baseCode.io.reader
Class SparseRaggedDouble2DNamedMatrixReader

java.lang.Object
  baseCode.io.reader.AbstractNamedMatrixReader
      baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader

public class SparseRaggedDouble2DNamedMatrixReader

extends AbstractNamedMatrixReader

Best data structure for reading really big, really sparse matrices when a matrix represetation is needed. *

The standard format looks like this:

 
  
   
    
     
      
       
        
         
          
           
            
             
              
               
                
                                         2          <--- number of items - the first line of the file only. NOTE - this line is often blank or not present.
                                         1 2        <--- items 1 has 2 edges
                                         1 2        <--- edge indices are to items 1 & 2
                                         0.1 100    <--- with the following weights
                                         2 2        <--- items 2 also has 2 edges
                                         1 2        <--- edge indices are also to items 1 & 2 (fully connected)
                                         100 0.1    <--- with the following weights
                
               
              
             
            
           
          
         
        
       
      
     
    
   
  
 

Copyright (c) 2004 Columbia University

Version:

$Id: SparseRaggedDouble2DNamedMatrixReader.java,v 1.22 2005/01/05 02:01:02 pavlidis Exp $

Author:

pavlidis

Field Summary

Fields inherited from class baseCode.io.reader.AbstractNamedMatrixReader

log

Constructor Summary

SparseRaggedDouble2DNamedMatrixReader()

Method Summary

NamedMatrix	read(java.io.InputStream stream) Read an entire sparse matrix from a stream (JW format).
NamedMatrix	read(java.io.InputStream stream, int offset) Read an entire sparse matrix from a stream (JW format).
NamedMatrix	read(java.lang.String fileName)
NamedMatrix	readFromAdjList(java.io.InputStream stream)
NamedMatrix	readFromAdjList(java.lang.String fileName) Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
NamedMatrix	readOneRow(java.io.BufferedReader dis)
NamedMatrix	readOneRow(java.io.BufferedReader dis, int offset) Use this to read one row from a matrix (JW format).

Methods inherited from class baseCode.io.reader.AbstractNamedMatrixReader

readHeader

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SparseRaggedDouble2DNamedMatrixReader

public SparseRaggedDouble2DNamedMatrixReader()

Method Detail

readFromAdjList

public NamedMatrix readFromAdjList(java.lang.String fileName)
                            throws java.io.IOException

Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:

 
  
   
    
     
      
       
        
         
          
           
            
                           item1 item2 weight
                           item1 item5 weight
             
            
           
          
         
        
       
      
     
    
   
  
 

IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not explicitly listed.

Returns:

Throws:

java.io.IOException

readFromAdjList

public NamedMatrix readFromAdjList(java.io.InputStream stream)
                            throws java.lang.NumberFormatException,
                                   java.io.IOException

Parameters:

stream -

Returns:

Throws:

java.io.IOException

java.lang.NumberFormatException - Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:

 
  
   
    
     
      
       
        
         
          
           
            
              item1 item2 weight
              item1 item5 weight
             
            
           
          
         
        
       
      
     
    
   
  
 

IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not explicitly listed.

read

public NamedMatrix read(java.lang.String fileName)
                 throws java.io.IOException

Specified by:

read in class AbstractNamedMatrixReader

Throws:

java.io.IOException

readOneRow

public NamedMatrix readOneRow(java.io.BufferedReader dis)
                       throws java.io.IOException

Specified by:

readOneRow in class AbstractNamedMatrixReader

Throws:

java.io.IOException

readOneRow

public NamedMatrix readOneRow(java.io.BufferedReader dis,
                              int offset)
                       throws java.io.IOException

Use this to read one row from a matrix (JW format). It does not close the reader. (this actually has to read several lines to get the data for one matrix row)

Parameters:

offset - A value indicating the lowest value for the indexes listed. This is here in case the indexes in the stream are numbered starting from 1 instead of zero.

Returns:

@throws IOException

Throws:

java.io.IOException

read

public NamedMatrix read(java.io.InputStream stream)
                 throws java.io.IOException

Read an entire sparse matrix from a stream (JW format).

Specified by:

read in class AbstractNamedMatrixReader

Parameters:

stream -

Returns:

@throws IOException

Throws:

java.io.IOException

read

public NamedMatrix read(java.io.InputStream stream,
                        int offset)
                 throws java.io.IOException

Read an entire sparse matrix from a stream (JW format).

Parameters:

stream -

offset - A value indicating the lowest value for the indexes listed. This is here in case the indexes in the stream are numbered starting from 1 instead of zero.

Returns:

@throws IOException

Throws:

java.io.IOException