Package ubic.basecode.io.reader

Class SparseRaggedMatrixReader

java.lang.Object

ubic.basecode.io.reader.AbstractMatrixReader<DoubleMatrix<String,String>,Double>

ubic.basecode.io.reader.DoubleMatrixReader

ubic.basecode.io.reader.SparseRaggedMatrixReader

public class SparseRaggedMatrixReader
extends DoubleMatrixReader

Best data structure for reading really big, really sparse matrices when a matrix represetation is needed. This uses a completely different file format than what we use for dense matrices.

Author:

pavlidis

See Also:

DoubleMatrixReader

Field Summary

Fields inherited from class ubic.basecode.io.reader.AbstractMatrixReader

log

Constructor Summary

Constructors

Constructor	Description
SparseRaggedMatrixReader()

Method Summary

Modifier and Type	Method	Description
DoubleMatrix<String,String>	read(InputStream stream, int offset)	Read an entire sparse matrix from a stream (JW format).
DoubleMatrix<String,String>	readFromAdjList(InputStream stream)
DoubleMatrix<String,String>	readFromAdjList(String fileName)	Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
DoubleMatrix<String,String>	readOneRow(BufferedReader dis, int offset)	Use this to read one row from a matrix (JW format).

Methods inherited from class ubic.basecode.io.reader.DoubleMatrixReader

createEmptyRow, createMatrix, read, read, read, read, read, read, read, read

Methods inherited from class ubic.basecode.io.reader.AbstractMatrixReader

readHeader

Methods inherited from class java.lang.Object

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

Constructor Detail

SparseRaggedMatrixReader

public SparseRaggedMatrixReader()

Method Detail

read

public DoubleMatrix<String,String> read(InputStream stream,
                                              int offset)
                                       throws 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

readFromAdjList

public DoubleMatrix<String,String> readFromAdjList(InputStream stream)
                                                  throws NumberFormatException,
                                                         IOException

Parameters:

stream -

Returns:

Throws:

IOException

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.

readFromAdjList

public DoubleMatrix<String,String> readFromAdjList(String fileName)
                                                  throws 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.

Parameters:

name - of file

Returns:

Throws:

IOException

readOneRow

public DoubleMatrix<String,String> readOneRow(BufferedReader dis,
                                                    int offset)
                                             throws 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:

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