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: 143   Methods: 4
NCLOC: 82   Classes: 1
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 Source file Conditionals Statements Methods TOTAL
AffymetrixProbeNameFilter.java 0% 0% 0% 0%
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: AffymetrixProbeNameFilter.java,v 1.12 2004/08/17 21:17:40 pavlidis Exp $
 19    
  */
 20    
 public class AffymetrixProbeNameFilter 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  0 
    public AffymetrixProbeNameFilter( int[] criteria ) {
 57  0 
       this.setCriteria( criteria );
 58    
    }
 59    
 
 60    
    /**
 61    
     * Filter probes with all criteria switched on.
 62    
     *
 63    
     */
 64  0 
    public AffymetrixProbeNameFilter(   ) {
 65  0 
       this.setCriteria( new int[] {1,2,3,4,5} );
 66    
    }
 67    
 
 68    
 
 69  0 
    private void setCriteria( int[] criteria ) {
 70  0 
       for ( int i = 0; i < criteria.length; i++ ) {
 71  0 
          switch ( criteria[i] ) {
 72    
             case ST: {
 73  0 
                skip_ST = true;
 74    
             }
 75    
             case AFFX: {
 76  0 
                skip_AFFX = true;
 77    
             }
 78    
             case F: {
 79  0 
                skip_F = true;
 80    
             }
 81    
             case X: {
 82  0 
                skip_X = true;
 83    
             }
 84    
             case G: {
 85  0 
                skip_G = true;
 86    
             }
 87    
             default: {
 88  0 
                break;
 89    
             }
 90    
          }
 91    
       }
 92    
    }
 93    
 
 94  0 
    public NamedMatrix filter( NamedMatrix data ) {
 95  0 
       Vector MTemp = new Vector();
 96  0 
       Vector rowNames = new Vector();
 97  0 
       int numRows = data.rows();
 98  0 
       int numCols = data.columns();
 99    
 
 100  0 
       int kept = 0;
 101  0 
       for ( int i = 0; i < numRows; i++ ) {
 102  0 
          String name = data.getRowName( i );
 103    
 
 104    
          // apply the rules.
 105  0 
          if ( skip_ST && name.endsWith( "_st" ) ) { // 'st' means sense strand.
 106  0 
             continue;
 107    
          }
 108    
 
 109  0 
          if ( skip_AFFX && name.startsWith( "AFFX" ) ) {
 110  0 
             continue;
 111    
          }
 112    
 
 113  0 
          if ( skip_F && name.endsWith( "_f_at" ) ) { // gene family. We don't
 114    
             // like.
 115  0 
             continue;
 116    
          }
 117    
 
 118  0 
          if ( skip_X && name.endsWith( "_x_at" ) ) {
 119  0 
             continue;
 120    
          }
 121  0 
          if ( skip_G && name.endsWith( "_g_at" ) ) {
 122  0 
             continue;
 123    
          }
 124  0 
          MTemp.add( data.getRowObj( i ) );
 125  0 
          rowNames.add( name );
 126  0 
          kept++;
 127    
       }
 128    
 
 129  0 
       NamedMatrix returnval = getOutputMatrix( data, MTemp.size(), numCols );
 130    
 
 131  0 
       for ( int i = 0; i < MTemp.size(); i++ ) {
 132  0 
          for ( int j = 0; j < numCols; j++ ) {
 133  0 
             returnval.set( i, j, ( ( Object[] ) MTemp.get( i ) )[j] );
 134    
          }
 135    
       }
 136  0 
       returnval.setColumnNames( data.getColNames() );
 137  0 
       returnval.setRowNames( rowNames );
 138  0 
       log.info( "There are " + kept + " rows left after filtering." );
 139    
 
 140  0 
       return ( returnval );
 141    
 
 142    
    }
 143    
 }
 
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.