Class DoubleMatrixReader

java.lang.Object

ubic.gemma.core.util.matrix.AbstractMatrixReader<DoubleMatrix<String,String>, Double>

ubic.gemma.core.util.matrix.DoubleMatrixReader

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

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

Ported in-tree from ubic.basecode.io.reader.DoubleMatrixReader as part of the baseCode in-tree migration; previously consumed via the MatrixUtil.fromBaseCode shim.

Author:

Paul Pavlidis

Field Summary

Fields inherited from class AbstractMatrixReader

log

Constructor Summary

Constructors

Constructor	Description
DoubleMatrixReader()

Method Summary

Modifier and Type	Method	Description
protected DoubleArrayList	createEmptyRow(int numColumns)
protected DoubleMatrix<String,String>	createMatrix(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 AbstractMatrixReader

readHeader

Methods inherited from class Object

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

Constructor Details

DoubleMatrixReader

public DoubleMatrixReader()

Method Details

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 - on I/O error

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 - on I/O error

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.

skipColumns - the number of data columns to skip after the row label

maxRows - maximum number of rows to read; -1 means no limit

Returns:

matrix

Throws:

IOException - on I/O error

read

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

Parameters:

stream - input stream

wantedRowNames - optional filter of row names to keep

numberOfColumnsToSkip - data columns to skip after the row label

Returns:

matrix

Throws:

IOException - on I/O error

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 - on I/O error

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 - on I/O error

read

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

Parameters:

fileName - file name

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:

matrix

Throws:

IOException - on I/O error

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 DoubleArrayList createEmptyRow(int numColumns)

createMatrix

protected DoubleMatrix<String,String> createMatrix(List<DoubleArrayList> MTemp,
 List<String> rowNames,
 List<String> colNames1)