jari 2172                                     numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2173                                 }
2 26 Feb 07 jari 2174                                 okPressed = true;
2 26 Feb 07 jari 2175                                 dispose();
2 26 Feb 07 jari 2176                             } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2177                                 JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2178                             }
2 26 Feb 07 jari 2179                         }
2 26 Feb 07 jari 2180                     } else if (getStudyDesign() == SAMInitDialog.CENSORED_SURVIVAL) {
2 26 Feb 07 jari 2181                         try {
2 26 Feb 07 jari 2182                             boolean allSame = true;
2 26 Feb 07 jari 2183                             int selectedCounter = 0;
2 26 Feb 07 jari 2184                             double previousTime = 0;
2 26 Feb 07 jari 2185                             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 2186                                 if (csPanel.fields[i].inAnalysisCheckBox.isSelected()) {
2 26 Feb 07 jari 2187                                     selectedCounter++;
2 26 Feb 07 jari 2188                                     double d = (new Double(csPanel.fields[i].timeInputField.getText())).doubleValue();
2 26 Feb 07 jari 2189                                     if (i > 0) {
2 26 Feb 07 jari 2190                                         if (previousTime != d) {
2 26 Feb 07 jari 2191                                             allSame = false;
2 26 Feb 07 jari 2192                                         }
2 26 Feb 07 jari 2193                                     }
2 26 Feb 07 jari 2194                                     previousTime = d;
2 26 Feb 07 jari 2195                                 }
2 26 Feb 07 jari 2196                             }
2 26 Feb 07 jari 2197                             int numCombs = 0;
2 26 Feb 07 jari 2198                             //if (!useAllCombs()) {
2 26 Feb 07 jari 2199                             numCombs = getUserNumCombs();
2 26 Feb 07 jari 2200                             //}
2 26 Feb 07 jari 2201                             int numNeibs = 0;
2 26 Feb 07 jari 2202                             if (useKNearest()) {
2 26 Feb 07 jari 2203                                 numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2204                             }
2 26 Feb 07 jari 2205                             if (selectedCounter < 2) {
2 26 Feb 07 jari 2206                                 JOptionPane.showMessageDialog(null, "At least 2 samples must be selected!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2207                             } else if (allSame) {
2 26 Feb 07 jari 2208                                 JOptionPane.showMessageDialog(null, "At least one of the survival time values must be different from the rest!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2209                             } else {
2 26 Feb 07 jari 2210                                 okPressed = true;
2 26 Feb 07 jari 2211                                 dispose();
2 26 Feb 07 jari 2212                             }
2 26 Feb 07 jari 2213                         } catch (NumberFormatException nfe){
2 26 Feb 07 jari 2214                             JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2215                         }
2 26 Feb 07 jari 2216                     }
2 26 Feb 07 jari 2217                 }
2 26 Feb 07 jari 2218             });
2 26 Feb 07 jari 2219             
2 26 Feb 07 jari 2220             cancelButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 2221                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 2222                     //  if (evt.getSource() == cancelButton) {
2 26 Feb 07 jari 2223                     okPressed = false;
2 26 Feb 07 jari 2224                     //hide();
2 26 Feb 07 jari 2225                     dispose();
2 26 Feb 07 jari 2226                     // }
2 26 Feb 07 jari 2227                 }
2 26 Feb 07 jari 2228             });
2 26 Feb 07 jari 2229             
2 26 Feb 07 jari 2230             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 2231             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 2232             this.setLayout(gridbag);
2 26 Feb 07 jari 2233             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 2234             buildConstraints(constraints, 0, 0, 2, 1, 0, 50);
2 26 Feb 07 jari 2235             gridbag.setConstraints(drawTreesBox, constraints);
2 26 Feb 07 jari 2236             this.add(drawTreesBox);
2 26 Feb 07 jari 2237             
2 26 Feb 07 jari 2238             buildConstraints(constraints, 0, 1, 1, 1, 50, 50);
2 26 Feb 07 jari 2239             //constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 2240             gridbag.setConstraints(okButton, constraints);
2 26 Feb 07 jari 2241             this.add(okButton);
2 26 Feb 07 jari 2242             
2 26 Feb 07 jari 2243             buildConstraints(constraints, 1, 1, 1, 1, 50, 0);
2 26 Feb 07 jari 2244             //constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 2245             gridbag.setConstraints(cancelButton, constraints);
2 26 Feb 07 jari 2246             this.add(cancelButton);
2 26 Feb 07 jari 2247         }
2 26 Feb 07 jari 2248     }
2 26 Feb 07 jari 2249     
2 26 Feb 07 jari 2250     
2 26 Feb 07 jari 2251     public int getStudyDesign() {
2 26 Feb 07 jari 2252         int studyDesign = TWO_CLASS_UNPAIRED;
2 26 Feb 07 jari 2253         if (tabPane.getSelectedIndex() == 0) {
2 26 Feb 07 jari 2254             studyDesign = TWO_CLASS_UNPAIRED;
2 26 Feb 07 jari 2255         } else if (tabPane.getSelectedIndex() == 1) {
2 26 Feb 07 jari 2256             studyDesign = SAMInitDialog.TWO_CLASS_PAIRED;
2 26 Feb 07 jari 2257         } else if (tabPane.getSelectedIndex() == 2) {
2 26 Feb 07 jari 2258             studyDesign = SAMInitDialog.MULTI_CLASS;
2 26 Feb 07 jari 2259         } else if (tabPane.getSelectedIndex() == 3) {
2 26 Feb 07 jari 2260             studyDesign = SAMInitDialog.CENSORED_SURVIVAL;
2 26 Feb 07 jari 2261         } else if (tabPane.getSelectedIndex() == 4) {
2 26 Feb 07 jari 2262             studyDesign = SAMInitDialog.ONE_CLASS;
2 26 Feb 07 jari 2263         }
2 26 Feb 07 jari 2264         return studyDesign;
2 26 Feb 07 jari 2265     }
2 26 Feb 07 jari 2266     
2 26 Feb 07 jari 2267     public int[] getGroupAssignments() {
2 26 Feb 07 jari 2268         int[] groupAssignments = new int[exptNames.size()];
2 26 Feb 07 jari 2269         if (getStudyDesign() == TWO_CLASS_UNPAIRED) {
2 26 Feb 07 jari 2270             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 2271                 if (gPanel.groupARadioButtons[i].isSelected()) {
2 26 Feb 07 jari 2272                     groupAssignments[i] = GROUP_A;
2 26 Feb 07 jari 2273                 } else if (gPanel.groupBRadioButtons[i].isSelected()) {
2 26 Feb 07 jari 2274                     groupAssignments[i] = GROUP_B;
2 26 Feb 07 jari 2275                 } else {
2 26 Feb 07 jari 2276                     groupAssignments[i] = NEITHER_GROUP;
2 26 Feb 07 jari 2277                 }
2 26 Feb 07 jari 2278             }
2 26 Feb 07 jari 2279         } else if (getStudyDesign() == MULTI_CLASS) { //  THAT "NOT IN GROUP" IS STORED AS ZERO, AND GROUP J IS STORED AS THE INTEGER J (I.E., THERE IS NO GROUP 0)
2 26 Feb 07 jari 2280             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 2281                 if (mPanel.mulgPanel.notInGroupRadioButtons[i].isSelected()) {
2 26 Feb 07 jari 2282                     groupAssignments[i] = 0;
2 26 Feb 07 jari 2283                 } else {
2 26 Feb 07 jari 2284                     for (int j = 0; j < mPanel.mulgPanel.exptGroupRadioButtons.length; j++) {
2 26 Feb 07 jari 2285                         if (mPanel.mulgPanel.exptGroupRadioButtons[j][i].isSelected()) {
2 26 Feb 07 jari 2286                             groupAssignments[i] = j + 1;
2 26 Feb 07 jari 2287                             break;
2 26 Feb 07 jari 2288                         }
2 26 Feb 07 jari 2289                     }
2 26 Feb 07 jari 2290                 }
2 26 Feb 07 jari 2291             }
2 26 Feb 07 jari 2292         } else if (getStudyDesign() == ONE_CLASS) {
2 26 Feb 07 jari 2293             return getOneClassAssignments();
2 26 Feb 07 jari 2294         }
2 26 Feb 07 jari 2295         
2 26 Feb 07 jari 2296         return groupAssignments;
2 26 Feb 07 jari 2297     }
2 26 Feb 07 jari 2298     
2 26 Feb 07 jari 2299     public int[] getOneClassAssignments() {
2 26 Feb 07 jari 2300         int[] oneClassAssignments = new int[oneCPanel.includeExpts.length];
2 26 Feb 07 jari 2301         
2 26 Feb 07 jari 2302         for (int i = 0; i < oneClassAssignments.length; i++) {
2 26 Feb 07 jari 2303             if (oneCPanel.includeExpts[i].isSelected()) {
2 26 Feb 07 jari 2304                 oneClassAssignments[i] = 1;
2 26 Feb 07 jari 2305             } else {
2 26 Feb 07 jari 2306                 oneClassAssignments[i] = 0;
2 26 Feb 07 jari 2307             }
2 26 Feb 07 jari 2308         }
2 26 Feb 07 jari 2309         
2 26 Feb 07 jari 2310         return oneClassAssignments;
2 26 Feb 07 jari 2311     }    
2 26 Feb 07 jari 2312     
2 26 Feb 07 jari 2313     public double getOneClassMean() {
2 26 Feb 07 jari 2314         return Double.parseDouble(oneCPanel.meanField.getText());
2 26 Feb 07 jari 2315     }    
2 26 Feb 07 jari 2316     
2 26 Feb 07 jari 2317     public int getMultiClassNumGroups() {
2 26 Feb 07 jari 2318         return Integer.parseInt(mPanel.ngPanel.numGroupsField.getText());
2 26 Feb 07 jari 2319     }
2 26 Feb 07 jari 2320     
2 26 Feb 07 jari 2321     public int getNumValidOneClassExpts() {
2 26 Feb 07 jari 2322         int validNum = 0;
2 26 Feb 07 jari 2323         int[] oca = getOneClassAssignments();
2 26 Feb 07 jari 2324         
2 26 Feb 07 jari 2325         for (int i =0; i < oca.length; i++) {
2 26 Feb 07 jari 2326             if (oca[i] == 1) {
2 26 Feb 07 jari 2327                 validNum++;
2 26 Feb 07 jari 2328             }
2 26 Feb 07 jari 2329         }
2 26 Feb 07 jari 2330         
2 26 Feb 07 jari 2331         return validNum;
2 26 Feb 07 jari 2332     }    
2 26 Feb 07 jari 2333     
2 26 Feb 07 jari 2334     
2 26 Feb 07 jari 2335     public int[] getGroupCount() {
2 26 Feb 07 jari 2336         int[] groupAssignments = getGroupAssignments();
2 26 Feb 07 jari 2337         int groupACount = 0;
2 26 Feb 07 jari 2338         int groupBCount = 0;
2 26 Feb 07 jari 2339         
2 26 Feb 07 jari 2340         for (int i = 0; i < groupAssignments.length; i++) {
2 26 Feb 07 jari 2341             if (groupAssignments[i] == GROUP_A) {
2 26 Feb 07 jari 2342                 groupACount++;
2 26 Feb 07 jari 2343             } else if (groupAssignments[i] == GROUP_B) {
2 26 Feb 07 jari 2344                 groupBCount++;
2 26 Feb 07 jari 2345             }
2 26 Feb 07 jari 2346         }
2 26 Feb 07 jari 2347         
2 26 Feb 07 jari 2348         int[] groupCount = new int[2];
2 26 Feb 07 jari 2349         groupCount[0] = groupACount;
2 26 Feb 07 jari 2350         groupCount[1] = groupBCount;
2 26 Feb 07 jari 2351         
2 26 Feb 07 jari 2352         return groupCount;
2 26 Feb 07 jari 2353     }
2 26 Feb 07 jari 2354     
2 26 Feb 07 jari 2355     public boolean[] isInSurvivalAnalysis() {
2 26 Feb 07 jari 2356         boolean[] inAnalysis = new boolean[csPanel.fields.length];
2 26 Feb 07 jari 2357         for (int i = 0; i < inAnalysis.length; i++) {
2 26 Feb 07 jari 2358             if (csPanel.fields[i].inAnalysisCheckBox.isSelected()) {
2 26 Feb 07 jari 2359                 inAnalysis[i] = true;
2 26 Feb 07 jari 2360             } else {
2 26 Feb 07 jari 2361                 inAnalysis[i] = false;
2 26 Feb 07 jari 2362             }
2 26 Feb 07 jari 2363         }
2 26 Feb 07 jari 2364         return inAnalysis;
2 26 Feb 07 jari 2365     }
2 26 Feb 07 jari 2366     
2 26 Feb 07 jari 2367     public double[] getSurvivalTimes() {
2 26 Feb 07 jari 2368         double[] survivalTimes = new double[exptNames.size()];
2 26 Feb 07 jari 2369         for (int i = 0; i < survivalTimes.length; i++) {
2 26 Feb 07 jari 2370             try {
2 26 Feb 07 jari 2371                 String s = csPanel.fields[i].timeInputField.getText();
2 26 Feb 07 jari 2372                 double d = (new Double(s)).doubleValue();
2 26 Feb 07 jari 2373                 survivalTimes[i] = d;
2 26 Feb 07 jari 2374                 //System.out.println("SAMInitDialog.getSurvivalTimes(): i =  " + i + ", s = " + s + ", d = " + d);
2 26 Feb 07 jari 2375             } catch (NumberFormatException nfe){
2 26 Feb 07 jari 2376                 //nfe.printStackTrace();
2 26 Feb 07 jari 2377                 survivalTimes[i] = 0;
2 26 Feb 07 jari 2378             }
2 26 Feb 07 jari 2379         }
2 26 Feb 07 jari 2380         return survivalTimes;
2 26 Feb 07 jari 2381     }
2 26 Feb 07 jari 2382     
2 26 Feb 07 jari 2383     public boolean[] isCensored() {
2 26 Feb 07 jari 2384         boolean[] censored = new boolean[exptNames.size()];
2 26 Feb 07 jari 2385         for (int i = 0; i  < censored.length; i++) {
2 26 Feb 07 jari 2386             if (csPanel.fields[i].censoredRadioButton.isSelected()) {
2 26 Feb 07 jari 2387                 censored[i] = true;
2 26 Feb 07 jari 2388             } else {
2 26 Feb 07 jari 2389                 censored[i] = false;
2 26 Feb 07 jari 2390             }
2 26 Feb 07 jari 2391         }
2 26 Feb 07 jari 2392         return censored;
2 26 Feb 07 jari 2393     }
2 26 Feb 07 jari 2394     
2 26 Feb 07 jari 2395     public Vector getPairedAExpts() {
2 26 Feb 07 jari 2396         return tcpmPanel.tcpPanel.pairedAExpts;
2 26 Feb 07 jari 2397     }
2 26 Feb 07 jari 2398     
2 26 Feb 07 jari 2399     public Vector getPairedBExpts() {
2 26 Feb 07 jari 2400         return tcpmPanel.tcpPanel.pairedBExpts;
2 26 Feb 07 jari 2401     }
2 26 Feb 07 jari 2402     
2 26 Feb 07 jari 2403     private long factorial(int n) {
2 26 Feb 07 jari 2404         if ((n==1) || (n == 0)) {
2 26 Feb 07 jari 2405             return 1;
2 26 Feb 07 jari 2406         }
2 26 Feb 07 jari 2407         else {
2 26 Feb 07 jari 2408             return factorial(n-1) * n;
2 26 Feb 07 jari 2409         }
2 26 Feb 07 jari 2410     }
2 26 Feb 07 jari 2411     
2 26 Feb 07 jari 2412     private int getNumCombs(int n, int k) { // nCk
2 26 Feb 07 jari 2413         
2 26 Feb 07 jari 2414         /*
2 26 Feb 07 jari 2415         System.out.println("n = " + n);
2 26 Feb 07 jari 2416         System.out.println("k = " + k);
2 26 Feb 07 jari 2417         System.out.println("Numerator: factorial(n) = " + factorial(n));
2 26 Feb 07 jari 2418         System.out.println("factorial(k) = " + factorial(k));
2 26 Feb 07 jari 2419         System.out.println("factorial(n-k) = " + factorial(n-k));
2 26 Feb 07 jari 2420          */
2 26 Feb 07 jari 2421         return Math.round(factorial(n)/(factorial(k)*factorial(n-k)));
2 26 Feb 07 jari 2422     }
2 26 Feb 07 jari 2423     
2 26 Feb 07 jari 2424     public int getNumNeighbors() {
2 26 Feb 07 jari 2425         String s = iPanel.numNeighborsField.getText();
2 26 Feb 07 jari 2426         return Integer.parseInt(s);
2 26 Feb 07 jari 2427     }
2 26 Feb 07 jari 2428     
2 26 Feb 07 jari 2429     public int getUserNumCombs() {
2 26 Feb 07 jari 2430         String s = pPanel.numPermsInputField.getText();
2 26 Feb 07 jari 2431         return Integer.parseInt(s);
2 26 Feb 07 jari 2432     }
2 26 Feb 07 jari 2433     
2 26 Feb 07 jari 2434     
2 26 Feb 07 jari 2435     public boolean useKNearest() {
2 26 Feb 07 jari 2436         return iPanel.kNearestButton.isSelected();
2 26 Feb 07 jari 2437     }
2 26 Feb 07 jari 2438     
2 26 Feb 07 jari 2439     /*
2 26 Feb 07 jari 2440     public boolean useAllCombs() {
2 26 Feb 07 jari 2441         return pPanel.useAllPermsButton.isSelected();
2 26 Feb 07 jari 2442     }
2 26 Feb 07 jari 2443      */
2 26 Feb 07 jari 2444     
2 26 Feb 07 jari 2445     public boolean drawTrees() {
2 26 Feb 07 jari 2446         return this.hclOpsPanel.isHCLSelected();
2 26 Feb 07 jari 2447     }
2 26 Feb 07 jari 2448     
2 26 Feb 07 jari 2449     public boolean drawSigTreesOnly() {
2 26 Feb 07 jari 2450         return hclOpsPanel.drawSigTreesOnly();
2 26 Feb 07 jari 2451     }    
2 26 Feb 07 jari 2452     
2 26 Feb 07 jari 2453     public boolean useTusherEtAlS0() {
2 26 Feb 07 jari 2454         if (sqPanel.s0SelectBox.getSelectedIndex() == 0) {
2 26 Feb 07 jari 2455             return true;
2 26 Feb 07 jari 2456         } else {
2 26 Feb 07 jari 2457             return false;
2 26 Feb 07 jari 2458         }
2 26 Feb 07 jari 2459     }
2 26 Feb 07 jari 2460     
2 26 Feb 07 jari 2461     public double getPercentile() {
2 26 Feb 07 jari 2462         if (sqPanel.s0SelectButton.isSelected()) {
2 26 Feb 07 jari 2463             int index = sqPanel.s0SelectBox.getSelectedIndex();
2 26 Feb 07 jari 2464             if (index == 0) {
2 26 Feb 07 jari 2465                 return -1d;
2 26 Feb 07 jari 2466             } else if (index == 1) {
2 26 Feb 07 jari 2467                 return 5d;
2 26 Feb 07 jari 2468             } else if (index == 2) {
2 26 Feb 07 jari 2469                 return 50d;
2 26 Feb 07 jari 2470             } else if (index == 3) {
2 26 Feb 07 jari 2471                 return 90d;
2 26 Feb 07 jari 2472             } else if (index == 4) {
2 26 Feb 07 jari 2473                 return 0d;
2 26 Feb 07 jari 2474             }
2 26 Feb 07 jari 2475         } else {
2 26 Feb 07 jari 2476             return Double.parseDouble(sqPanel.s0EntryField.getText());
2 26 Feb 07 jari 2477         }
2 26 Feb 07 jari 2478         return 0d;
2 26 Feb 07 jari 2479     }
2 26 Feb 07 jari 2480     
2 26 Feb 07 jari 2481     public boolean calculateQLowestFDR() {
2 26 Feb 07 jari 2482         if (sqPanel.qYesButton.isSelected()){
2 26 Feb 07 jari 2483             return true;
2 26 Feb 07 jari 2484         } else {
2 26 Feb 07 jari 2485             return false;
2 26 Feb 07 jari 2486         }
2 26 Feb 07 jari 2487     }
2 26 Feb 07 jari 2488     
2 26 Feb 07 jari 2489     public int getNumUniquePerms() {
2 26 Feb 07 jari 2490         return this.numUniquePerms;
2 26 Feb 07 jari 2491     }
2 26 Feb 07 jari 2492     
2 26 Feb 07 jari 2493     public boolean useAllUniquePerms() {
2 26 Feb 07 jari 2494         return this.allUniquePermsUsed;
2 26 Feb 07 jari 2495     }
2 26 Feb 07 jari 2496     
2 26 Feb 07 jari 2497     private int getNumUnique2ClassUnpairedPerms(int n, int k) { // nCk
2 26 Feb 07 jari 2498         return Math.round(factorial(n)/(factorial(k)*factorial(n-k)));
2 26 Feb 07 jari 2499     }    
2 26 Feb 07 jari 2500     
2 26 Feb 07 jari 2501     
2 26 Feb 07 jari 2502     public class EventListener extends WindowAdapter implements ActionListener{
2 26 Feb 07 jari 2503         public void actionPerformed(ActionEvent ae){
2 26 Feb 07 jari 2504             String command = ae.getActionCommand();
2 26 Feb 07 jari 2505             if(command.equals("ok-command")){
2 26 Feb 07 jari 2506                 try {
2 26 Feb 07 jari 2507                     if (sqPanel.s0EntryButton.isSelected()) {
2 26 Feb 07 jari 2508                         double d = Double.parseDouble(sqPanel.s0EntryField.getText());
2 26 Feb 07 jari 2509                         if ((d < 0)||(d > 100)) {
2 26 Feb 07 jari 2510                             JOptionPane.showMessageDialog(null, "Enter a valid percentile between 0 and 100!", "Error!", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2511                             return;                          
2 26 Feb 07 jari 2512                         }
2 26 Feb 07 jari 2513                     }
2 26 Feb 07 jari 2514                 } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2515                     JOptionPane.showMessageDialog(null, "Enter a valid percentile between 0 and 100!", "Error!", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2516                     return;
2 26 Feb 07 jari 2517                 }
2 26 Feb 07 jari 2518                 
2 26 Feb 07 jari 2519                 try {
2 26 Feb 07 jari 2520                     int numCombs = 0;
2 26 Feb 07 jari 2521                     //if (!useAllCombs()) {
2 26 Feb 07 jari 2522                     numCombs = getUserNumCombs();
2 26 Feb 07 jari 2523                     //}
2 26 Feb 07 jari 2524                     int numNeibs = 0;
2 26 Feb 07 jari 2525                     if (useKNearest()) {
2 26 Feb 07 jari 2526                         numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2527                     }                  
2 26 Feb 07 jari 2528                     
2 26 Feb 07 jari 2529                 } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2530                     JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE); 
2 26 Feb 07 jari 2531                     return;
2 26 Feb 07 jari 2532                 }
2 26 Feb 07 jari 2533                 if (getStudyDesign() == SAMInitDialog.TWO_CLASS_UNPAIRED) {
2 26 Feb 07 jari 2534                     // if (evt.getSource() == okButton) {
2 26 Feb 07 jari 2535                     int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 2536                     int grpACounter = 0;
2 26 Feb 07 jari 2537                     int grpBCounter = 0;
2 26 Feb 07 jari 2538                     for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2539                         if (grpAssignments[i] == GROUP_A) {
2 26 Feb 07 jari 2540                             grpACounter++;
2 26 Feb 07 jari 2541                         } else if (grpAssignments[i] == GROUP_B) {
2 26 Feb 07 jari 2542                             grpBCounter++;
2 26 Feb 07 jari 2543                         }
2 26 Feb 07 jari 2544                     }
2 26 Feb 07 jari 2545                     if ((grpACounter < 2) || (grpBCounter < 2)) {
2 26 Feb 07 jari 2546                         JOptionPane.showMessageDialog(null, "Group A and Group B must contain more than one sample.", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2547                     } /*else if ((Integer.parseInt(iPanel.numNeighborsField.getText()) > numGenes) || (Integer.parseInt(iPanel.numNeighborsField.getText()) <= 0)) {
2 26 Feb 07 jari 2548                             JOptionPane.showMessageDialog(null, "Number of neighbors must be  > 0, and <= the total number of genes", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2549                         } else if (Integer.parseInt(pPanel.numPermsInputField.getText()) < 0) {
2 26 Feb 07 jari 2550                             JOptionPane.showMessageDialog(null, "Number of permutations must be > 0", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2551                         } */else {
2 26 Feb 07 jari 2552                             try {
2 26 Feb 07 jari 2553                                 
2 26 Feb 07 jari 2554                                 int numCombs = 0;
2 26 Feb 07 jari 2555                                 //if (!useAllCombs()) {
2 26 Feb 07 jari 2556                                 numCombs = getUserNumCombs();
2 26 Feb 07 jari 2557                                 //}
2 26 Feb 07 jari 2558                                 int numNeibs = 0;
2 26 Feb 07 jari 2559                                 if (useKNearest()) {
2 26 Feb 07 jari 2560                                     numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2561                                 }
2 26 Feb 07 jari 2562                                  
2 26 Feb 07 jari 2563                                 if ((grpACounter + grpBCounter) <= 20) {
2 26 Feb 07 jari 2564                                     numUniquePerms = getNumUnique2ClassUnpairedPerms((grpACounter + grpBCounter), grpACounter);
2 26 Feb 07 jari 2565                                     SAMAllPermsDialog sapDialog = new SAMAllPermsDialog(SAMGUI.SAMFrame, true, numUniquePerms, numCombs);
2 26 Feb 07 jari 2566                                     sapDialog.setVisible(true);
2 26 Feb 07 jari 2567                                     allUniquePermsUsed = sapDialog.useAllPerms();
2 26 Feb 07 jari 2568                                 }
2 26 Feb 07 jari 2569                                 okPressed = true;
2 26 Feb 07 jari 2570                                 javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2571                                 
2 26 Feb 07 jari 2572                                 dispose();
2 26 Feb 07 jari 2573                             } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2574                                 JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2575                             }
2 26 Feb 07 jari 2576                             
2 26 Feb 07 jari 2577                             //okPressed = true;
2 26 Feb 07 jari 2578                             //hide();
2 26 Feb 07 jari 2579                             //dispose();
2 26 Feb 07 jari 2580                         }
2 26 Feb 07 jari 2581                     // }
2 26 Feb 07 jari 2582                 } else if (getStudyDesign() == SAMInitDialog.TWO_CLASS_PAIRED) {
2 26 Feb 07 jari 2583                     if (tcpmPanel.tcpPanel.pairedListModel.size() < 2) {
2 26 Feb 07 jari 2584                         JOptionPane.showMessageDialog(null, "Need at least two pairs of samples!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2585                     } else {
2 26 Feb 07 jari 2586                         if (tcpmPanel.tcpPanel.pairedListModel.size() <= 29) {
2 26 Feb 07 jari 2587                             int numCombs = getUserNumCombs();
2 26 Feb 07 jari 2588                             numUniquePerms = (int)(Math.pow(2, tcpmPanel.tcpPanel.pairedListModel.size()));
2 26 Feb 07 jari 2589                             SAMAllPermsDialog sapDialog = new SAMAllPermsDialog(SAMGUI.SAMFrame, true, numUniquePerms, numCombs);
2 26 Feb 07 jari 2590                             sapDialog.setVisible(true);
2 26 Feb 07 jari 2591                             allUniquePermsUsed = sapDialog.useAllPerms();                            
2 26 Feb 07 jari 2592                         }
2 26 Feb 07 jari 2593                         okPressed = true;
2 26 Feb 07 jari 2594                         javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2595                         dispose();
2 26 Feb 07 jari 2596                     }
2 26 Feb 07 jari 2597                     
2 26 Feb 07 jari 2598                 } else if (getStudyDesign() == SAMInitDialog.MULTI_CLASS) {
2 26 Feb 07 jari 2599                     boolean tooFew = false;
2 26 Feb 07 jari 2600                     int[] grpAssignments = getGroupAssignments();
2 26 Feb 07 jari 2601                     int numGroups = getMultiClassNumGroups();
2 26 Feb 07 jari 2602                     int[] groupSize = new int[numGroups];
2 26 Feb 07 jari 2603                     
2 26 Feb 07 jari 2604                     for (int i = 0; i < groupSize.length; i++) {
2 26 Feb 07 jari 2605                         groupSize[i] = 0;
2 26 Feb 07 jari 2606                     }
2 26 Feb 07 jari 2607                     
2 26 Feb 07 jari 2608                     for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2609                         int currentGroup = grpAssignments[i];
2 26 Feb 07 jari 2610                         if (currentGroup != 0) {
2 26 Feb 07 jari 2611                             groupSize[currentGroup - 1]++;
2 26 Feb 07 jari 2612                         }
2 26 Feb 07 jari 2613                     }
2 26 Feb 07 jari 2614                     
2 26 Feb 07 jari 2615                         /*
2 26 Feb 07 jari 2616                         for (int i = 0; i < grpAssignments.length; i++) {
2 26 Feb 07 jari 2617                             System.out.println("grpAssignments[" + i + "] = "  + grpAssignments[i]);
2 26 Feb 07 jari 2618                         }
2 26 Feb 07 jari 2619                          
2 26 Feb 07 jari 2620                         for (int i = 0; i < groupSize.length; i++) {
2 26 Feb 07 jari 2621                             System.out.println("groupSize[" + i + "] = " + groupSize[i] + " (group " + (i +1) + ")");
2 26 Feb 07 jari 2622                         }
2 26 Feb 07 jari 2623                          */
2 26 Feb 07 jari 2624                     
2 26 Feb 07 jari 2625                     for (int i = 0; i < groupSize.length; i++) {
2 26 Feb 07 jari 2626                         if (groupSize[i] <= 1) {
2 26 Feb 07 jari 2627                             JOptionPane.showMessageDialog(null, "Each group must contain more than one sample.", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 2628                             tooFew = true;
2 26 Feb 07 jari 2629                             break;
2 26 Feb 07 jari 2630                         }
2 26 Feb 07 jari 2631                     }
2 26 Feb 07 jari 2632                     
2 26 Feb 07 jari 2633                     if (!tooFew) {
2 26 Feb 07 jari 2634                         try {
2 26 Feb 07 jari 2635                             int numCombs = 0;
2 26 Feb 07 jari 2636                             //if (!useAllCombs()) {
2 26 Feb 07 jari 2637                             numCombs = getUserNumCombs();
2 26 Feb 07 jari 2638                             //}
2 26 Feb 07 jari 2639                             int numNeibs = 0;
2 26 Feb 07 jari 2640                             if (useKNearest()) {
2 26 Feb 07 jari 2641                                 numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2642                             }
2 26 Feb 07 jari 2643                             okPressed = true;
2 26 Feb 07 jari 2644                             javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2645                             
2 26 Feb 07 jari 2646                             dispose();
2 26 Feb 07 jari 2647                         } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2648                             JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2649                         }
2 26 Feb 07 jari 2650                     }
2 26 Feb 07 jari 2651                      
2 26 Feb 07 jari 2652                 } else if (getStudyDesign() == SAMInitDialog.CENSORED_SURVIVAL) {
2 26 Feb 07 jari 2653                     try {
2 26 Feb 07 jari 2654                         boolean allSame = true;
2 26 Feb 07 jari 2655                         int selectedCounter = 0;
2 26 Feb 07 jari 2656                         double previousTime = 0;
2 26 Feb 07 jari 2657                         for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 2658                             if (csPanel.fields[i].inAnalysisCheckBox.isSelected()) {
2 26 Feb 07 jari 2659                                 selectedCounter++;
2 26 Feb 07 jari 2660                                 double d = (new Double(csPanel.fields[i].timeInputField.getText())).doubleValue();
2 26 Feb 07 jari 2661                                 if (i > 0) {
2 26 Feb 07 jari 2662                                     if (previousTime != d) {
2 26 Feb 07 jari 2663                                         allSame = false;
2 26 Feb 07 jari 2664                                     }
2 26 Feb 07 jari 2665                                 }
2 26 Feb 07 jari 2666                                 previousTime = d;
2 26 Feb 07 jari 2667                             }
2 26 Feb 07 jari 2668                         }
2 26 Feb 07 jari 2669                         int numCombs = 0;
2 26 Feb 07 jari 2670                         //if (!useAllCombs()) {
2 26 Feb 07 jari 2671                         numCombs = getUserNumCombs();
2 26 Feb 07 jari 2672                         //}
2 26 Feb 07 jari 2673                         int numNeibs = 0;
2 26 Feb 07 jari 2674                         if (useKNearest()) {
2 26 Feb 07 jari 2675                             numNeibs = getNumNeighbors();
2 26 Feb 07 jari 2676                         }
2 26 Feb 07 jari 2677                         if (selectedCounter < 2) {
2 26 Feb 07 jari 2678                             JOptionPane.showMessageDialog(null, "At least 2 samples must be selected!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2679                         } else if (allSame) {
2 26 Feb 07 jari 2680                             JOptionPane.showMessageDialog(null, "At least one of the survival time values must be different from the rest!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2681                         } else {
2 26 Feb 07 jari 2682                             if (selectedCounter <= 10) {
2 26 Feb 07 jari 2683                                 numUniquePerms = (int)(factorial(selectedCounter));
2 26 Feb 07 jari 2684                                 SAMAllPermsDialog sapDialog = new SAMAllPermsDialog(SAMGUI.SAMFrame, true, numUniquePerms, numCombs);
2 26 Feb 07 jari 2685                                 sapDialog.setVisible(true);
2 26 Feb 07 jari 2686                                 allUniquePermsUsed = sapDialog.useAllPerms();
2 26 Feb 07 jari 2687                             }                            
2 26 Feb 07 jari 2688                             okPressed = true;
2 26 Feb 07 jari 2689                             javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2690                             dispose();
2 26 Feb 07 jari 2691                         }
2 26 Feb 07 jari 2692                     } catch (NumberFormatException nfe){
2 26 Feb 07 jari 2693                         JOptionPane.showMessageDialog(null, "Invalid parameter value(s)!", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 2694                     }
2 26 Feb 07 jari 2695                 } else if (getStudyDesign() == SAMInitDialog.ONE_CLASS) {
2 26 Feb 07 jari 2696                     try {
2 26 Feb 07 jari 2697                         double ocm = getOneClassMean();
2 26 Feb 07 jari 2698                         if (getNumValidOneClassExpts() < 2) {
2 26 Feb 07 jari 2699                             JOptionPane.showMessageDialog(null, "At least 2 samples must be selected for one-class test!", "Error", JOptionPane.ERROR_MESSAGE);                            
2 26 Feb 07 jari 2700                         } else {
2 26 Feb 07 jari 2701                             if (getNumValidOneClassExpts() <= 29) {
2 26 Feb 07 jari 2702                                 int numCombs = getUserNumCombs();
2 26 Feb 07 jari 2703                                 numUniquePerms = (int)(Math.pow(2, getNumValidOneClassExpts()));
2 26 Feb 07 jari 2704                                 SAMAllPermsDialog sapDialog = new SAMAllPermsDialog(SAMGUI.SAMFrame, true, numUniquePerms, numCombs);
2 26 Feb 07 jari 2705                                 sapDialog.setVisible(true);
2 26 Feb 07 jari 2706                                 allUniquePermsUsed = sapDialog.useAllPerms();
2 26 Feb 07 jari 2707                             }                            
2 26 Feb 07 jari 2708                             okPressed = true;
2 26 Feb 07 jari 2709                             javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2710                             dispose();
2 26 Feb 07 jari 2711                         }
2 26 Feb 07 jari 2712                     } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 2713                         JOptionPane.showMessageDialog(null, "Invalid value for one-class mean!", "Error", JOptionPane.ERROR_MESSAGE);                        
2 26 Feb 07 jari 2714                     }
2 26 Feb 07 jari 2715                 }
2 26 Feb 07 jari 2716             }  // ends handling ok-command
2 26 Feb 07 jari 2717             else if(command.equals("reset-command")){
2 26 Feb 07 jari 2718                 if(getStudyDesign() == SAMInitDialog.TWO_CLASS_UNPAIRED)
2 26 Feb 07 jari 2719                     gPanel.reset();
2 26 Feb 07 jari 2720                 else if(getStudyDesign() == SAMInitDialog.MULTI_CLASS && mPanel.mulgPanel != null)
2 26 Feb 07 jari 2721                     mPanel.reset();
2 26 Feb 07 jari 2722                 else if(getStudyDesign() == SAMInitDialog.CENSORED_SURVIVAL)
2 26 Feb 07 jari 2723                     csPanel.reset();
2 26 Feb 07 jari 2724                 sqPanel.reset();
2 26 Feb 07 jari 2725                 pPanel.reset();
2 26 Feb 07 jari 2726                 iPanel.reset();
2 26 Feb 07 jari 2727                 tcpmPanel.tcpPanel.reset();
2 26 Feb 07 jari 2728                 hclOpsPanel.setHCLSelected(false);
2 26 Feb 07 jari 2729             }
2 26 Feb 07 jari 2730             else if(command.equals("cancel-command")){
2 26 Feb 07 jari 2731                 okPressed = false;
2 26 Feb 07 jari 2732                 //hide();
2 26 Feb 07 jari 2733                 javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2734                 dispose();
2 26 Feb 07 jari 2735             }
2 26 Feb 07 jari 2736             else if(command.equals("info-command")){
2 26 Feb 07 jari 2737                 HelpWindow help = new HelpWindow(SAMInitDialog.this, "SAM Initialization Dialog");
2 26 Feb 07 jari 2738                 if(help.getWindowContent()){
2 26 Feb 07 jari 2739                     help.setSize(500,650);
2 26 Feb 07 jari 2740                     help.setLocation();
2 26 Feb 07 jari 2741                     help.show();
2 26 Feb 07 jari 2742                     return;
2 26 Feb 07 jari 2743                 }
2 26 Feb 07 jari 2744             }
2 26 Feb 07 jari 2745         }
2 26 Feb 07 jari 2746         
2 26 Feb 07 jari 2747         public void windowClosing(WindowEvent we){
2 26 Feb 07 jari 2748             javax.swing.UIManager.put("TabbedPane.selected", Color.lightGray);
2 26 Feb 07 jari 2749             //System.out.println("Sam is closed");
2 26 Feb 07 jari 2750         }
2 26 Feb 07 jari 2751         
2 26 Feb 07 jari 2752     }
2 26 Feb 07 jari 2753     
2 26 Feb 07 jari 2754     public static void main(String[] args) {
2 26 Feb 07 jari 2755         
2 26 Feb 07 jari 2756         JFrame dummyFrame = new JFrame();
2 26 Feb 07 jari 2757         Vector dummyVect = new Vector();
2 26 Feb 07 jari 2758         for (int i = 0; i < 100; i++) {
2 26 Feb 07 jari 2759             dummyVect.add("Expt " + i);
2 26 Feb 07 jari 2760         }
2 26 Feb 07 jari 2761         SAMInitDialog sDialog = new SAMInitDialog(dummyFrame, true, dummyVect, 5);
2 26 Feb 07 jari 2762         sDialog.setVisible(true);
2 26 Feb 07 jari 2763         System.exit(0);
2 26 Feb 07 jari 2764         
2 26 Feb 07 jari 2765     }
2 26 Feb 07 jari 2766     
2 26 Feb 07 jari 2767 }

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