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: 91   Classes: 1
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 Source file Conditionals Statements Methods TOTAL
StringMatrixReader.java 76.9% 85.2% 33.3% 80.7%
coverage coverage
 1    
 package baseCode.io.reader;
 2    
 
 3    
 import java.io.BufferedReader;
 4    
 import java.io.File;
 5    
 import java.io.FileInputStream;
 6    
 import java.io.IOException;
 7    
 import java.io.InputStream;
 8    
 import java.io.InputStreamReader;
 9    
 import java.util.StringTokenizer;
 10    
 import java.util.Vector;
 11    
 
 12    
 import baseCode.dataStructure.matrix.NamedMatrix;
 13    
 import baseCode.dataStructure.matrix.StringMatrix2DNamed;
 14    
 
 15    
 /**
 16    
  * Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
 17    
  * <p>
 18    
  * Copyright (c) 2004
 19    
  * </p>
 20    
  * <p>
 21    
  * Institution:: Columbia University
 22    
  * </p>
 23    
  *
 24    
  * @author Paul Pavlidis
 25    
  * @version $Id: StringMatrixReader.java,v 1.3 2004/08/11 22:53:43 pavlidis Exp $
 26    
  */
 27    
 public class StringMatrixReader extends AbstractNamedMatrixReader {
 28    
 
 29  0 
    public NamedMatrix read( String filename ) throws IOException {
 30  0 
       File infile = new File( filename );
 31  0 
       if ( !infile.exists() || !infile.canRead() ) {
 32  0 
          throw new IllegalArgumentException( "Could not read from " + filename );
 33    
       }
 34  0 
       FileInputStream stream = new FileInputStream( infile );
 35  0 
       return read( stream );
 36    
    }
 37    
 
 38    
    /**
 39    
     * Missing values are entered as an empty string.
 40    
     *
 41    
     * @param stream InputStream
 42    
     * @return NamedMatrix
 43    
     * @throws IOException
 44    
     */
 45  113 
    public NamedMatrix read( InputStream stream ) throws IOException {
 46  113 
       StringMatrix2DNamed matrix = null;
 47  113 
       Vector MTemp = new Vector();
 48  113 
       Vector rowNames = new Vector();
 49  113 
       Vector columnNames;
 50  113 
       BufferedReader dis = new BufferedReader( new InputStreamReader( stream ) );
 51    
       //    BufferedReader dis = new BufferedReader( new FileReader( filename ) );
 52  113 
       int columnNumber = 0;
 53  113 
       int rowNumber = 0;
 54  113 
       String row;
 55    
 
 56  113 
       columnNames = readHeader( dis );
 57  113 
       int numHeadings = columnNames.size();
 58    
 
 59  ? 
       while ( ( row = dis.readLine() ) != null ) {
 60  3390 
          StringTokenizer st = new StringTokenizer( row, "\t", true );
 61  3390 
          Vector rowTemp = new Vector();
 62  3390 
          columnNumber = 0;
 63  3390 
          String previousToken = "";
 64    
 
 65  3390 
          while ( st.hasMoreTokens() ) {
 66  83991 
             String s = st.nextToken();
 67    
 
 68  83991 
             boolean missing = false;
 69    
 
 70  83991 
             if ( s.compareTo( "\t" ) == 0 ) {
 71    
                /* two tabs in a row */
 72  40680 
                if ( previousToken.compareTo( "\t" ) == 0 ) {
 73  659 
                   missing = true;
 74  40021 
                } else if ( !st.hasMoreTokens() ) { // at end of line.
 75  50 
                   missing = true;
 76    
                } else {
 77  39971 
                   previousToken = s;
 78  39971 
                   continue;
 79    
                }
 80    
             }
 81    
 
 82  44020 
             if ( columnNumber > 0 ) {
 83  40630 
                if ( missing ) {
 84    
                   //rowTemp.add(Double.toString(Double.NaN));
 85  709 
                   rowTemp.add( "" );
 86    
                } else {
 87  39921 
                   rowTemp.add( s );
 88    
                }
 89    
             } else {
 90  3390 
                if ( missing ) {
 91  0 
                   throw new IOException(
 92    
                         "Missing values not allowed for row labels" );
 93    
                }
 94  3390 
                rowNames.add( s );
 95    
             }
 96    
 
 97  44020 
             columnNumber++;
 98  44020 
             previousToken = s;
 99    
          }
 100  3390 
          MTemp.add( rowTemp );
 101  3390 
          if ( rowTemp.size() > numHeadings ) {
 102  0 
             throw new IOException( "Warning: too many values ("
 103    
                   + rowTemp.size() + ") in row " + rowNumber
 104    
                   + " (based on headings count of " + numHeadings + ")" );
 105    
          }
 106  3390 
          rowNumber++;
 107    
       }
 108    
 
 109  113 
       matrix = new StringMatrix2DNamed( rowNumber, numHeadings );
 110  113 
       matrix.setColumnNames( columnNames );
 111  113 
       matrix.setRowNames( rowNames );
 112    
 
 113  113 
       for ( int i = 0; i < matrix.rows(); i++ ) {
 114  3390 
          for ( int j = 0; j < matrix.columns(); j++ ) {
 115  40680 
             if ( ( ( Vector ) MTemp.get( i ) ).size() < j + 1 ) {
 116  50 
                matrix.set( i, j, "" );
 117    
                // this allows the input file to have ragged ends.
 118    
             } else {
 119  40630 
                matrix.set( i, j, ( ( Vector ) MTemp.get( i ) ).get( j ) );
 120    
             }
 121    
          }
 122    
       }
 123  113 
       stream.close();
 124  113 
       return matrix;
 125    
 
 126    
    }
 127    
 
 128    
    /* (non-Javadoc)
 129    
     * @see baseCode.io.reader.AbstractNamedMatrixReader#readOneRow(java.io.BufferedReader)
 130    
     */
 131  0 
    public NamedMatrix readOneRow( BufferedReader dis ) throws IOException {
 132  0 
      throw new UnsupportedOperationException();
 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.