mev-4.0.01/source/org/tigr/microarray/mev/cgh/CGHDataModel/CGHChartDataModelDyeSwap.java

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2 26 Feb 07 jari 1 /*
2 26 Feb 07 jari 2  * CGHChartDataModelDyeSwap.java
2 26 Feb 07 jari 3  *
2 26 Feb 07 jari 4  * Created on July 5, 2003, 11:15 PM
2 26 Feb 07 jari 5  */
2 26 Feb 07 jari 6
2 26 Feb 07 jari 7 package org.tigr.microarray.mev.cgh.CGHDataModel;
2 26 Feb 07 jari 8
2 26 Feb 07 jari 9 /*
2 26 Feb 07 jari 10 import com.klg.jclass.chart.ChartDataModel;
2 26 Feb 07 jari 11 import com.klg.jclass.chart.LabelledChartDataModel;
2 26 Feb 07 jari 12 import com.klg.jclass.chart.ChartDataSupport;
2 26 Feb 07 jari 13 import com.klg.jclass.chart.ChartDataEvent;
2 26 Feb 07 jari 14 import com.klg.jclass.chart.ChartDataManageable;
2 26 Feb 07 jari 15 */
2 26 Feb 07 jari 16 import org.tigr.microarray.mev.ISlideData;
2 26 Feb 07 jari 17 import org.tigr.microarray.mev.cluster.gui.IData;
2 26 Feb 07 jari 18 import org.tigr.microarray.mev.cluster.gui.IFramework;
2 26 Feb 07 jari 19 /*
2 26 Feb 07 jari 20 import java.util.Vector;
2 26 Feb 07 jari 21 import java.util.Iterator;
2 26 Feb 07 jari 22 import java.util.Hashtable;
2 26 Feb 07 jari 23 import javax.swing.event.ChangeListener;
2 26 Feb 07 jari 24
2 26 Feb 07 jari 25 import java.awt.Color;
2 26 Feb 07 jari 26
2 26 Feb 07 jari 27 import org.tigr.microarray.mev.cgh.CGHDataObj.*;
2 26 Feb 07 jari 28 //import org.tigr.microarray.mev.cgh.CGHFcdObj.CGHMultipleArrayDataFcd;
2 26 Feb 07 jari 29 import cern.jet.math.Arithmetic;
2 26 Feb 07 jari 30
2 26 Feb 07 jari 31 import cern.jet.stat.Probability;
2 26 Feb 07 jari 32 */
2 26 Feb 07 jari 33 /**
2 26 Feb 07 jari 34  *
2 26 Feb 07 jari 35  * @author  Adam Margolin
2 26 Feb 07 jari 36  * @author Raktim Sinha
2 26 Feb 07 jari 37  */
2 26 Feb 07 jari 38
2 26 Feb 07 jari 39 public class CGHChartDataModelDyeSwap extends CGHChartDataModel {
2 26 Feb 07 jari 40
2 26 Feb 07 jari 41     /** Creates a new instance of CGHChartDataModelDyeSwap */
2 26 Feb 07 jari 42     public CGHChartDataModelDyeSwap(/*CGHMultipleArrayDataFcd fcd,*/ IFramework framework, int experimentIndex, int chromosomeIndex){
2 26 Feb 07 jari 43         super(/*fcd,*/ framework, experimentIndex, chromosomeIndex);
2 26 Feb 07 jari 44     }
2 26 Feb 07 jari 45
2 26 Feb 07 jari 46     /*
2 26 Feb 07 jari 47      * @return the number of experiments if viewing all experiments, 2 otherwise
2 26 Feb 07 jari 48      * representing the cy3 and cy5 experiments
2 26 Feb 07 jari 49      */
2 26 Feb 07 jari 50     public int getNumSeries() {
2 26 Feb 07 jari 51         switch(adaptor.cloneValueType){
2 26 Feb 07 jari 52             case CGHBrowserModelAdaptor.CLONE_VALUES_DYE_SWAP:
2 26 Feb 07 jari 53                 return adaptor.experimentIndices.length * 2;
2 26 Feb 07 jari 54             case CGHBrowserModelAdaptor.CLONE_VALUES_LOG_AVERAGE_INVERTED:
2 26 Feb 07 jari 55                 return adaptor.experimentIndices.length;
2 26 Feb 07 jari 56             case CGHBrowserModelAdaptor.CLONE_VALUES_LOG_DYE_SWAP:
2 26 Feb 07 jari 57                 return adaptor.experimentIndices.length * 2;
2 26 Feb 07 jari 58             case CGHBrowserModelAdaptor.CLONE_VALUES_P_SCORE:
2 26 Feb 07 jari 59                 return adaptor.experimentIndices.length * 2;
2 26 Feb 07 jari 60             default:
2 26 Feb 07 jari 61                 return 0;
2 26 Feb 07 jari 62         }
2 26 Feb 07 jari 63     }
2 26 Feb 07 jari 64
2 26 Feb 07 jari 65     public String[] getSeriesLabels() {
2 26 Feb 07 jari 66         int numSeries = getNumSeries();
2 26 Feb 07 jari 67         String[] seriesLabels = new String[numSeries];
2 26 Feb 07 jari 68         for(int labelIndex = 0; labelIndex < numSeries; labelIndex++){
2 26 Feb 07 jari 69             String label = "";
2 26 Feb 07 jari 70             int dyeSwapIndex = labelIndex % 2;
2 26 Feb 07 jari 71             int experimentIndex = labelIndex / 2;
2 26 Feb 07 jari 72             String sampleName = data.getSampleName(adaptor.experimentIndices[experimentIndex]);
2 26 Feb 07 jari 73             switch(adaptor.cloneValueType){
2 26 Feb 07 jari 74                 case CGHBrowserModelAdaptor.CLONE_VALUES_DYE_SWAP:
2 26 Feb 07 jari 75                     if(dyeSwapIndex == 0){
2 26 Feb 07 jari 76                         label = sampleName + " Cy3";
2 26 Feb 07 jari 77                     }else if(dyeSwapIndex == 1){
2 26 Feb 07 jari 78                         label = sampleName + " Cy5";
2 26 Feb 07 jari 79                     }
2 26 Feb 07 jari 80                     break;
2 26 Feb 07 jari 81                 case CGHBrowserModelAdaptor.CLONE_VALUES_LOG_AVERAGE_INVERTED:
2 26 Feb 07 jari 82                     //label = data.getSampleName(experimentIndices[experimentIndex]);
2 26 Feb 07 jari 83                     label = sampleName;
2 26 Feb 07 jari 84                     break;
2 26 Feb 07 jari 85                 case CGHBrowserModelAdaptor.CLONE_VALUES_LOG_DYE_SWAP:
2 26 Feb 07 jari 86                     if(dyeSwapIndex == 0){
2 26 Feb 07 jari 87                         label = sampleName + " Cy3";
2 26 Feb 07 jari 88                     }else if(dyeSwapIndex == 1){
2 26 Feb 07 jari 89                         label = sampleName + " Cy5";
2 26 Feb 07 jari 90                     }
2 26 Feb 07 jari 91                     break;
2 26 Feb 07 jari 92                 case CGHBrowserModelAdaptor.CLONE_VALUES_P_SCORE:
2 26 Feb 07 jari 93                     if(dyeSwapIndex == 0){
2 26 Feb 07 jari 94                         label = sampleName + " Cy3";
2 26 Feb 07 jari 95                     }else if(dyeSwapIndex == 1){
2 26 Feb 07 jari 96                         label = sampleName + " Cy5";
2 26 Feb 07 jari 97                     }
2 26 Feb 07 jari 98                     break;
2 26 Feb 07 jari 99             }
2 26 Feb 07 jari 100             seriesLabels[labelIndex] = label;
2 26 Feb 07 jari 101         }
2 26 Feb 07 jari 102         return seriesLabels;
2 26 Feb 07 jari 103     }
2 26 Feb 07 jari 104
2 26 Feb 07 jari 105     public double[] getYSeries(int index) {
2 26 Feb 07 jari 106         switch(adaptor.cloneValueType){
2 26 Feb 07 jari 107             case CGHBrowserModelAdaptor.CLONE_VALUES_DYE_SWAP:
2 26 Feb 07 jari 108                 return generateDyeSwapYSeries(index);
2 26 Feb 07 jari 109             case CGHBrowserModelAdaptor.CLONE_VALUES_LOG_AVERAGE_INVERTED:
2 26 Feb 07 jari 110                 return generateLogAverageInvertedYSeries(index);
2 26 Feb 07 jari 111             case CGHBrowserModelAdaptor.CLONE_VALUES_LOG_DYE_SWAP:
2 26 Feb 07 jari 112                 return generateLogDyeSwapYSeries(index);
2 26 Feb 07 jari 113             case CGHBrowserModelAdaptor.CLONE_VALUES_P_SCORE:
2 26 Feb 07 jari 114                 return generateCloneDistributionPScoreYSeries(index);
2 26 Feb 07 jari 115             default:
2 26 Feb 07 jari 116                 return null;
2 26 Feb 07 jari 117         }
2 26 Feb 07 jari 118     }
2 26 Feb 07 jari 119
2 26 Feb 07 jari 120     /**
2 26 Feb 07 jari 121      * Remember getRatio Glitch
2 26 Feb 07 jari 122      * @param index
2 26 Feb 07 jari 123      * @return
2 26 Feb 07 jari 124      */
2 26 Feb 07 jari 125     private double[] generateDyeSwapYSeries(int index){
2 26 Feb 07 jari 126         double[] ySeries = new double[getSeriesSize()];
2 26 Feb 07 jari 127
2 26 Feb 07 jari 128         int dyeSwapIndex = index % 2;
2 26 Feb 07 jari 129         int experimentIndex = index / 2;
2 26 Feb 07 jari 130         for(int i = 0; i < ySeries.length; i++){
2 26 Feb 07 jari 131             if(smoothUnconfirmed){
2 26 Feb 07 jari 132                 int copyNumber = data.getCopyNumberDetermination(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 133                 if(copyNumber == IData.BAD_CLONE || copyNumber == IData.NO_COPY_CHANGE){
2 26 Feb 07 jari 134                     ySeries[i] = 1;
2 26 Feb 07 jari 135                     continue;
2 26 Feb 07 jari 136                 }
2 26 Feb 07 jari 137             }
2 26 Feb 07 jari 138
2 26 Feb 07 jari 139             if(dyeSwapIndex == 0){
2 26 Feb 07 jari 140                 ySeries[i] = data.getRatio(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i), ISlideData.CY3_SLIDES);
2 26 Feb 07 jari 141
2 26 Feb 07 jari 142             }else if(dyeSwapIndex == 1){
2 26 Feb 07 jari 143                 ySeries[i] = data.getRatio(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i), ISlideData.CY5_SLIDES);
2 26 Feb 07 jari 144             }
2 26 Feb 07 jari 145         }
2 26 Feb 07 jari 146         return ySeries;
2 26 Feb 07 jari 147     }
2 26 Feb 07 jari 148
2 26 Feb 07 jari 149     private double[] generateLogDyeSwapYSeries(int index){
2 26 Feb 07 jari 150         double[] ySeries = new double[getSeriesSize()];
2 26 Feb 07 jari 151
2 26 Feb 07 jari 152         int dyeSwapIndex = index % 2;
2 26 Feb 07 jari 153         int experimentIndex = index / 2;
2 26 Feb 07 jari 154         float val = Float.NaN;
2 26 Feb 07 jari 155         for(int i = 0; i < ySeries.length; i++){
2 26 Feb 07 jari 156             if(smoothUnconfirmed){
2 26 Feb 07 jari 157                 int copyNumber = data.getCopyNumberDetermination(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 158                 if(copyNumber == IData.BAD_CLONE || copyNumber == IData.NO_COPY_CHANGE){
2 26 Feb 07 jari 159                     ySeries[i] = 0;
2 26 Feb 07 jari 160                     continue;
2 26 Feb 07 jari 161                 }
2 26 Feb 07 jari 162             }
2 26 Feb 07 jari 163
2 26 Feb 07 jari 164             if(dyeSwapIndex == 0){
2 26 Feb 07 jari 165                 //val = data.getRatio(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i), ISlideData.CY3_SLIDES, true);
2 26 Feb 07 jari 166               val = data.getCY3(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 167             }else if(dyeSwapIndex == 1){
2 26 Feb 07 jari 168                 //val = data.getRatio(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i), ISlideData.CY5_SLIDES, true);
2 26 Feb 07 jari 169               val = data.getCY5(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 170             }
2 26 Feb 07 jari 171             if(Float.isNaN(val) || Float.isInfinite(val)){
2 26 Feb 07 jari 172
2 26 Feb 07 jari 173             }else{
2 26 Feb 07 jari 174                 ySeries[i] = val;
2 26 Feb 07 jari 175             }
2 26 Feb 07 jari 176         }
2 26 Feb 07 jari 177         return ySeries;
2 26 Feb 07 jari 178     }
2 26 Feb 07 jari 179
2 26 Feb 07 jari 180     private double[] generateLogAverageInvertedYSeries(int index){
2 26 Feb 07 jari 181         double[] ySeries = new double[getSeriesSize()];
2 26 Feb 07 jari 182         for(int i = 0; i < ySeries.length; i++){
2 26 Feb 07 jari 183             if(smoothUnconfirmed){
2 26 Feb 07 jari 184                 int copyNumber = data.getCopyNumberDetermination(adaptor.experimentIndices[index], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 185                 if(copyNumber == IData.BAD_CLONE || copyNumber == IData.NO_COPY_CHANGE){
2 26 Feb 07 jari 186                     ySeries[i] = 0;
2 26 Feb 07 jari 187                     continue;
2 26 Feb 07 jari 188                 }
2 26 Feb 07 jari 189             }
2 26 Feb 07 jari 190
2 26 Feb 07 jari 191             float val = data.getLogAverageInvertedValue(adaptor.experimentIndices[index], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 192             if(Float.isNaN(val) || Float.isInfinite(val)){
2 26 Feb 07 jari 193                 //ySeries[i] = Double.NaN;
2 26 Feb 07 jari 194             }else{
2 26 Feb 07 jari 195                 ySeries[i] = val;
2 26 Feb 07 jari 196             }
2 26 Feb 07 jari 197         }
2 26 Feb 07 jari 198         return ySeries;
2 26 Feb 07 jari 199     }
2 26 Feb 07 jari 200
2 26 Feb 07 jari 201     private double[] generateCloneDistributionPScoreYSeries(int index){
2 26 Feb 07 jari 202         double[] ySeries = new double[getSeriesSize()];
2 26 Feb 07 jari 203
2 26 Feb 07 jari 204         int dyeSwapIndex = index % 2;
2 26 Feb 07 jari 205         int experimentIndex = index / 2;
2 26 Feb 07 jari 206         for(int i = 0; i < ySeries.length; i++){
2 26 Feb 07 jari 207             if(smoothUnconfirmed){
2 26 Feb 07 jari 208                 int copyNumber = data.getCopyNumberDetermination(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 209                 if(copyNumber == IData.BAD_CLONE || copyNumber == IData.NO_COPY_CHANGE){
2 26 Feb 07 jari 210                     ySeries[i] = .5;
2 26 Feb 07 jari 211                     continue;
2 26 Feb 07 jari 212                 }
2 26 Feb 07 jari 213             }
2 26 Feb 07 jari 214
2 26 Feb 07 jari 215             if(dyeSwapIndex == 0){
2 26 Feb 07 jari 216                 ySeries[i] = data.getPValueByLogCloneDistribution(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 217
2 26 Feb 07 jari 218             }else if(dyeSwapIndex == 1){
2 26 Feb 07 jari 219                 ySeries[i] = data.getPValueByLogCloneDistribution(adaptor.experimentIndices[experimentIndex], adaptor.getCloneIndex(i));
2 26 Feb 07 jari 220             }
2 26 Feb 07 jari 221         }
2 26 Feb 07 jari 222         return ySeries;
2 26 Feb 07 jari 223     }
2 26 Feb 07 jari 224 }

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