baseCode.io.reader
Class DoubleMatrixReader

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

public class DoubleMatrixReader

extends AbstractNamedMatrixReader

Reader for DenseDoubleMatrix2DNamed.

Copyright (c) 2004

Institution: Columbia University

Version:

$Id: DoubleMatrixReader.java,v 1.7 2005/03/21 18:01:04 pavlidis Exp $

Author:

Paul Pavlidis

Field Summary

Fields inherited from class baseCode.io.reader.AbstractNamedMatrixReader

log

Constructor Summary

DoubleMatrixReader()

Method Summary

protected cern.colt.list.DoubleArrayList	createEmptyRow(int numColumns)
protected DenseDoubleMatrix2DNamed	createMatrix(java.util.List MTemp, int rowCount, int colCount, java.util.List rowNames, java.util.List colNames)
NamedMatrix	read(java.io.InputStream stream)
NamedMatrix	read(java.io.InputStream stream, java.util.Set wantedRowNames)
NamedMatrix	read(java.io.InputStream stream, java.util.Set wantedRowNames, boolean createEmptyRows)
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	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

DoubleMatrixReader

public DoubleMatrixReader()

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.io.InputStream stream,
                        java.util.Set wantedRowNames)
                 throws java.io.IOException

Parameters:

stream - InputStream

wantedRowNames - Set

Returns:

read( stream, wantedRowNames, createEmptyRows ) with createEmptyRows set to true.

Throws:

java.io.IOException

read

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

Parameters:

stream - InputStream

wantedRowNames - Set

createEmptyRows - if a row contained in wantedRowNames is not found in the file, create an empty row filled with Double.NaN iff this param is true.

Returns:

matrix

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

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

createMatrix

protected DenseDoubleMatrix2DNamed createMatrix(java.util.List MTemp,
                                                int rowCount,
                                                int colCount,
                                                java.util.List rowNames,
                                                java.util.List colNames)

createEmptyRow

protected cern.colt.list.DoubleArrayList createEmptyRow(int numColumns)