Class AbstractMatrixReader<M extends Matrix2D<String,String,V>, V>

java.lang.Object

ubic.gemma.core.util.matrix.AbstractMatrixReader<M,V>

Direct Known Subclasses:

DoubleMatrixReader, StringMatrixReader

public abstract class AbstractMatrixReader<M extends Matrix2D<String,String,V>, V>
extends Object

Abstract class representing an object that can read in a Matrix2D from a file.

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

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected static final org.slf4j.Logger	log

Constructor Summary

Constructors

Constructor	Description
AbstractMatrixReader()

Method Summary

Modifier and Type	Method	Description
abstract M	read(InputStream stream)
abstract M	read(String filename)
abstract M	read(String filename, int maxRows)
protected List<String>	readHeader(BufferedReader dis, int skipColumns)

Methods inherited from class Object

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

Field Details

log

protected static final org.slf4j.Logger log

Constructor Details

AbstractMatrixReader

public AbstractMatrixReader()

Method Details

read

public abstract M read(InputStream stream)
                throws IOException

Throws:

IOException

read

public abstract M read(String filename)
                throws IOException

Throws:

IOException

read

public abstract M read(String filename,
 int maxRows)
                throws IOException

Throws:

IOException

readHeader

protected List<String> readHeader(BufferedReader dis,
 int skipColumns)
                           throws IOException

Parameters:

dis - input reader positioned at the start of the header line

skipColumns - how many data columns should be ignored

Returns:

list of column header names (excluding the corner cell)

Throws:

IOException - on I/O error or malformed header