baseCode - 0.2.5

Clover coverage report - baseCode - 0.2.5

Coverage timestamp: Tue Apr 12 2005 11:31:58 EDT

FRAMES NO FRAMES

file stats:	LOC:	87		Methods:	1
	NCLOC:	53		Classes:	1

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Source file

Conditionals

Statements

Methods

TOTAL

AbstractNamedMatrixReader.java

72.2%

85.2%

100%

80.4%

 package baseCode.io.reader;
 
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
 import baseCode.dataStructure.matrix.NamedMatrix;
 
 /**
  * Abstract class representing an object that can read in a {@link NamedMatrix}from a file.
  * <p>
  * Copyright (c) 2004
  * </p>
  * <p>
  * Institution:: Columbia University
  * </p>
  * 
  * @author Paul Pavlidis
  * @version $Id: AbstractNamedMatrixReader.java,v 1.3 2004/08/11 22:53:43 pavlidis Exp $
  */
 public abstract class AbstractNamedMatrixReader {
 
    public abstract NamedMatrix read( String filename ) throws IOException;
 
    public abstract NamedMatrix read( InputStream stream ) throws IOException;
    
    public abstract NamedMatrix readOneRow(BufferedReader dis ) throws IOException;
    
    
    protected static final Log log = LogFactory
          .getLog( AbstractNamedMatrixReader.class );
 
    protected Vector readHeader( BufferedReader dis ) throws IOException {
       Vector headerVec = new Vector();
       String header = dis.readLine();
       StringTokenizer st = new StringTokenizer( header, "\t", true ); // return
       // delims.
 
       String previousToken = "";
       int columnNumber = 0;
       while ( st.hasMoreTokens() ) {
          String s = st.nextToken();
          boolean missing = false;
 
          if ( s.compareTo( "\t" ) == 0 ) {
             /* two tabs in a row */
             if ( previousToken.compareTo( "\t" ) == 0 ) {
                missing = true;
             } else if ( !st.hasMoreTokens() ) { // at end of line.
                missing = true;
             } else {
                previousToken = s;
                continue;
             }
          } else if ( s.compareTo( " " ) == 0 ) {
             if ( previousToken.compareTo( "\t" ) == 0 ) {
                missing = true;
             }
          }
 
          if ( missing ) {
             throw new IOException(
                   "Warning: Missing values not allowed in the header (column "
                         + columnNumber + ")" );
          } else if ( columnNumber > 0 ) {
             headerVec.add( s );
          }
          // otherwise, just the corner string.
          columnNumber++;
          previousToken = s;
       }
 
       //return columnNumber - 1;
       if ( headerVec.size() == 0 ) {
          log.warn( "No headings found" );
       }
 
       return headerVec;
 
    }
 
 }

1		package baseCode.io.reader;
2
3		import java.io.BufferedReader;
4		import java.io.IOException;
5		import java.io.InputStream;
6		import java.util.StringTokenizer;
7		import java.util.Vector;
8
9		import org.apache.commons.logging.Log;
10		import org.apache.commons.logging.LogFactory;
11
12		import baseCode.dataStructure.matrix.NamedMatrix;
13
14		/**
15		* Abstract class representing an object that can read in a {@link NamedMatrix}from a file.
16		* <p>
17		* Copyright (c) 2004
18		* </p>
19		* <p>
20		* Institution:: Columbia University
21		* </p>
22		*
23		* @author Paul Pavlidis
24		* @version $Id: AbstractNamedMatrixReader.java,v 1.3 2004/08/11 22:53:43 pavlidis Exp $
25		*/
26		public abstract class AbstractNamedMatrixReader {
27
28		public abstract NamedMatrix read( String filename ) throws IOException;
29
30		public abstract NamedMatrix read( InputStream stream ) throws IOException;
31
32		public abstract NamedMatrix readOneRow(BufferedReader dis ) throws IOException;
33
34
35		protected static final Log log = LogFactory
36		.getLog( AbstractNamedMatrixReader.class );
37
38	229	protected Vector readHeader( BufferedReader dis ) throws IOException {
39	229	Vector headerVec = new Vector();
40	229	String header = dis.readLine();
41	229	StringTokenizer st = new StringTokenizer( header, "\t", true ); // return
42		// delims.
43
44	229	String previousToken = "";
45	229	int columnNumber = 0;
46	229	while ( st.hasMoreTokens() ) {
47	5762	String s = st.nextToken();
48	5762	boolean missing = false;
49
50	5762	if ( s.compareTo( "\t" ) == 0 ) {
51		/* two tabs in a row */
52	2767	if ( previousToken.compareTo( "\t" ) == 0 ) {
53	0	missing = true;
54	2767	} else if ( !st.hasMoreTokens() ) { // at end of line.
55	1	missing = true;
56		} else {
57	2766	previousToken = s;
58	2766	continue;
59		}
60	2995	} else if ( s.compareTo( " " ) == 0 ) {
61	0	if ( previousToken.compareTo( "\t" ) == 0 ) {
62	0	missing = true;
63		}
64		}
65
66	2996	if ( missing ) {
67	1	throw new IOException(
68		"Warning: Missing values not allowed in the header (column "
69		+ columnNumber + ")" );
70	2995	} else if ( columnNumber > 0 ) {
71	2766	headerVec.add( s );
72		}
73		// otherwise, just the corner string.
74	2995	columnNumber++;
75	2995	previousToken = s;
76		}
77
78		//return columnNumber - 1;
79	228	if ( headerVec.size() == 0 ) {
80	0	log.warn( "No headings found" );
81		}
82
83	228	return headerVec;
84
85		}
86
87		}