mev-4.0.01/source/org/tigr/microarray/mev/cgh/CGHAlgorithms/AlterationsComparator/CompareExperiments.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2  * CompareExperiments.java
2 26 Feb 07 jari 3  *
2 26 Feb 07 jari 4  * Created on November 22, 2003, 4:05 AM
2 26 Feb 07 jari 5  */
2 26 Feb 07 jari 6
2 26 Feb 07 jari 7 package org.tigr.microarray.mev.cgh.CGHAlgorithms.AlterationsComparator;
2 26 Feb 07 jari 8
2 26 Feb 07 jari 9 import java.util.Vector;
2 26 Feb 07 jari 10 import java.util.ArrayList;
2 26 Feb 07 jari 11 import javax.swing.JOptionPane;
2 26 Feb 07 jari 12 import javax.swing.tree.DefaultMutableTreeNode;
2 26 Feb 07 jari 13
2 26 Feb 07 jari 14 import org.tigr.microarray.mev.ISlideData;
2 26 Feb 07 jari 15 import org.tigr.microarray.mev.cgh.CGHAlgorithms.NumberOfAlterations.NumberOfAlterationsCalculator;
2 26 Feb 07 jari 16 import org.tigr.microarray.mev.cgh.CGHDataGenerator.ComparisonFlankingRegionCalculator;
2 26 Feb 07 jari 17 import org.tigr.microarray.mev.cgh.CGHDataObj.ICGHDataRegion;
2 26 Feb 07 jari 18 import org.tigr.microarray.mev.cgh.CGHGuiObj.AlgorithmResultsViewers.NumberOfAlterationsViewers.AlterationParametersViewer;
2 26 Feb 07 jari 19 import org.tigr.microarray.mev.cgh.CGHGuiObj.AlgorithmResultsViewers.NumberOfAlterationsViewers.DataRegionsDataModel;
2 26 Feb 07 jari 20 import org.tigr.microarray.mev.cgh.CGHGuiObj.AlgorithmResultsViewers.NumberOfAlterationsViewers.NumberOfAlterationsViewer;
2 26 Feb 07 jari 21 import org.tigr.microarray.mev.cgh.CGHGuiObj.GuiUtil.GroupExperimentsPanel;
2 26 Feb 07 jari 22 import org.tigr.microarray.mev.cluster.algorithm.AbortException;
2 26 Feb 07 jari 23 import org.tigr.microarray.mev.cluster.algorithm.AlgorithmException;
2 26 Feb 07 jari 24 import org.tigr.microarray.mev.cluster.gui.ICGHCloneValueMenu;
2 26 Feb 07 jari 25 import org.tigr.microarray.mev.cluster.gui.IData;
2 26 Feb 07 jari 26 import org.tigr.microarray.mev.cluster.gui.IFramework;
2 26 Feb 07 jari 27 import org.tigr.microarray.mev.cluster.gui.IViewer;
2 26 Feb 07 jari 28 import org.tigr.microarray.mev.cluster.gui.LeafInfo;
2 26 Feb 07 jari 29
2 26 Feb 07 jari 30 /**
2 26 Feb 07 jari 31  *
2 26 Feb 07 jari 32  * @author  Adam Margolin
2 26 Feb 07 jari 33  * @author Raktim Sinha
2 26 Feb 07 jari 34  */
2 26 Feb 07 jari 35 public class CompareExperiments extends NumberOfAlterationsCalculator {
2 26 Feb 07 jari 36     //MultipleArrayData data;
2 26 Feb 07 jari 37   IData data;
2 26 Feb 07 jari 38     int[] deletionsAOnly, deletionsBOnly, deletionsAandB, amplificationsAOnly, amplificationsBOnly, amplificationsAandB;
2 26 Feb 07 jari 39     String exprA;
2 26 Feb 07 jari 40     String exprB;
2 26 Feb 07 jari 41
2 26 Feb 07 jari 42     /** Creates a new instance of CompareExperiments */
2 26 Feb 07 jari 43     public CompareExperiments() {
2 26 Feb 07 jari 44     }
2 26 Feb 07 jari 45
2 26 Feb 07 jari 46     /** This method should return a tree with calculation results or
2 26 Feb 07 jari 47      * null, if analysis start was canceled.
2 26 Feb 07 jari 48      *
2 26 Feb 07 jari 49      * @param framework the reference to <code>IFramework</code> implementation,
2 26 Feb 07 jari 50      *        which is used to obtain an initial analysis data and parameters.
2 26 Feb 07 jari 51      * @throws AlgorithmException if calculation was failed.
2 26 Feb 07 jari 52      * @throws AbortException if calculation was canceled.
2 26 Feb 07 jari 53      * @see IFramework
2 26 Feb 07 jari 54      */
2 26 Feb 07 jari 55     public DefaultMutableTreeNode execute(IFramework framework) throws AlgorithmException {
2 26 Feb 07 jari 56         ComparisonFlankingRegionCalculator frCalc = new ComparisonFlankingRegionCalculator();
2 26 Feb 07 jari 57         this.framework = framework;
2 26 Feb 07 jari 58         this.data = framework.getData();
2 26 Feb 07 jari 59
2 26 Feb 07 jari 60         ExperimentsComparatorInitDlg initDlg = new ExperimentsComparatorInitDlg(framework.getFrame(), data.getFeaturesList());
2 26 Feb 07 jari 61         if(initDlg.showModal() != JOptionPane.OK_OPTION){
2 26 Feb 07 jari 62             return null;
2 26 Feb 07 jari 63         }
2 26 Feb 07 jari 64
2 26 Feb 07 jari 65         GroupExperimentsPanel gPanel = initDlg.getGroupExperimentsPanel();
2 26 Feb 07 jari 66         int[] groupAssignments = gPanel.getGroupAssignments();
2 26 Feb 07 jari 67
2 26 Feb 07 jari 68         //this.nodeName = data.getSampleName(groupAssignments[0]) + " vs. " + data.getSampleName(groupAssignments[1]);
2 26 Feb 07 jari 69         this.nodeName = "CompareExperiments";
2 26 Feb 07 jari 70         this.exprA = data.getSampleName(groupAssignments[0]);
2 26 Feb 07 jari 71         this.exprB = data.getSampleName(groupAssignments[1]);
2 26 Feb 07 jari 72
2 26 Feb 07 jari 73         DefaultMutableTreeNode root = new DefaultMutableTreeNode(nodeName);
2 26 Feb 07 jari 74
2 26 Feb 07 jari 75         TwoExperimentAlterationComparator comparator = new TwoExperimentAlterationComparator();
2 26 Feb 07 jari 76         comparator.compareExperiments(this.data, groupAssignments[0], groupAssignments[1], TwoExperimentAlterationComparator.DELETION);
2 26 Feb 07 jari 77
2 26 Feb 07 jari 78         DefaultMutableTreeNode deletionsNode = new DefaultMutableTreeNode("Deletions");
2 26 Feb 07 jari 79
2 26 Feb 07 jari 80         DefaultMutableTreeNode cloneDeletionsNode = new DefaultMutableTreeNode("Clone Deletions");
2 26 Feb 07 jari 81         deletionsAOnly = comparator.getAOnly();
2 26 Feb 07 jari 82         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(deletionsAOnly))));
2 26 Feb 07 jari 83         deletionsBOnly = comparator.getBOnly();
2 26 Feb 07 jari 84         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(deletionsBOnly))));
2 26 Feb 07 jari 85         deletionsAandB = comparator.getAAndB();
2 26 Feb 07 jari 86         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(deletionsAandB))));
2 26 Feb 07 jari 87
2 26 Feb 07 jari 88         DefaultMutableTreeNode regionDeletionsNode = new DefaultMutableTreeNode("Region Amplifications");
2 26 Feb 07 jari 89         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAOnly(), comparator.getBOnly(), groupAssignments[0])))));
2 26 Feb 07 jari 90         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getBOnly(), comparator.getAOnly(), groupAssignments[1])))));
2 26 Feb 07 jari 91         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAAndB(), null, groupAssignments)))));
2 26 Feb 07 jari 92
2 26 Feb 07 jari 93         deletionsNode.add(cloneDeletionsNode);
2 26 Feb 07 jari 94         deletionsNode.add(regionDeletionsNode);
2 26 Feb 07 jari 95
2 26 Feb 07 jari 96         root.add(deletionsNode);
2 26 Feb 07 jari 97
2 26 Feb 07 jari 98         comparator.compareExperiments(this.data, groupAssignments[0], groupAssignments[1], TwoExperimentAlterationComparator.AMPLIFICATION);
2 26 Feb 07 jari 99
2 26 Feb 07 jari 100         DefaultMutableTreeNode amplificationsNode = new DefaultMutableTreeNode("Amplifications");
2 26 Feb 07 jari 101
2 26 Feb 07 jari 102         DefaultMutableTreeNode cloneAmplificationsNode = new DefaultMutableTreeNode("Clone Amplifications");
2 26 Feb 07 jari 103         amplificationsAOnly = comparator.getAOnly();
2 26 Feb 07 jari 104         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(amplificationsAOnly))));
2 26 Feb 07 jari 105         amplificationsBOnly = comparator.getBOnly();
2 26 Feb 07 jari 106         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(amplificationsBOnly))));
2 26 Feb 07 jari 107         amplificationsAandB = comparator.getAAndB();
2 26 Feb 07 jari 108         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(amplificationsAandB))));
2 26 Feb 07 jari 109
2 26 Feb 07 jari 110         DefaultMutableTreeNode regionAmplificationsNode = new DefaultMutableTreeNode("Region Amplifications");
2 26 Feb 07 jari 111         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAOnly(), comparator.getBOnly(), groupAssignments[0])))));
2 26 Feb 07 jari 112         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getBOnly(), comparator.getAOnly(), groupAssignments[1])))));
2 26 Feb 07 jari 113         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAAndB(), null, groupAssignments)))));
2 26 Feb 07 jari 114
2 26 Feb 07 jari 115         amplificationsNode.add(cloneAmplificationsNode);
2 26 Feb 07 jari 116         amplificationsNode.add(regionAmplificationsNode);
2 26 Feb 07 jari 117
2 26 Feb 07 jari 118         root.add(amplificationsNode);
2 26 Feb 07 jari 119
2 26 Feb 07 jari 120         addGeneralInfo(root);
2 26 Feb 07 jari 121         return root;
2 26 Feb 07 jari 122     }
2 26 Feb 07 jari 123     
2 26 Feb 07 jari 124     /**
2 26 Feb 07 jari 125      * Raktim 4/27
2 26 Feb 07 jari 126      * Added for State Saving
2 26 Feb 07 jari 127      * @param framework
2 26 Feb 07 jari 128      * @param groupAssignments
2 26 Feb 07 jari 129      * @return
2 26 Feb 07 jari 130      * @throws AlgorithmException
2 26 Feb 07 jari 131      */
2 26 Feb 07 jari 132     public DefaultMutableTreeNode execute(IFramework framework, int[] groupAssignments) throws AlgorithmException {
2 26 Feb 07 jari 133         ComparisonFlankingRegionCalculator frCalc = new ComparisonFlankingRegionCalculator();
2 26 Feb 07 jari 134         this.framework = framework;
2 26 Feb 07 jari 135         this.data = framework.getData();
2 26 Feb 07 jari 136
2 26 Feb 07 jari 137         //this.nodeName = data.getSampleName(groupAssignments[0]) + " vs. " + data.getSampleName(groupAssignments[1]);
2 26 Feb 07 jari 138         this.nodeName = "CompareExperiments";
2 26 Feb 07 jari 139         this.exprA = data.getSampleName(groupAssignments[0]);
2 26 Feb 07 jari 140         this.exprB = data.getSampleName(groupAssignments[1]);
2 26 Feb 07 jari 141
2 26 Feb 07 jari 142         DefaultMutableTreeNode root = new DefaultMutableTreeNode(nodeName);
2 26 Feb 07 jari 143
2 26 Feb 07 jari 144         TwoExperimentAlterationComparator comparator = new TwoExperimentAlterationComparator();
2 26 Feb 07 jari 145         comparator.compareExperiments(this.data, groupAssignments[0], groupAssignments[1], TwoExperimentAlterationComparator.DELETION);
2 26 Feb 07 jari 146
2 26 Feb 07 jari 147         DefaultMutableTreeNode deletionsNode = new DefaultMutableTreeNode("Deletions");
2 26 Feb 07 jari 148
2 26 Feb 07 jari 149         DefaultMutableTreeNode cloneDeletionsNode = new DefaultMutableTreeNode("Clone Deletions");
2 26 Feb 07 jari 150         deletionsAOnly = comparator.getAOnly();
2 26 Feb 07 jari 151         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(deletionsAOnly))));
2 26 Feb 07 jari 152         deletionsBOnly = comparator.getBOnly();
2 26 Feb 07 jari 153         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(deletionsBOnly))));
2 26 Feb 07 jari 154         deletionsAandB = comparator.getAAndB();
2 26 Feb 07 jari 155         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(deletionsAandB))));
2 26 Feb 07 jari 156
2 26 Feb 07 jari 157         DefaultMutableTreeNode regionDeletionsNode = new DefaultMutableTreeNode("Region Amplifications");
2 26 Feb 07 jari 158         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAOnly(), comparator.getBOnly(), groupAssignments[0])))));
2 26 Feb 07 jari 159         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getBOnly(), comparator.getAOnly(), groupAssignments[1])))));
2 26 Feb 07 jari 160         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAAndB(), null, groupAssignments)))));
2 26 Feb 07 jari 161
2 26 Feb 07 jari 162         deletionsNode.add(cloneDeletionsNode);
2 26 Feb 07 jari 163         deletionsNode.add(regionDeletionsNode);
2 26 Feb 07 jari 164
2 26 Feb 07 jari 165         root.add(deletionsNode);
2 26 Feb 07 jari 166
2 26 Feb 07 jari 167         comparator.compareExperiments(this.data, groupAssignments[0], groupAssignments[1], TwoExperimentAlterationComparator.AMPLIFICATION);
2 26 Feb 07 jari 168
2 26 Feb 07 jari 169         DefaultMutableTreeNode amplificationsNode = new DefaultMutableTreeNode("Amplifications");
2 26 Feb 07 jari 170
2 26 Feb 07 jari 171         DefaultMutableTreeNode cloneAmplificationsNode = new DefaultMutableTreeNode("Clone Amplifications");
2 26 Feb 07 jari 172         amplificationsAOnly = comparator.getAOnly();
2 26 Feb 07 jari 173         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(amplificationsAOnly))));
2 26 Feb 07 jari 174         amplificationsBOnly = comparator.getBOnly();
2 26 Feb 07 jari 175         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(amplificationsBOnly))));
2 26 Feb 07 jari 176         amplificationsAandB = comparator.getAAndB();
2 26 Feb 07 jari 177         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(amplificationsAandB))));
2 26 Feb 07 jari 178
2 26 Feb 07 jari 179         DefaultMutableTreeNode regionAmplificationsNode = new DefaultMutableTreeNode("Region Amplifications");
2 26 Feb 07 jari 180         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAOnly(), comparator.getBOnly(), groupAssignments[0])))));
2 26 Feb 07 jari 181         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getBOnly(), comparator.getAOnly(), groupAssignments[1])))));
2 26 Feb 07 jari 182         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAAndB(), null, groupAssignments)))));
2 26 Feb 07 jari 183
2 26 Feb 07 jari 184         amplificationsNode.add(cloneAmplificationsNode);
2 26 Feb 07 jari 185         amplificationsNode.add(regionAmplificationsNode);
2 26 Feb 07 jari 186
2 26 Feb 07 jari 187         root.add(amplificationsNode);
2 26 Feb 07 jari 188
2 26 Feb 07 jari 189         addGeneralInfo(root);
2 26 Feb 07 jari 190         return root;
2 26 Feb 07 jari 191     }
2 26 Feb 07 jari 192
2 26 Feb 07 jari 193
2 26 Feb 07 jari 194     /**
2 26 Feb 07 jari 195      * Old UNUSED
2 26 Feb 07 jari 196      */
2 26 Feb 07 jari 197     public DefaultMutableTreeNode execute2(IFramework framework) throws AlgorithmException {
2 26 Feb 07 jari 198         ComparisonFlankingRegionCalculator frCalc = new ComparisonFlankingRegionCalculator();
2 26 Feb 07 jari 199         this.framework = framework;
2 26 Feb 07 jari 200         this.data = framework.getData();
2 26 Feb 07 jari 201
2 26 Feb 07 jari 202         ExperimentsComparatorInitDlg initDlg = new ExperimentsComparatorInitDlg(framework.getFrame(), data.getFeaturesList());
2 26 Feb 07 jari 203         if(initDlg.showModal() != JOptionPane.OK_OPTION){
2 26 Feb 07 jari 204             return null;
2 26 Feb 07 jari 205         }
2 26 Feb 07 jari 206
2 26 Feb 07 jari 207         GroupExperimentsPanel gPanel = initDlg.getGroupExperimentsPanel();
2 26 Feb 07 jari 208         int[] groupAssignments = gPanel.getGroupAssignments();
2 26 Feb 07 jari 209
2 26 Feb 07 jari 210         this.nodeName = data.getSampleName(groupAssignments[0]) + " vs. " + data.getSampleName(groupAssignments[1]);
2 26 Feb 07 jari 211
2 26 Feb 07 jari 212         DefaultMutableTreeNode root = new DefaultMutableTreeNode(nodeName);
2 26 Feb 07 jari 213         root.add(new DefaultMutableTreeNode(new LeafInfo("Parameters", createParametersViewer())));
2 26 Feb 07 jari 214
2 26 Feb 07 jari 215         TwoExperimentAlterationComparator comparator = new TwoExperimentAlterationComparator();
2 26 Feb 07 jari 216         comparator.compareExperiments(this.data, groupAssignments[0], groupAssignments[1], TwoExperimentAlterationComparator.DELETION);
2 26 Feb 07 jari 217
2 26 Feb 07 jari 218         DefaultMutableTreeNode deletionsNode = new DefaultMutableTreeNode("Deletions");
2 26 Feb 07 jari 219
2 26 Feb 07 jari 220         DefaultMutableTreeNode cloneDeletionsNode = new DefaultMutableTreeNode("Clone Deletions");
2 26 Feb 07 jari 221         deletionsAOnly = comparator.getAOnly();
2 26 Feb 07 jari 222         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(deletionsAOnly))));
2 26 Feb 07 jari 223         deletionsBOnly = comparator.getBOnly();
2 26 Feb 07 jari 224         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(deletionsBOnly))));
2 26 Feb 07 jari 225         deletionsAandB = comparator.getAAndB();
2 26 Feb 07 jari 226         cloneDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(deletionsAandB))));
2 26 Feb 07 jari 227
2 26 Feb 07 jari 228         DefaultMutableTreeNode regionDeletionsNode = new DefaultMutableTreeNode("Region Amplifications");
2 26 Feb 07 jari 229         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAOnly(), comparator.getBOnly(), groupAssignments[0])))));
2 26 Feb 07 jari 230         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getBOnly(), comparator.getAOnly(), groupAssignments[1])))));
2 26 Feb 07 jari 231         regionDeletionsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAAndB(), null, groupAssignments)))));
2 26 Feb 07 jari 232
2 26 Feb 07 jari 233         deletionsNode.add(cloneDeletionsNode);
2 26 Feb 07 jari 234         deletionsNode.add(regionDeletionsNode);
2 26 Feb 07 jari 235
2 26 Feb 07 jari 236         root.add(deletionsNode);
2 26 Feb 07 jari 237
2 26 Feb 07 jari 238         comparator.compareExperiments(this.data, groupAssignments[0], groupAssignments[1], TwoExperimentAlterationComparator.AMPLIFICATION);
2 26 Feb 07 jari 239
2 26 Feb 07 jari 240         DefaultMutableTreeNode amplificationsNode = new DefaultMutableTreeNode("Amplifications");
2 26 Feb 07 jari 241
2 26 Feb 07 jari 242         DefaultMutableTreeNode cloneAmplificationsNode = new DefaultMutableTreeNode("Clone Amplifications");
2 26 Feb 07 jari 243         amplificationsAOnly = comparator.getAOnly();
2 26 Feb 07 jari 244         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(amplificationsAOnly))));
2 26 Feb 07 jari 245         amplificationsBOnly = comparator.getBOnly();
2 26 Feb 07 jari 246         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(amplificationsBOnly))));
2 26 Feb 07 jari 247         amplificationsAandB = comparator.getAAndB();
2 26 Feb 07 jari 248         cloneAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(amplificationsAandB))));
2 26 Feb 07 jari 249
2 26 Feb 07 jari 250         DefaultMutableTreeNode regionAmplificationsNode = new DefaultMutableTreeNode("Region Amplifications");
2 26 Feb 07 jari 251         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAOnly(), comparator.getBOnly(), groupAssignments[0])))));
2 26 Feb 07 jari 252         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("B Only", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getBOnly(), comparator.getAOnly(), groupAssignments[1])))));
2 26 Feb 07 jari 253         regionAmplificationsNode.add(new DefaultMutableTreeNode(new LeafInfo("A and B", createComparisonViewer(frCalc.calculateFlankingRegions(this.data, comparator.getAAndB(), null, groupAssignments)))));
2 26 Feb 07 jari 254
2 26 Feb 07 jari 255         amplificationsNode.add(cloneAmplificationsNode);
2 26 Feb 07 jari 256         amplificationsNode.add(regionAmplificationsNode);
2 26 Feb 07 jari 257
2 26 Feb 07 jari 258         root.add(amplificationsNode);
2 26 Feb 07 jari 259
2 26 Feb 07 jari 260         root.add(new DefaultMutableTreeNode(new LeafInfo("Summary", createSummaryViewer())));
2 26 Feb 07 jari 261         return root;
2 26 Feb 07 jari 262     }
2 26 Feb 07 jari 263
2 26 Feb 07 jari 264     private IViewer createComparisonViewer(Vector dataRegions){
2 26 Feb 07 jari 265         ICGHDataRegion[] alterationRegions = (ICGHDataRegion[])dataRegions.toArray(new ICGHDataRegion[0]);
2 26 Feb 07 jari 266         DataRegionsDataModel dataModel = new DataRegionsDataModel(alterationRegions);
2 26 Feb 07 jari 267
2 26 Feb 07 jari 268         NumberOfAlterationsViewer viewer = new NumberOfAlterationsViewer();
2 26 Feb 07 jari 269         viewer.setData(data);
2 26 Feb 07 jari 270         viewer.setDataModel(dataModel);
2 26 Feb 07 jari 271
2 26 Feb 07 jari 272         return viewer;
2 26 Feb 07 jari 273
2 26 Feb 07 jari 274     }
2 26 Feb 07 jari 275
2 26 Feb 07 jari 276     private IViewer createComparisonViewer(int[] cloneIndices){
2 26 Feb 07 jari 277
2 26 Feb 07 jari 278         ICGHDataRegion[] alterationRegions = new ICGHDataRegion[cloneIndices.length];
2 26 Feb 07 jari 279
2 26 Feb 07 jari 280         for(int i = 0; i < cloneIndices.length; i++){
2 26 Feb 07 jari 281             alterationRegions[i] = data.getCloneAt(cloneIndices[i]);
2 26 Feb 07 jari 282         }
2 26 Feb 07 jari 283
2 26 Feb 07 jari 284         DataRegionsDataModel dataModel = new DataRegionsDataModel(alterationRegions);
2 26 Feb 07 jari 285
2 26 Feb 07 jari 286         NumberOfAlterationsViewer viewer = new NumberOfAlterationsViewer();
2 26 Feb 07 jari 287         viewer.setData(data);
2 26 Feb 07 jari 288         viewer.setDataModel(dataModel);
2 26 Feb 07 jari 289
2 26 Feb 07 jari 290         return viewer;
2 26 Feb 07 jari 291     }
2 26 Feb 07 jari 292
2 26 Feb 07 jari 293     private IViewer createSummaryViewer(){
2 26 Feb 07 jari 294         StringBuffer sb = new StringBuffer();
2 26 Feb 07 jari 295         sb.append("Deletions A Only " + deletionsAOnly.length + "\n");
2 26 Feb 07 jari 296         sb.append("Deletions B Only " + deletionsBOnly.length + "\n");
2 26 Feb 07 jari 297         sb.append("Deletions A and B " + deletionsAandB.length + "\n\n");
2 26 Feb 07 jari 298
2 26 Feb 07 jari 299         sb.append("Amplifications A Only " + amplificationsAOnly.length + "\n");
2 26 Feb 07 jari 300         sb.append("Amplifications B Only " + amplificationsBOnly.length + "\n");
2 26 Feb 07 jari 301         sb.append("Amplifications A and B " + amplificationsAandB.length + "\n\n");
2 26 Feb 07 jari 302
2 26 Feb 07 jari 303         return new AlterationParametersViewer(sb.toString());
2 26 Feb 07 jari 304     }
2 26 Feb 07 jari 305
2 26 Feb 07 jari 306     /**
2 26 Feb 07 jari 307      * Adds node with general iformation.
2 26 Feb 07 jari 308      */
2 26 Feb 07 jari 309     private void addGeneralInfo(DefaultMutableTreeNode root) {
2 26 Feb 07 jari 310       ICGHCloneValueMenu menu = framework.getCghCloneValueMenu();
2 26 Feb 07 jari 311       DefaultMutableTreeNode node = new DefaultMutableTreeNode("General Information");
2 26 Feb 07 jari 312         node.add(new DefaultMutableTreeNode("Amplification Threshold: " + menu.getAmpThresh()));
2 26 Feb 07 jari 313         node.add(new DefaultMutableTreeNode("Deletion Threshold: " + menu.getDelThresh()));
2 26 Feb 07 jari 314         node.add(new DefaultMutableTreeNode("Amplification 2 Copy Threshold: " + menu.getAmpThresh2Copy()));
2 26 Feb 07 jari 315         node.add(new DefaultMutableTreeNode("Deletion 2 Copy Threshold: " + menu.getDelThresh2Copy()));
2 26 Feb 07 jari 316
2 26 Feb 07 jari 317         node.add(new DefaultMutableTreeNode("Experiment A: " + this.exprA));
2 26 Feb 07 jari 318         node.add(new DefaultMutableTreeNode("Experiment B: " + this.exprB));
2 26 Feb 07 jari 319         node.add(new DefaultMutableTreeNode("Deletions A Only: " + deletionsAOnly.length));
2 26 Feb 07 jari 320         node.add(new DefaultMutableTreeNode("Deletions B Only: " + deletionsBOnly.length));
2 26 Feb 07 jari 321         node.add(new DefaultMutableTreeNode("Deletions A and B: " + deletionsAandB.length));
2 26 Feb 07 jari 322
2 26 Feb 07 jari 323         node.add(new DefaultMutableTreeNode("Amplifications A Only: " + amplificationsAOnly.length));
2 26 Feb 07 jari 324         node.add(new DefaultMutableTreeNode("Amplifications B Only: " + amplificationsBOnly.length));
2 26 Feb 07 jari 325         node.add(new DefaultMutableTreeNode("Amplifications A and B: " + amplificationsAandB.length));
2 26 Feb 07 jari 326         root.add(node);
2 26 Feb 07 jari 327     }
2 26 Feb 07 jari 328     
2 26 Feb 07 jari 329 }

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