mev-4.0.01/source/org/tigr/microarray/mev/cluster/gui/impl/tfa/TFAInitBox2.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2 Copyright @ 1999-2005, The Institute for Genomic Research (TIGR).
2 26 Feb 07 jari 3 All rights reserved.
2 26 Feb 07 jari 4 */
2 26 Feb 07 jari 5 /*
2 26 Feb 07 jari 6  * TFAInitBox2.java
2 26 Feb 07 jari 7  *
2 26 Feb 07 jari 8  * Created on February 12, 2004, 4:15 PM
2 26 Feb 07 jari 9  */
2 26 Feb 07 jari 10
2 26 Feb 07 jari 11 package org.tigr.microarray.mev.cluster.gui.impl.tfa;
2 26 Feb 07 jari 12
2 26 Feb 07 jari 13 import java.awt.Color;
2 26 Feb 07 jari 14 import java.awt.Dimension;
2 26 Feb 07 jari 15 import java.awt.Font;
2 26 Feb 07 jari 16 import java.awt.GridBagConstraints;
2 26 Feb 07 jari 17 import java.awt.GridBagLayout;
2 26 Feb 07 jari 18 import java.awt.Insets;
2 26 Feb 07 jari 19 import java.awt.Toolkit;
2 26 Feb 07 jari 20 import java.awt.event.ActionEvent;
2 26 Feb 07 jari 21 import java.awt.event.ActionListener;
2 26 Feb 07 jari 22 import java.awt.event.WindowAdapter;
2 26 Feb 07 jari 23 import java.io.BufferedReader;
2 26 Feb 07 jari 24 import java.io.File;
2 26 Feb 07 jari 25 import java.io.FileOutputStream;
2 26 Feb 07 jari 26 import java.io.FileReader;
2 26 Feb 07 jari 27 import java.io.PrintWriter;
2 26 Feb 07 jari 28 import java.util.Vector;
2 26 Feb 07 jari 29
2 26 Feb 07 jari 30 import javax.swing.BorderFactory;
2 26 Feb 07 jari 31 import javax.swing.ButtonGroup;
2 26 Feb 07 jari 32 import javax.swing.JButton;
2 26 Feb 07 jari 33 import javax.swing.JFileChooser;
2 26 Feb 07 jari 34 import javax.swing.JFrame;
2 26 Feb 07 jari 35 import javax.swing.JLabel;
2 26 Feb 07 jari 36 import javax.swing.JOptionPane;
2 26 Feb 07 jari 37 import javax.swing.JPanel;
2 26 Feb 07 jari 38 import javax.swing.JRadioButton;
2 26 Feb 07 jari 39 import javax.swing.JScrollPane;
2 26 Feb 07 jari 40 import javax.swing.JTextField;
2 26 Feb 07 jari 41 import javax.swing.ScrollPaneConstants;
2 26 Feb 07 jari 42 import javax.swing.UIManager;
2 26 Feb 07 jari 43 import javax.swing.border.BevelBorder;
2 26 Feb 07 jari 44 import javax.swing.border.EtchedBorder;
2 26 Feb 07 jari 45 import javax.swing.border.TitledBorder;
2 26 Feb 07 jari 46
2 26 Feb 07 jari 47 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.AlgorithmDialog;
2 26 Feb 07 jari 48 import org.tigr.microarray.mev.cluster.gui.impl.dialogs.HCLSigOnlyPanel;
2 26 Feb 07 jari 49 import org.tigr.util.StringSplitter;
2 26 Feb 07 jari 50
2 26 Feb 07 jari 51
2 26 Feb 07 jari 52 /**
2 26 Feb 07 jari 53  *
2 26 Feb 07 jari 54  * @author  nbhagaba
2 26 Feb 07 jari 55  */
2 26 Feb 07 jari 56 public class TFAInitBox2 extends AlgorithmDialog {
2 26 Feb 07 jari 57     
2 26 Feb 07 jari 58     public static final int JUST_ALPHA = 4;
2 26 Feb 07 jari 59     public static final int STD_BONFERRONI = 5;
2 26 Feb 07 jari 60     public static final int ADJ_BONFERRONI = 6;    
2 26 Feb 07 jari 61     public static final int MAX_T = 9;
2 26 Feb 07 jari 62     public static final int MIN_P = 10;
2 26 Feb 07 jari 63     
2 26 Feb 07 jari 64     boolean okPressed = false;
2 26 Feb 07 jari 65     private boolean oneSamplePerCell = false;
2 26 Feb 07 jari 66     Vector exptNames;
2 26 Feb 07 jari 67     String[] factorNames;
2 26 Feb 07 jari 68     int[] numFactorLevels;
2 26 Feb 07 jari 69     GroupExptsPanel gPanel;
2 26 Feb 07 jari 70     PValuePanel pPanel;
2 26 Feb 07 jari 71     PValueAdjustmentPanel pAdjPanel;
2 26 Feb 07 jari 72     HCLSigOnlyPanel hclOpsPanel;    
2 26 Feb 07 jari 73     //HCLSelectionPanel hclOpsPanel;
2 26 Feb 07 jari 74     /** Creates a new instance of TFAInitBox2 */
2 26 Feb 07 jari 75     public TFAInitBox2(JFrame parentFrame, boolean modality, Vector exptNames, String[] factorNames, int[] numFactorLevels) {
2 26 Feb 07 jari 76         super(parentFrame, "Two-factor ANOVA Initialization", modality);
2 26 Feb 07 jari 77         this.exptNames = exptNames;
2 26 Feb 07 jari 78         this.factorNames = factorNames;
2 26 Feb 07 jari 79         this.numFactorLevels = numFactorLevels;
2 26 Feb 07 jari 80         
2 26 Feb 07 jari 81         setBounds(0, 0, 800, 720);
2 26 Feb 07 jari 82         setBackground(Color.white);
2 26 Feb 07 jari 83         setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
2 26 Feb 07 jari 84         GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 85         GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 86         constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 87         
2 26 Feb 07 jari 88         JPanel pane = new JPanel();
2 26 Feb 07 jari 89         pane.setLayout(gridbag);
2 26 Feb 07 jari 90         
2 26 Feb 07 jari 91         gPanel = new GroupExptsPanel();
2 26 Feb 07 jari 92         
2 26 Feb 07 jari 93         buildConstraints(constraints, 0, 0, 1, 1, 100, 80);
2 26 Feb 07 jari 94         gridbag.setConstraints(gPanel, constraints);
2 26 Feb 07 jari 95         pane.add(gPanel);
2 26 Feb 07 jari 96         
2 26 Feb 07 jari 97         pPanel = new PValuePanel();
2 26 Feb 07 jari 98         buildConstraints(constraints, 0, 1, 1, 1, 0, 8);
2 26 Feb 07 jari 99         gridbag.setConstraints(pPanel, constraints);
2 26 Feb 07 jari 100         pane.add(pPanel);
2 26 Feb 07 jari 101         
2 26 Feb 07 jari 102         pAdjPanel = new PValueAdjustmentPanel();
2 26 Feb 07 jari 103         buildConstraints(constraints, 0, 2, 1, 1, 0, 8);
2 26 Feb 07 jari 104         gridbag.setConstraints(pAdjPanel, constraints);
2 26 Feb 07 jari 105         pane.add(pAdjPanel);
2 26 Feb 07 jari 106         
2 26 Feb 07 jari 107         hclOpsPanel = new HCLSigOnlyPanel();
2 26 Feb 07 jari 108         buildConstraints(constraints, 0, 3, 1, 1, 0, 4);
2 26 Feb 07 jari 109         gridbag.setConstraints(hclOpsPanel, constraints);
2 26 Feb 07 jari 110         pane.add(hclOpsPanel);
2 26 Feb 07 jari 111         
2 26 Feb 07 jari 112         addContent(pane);
2 26 Feb 07 jari 113         EventListener listener = new EventListener();
2 26 Feb 07 jari 114         setActionListeners(listener);
2 26 Feb 07 jari 115         this.addWindowListener(listener);
2 26 Feb 07 jari 116     }
2 26 Feb 07 jari 117     
2 26 Feb 07 jari 118     void buildConstraints(GridBagConstraints gbc, int gx, int gy, int gw, int gh, int wx, int wy) {
2 26 Feb 07 jari 119         gbc.gridx = gx;
2 26 Feb 07 jari 120         gbc.gridy = gy;
2 26 Feb 07 jari 121         gbc.gridwidth = gw;
2 26 Feb 07 jari 122         gbc.gridheight = gh;
2 26 Feb 07 jari 123         gbc.weightx = wx;
2 26 Feb 07 jari 124         gbc.weighty = wy;
2 26 Feb 07 jari 125     }
2 26 Feb 07 jari 126     
2 26 Feb 07 jari 127     class GroupExptsPanel extends JPanel {
2 26 Feb 07 jari 128         MultiGroupExperimentsPanel factorAPanel, factorBPanel;
2 26 Feb 07 jari 129         JPanel panel2;
2 26 Feb 07 jari 130         GroupExptsPanel() {
2 26 Feb 07 jari 131             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 132             setBackground(Color.white);
2 26 Feb 07 jari 133             factorAPanel = new MultiGroupExperimentsPanel(factorNames[0], numFactorLevels[0]);
2 26 Feb 07 jari 134             factorBPanel = new MultiGroupExperimentsPanel(factorNames[1], numFactorLevels[1]);
2 26 Feb 07 jari 135             
2 26 Feb 07 jari 136             GridBagLayout grid1 = new GridBagLayout();
2 26 Feb 07 jari 137             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 138             this.setLayout(grid1);
2 26 Feb 07 jari 139             
2 26 Feb 07 jari 140             buildConstraints(constraints, 0, 0, 1, 1, 50, 90);
2 26 Feb 07 jari 141             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 142             grid1.setConstraints(factorAPanel, constraints);
2 26 Feb 07 jari 143             this.add(factorAPanel);
2 26 Feb 07 jari 144             
2 26 Feb 07 jari 145             buildConstraints(constraints, 1, 0, 1, 1, 50, 0);
2 26 Feb 07 jari 146             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 147             grid1.setConstraints(factorBPanel, constraints);
2 26 Feb 07 jari 148             this.add(factorBPanel);
2 26 Feb 07 jari 149             
2 26 Feb 07 jari 150             JPanel panel2 = new JPanel();
2 26 Feb 07 jari 151             GridBagLayout gridbag3 = new GridBagLayout();
2 26 Feb 07 jari 152             panel2.setLayout(gridbag3);
2 26 Feb 07 jari 153             panel2.setBackground(Color.white);
2 26 Feb 07 jari 154             JButton saveButton = new JButton("  Save settings  ");
2 26 Feb 07 jari 155             saveButton.setFocusPainted(false);
2 26 Feb 07 jari 156             saveButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 157             JButton loadButton = new JButton("  Load settings  ");
2 26 Feb 07 jari 158             loadButton.setFocusPainted(false);
2 26 Feb 07 jari 159             loadButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 160             JButton resetButton = new JButton("  Reset  ");
2 26 Feb 07 jari 161             resetButton.setFocusPainted(false);
2 26 Feb 07 jari 162             resetButton.setBorder(BorderFactory.createBevelBorder(BevelBorder.RAISED, Color.lightGray, Color.darkGray));
2 26 Feb 07 jari 163             
2 26 Feb 07 jari 164             
2 26 Feb 07 jari 165             //final int finNum = exptNames.size();
2 26 Feb 07 jari 166             
2 26 Feb 07 jari 167             resetButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 168                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 169                     factorAPanel.reset();
2 26 Feb 07 jari 170                     factorBPanel.reset();
2 26 Feb 07 jari 171                 }
2 26 Feb 07 jari 172             });
2 26 Feb 07 jari 173             
2 26 Feb 07 jari 174             final JFileChooser fc = new JFileChooser();
2 26 Feb 07 jari 175             fc.setCurrentDirectory(new File("Data"));
2 26 Feb 07 jari 176             
2 26 Feb 07 jari 177             saveButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 178                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 179                     int returnVal = fc.showSaveDialog(GroupExptsPanel.this);
2 26 Feb 07 jari 180                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 181                         File file = fc.getSelectedFile();
2 26 Feb 07 jari 182                         try {
2 26 Feb 07 jari 183                             PrintWriter out = new PrintWriter(new FileOutputStream(file));
2 26 Feb 07 jari 184                             int[] factorAGroupAssgn = factorAPanel.getGroupAssignments();
2 26 Feb 07 jari 185                             int[] factorBGroupAssgn = factorBPanel.getGroupAssignments();
2 26 Feb 07 jari 186                             for (int i = 0; i < factorAGroupAssgn.length; i++) {
2 26 Feb 07 jari 187                                 out.print(factorAGroupAssgn[i]);
2 26 Feb 07 jari 188                                 if (i < factorAGroupAssgn.length - 1) {
2 26 Feb 07 jari 189                                     out.print("\t");
2 26 Feb 07 jari 190                                 }
2 26 Feb 07 jari 191                             }
2 26 Feb 07 jari 192                             out.println();
2 26 Feb 07 jari 193                             
2 26 Feb 07 jari 194                             for (int i = 0; i < factorBGroupAssgn.length; i++) {
2 26 Feb 07 jari 195                                 out.print(factorBGroupAssgn[i]);
2 26 Feb 07 jari 196                                 if (i < factorBGroupAssgn.length - 1) {
2 26 Feb 07 jari 197                                     out.print("\t");
2 26 Feb 07 jari 198                                 }
2 26 Feb 07 jari 199                             }
2 26 Feb 07 jari 200                             out.println();
2 26 Feb 07 jari 201                             
2 26 Feb 07 jari 202                             out.flush();
2 26 Feb 07 jari 203                             out.close();
2 26 Feb 07 jari 204                         } catch (Exception e) {
2 26 Feb 07 jari 205                             //e.printStackTrace();
2 26 Feb 07 jari 206                         }
2 26 Feb 07 jari 207                         //this is where a real application would save the file.
2 26 Feb 07 jari 208                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 209                     } else {
2 26 Feb 07 jari 210                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 211                     }
2 26 Feb 07 jari 212                 }
2 26 Feb 07 jari 213             });
2 26 Feb 07 jari 214             
2 26 Feb 07 jari 215             
2 26 Feb 07 jari 216             
2 26 Feb 07 jari 217             
2 26 Feb 07 jari 218             loadButton.addActionListener(new ActionListener(){
2 26 Feb 07 jari 219                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 220                     int returnVal = fc.showOpenDialog(GroupExptsPanel.this);
2 26 Feb 07 jari 221                     if (returnVal == JFileChooser.APPROVE_OPTION) {
2 26 Feb 07 jari 222                         try {
2 26 Feb 07 jari 223                             FileReader file = new FileReader(fc.getSelectedFile());
2 26 Feb 07 jari 224                             BufferedReader buff = new BufferedReader(file);
2 26 Feb 07 jari 225                             String line = buff.readLine();
2 26 Feb 07 jari 226                             //System.out.println(line);
2 26 Feb 07 jari 227                             StringSplitter st = new StringSplitter('\t');
2 26 Feb 07 jari 228                             st.init(line);
2 26 Feb 07 jari 229                             Vector factorAGroupsVector = new Vector();
2 26 Feb 07 jari 230                             Vector factorBGroupsVector = new Vector();
2 26 Feb 07 jari 231                             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 232                                 String current = st.nextToken();
2 26 Feb 07 jari 233                                 factorAGroupsVector.add(new Integer(current));
2 26 Feb 07 jari 234                                 //System.out.print(current);
2 26 Feb 07 jari 235                             }
2 26 Feb 07 jari 236                             
2 26 Feb 07 jari 237                             line = buff.readLine();
2 26 Feb 07 jari 238                             st.init(line);
2 26 Feb 07 jari 239                             while (st.hasMoreTokens()) {
2 26 Feb 07 jari 240                                 String current = st.nextToken();
2 26 Feb 07 jari 241                                 factorBGroupsVector.add(new Integer(current));
2 26 Feb 07 jari 242                                 //System.out.print(current);
2 26 Feb 07 jari 243                             }
2 26 Feb 07 jari 244                             
2 26 Feb 07 jari 245                             buff.close();
2 26 Feb 07 jari 246                             int[] factorAGroupAssgn = factorAPanel.getGroupAssignments();
2 26 Feb 07 jari 247                             int[] factorBGroupAssgn = factorBPanel.getGroupAssignments();
2 26 Feb 07 jari 248                             if ((factorAGroupsVector.size() != factorAGroupAssgn.length) || (factorBGroupsVector.size() != factorBGroupAssgn.length)){
2 26 Feb 07 jari 249                                 JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 250                             } else {
2 26 Feb 07 jari 251                                 int[] factorAAssignments = new int[factorAGroupsVector.size()];
2 26 Feb 07 jari 252                                 int[] factorBAssignments = new int[factorBGroupsVector.size()];
2 26 Feb 07 jari 253                                 for (int i = 0; i < factorAAssignments.length; i++) {
2 26 Feb 07 jari 254                                     factorAAssignments[i] = ((Integer)(factorAGroupsVector.get(i))).intValue();
2 26 Feb 07 jari 255                                     factorBAssignments[i] = ((Integer)(factorBGroupsVector.get(i))).intValue();
2 26 Feb 07 jari 256                                 }
2 26 Feb 07 jari 257                                 
2 26 Feb 07 jari 258                                 factorAPanel.setGroupAssignments(factorAAssignments);
2 26 Feb 07 jari 259                                 factorBPanel.setGroupAssignments(factorBAssignments);
2 26 Feb 07 jari 260                             }
2 26 Feb 07 jari 261                         } catch (Exception e) {
2 26 Feb 07 jari 262                             JOptionPane.showMessageDialog(gPanel, "Incompatible file!", "Error", JOptionPane.WARNING_MESSAGE);
2 26 Feb 07 jari 263                             factorAPanel.reset();
2 26 Feb 07 jari 264                             factorBPanel.reset();
2 26 Feb 07 jari 265                             //e.printStackTrace();
2 26 Feb 07 jari 266                         }
2 26 Feb 07 jari 267                         
2 26 Feb 07 jari 268                         //this is where a real application would save the file.
2 26 Feb 07 jari 269                         //log.append("Saving: " + file.getName() + "." + newline);
2 26 Feb 07 jari 270                     } else {
2 26 Feb 07 jari 271                         //log.append("Save command cancelled by user." + newline);
2 26 Feb 07 jari 272                     }
2 26 Feb 07 jari 273                 }
2 26 Feb 07 jari 274             });
2 26 Feb 07 jari 275             //
2 26 Feb 07 jari 276             
2 26 Feb 07 jari 277             
2 26 Feb 07 jari 278             
2 26 Feb 07 jari 279             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 280             constraints.fill = GridBagConstraints.NONE;
2 26 Feb 07 jari 281             constraints.insets = new Insets(5,5,5,5);
2 26 Feb 07 jari 282             buildConstraints(constraints, 0, 0, 1, 1, 33, 100);
2 26 Feb 07 jari 283             gridbag3.setConstraints(saveButton, constraints);
2 26 Feb 07 jari 284             panel2.add(saveButton);
2 26 Feb 07 jari 285             
2 26 Feb 07 jari 286             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 287             gridbag3.setConstraints(loadButton, constraints);
2 26 Feb 07 jari 288             panel2.add(loadButton);
2 26 Feb 07 jari 289             
2 26 Feb 07 jari 290             buildConstraints(constraints, 2, 0, 1, 1, 34, 0);
2 26 Feb 07 jari 291             gridbag3.setConstraints(resetButton, constraints);
2 26 Feb 07 jari 292             panel2.add(resetButton);
2 26 Feb 07 jari 293             constraints.insets = new Insets(0,0,0,0);
2 26 Feb 07 jari 294             
2 26 Feb 07 jari 295             buildConstraints(constraints, 0, 1, 2, 1, 100, 5);
2 26 Feb 07 jari 296             constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 297             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 298             grid1.setConstraints(panel2, constraints);
2 26 Feb 07 jari 299             this.add(panel2);
2 26 Feb 07 jari 300             
2 26 Feb 07 jari 301         }
2 26 Feb 07 jari 302         
2 26 Feb 07 jari 303         public void reset() {
2 26 Feb 07 jari 304             factorAPanel.reset();
2 26 Feb 07 jari 305             factorBPanel.reset();
2 26 Feb 07 jari 306         }
2 26 Feb 07 jari 307     }
2 26 Feb 07 jari 308     
2 26 Feb 07 jari 309     class MultiGroupExperimentsPanel extends JPanel {
2 26 Feb 07 jari 310         JLabel[] expLabels;
2 26 Feb 07 jari 311         JRadioButton[][] exptGroupRadioButtons;
2 26 Feb 07 jari 312         JRadioButton[] notInGroupRadioButtons;
2 26 Feb 07 jari 313         int numGroups;
2 26 Feb 07 jari 314         
2 26 Feb 07 jari 315         MultiGroupExperimentsPanel(String factorName, int numGroups) {
2 26 Feb 07 jari 316             this.setBorder(new TitledBorder(new EtchedBorder(), factorName + " assignments", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 317             this.numGroups = numGroups;
2 26 Feb 07 jari 318             setBackground(Color.white);
2 26 Feb 07 jari 319             JPanel panel1 = new JPanel();
2 26 Feb 07 jari 320             expLabels = new JLabel[exptNames.size()];
2 26 Feb 07 jari 321             exptGroupRadioButtons = new JRadioButton[numGroups][exptNames.size()];
2 26 Feb 07 jari 322             //groupARadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 323             //groupBRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 324             notInGroupRadioButtons = new JRadioButton[exptNames.size()];
2 26 Feb 07 jari 325             ButtonGroup chooseGroup[] = new ButtonGroup[exptNames.size()];
2 26 Feb 07 jari 326             
2 26 Feb 07 jari 327             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 328             GridBagLayout gridbag2 = new GridBagLayout();
2 26 Feb 07 jari 329             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 330             this.setLayout(gridbag2);
2 26 Feb 07 jari 331             panel1.setLayout(gridbag);
2 26 Feb 07 jari 332             
2 26 Feb 07 jari 333             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 334                 String s1 = (String)(exptNames.get(i));
2 26 Feb 07 jari 335                 expLabels[i] = new JLabel(s1);
2 26 Feb 07 jari 336                 chooseGroup[i] = new ButtonGroup();
2 26 Feb 07 jari 337                 for (int j = 0; j < numGroups; j++) {
2 26 Feb 07 jari 338                     exptGroupRadioButtons[j][i] = new JRadioButton("Group " + (j + 1) + "     ", j == 0? true: false);
2 26 Feb 07 jari 339                     chooseGroup[i].add(exptGroupRadioButtons[j][i]);
2 26 Feb 07 jari 340                 }
2 26 Feb 07 jari 341                 
2 26 Feb 07 jari 342                 notInGroupRadioButtons[i] = new JRadioButton("Not in groups", false);
2 26 Feb 07 jari 343                 chooseGroup[i].add(notInGroupRadioButtons[i]);
2 26 Feb 07 jari 344                 
2 26 Feb 07 jari 345                 for (int j = 0; j < numGroups; j++) {
2 26 Feb 07 jari 346                     buildConstraints(constraints, j, i, 1, 1, 100, 100);
2 26 Feb 07 jari 347                     //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 348                     gridbag.setConstraints(exptGroupRadioButtons[j][i], constraints);
2 26 Feb 07 jari 349                     panel1.add(exptGroupRadioButtons[j][i]);
2 26 Feb 07 jari 350                 }
2 26 Feb 07 jari 351                 
2 26 Feb 07 jari 352                 buildConstraints(constraints, (numGroups + 1), i, 1, 1, 100, 100);
2 26 Feb 07 jari 353                 //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 354                 gridbag.setConstraints(notInGroupRadioButtons[i], constraints);
2 26 Feb 07 jari 355                 panel1.add(notInGroupRadioButtons[i]);
2 26 Feb 07 jari 356             }
2 26 Feb 07 jari 357             
2 26 Feb 07 jari 358             int maxLabelWidth = 0;
2 26 Feb 07 jari 359             
2 26 Feb 07 jari 360             for (int i = 0; i < expLabels.length; i++) {
2 26 Feb 07 jari 361                 if (expLabels[i].getPreferredSize().getWidth() > maxLabelWidth) {
2 26 Feb 07 jari 362                     maxLabelWidth = (int)Math.ceil(expLabels[i].getPreferredSize().getWidth());
2 26 Feb 07 jari 363                 }
2 26 Feb 07 jari 364             }
2 26 Feb 07 jari 365             
2 26 Feb 07 jari 366             JScrollPane scroll = new JScrollPane(panel1);
2 26 Feb 07 jari 367             scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 368             scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
2 26 Feb 07 jari 369             
2 26 Feb 07 jari 370             JPanel exptNameHeaderPanel = new JPanel();
2 26 Feb 07 jari 371             GridBagLayout exptHeaderGridbag = new GridBagLayout();
2 26 Feb 07 jari 372             //exptNameHeaderPanel.HEIGHT = panel1.getHeight();
2 26 Feb 07 jari 373             //System.out.println("panel1.preferredSise().height = " + panel1.getPreferredSize().height);
2 26 Feb 07 jari 374             exptNameHeaderPanel.setSize(50, panel1.getPreferredSize().height);
2 26 Feb 07 jari 375             exptNameHeaderPanel.setPreferredSize(new Dimension(maxLabelWidth + 10, panel1.getPreferredSize().height));
2 26 Feb 07 jari 376             exptNameHeaderPanel.setLayout(exptHeaderGridbag);
2 26 Feb 07 jari 377             //scroll.getRowHeader().setLayout(exptHeaderGridbag);
2 26 Feb 07 jari 378             
2 26 Feb 07 jari 379             
2 26 Feb 07 jari 380             for (int i = 0; i < expLabels.length; i++) {
2 26 Feb 07 jari 381                 buildConstraints(constraints, 0, i, 1, 1, 100, 100);
2 26 Feb 07 jari 382                 constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 383                 exptHeaderGridbag.setConstraints(expLabels[i], constraints);
2 26 Feb 07 jari 384                 exptNameHeaderPanel.add(expLabels[i]);
2 26 Feb 07 jari 385             }
2 26 Feb 07 jari 386             
2 26 Feb 07 jari 387             scroll.setRowHeaderView(exptNameHeaderPanel);
2 26 Feb 07 jari 388             
2 26 Feb 07 jari 389             buildConstraints(constraints, 0, 0, 1, 1, 100, 100);
2 26 Feb 07 jari 390             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 391             gridbag2.setConstraints(scroll, constraints);
2 26 Feb 07 jari 392             this.add(scroll);
2 26 Feb 07 jari 393             
2 26 Feb 07 jari 394         }
2 26 Feb 07 jari 395         
2 26 Feb 07 jari 396         public void reset() {
2 26 Feb 07 jari 397             for (int i = 0; i < exptNames.size(); i++) {
2 26 Feb 07 jari 398                 exptGroupRadioButtons[0][i].setSelected(true);
2 26 Feb 07 jari 399             }
2 26 Feb 07 jari 400         }
2 26 Feb 07 jari 401         
2 26 Feb 07 jari 402         
2 26 Feb 07 jari 403         public int[] getGroupAssignments() {
2 26 Feb 07 jari 404             int[] groupAssignments = new int[exptNames.size()];
2 26 Feb 07 jari 405             
2 26 Feb 07 jari 406             for (int i = 0; i < groupAssignments.length; i++) {
2 26 Feb 07 jari 407                 groupAssignments[i] = 0;
2 26 Feb 07 jari 408             }
2 26 Feb 07 jari 409             
2 26 Feb 07 jari 410             for (int i = 0; i < groupAssignments.length; i++) {
2 26 Feb 07 jari 411                 for (int j = 0; j < numGroups; j++) {
2 26 Feb 07 jari 412                     if (exptGroupRadioButtons[j][i].isSelected()) {
2 26 Feb 07 jari 413                         groupAssignments[i] = j + 1;
2 26 Feb 07 jari 414                         break;
2 26 Feb 07 jari 415                     }
2 26 Feb 07 jari 416                 }
2 26 Feb 07 jari 417             }
2 26 Feb 07 jari 418             
2 26 Feb 07 jari 419             return groupAssignments;
2 26 Feb 07 jari 420         }
2 26 Feb 07 jari 421         
2 26 Feb 07 jari 422         public void setGroupAssignments(int[] assignments) {
2 26 Feb 07 jari 423             for (int i = 0; i < assignments.length; i++) {
2 26 Feb 07 jari 424                 if (assignments[i] == 0) {
2 26 Feb 07 jari 425                     notInGroupRadioButtons[i].setSelected(true);
2 26 Feb 07 jari 426                 } else {
2 26 Feb 07 jari 427                     exptGroupRadioButtons[assignments[i] - 1][i].setSelected(true);
2 26 Feb 07 jari 428                 }
2 26 Feb 07 jari 429             }
2 26 Feb 07 jari 430         }
2 26 Feb 07 jari 431         
2 26 Feb 07 jari 432     }
2 26 Feb 07 jari 433     
2 26 Feb 07 jari 434     class PValuePanel extends JPanel {
2 26 Feb 07 jari 435         JRadioButton tDistButton, permutButton; // randomGroupsButton, allCombsButton;
2 26 Feb 07 jari 436         JLabel numPermsLabel;
2 26 Feb 07 jari 437         JTextField timesField, alphaInputField;
2 26 Feb 07 jari 438         //JButton permParamButton;
2 26 Feb 07 jari 439         
2 26 Feb 07 jari 440         PValuePanel() {
2 26 Feb 07 jari 441             // this.setBorder(new TitledBorder(new EtchedBorder(), "P-Value parameters"));
2 26 Feb 07 jari 442             this.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "P-Value Parameters", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 443             this.setBackground(Color.white);
2 26 Feb 07 jari 444             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 445             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 446             //constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 447             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 448             this.setLayout(gridbag);
2 26 Feb 07 jari 449             
2 26 Feb 07 jari 450             //permParamButton = new JButton("Permutation parameters");
2 26 Feb 07 jari 451             //permParamButton.setEnabled(false);
2 26 Feb 07 jari 452             
2 26 Feb 07 jari 453             ButtonGroup chooseP = new ButtonGroup();
2 26 Feb 07 jari 454             
2 26 Feb 07 jari 455             tDistButton = new JRadioButton("p-values based on F-distribution", true);
2 26 Feb 07 jari 456             tDistButton.setFocusPainted(false);
2 26 Feb 07 jari 457             tDistButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 458             tDistButton.setBackground(Color.white);
2 26 Feb 07 jari 459             
2 26 Feb 07 jari 460             numPermsLabel = new JLabel("Enter number of permutations");
2 26 Feb 07 jari 461             numPermsLabel.setEnabled(false);
2 26 Feb 07 jari 462             
2 26 Feb 07 jari 463             timesField = new JTextField("1000", 7);
2 26 Feb 07 jari 464             timesField.setEnabled(false);
2 26 Feb 07 jari 465             timesField.setBackground(Color.darkGray);
2 26 Feb 07 jari 466             
2 26 Feb 07 jari 467             tDistButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 468                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 469                     numPermsLabel.setEnabled(false);
2 26 Feb 07 jari 470                     timesField.setEnabled(false);
2 26 Feb 07 jari 471                     timesField.setBackground(Color.darkGray);                  
2 26 Feb 07 jari 472                     pAdjPanel.maxTButton.setEnabled(false);
2 26 Feb 07 jari 473                     pAdjPanel.minPButton.setEnabled(false);
2 26 Feb 07 jari 474                 }
2 26 Feb 07 jari 475             });
2 26 Feb 07 jari 476             
2 26 Feb 07 jari 477             chooseP.add(tDistButton);
2 26 Feb 07 jari 478             
2 26 Feb 07 jari 479             permutButton = new JRadioButton("p-values based on permutation:  ", false);
2 26 Feb 07 jari 480             permutButton.setFocusPainted(false);
2 26 Feb 07 jari 481             permutButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 482             permutButton.setBackground(Color.white);
2 26 Feb 07 jari 483             
2 26 Feb 07 jari 484             permutButton.addActionListener(new ActionListener() {
2 26 Feb 07 jari 485                 public void actionPerformed(ActionEvent evt) {
2 26 Feb 07 jari 486                     numPermsLabel.setEnabled(true);
2 26 Feb 07 jari 487                     timesField.setEnabled(true);
2 26 Feb 07 jari 488                     timesField.setBackground(Color.white);                  
2 26 Feb 07 jari 489                     //pAdjPanel.maxTButton.setEnabled(true);  //UNCOMMENT THIS WHEN MAXT METHOD HAS BEEN IMPLEMEMTED
2 26 Feb 07 jari 490                     //pAdjPanel.minPButton.setEnabled(true);  //UNCOMMENT THIS WHEN MINP METHOD HAS BEEN DEBUGGED                  
2 26 Feb 07 jari 491                 }                
2 26 Feb 07 jari 492             });
2 26 Feb 07 jari 493             
2 26 Feb 07 jari 494             chooseP.add(permutButton);
2 26 Feb 07 jari 495             
2 26 Feb 07 jari 496             
2 26 Feb 07 jari 497             //constraints.anchor = GridBagConstraints.CENTER;
2 26 Feb 07 jari 498             
2 26 Feb 07 jari 499             //numCombsLabel = new JLabel("                                       ");
2 26 Feb 07 jari 500             //numCombsLabel.setOpaque(false);
2 26 Feb 07 jari 501             /*
2 26 Feb 07 jari 502             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 503             buildConstraints(constraints, 1, 2, 1, 1, 0, 0);
2 26 Feb 07 jari 504             gridbag.setConstraints(numCombsLabel, constraints);
2 26 Feb 07 jari 505             this.add(numCombsLabel);
2 26 Feb 07 jari 506              */
2 26 Feb 07 jari 507             
2 26 Feb 07 jari 508             
2 26 Feb 07 jari 509             buildConstraints(constraints, 0, 0, 3, 1, 100, 30);
2 26 Feb 07 jari 510             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 511             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 512             gridbag.setConstraints(tDistButton, constraints);
2 26 Feb 07 jari 513             this.add(tDistButton);
2 26 Feb 07 jari 514             
2 26 Feb 07 jari 515             buildConstraints(constraints, 0, 1, 1, 1, 30, 30);
2 26 Feb 07 jari 516             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 517             gridbag.setConstraints(permutButton, constraints);
2 26 Feb 07 jari 518             this.add(permutButton);
2 26 Feb 07 jari 519             
2 26 Feb 07 jari 520             //JLabel numPermsLabel = new JLabel("Enter number of permutations");
2 26 Feb 07 jari 521             //numPermsLabel.setEnabled(false);
2 26 Feb 07 jari 522             buildConstraints(constraints, 1, 1, 1, 1, 30, 0);
2 26 Feb 07 jari 523             gridbag.setConstraints(numPermsLabel, constraints);
2 26 Feb 07 jari 524             this.add(numPermsLabel);
2 26 Feb 07 jari 525             
2 26 Feb 07 jari 526             buildConstraints(constraints, 2, 1, 1, 1, 40, 0);
2 26 Feb 07 jari 527             gridbag.setConstraints(timesField, constraints);
2 26 Feb 07 jari 528             this.add(timesField);
2 26 Feb 07 jari 529             
2 26 Feb 07 jari 530             JLabel alphaLabel = new JLabel("Enter critical p-value");
2 26 Feb 07 jari 531             buildConstraints(constraints, 0, 2, 2, 1, 60, 40);
2 26 Feb 07 jari 532             //constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 533             gridbag.setConstraints(alphaLabel, constraints);
2 26 Feb 07 jari 534             this.add(alphaLabel);
2 26 Feb 07 jari 535             
2 26 Feb 07 jari 536             alphaInputField = new JTextField("0.01", 7);
2 26 Feb 07 jari 537             buildConstraints(constraints, 1, 2, 1, 1, 40, 0);
2 26 Feb 07 jari 538             constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 539             gridbag.setConstraints(alphaInputField, constraints);
2 26 Feb 07 jari 540             this.add(alphaInputField);
2 26 Feb 07 jari 541         }
2 26 Feb 07 jari 542     }
2 26 Feb 07 jari 543     
2 26 Feb 07 jari 544     class PValueAdjustmentPanel extends JPanel {
2 26 Feb 07 jari 545         JRadioButton minPButton, maxTButton, justAlphaButton, stdBonfButton, adjBonfButton;
2 26 Feb 07 jari 546         PValueAdjustmentPanel() {
2 26 Feb 07 jari 547             //      this.setBorder(new TitledBorder(new EtchedBorder(), "Significance based on: "));
2 26 Feb 07 jari 548             this.setBorder(new TitledBorder(new EtchedBorder(EtchedBorder.LOWERED), "Alpha Corrections", TitledBorder.DEFAULT_JUSTIFICATION, TitledBorder.DEFAULT_POSITION, new Font("Dialog", Font.BOLD, 12), Color.black));
2 26 Feb 07 jari 549             this.setBackground(Color.white);
2 26 Feb 07 jari 550             GridBagLayout gridbag = new GridBagLayout();
2 26 Feb 07 jari 551             GridBagConstraints constraints = new GridBagConstraints();
2 26 Feb 07 jari 552             this.setLayout(gridbag);
2 26 Feb 07 jari 553             
2 26 Feb 07 jari 554             /*
2 26 Feb 07 jari 555             JLabel sigLabel = new JLabel("Significance based on: ");
2 26 Feb 07 jari 556             buildConstraints(constraints, 0, 0, 3, 1, 0, 50);
2 26 Feb 07 jari 557             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 558             gridbag.setConstraints(sigLabel, constraints);
2 26 Feb 07 jari 559             this.add(sigLabel);
2 26 Feb 07 jari 560              */
2 26 Feb 07 jari 561             
2 26 Feb 07 jari 562             ButtonGroup sigGroup = new ButtonGroup();
2 26 Feb 07 jari 563             
2 26 Feb 07 jari 564             justAlphaButton = new JRadioButton("just alpha (no correction)", true);
2 26 Feb 07 jari 565             justAlphaButton.setFocusPainted(false);
2 26 Feb 07 jari 566             justAlphaButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 567             justAlphaButton.setBackground(Color.white);
2 26 Feb 07 jari 568             sigGroup.add(justAlphaButton);
2 26 Feb 07 jari 569             
2 26 Feb 07 jari 570             stdBonfButton = new JRadioButton("standard Bonferroni correction", false);
2 26 Feb 07 jari 571             stdBonfButton.setEnabled(false);//enable this button when this option is implemented
2 26 Feb 07 jari 572             stdBonfButton.setFocusPainted(false);
2 26 Feb 07 jari 573             stdBonfButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 574             stdBonfButton.setBackground(Color.white);
2 26 Feb 07 jari 575             sigGroup.add(stdBonfButton);
2 26 Feb 07 jari 576             
2 26 Feb 07 jari 577             adjBonfButton = new JRadioButton("adjusted Bonferroni correction", false);
2 26 Feb 07 jari 578             adjBonfButton.setEnabled(false);//enable this button when this option is implemented
2 26 Feb 07 jari 579             adjBonfButton.setFocusPainted(false);
2 26 Feb 07 jari 580             adjBonfButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 581             adjBonfButton.setBackground(Color.white);
2 26 Feb 07 jari 582             sigGroup.add(adjBonfButton);
2 26 Feb 07 jari 583             
2 26 Feb 07 jari 584             minPButton = new JRadioButton("minP", false);
2 26 Feb 07 jari 585             minPButton.setEnabled(false);
2 26 Feb 07 jari 586             minPButton.setFocusPainted(false);
2 26 Feb 07 jari 587             minPButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 588             minPButton.setBackground(Color.white);
2 26 Feb 07 jari 589             sigGroup.add(minPButton);
2 26 Feb 07 jari 590             
2 26 Feb 07 jari 591             maxTButton = new JRadioButton("maxT", false);
2 26 Feb 07 jari 592             maxTButton.setEnabled(false);
2 26 Feb 07 jari 593             maxTButton.setFocusPainted(false);
2 26 Feb 07 jari 594             maxTButton.setForeground(UIManager.getColor("Label.foreground"));
2 26 Feb 07 jari 595             maxTButton.setBackground(Color.white);
2 26 Feb 07 jari 596             sigGroup.add(maxTButton);
2 26 Feb 07 jari 597             
2 26 Feb 07 jari 598             buildConstraints(constraints, 0, 0, 1, 1, 33, 50);
2 26 Feb 07 jari 599             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 600             gridbag.setConstraints(justAlphaButton, constraints);
2 26 Feb 07 jari 601             this.add(justAlphaButton);
2 26 Feb 07 jari 602             
2 26 Feb 07 jari 603             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 604             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 605             gridbag.setConstraints(stdBonfButton, constraints);
2 26 Feb 07 jari 606             this.add(stdBonfButton);
2 26 Feb 07 jari 607             
2 26 Feb 07 jari 608             buildConstraints(constraints, 2, 0, 1, 1, 34, 0);
2 26 Feb 07 jari 609             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 610             gridbag.setConstraints(adjBonfButton, constraints);
2 26 Feb 07 jari 611             this.add(adjBonfButton);
2 26 Feb 07 jari 612             
2 26 Feb 07 jari 613             JPanel westfallYoungPanel = new JPanel();
2 26 Feb 07 jari 614             westfallYoungPanel.setBackground(Color.white);
2 26 Feb 07 jari 615             westfallYoungPanel.setBorder(new EtchedBorder());
2 26 Feb 07 jari 616             GridBagLayout grid2 = new GridBagLayout();
2 26 Feb 07 jari 617             westfallYoungPanel.setLayout(grid2);
2 26 Feb 07 jari 618             
2 26 Feb 07 jari 619             JLabel stepDownLabel = new JLabel("Step-down Westfall and Young methods (for permutations only): ");
2 26 Feb 07 jari 620             buildConstraints(constraints, 0, 0, 1, 1, 34, 100);
2 26 Feb 07 jari 621             //buildConstraints(constraints, 0, 1, 1, 1, 34, 50);
2 26 Feb 07 jari 622             ////constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 623             //constraints.anchor = GridBagConstraints.EAST;
2 26 Feb 07 jari 624             //gridbag.setConstraints(stepDownLabel, constraints);
2 26 Feb 07 jari 625             grid2.setConstraints(stepDownLabel, constraints);
2 26 Feb 07 jari 626             //this.add(stepDownLabel);
2 26 Feb 07 jari 627             westfallYoungPanel.add(stepDownLabel);
2 26 Feb 07 jari 628             
2 26 Feb 07 jari 629             //buildConstraints(constraints, 1, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 630             buildConstraints(constraints, 1, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 631             ////constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 632             //constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 633             //gridbag.setConstraints(minPButton, constraints);
2 26 Feb 07 jari 634             grid2.setConstraints(minPButton, constraints);
2 26 Feb 07 jari 635             //this.add(minPButton);
2 26 Feb 07 jari 636             westfallYoungPanel.add(minPButton);
2 26 Feb 07 jari 637             
2 26 Feb 07 jari 638             
2 26 Feb 07 jari 639             //buildConstraints(constraints, 2, 1, 1, 1, 33, 0);
2 26 Feb 07 jari 640             buildConstraints(constraints, 2, 0, 1, 1, 33, 0);
2 26 Feb 07 jari 641             ////constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 642             //constraints.anchor = GridBagConstraints.WEST;
2 26 Feb 07 jari 643             //gridbag.setConstraints(maxTButton, constraints);
2 26 Feb 07 jari 644             grid2.setConstraints(maxTButton, constraints);
2 26 Feb 07 jari 645             //this.add(maxTButton);
2 26 Feb 07 jari 646             westfallYoungPanel.add(maxTButton);
2 26 Feb 07 jari 647             
2 26 Feb 07 jari 648             buildConstraints(constraints, 0, 1, 3, 1, 100, 50);
2 26 Feb 07 jari 649             //constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 650             gridbag.setConstraints(westfallYoungPanel, constraints);
2 26 Feb 07 jari 651             this.add(westfallYoungPanel);
2 26 Feb 07 jari 652             /*
2 26 Feb 07 jari 653             JButton sButton = new JButton("significancePanel");
2 26 Feb 07 jari 654             buildConstraints(constraints, 0, 0, 1, 1, 100, 100);
2 26 Feb 07 jari 655             constraints.fill = GridBagConstraints.BOTH;
2 26 Feb 07 jari 656             gridbag.setConstraints(sButton, constraints);
2 26 Feb 07 jari 657             this.add(sButton);
2 26 Feb 07 jari 658              */
2 26 Feb 07 jari 659             
2 26 Feb 07 jari 660         }
2 26 Feb 07 jari 661     }
2 26 Feb 07 jari 662     
2 26 Feb 07 jari 663     public boolean allCellsHaveOneSample() {
2 26 Feb 07 jari 664         return this.oneSamplePerCell;
2 26 Feb 07 jari 665     }
2 26 Feb 07 jari 666     
2 26 Feb 07 jari 667     public boolean usePerms() {
2 26 Feb 07 jari 668         return pPanel.permutButton.isSelected();
2 26 Feb 07 jari 669     }
2 26 Feb 07 jari 670     
2 26 Feb 07 jari 671     public float getAlpha() {
2 26 Feb 07 jari 672         return Float.parseFloat(pPanel.alphaInputField.getText());
2 26 Feb 07 jari 673     }
2 26 Feb 07 jari 674     
2 26 Feb 07 jari 675     public int getNumPerms() {
2 26 Feb 07 jari 676         return Integer.parseInt(pPanel.timesField.getText());
2 26 Feb 07 jari 677     }
2 26 Feb 07 jari 678     
2 26 Feb 07 jari 679     public boolean isBalancedDesign() {
2 26 Feb 07 jari 680         boolean balanced = true;
2 26 Feb 07 jari 681         Vector[][] bothFactorAssignments = getBothFactorAssignments();     
2 26 Feb 07 jari 682         int[] cellSizes =new int[bothFactorAssignments.length*bothFactorAssignments[0].length];
2 26 Feb 07 jari 683         //System.out.println("cellSizes.length = " + cellSizes.length);
2 26 Feb 07 jari 684         int cellCounter = 0;
2 26 Feb 07 jari 685         for (int i = 0; i < bothFactorAssignments.length; i++) {
2 26 Feb 07 jari 686             for (int j = 0; j < bothFactorAssignments[i].length; j++) {
2 26 Feb 07 jari 687                 cellSizes[cellCounter] = bothFactorAssignments[i][j].size();
2 26 Feb 07 jari 688                 cellCounter++;
2 26 Feb 07 jari 689             }
2 26 Feb 07 jari 690         } 
2 26 Feb 07 jari 691         
2 26 Feb 07 jari 692         int numPerCell = cellSizes[0];
2 26 Feb 07 jari 693         
2 26 Feb 07 jari 694         for (int i = 1; i < cellSizes.length; i++) {
2 26 Feb 07 jari 695             if (cellSizes[i] != numPerCell) {
2 26 Feb 07 jari 696                 balanced = false;
2 26 Feb 07 jari 697                 break;
2 26 Feb 07 jari 698             }
2 26 Feb 07 jari 699         }
2 26 Feb 07 jari 700         
2 26 Feb 07 jari 701         return balanced;
2 26 Feb 07 jari 702     }
2 26 Feb 07 jari 703     
2 26 Feb 07 jari 704     public int getAdjustmentMethod() {
2 26 Feb 07 jari 705         if (pAdjPanel.justAlphaButton.isSelected()) {
2 26 Feb 07 jari 706             return TFAInitBox2.JUST_ALPHA;
2 26 Feb 07 jari 707         } else if (pAdjPanel.stdBonfButton.isSelected()) {
2 26 Feb 07 jari 708             return TFAInitBox2.STD_BONFERRONI;
2 26 Feb 07 jari 709         } else if (pAdjPanel.adjBonfButton.isSelected()){
2 26 Feb 07 jari 710             return TFAInitBox2.ADJ_BONFERRONI;
2 26 Feb 07 jari 711         } else if (pAdjPanel.maxTButton.isSelected()) {
2 26 Feb 07 jari 712             return TFAInitBox2.MAX_T;
2 26 Feb 07 jari 713         } else if (pAdjPanel.minPButton.isSelected()) {
2 26 Feb 07 jari 714             return TFAInitBox2.MIN_P;
2 26 Feb 07 jari 715         } else {
2 26 Feb 07 jari 716             return -1;
2 26 Feb 07 jari 717         }
2 26 Feb 07 jari 718     }    
2 26 Feb 07 jari 719     
2 26 Feb 07 jari 720     public boolean drawTrees() {
2 26 Feb 07 jari 721         return this.hclOpsPanel.isHCLSelected();
2 26 Feb 07 jari 722     }
2 26 Feb 07 jari 723     
2 26 Feb 07 jari 724     public boolean drawSigTreesOnly() {
2 26 Feb 07 jari 725         return hclOpsPanel.drawSigTreesOnly();
2 26 Feb 07 jari 726     }    
2 26 Feb 07 jari 727     
2 26 Feb 07 jari 728     public boolean isOkPressed() {
2 26 Feb 07 jari 729         return okPressed;
2 26 Feb 07 jari 730     }
2 26 Feb 07 jari 731     
2 26 Feb 07 jari 732     public void setVisible(boolean visible) {
2 26 Feb 07 jari 733         Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
2 26 Feb 07 jari 734         setLocation((screenSize.width - getSize().width)/2, (screenSize.height - getSize().height)/2);
2 26 Feb 07 jari 735         super.setVisible(visible);
2 26 Feb 07 jari 736         if (visible) {
2 26 Feb 07 jari 737             //bPanel.okButton.requestFocus(); //UNCOMMMENT THIS LATER
2 26 Feb 07 jari 738         }
2 26 Feb 07 jari 739     }
2 26 Feb 07 jari 740
2 26 Feb 07 jari 741     
2 26 Feb 07 jari 742     public class EventListener extends WindowAdapter implements ActionListener{
2 26 Feb 07 jari 743         
2 26 Feb 07 jari 744         public void actionPerformed(ActionEvent ae){
2 26 Feb 07 jari 745             
2 26 Feb 07 jari 746             String command = ae.getActionCommand();
2 26 Feb 07 jari 747             if(command.equals("ok-command")){
2 26 Feb 07 jari 748                 Vector[][] bothFactorAssignments = getBothFactorAssignments();
2 26 Feb 07 jari 749                 int[] cellSizes =new int[bothFactorAssignments.length*bothFactorAssignments[0].length];
2 26 Feb 07 jari 750                 //System.out.println("cellSizes.length = " + cellSizes.length);
2 26 Feb 07 jari 751                 int cellCounter = 0;
2 26 Feb 07 jari 752                 for (int i = 0; i < bothFactorAssignments.length; i++) {
2 26 Feb 07 jari 753                     for (int j = 0; j < bothFactorAssignments[i].length; j++) {
2 26 Feb 07 jari 754                         cellSizes[cellCounter] = bothFactorAssignments[i][j].size();
2 26 Feb 07 jari 755                         cellCounter++;
2 26 Feb 07 jari 756                     }
2 26 Feb 07 jari 757                 }
2 26 Feb 07 jari 758                 if (cellSizes[0] == 1) {
2 26 Feb 07 jari 759                     boolean allOne = true;
2 26 Feb 07 jari 760                     for (int i = 1; i < cellSizes.length; i++) {
2 26 Feb 07 jari 761                         if (cellSizes[i] != 1) {
2 26 Feb 07 jari 762                             allOne = false;
2 26 Feb 07 jari 763                             //oneSamplePerCell = true;
2 26 Feb 07 jari 764                             break;
2 26 Feb 07 jari 765                         }
2 26 Feb 07 jari 766                     }
2 26 Feb 07 jari 767                     if (!allOne) {
2 26 Feb 07 jari 768                         JOptionPane.showMessageDialog(null, "All factor combinations must contain more than one sample, or else they must all contain exactly one sample each", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 769                         okPressed = false;
2 26 Feb 07 jari 770                         return;
2 26 Feb 07 jari 771                     } else {
2 26 Feb 07 jari 772                         oneSamplePerCell = true;
2 26 Feb 07 jari 773                     }
2 26 Feb 07 jari 774                 } else {
2 26 Feb 07 jari 775                     for (int i = 0; i < cellSizes.length; i++) {
2 26 Feb 07 jari 776                         if (cellSizes[i] < 2) {
2 26 Feb 07 jari 777                             JOptionPane.showMessageDialog(null, "All factor combinations must contain more than one sample, or else they must all contain exactly one sample each", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 778                             okPressed = false;
2 26 Feb 07 jari 779                             return;                            
2 26 Feb 07 jari 780                         }
2 26 Feb 07 jari 781                     }
2 26 Feb 07 jari 782                 }
2 26 Feb 07 jari 783                 
2 26 Feb 07 jari 784                 if (usePerms()) {
2 26 Feb 07 jari 785                     try {
2 26 Feb 07 jari 786                         int numPerms = getNumPerms();
2 26 Feb 07 jari 787                         if (numPerms <= 0) {
2 26 Feb 07 jari 788                             JOptionPane.showMessageDialog(null, "Number of permutations should be an integer > 0", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 789                             okPressed = false;
2 26 Feb 07 jari 790                             return;                         
2 26 Feb 07 jari 791                         }
2 26 Feb 07 jari 792                         } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 793                             JOptionPane.showMessageDialog(null, "Number of permutations should be an integer > 0", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 794                             okPressed = false;
2 26 Feb 07 jari 795                             return;
2 26 Feb 07 jari 796                         }
2 26 Feb 07 jari 797                 }
2 26 Feb 07 jari 798                 
2 26 Feb 07 jari 799                 try {
2 26 Feb 07 jari 800                     float alpha = getAlpha();
2 26 Feb 07 jari 801                     if ((alpha <= 0) || (alpha >= 1)) {
2 26 Feb 07 jari 802                         JOptionPane.showMessageDialog(null, "Critical p-value should be between 0 and 1", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 803                         okPressed = false;
2 26 Feb 07 jari 804                         return;                        
2 26 Feb 07 jari 805                     }
2 26 Feb 07 jari 806                 } catch (NumberFormatException nfe) {
2 26 Feb 07 jari 807                     JOptionPane.showMessageDialog(null, "Critical p-value should be between 0 and 1", "Error", JOptionPane.ERROR_MESSAGE);
2 26 Feb 07 jari 808                     okPressed = false;
2 26 Feb 07 jari 809                     return;                    
2 26 Feb 07 jari 810                 }
2 26 Feb 07 jari 811                 
2 26 Feb 07 jari 812                 okPressed = true;
2 26 Feb 07 jari 813                 hide();
2 26 Feb 07 jari 814                 dispose();                
2 26 Feb 07 jari 815             }
2 26 Feb 07 jari 816             else if(command.equals("reset-command")){
2 26 Feb 07 jari 817                 okPressed = false;
2 26 Feb 07 jari 818                 gPanel.reset();
2 26 Feb 07 jari 819                 return;
2 26 Feb 07 jari 820             }
2 26 Feb 07 jari 821             else if(command.equals("cancel-command")){
2 26 Feb 07 jari 822                 okPressed = false;
2 26 Feb 07 jari 823                 setVisible(false);
2 26 Feb 07 jari 824                 dispose();
2 26 Feb 07 jari 825             }
2 26 Feb 07 jari 826             else if(command.equals("info-command")){
2 26 Feb 07 jari 827             }
2 26 Feb 07 jari 828         }
2 26 Feb 07 jari 829         
2 26 Feb 07 jari 830     }
2 26 Feb 07 jari 831     
2 26 Feb 07 jari 832     public int[] getFactorAAssignments() {
2 26 Feb 07 jari 833         return gPanel.factorAPanel.getGroupAssignments();
2 26 Feb 07 jari 834     }
2 26 Feb 07 jari 835     
2 26 Feb 07 jari 836     public int[] getFactorBAssignments() {
2 26 Feb 07 jari 837         return gPanel.factorBPanel.getGroupAssignments();
2 26 Feb 07 jari 838     }   
2 26 Feb 07 jari 839     
2 26 Feb 07 jari 840     public Vector[][] getBothFactorAssignments() {
2 26 Feb 07 jari 841         Vector[][] bothFactorAssignments = new Vector[numFactorLevels[0]][numFactorLevels[1]];
2 26 Feb 07 jari 842         
2 26 Feb 07 jari 843         for (int i = 0; i < bothFactorAssignments.length; i++) {
2 26 Feb 07 jari 844             for (int j = 0; j < bothFactorAssignments[i].length; j++) {
2 26 Feb 07 jari 845                 bothFactorAssignments[i][j] = new Vector();
2 26 Feb 07 jari 846             }
2 26 Feb 07 jari 847         }
2 26 Feb 07 jari 848         
2 26 Feb 07 jari 849         int[] factorAAssgn = getFactorAAssignments();
2 26 Feb 07 jari 850         int[] factorBAssgn = getFactorBAssignments();
2 26 Feb 07 jari 851         
2 26 Feb 07 jari 852         for (int i = 0; i < factorAAssgn.length; i++) {
2 26 Feb 07 jari 853             if ((factorAAssgn[i] != 0)&&(factorBAssgn[i] != 0)) {
2 26 Feb 07 jari 854                 bothFactorAssignments[factorAAssgn[i] - 1][factorBAssgn[i] - 1].add(new Integer(i));
2 26 Feb 07 jari 855             }
2 26 Feb 07 jari 856         }
2 26 Feb 07 jari 857         
2 26 Feb 07 jari 858         return bothFactorAssignments;
2 26 Feb 07 jari 859     }
2 26 Feb 07 jari 860 }

Generated on Thu Jul 20 09:29:14 2023 (UTC) by svndigest 0.11.2pre (dev build 1672)