Class StringMatrixReader

java.lang.Object

ubic.gemma.core.util.matrix.AbstractMatrixReader<StringMatrix<String,String>, String>

ubic.gemma.core.util.matrix.StringMatrixReader

public class StringMatrixReader
extends AbstractMatrixReader<StringMatrix<String,String>, String>

Reader for StringMatrix.

Ported in-tree from ubic.basecode.io.reader.StringMatrixReader 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
StringMatrixReader()

Method Summary

Modifier and Type	Method	Description
StringMatrix<String,String>	read(InputStream stream)
StringMatrix<String,String>	read(InputStream stream, int maxRows, int numColumnsToSkip)
StringMatrix<String,String>	read(String filename)
StringMatrix<String,String>	read(String filename, int maxRows)
StringMatrix<String,String>	read(String filename, int maxRows, int numColumnsToSkip)

Methods inherited from class AbstractMatrixReader

readHeader

Methods inherited from class Object

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

Constructor Details

StringMatrixReader

public StringMatrixReader()

Method Details

read

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

Specified by:

read in class AbstractMatrixReader<StringMatrix<String,String>, String>

Throws:

IOException

read

public StringMatrix<String,String> read(InputStream stream,
 int maxRows,
 int numColumnsToSkip)
                                 throws IOException

Parameters:

stream - input stream

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

numColumnsToSkip - how many data columns to skip. 0 or -1 means none; 1 means one column will be skipped, etc.

Returns:

matrix

Throws:

IOException - on I/O error

read

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

Specified by:

read in class AbstractMatrixReader<StringMatrix<String,String>, String>

Throws:

IOException

read

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

Specified by:

read in class AbstractMatrixReader<StringMatrix<String,String>, String>

Throws:

IOException

read

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

Parameters:

filename - file name to read (can be compressed)

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

numColumnsToSkip - how many data columns to skip

Returns:

matrix

Throws:

IOException - on I/O error