baseCode.io.reader
Class SparseDoubleMatrixReader

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

public class SparseDoubleMatrixReader

extends AbstractNamedMatrixReader

Copyright (c) 2004 Columbia University

Version:

$Id: SparseDoubleMatrixReader.java,v 1.4 2004/08/16 02:06:01 pavlidis Exp $

Author:

pavlidis

Field Summary

Fields inherited from class baseCode.io.reader.AbstractNamedMatrixReader

log

Constructor Summary

SparseDoubleMatrixReader()

Method Summary

NamedMatrix	read(java.io.InputStream stream)
NamedMatrix	read(java.io.InputStream stream, java.util.Set wantedRowNames) Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
NamedMatrix	read(java.lang.String filename)
NamedMatrix	read(java.lang.String filename, java.util.Set wantedRowNames) Read a matrix from a file, subject to filtering criteria.
NamedMatrix	readJW(java.io.InputStream stream) Read a sparse matrix in "JW" (Jason Weston) format.
NamedMatrix	readOneRow(java.io.BufferedReader dis)

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

SparseDoubleMatrixReader

public SparseDoubleMatrixReader()

Method Detail

read

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

Specified by:

read in class AbstractNamedMatrixReader

Parameters:

filename - data file to read from

Returns:

NamedMatrix object constructed from the data file

Throws:

java.io.IOException

read

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

Specified by:

read in class AbstractNamedMatrixReader

Parameters:

stream - InputStream stream to read from

Returns:

NamedMatrix object constructed from the data file

Throws:

java.io.IOException

read

public NamedMatrix read(java.lang.String filename,
                        java.util.Set wantedRowNames)
                 throws java.io.IOException

Read a matrix from a file, subject to filtering criteria.

Parameters:

filename - data file to read from

wantedRowNames - contains names of rows we want to get

Returns:

NamedMatrix object constructed from the data file

Throws:

java.io.IOException

readJW

public NamedMatrix readJW(java.io.InputStream stream)
                   throws java.io.IOException,
                          java.lang.IllegalAccessException,
                          java.lang.NoSuchFieldException

Read a sparse matrix in "JW" (Jason Weston) format. The format is 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
 

Note that the item numbering starts at 1. This is a requirement.

Note that this cannot handle very large matrices - the limit to rows x columns is the number Integer.MAX_VALUE. This is an implementation problem for colt's sparse matrix.

Parameters:

stream -

Returns:

@throws IOException

Throws:

java.io.IOException

java.lang.IllegalAccessException

java.lang.NoSuchFieldException

read

public NamedMatrix read(java.io.InputStream stream,
                        java.util.Set wantedRowNames)
                 throws java.io.IOException

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

               item1 item2 weight
               item1 item5 weight
 

By definition the resulting matrix is square and symmetric.

Note that the ordering of the items will be as they are encountered in the file.

Parameters:

stream - InputStream

wantedRowNames - Set

Returns:

NamedMatrix

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