Clover coverage report - baseCode - 0.2.5
Coverage timestamp: Tue Apr 12 2005 11:31:58 EDT
Overview   Package   File
    FRAMES   NO FRAMES  
file stats: LOC: 134   Methods: 3
NCLOC: 79   Classes: 1
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 Source file Conditionals Statements Methods TOTAL
RowAffyNameFilter.java 94.4% 97.3% 100% 96.6%
coverage coverage
 1    
 package baseCode.dataFilter;
 2    
 
 3    
 import java.util.Vector;
 4    
 
 5    
 import baseCode.dataStructure.matrix.NamedMatrix;
 6    
 
 7    
 /**
 8    
  * Remove probes that have names meeting certain rules indicating they may have low reliability. This is targeted at
 9    
  * cases like "AFFX", "_st", "_f_at" and so forth.
 10    
  * <p>
 11    
  * Copyright (c) 2004
 12    
  * </p>
 13    
  * <p>
 14    
  * Institution:: Columbia University
 15    
  * </p>
 16    
  *
 17    
  * @author Paul Pavlidis
 18    
  * @version $Id: RowAffyNameFilter.java,v 1.3 2004/07/27 03:18:58 pavlidis Exp $
 19    
  */
 20    
 public class RowAffyNameFilter extends AbstractFilter implements Filter {
 21    
 
 22    
    private boolean skip_ST = false;
 23    
    private boolean skip_AFFX = false;
 24    
    private boolean skip_F = false;
 25    
    private boolean skip_X = false;
 26    
    private boolean skip_G = false;
 27    
 
 28    
    /**
 29    
     * Filter probes that contain the '_st' (sense strand) tag
 30    
     */
 31    
    public static final int ST = 1;
 32    
 
 33    
    /**
 34    
     * Filter probes that have the AFFX prefix.
 35    
     */
 36    
    public static final int AFFX = 2;
 37    
 
 38    
    /**
 39    
     * Filter probes that have the "_f_at" (family) tag.
 40    
     */
 41    
    public static final int F = 3;
 42    
 
 43    
    /**
 44    
     * Filter probes that have the "_x_at" tag.
 45    
     */
 46    
    public static final int X = 4;
 47    
 
 48    
    /**
 49    
     * Filter probes that have the "_g_at" (group) tag.
 50    
     */
 51    
    public static final int G = 5;
 52    
 
 53    
    /**
 54    
     * @param criteria int[] of constants indicating the criteria to use.
 55    
     */
 56  2 
    public RowAffyNameFilter( int[] criteria ) {
 57  2 
       this.setCriteria( criteria );
 58    
    }
 59    
 
 60  2 
    private void setCriteria( int[] criteria ) {
 61  2 
       for ( int i = 0; i < criteria.length; i++ ) {
 62  8 
          switch ( criteria[i] ) {
 63    
             case ST: {
 64  2 
                skip_ST = true;
 65    
             }
 66    
             case AFFX: {
 67  4 
                skip_AFFX = true;
 68    
             }
 69    
             case F: {
 70  6 
                skip_F = true;
 71    
             }
 72    
             case X: {
 73  8 
                skip_X = true;
 74    
             }
 75    
             case G: {
 76  8 
                skip_G = true;
 77    
             }
 78    
             default: {
 79  8 
                break;
 80    
             }
 81    
          }
 82    
       }
 83    
    }
 84    
 
 85  2 
    public NamedMatrix filter( NamedMatrix data ) {
 86  2 
       Vector MTemp = new Vector();
 87  2 
       Vector rowNames = new Vector();
 88  2 
       int numRows = data.rows();
 89  2 
       int numCols = data.columns();
 90    
 
 91  2 
       int kept = 0;
 92  2 
       for ( int i = 0; i < numRows; i++ ) {
 93  60 
          String name = data.getRowName( i );
 94    
 
 95    
          // apply the rules.
 96  60 
          if ( skip_ST && name.endsWith( "_st" ) ) { // 'st' means sense strand.
 97  0 
             continue;
 98    
          }
 99    
 
 100  60 
          if ( skip_AFFX && name.startsWith( "AFFX" ) ) {
 101  2 
             continue;
 102    
          }
 103    
 
 104  58 
          if ( skip_F && name.endsWith( "_f_at" ) ) { // gene family. We don't
 105    
             // like.
 106  4 
             continue;
 107    
          }
 108    
 
 109  54 
          if ( skip_X && name.endsWith( "_x_at" ) ) {
 110  2 
             continue;
 111    
          }
 112  52 
          if ( skip_G && name.endsWith( "_g_at" ) ) {
 113  2 
             continue;
 114    
          }
 115  50 
          MTemp.add( data.getRowObj( i ) );
 116  50 
          rowNames.add( name );
 117  50 
          kept++;
 118    
       }
 119    
 
 120  2 
       NamedMatrix returnval = getOutputMatrix( data, MTemp.size(), numCols );
 121    
 
 122  2 
       for ( int i = 0; i < MTemp.size(); i++ ) {
 123  50 
          for ( int j = 0; j < numCols; j++ ) {
 124  600 
             returnval.set( i, j, ( ( Object[] ) MTemp.get( i ) )[j] );
 125    
          }
 126    
       }
 127  2 
       returnval.setColumnNames( data.getColNames() );
 128  2 
       returnval.setRowNames( rowNames );
 129  2 
       log.info( "There are " + kept + " rows left after filtering." );
 130    
 
 131  2 
       return ( returnval );
 132    
 
 133    
    }
 134    
 }
 
CloverReport generated by Clover v1.2.3
Tue Apr 12 2005 11:31:59 EDT.		   30 day Evaluation Version distributed via the Maven Jar Repository. Clover is not free. You have 30 days to evaluate it.