Package ubic.basecode.io.reader

Class DoubleMatrixReader

java.lang.Object

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

ubic.basecode.io.reader.DoubleMatrixReader

Direct Known Subclasses:

SparseDoubleMatrixReader, SparseRaggedMatrixReader

public class DoubleMatrixReader
extends AbstractMatrixReader<DoubleMatrix<String,String>,Double>

Reader for basecode.dataStructure.matrix.DoubleMatrix. Lines beginning with "#" or "!" will be ignored.

Author:

Paul Pavlidis

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
DoubleMatrixReader()

Method Summary

Modifier and Type	Method	Description
protected cern.colt.list.DoubleArrayList	createEmptyRow(int numColumns)
protected DoubleMatrix<String,String>	createMatrix(List<cern.colt.list.DoubleArrayList> MTemp, List<String> rowNames, List<String> colNames1)
DoubleMatrix<String,String>	read(InputStream stream)
DoubleMatrix<String,String>	read(InputStream stream, Collection<String> wantedRowNames)
DoubleMatrix<String,String>	read(InputStream stream, Collection<String> wantedRowNames, boolean createEmptyRows, int skipColumns, int maxRows)
DoubleMatrix<String,String>	read(InputStream stream, Collection<String> wantedRowNames, int numberOfColumnsToSkip)
DoubleMatrix<String,String>	read(String filename)
DoubleMatrix<String,String>	read(String filename, int maxRows)
DoubleMatrix<String,String>	read(String filename, Collection<String> wantedRowNames)	Read a matrix from a file, subject to filtering criteria.
DoubleMatrix<String,String>	read(String fileName, Collection<String> wantedRowNames, int numberOfColumnsToSkip)

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

DoubleMatrixReader

public DoubleMatrixReader()

Method Detail

read

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

Specified by:

read in class AbstractMatrixReader<DoubleMatrix<String,String>,Double>

Parameters:

stream - InputStream stream to read from

Returns:

NamedMatrix object constructed from the data file

Throws:

IOException

read

public DoubleMatrix<String,String> read(InputStream stream,
                                              Collection<String> wantedRowNames)
                                       throws IOException

Parameters:

stream - InputStream

wantedRowNames - Set

Returns:

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

Throws:

IOException

read

public DoubleMatrix<String,String> read(InputStream stream,
                                              Collection<String> wantedRowNames,
                                              boolean createEmptyRows,
                                              int skipColumns,
                                              int maxRows)
                                       throws 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.

maxRows -

Returns:

matrix

Throws:

IOException

read

public DoubleMatrix<String,String> read(InputStream stream,
                                              Collection<String> wantedRowNames,
                                              int numberOfColumnsToSkip)
                                       throws IOException

Parameters:

stream -

wantedRowNames -

numberOfColumnsToSkip -

Returns:

Throws:

IOException

read

public DoubleMatrix<String,String> read(String filename)
                                       throws IOException

Specified by:

read in class AbstractMatrixReader<DoubleMatrix<String,String>,Double>

Parameters:

filename - data file to read from (can be compressed)

Returns:

NamedMatrix object constructed from the data file

Throws:

IOException

read

public DoubleMatrix<String,String> read(String filename,
                                              Collection<String> wantedRowNames)
                                       throws IOException

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

Parameters:

filename - data file to read from (can be compressed)

wantedRowNames - contains names of rows we want to get

Returns:

NamedMatrix object constructed from the data file

Throws:

IOException

read

public DoubleMatrix<String,String> read(String fileName,
                                              Collection<String> wantedRowNames,
                                              int numberOfColumnsToSkip)
                                       throws IOException

Parameters:

fileName -

wantedRowNames - if null, takes all rows

numberOfColumnsToSkip - how many columns to skip -- not counting the first column. So if you set this to 4, the first four data columns will be skipped. If you set it to zero, only the first column will be skipped.

Returns:

Throws:

IOException

read

public DoubleMatrix<String,String> read(String filename,
                                              int maxRows)
                                       throws IOException

Specified by:

read in class AbstractMatrixReader<DoubleMatrix<String,String>,Double>

Throws:

IOException

createEmptyRow

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

createMatrix

protected DoubleMatrix<String,String> createMatrix(List<cern.colt.list.DoubleArrayList> MTemp,
                                                         List<String> rowNames,
                                                         List<String> colNames1)