ubic.basecode.datafilter

Class AffymetrixProbeNameFilter<M extends Matrix2D<R,C,V>,R,C,V>

java.lang.Object

ubic.basecode.datafilter.AbstractFilter<M,R,C,V>

ubic.basecode.datafilter.AffymetrixProbeNameFilter<M,R,C,V>

All Implemented Interfaces:

Filter<M,R,C,V>

public class AffymetrixProbeNameFilter<M extends Matrix2D<R,C,V>,R,C,V>
extends AbstractFilter<M,R,C,V>

Remove probes that have names meeting certain rules indicating they may have low reliability. This is targeted at cases like "AFFX", "_st", "_f_at" and so forth.

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
static int	AFFX Filter probes that have the AFFX prefix.
static int	F Filter probes that have the "_f_at" (family) tag.
static int	G Filter probes that have the "_g_at" (group) tag.
static int	ST Filter probes that contain the '_st' (sense strand) tag
static int	X Filter probes that have the "_x_at" tag.

Fields inherited from class ubic.basecode.datafilter.AbstractFilter

log

Constructor Summary

Constructors

Constructor and Description
AffymetrixProbeNameFilter() Filter probes with all criteria switched on.
AffymetrixProbeNameFilter(int[] criteria)

Method Summary

Modifier and Type	Method and Description
M	filter(M data) Filter the data

Methods inherited from class ubic.basecode.datafilter.AbstractFilter

getOutputMatrix

Methods inherited from class java.lang.Object

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

Field Detail

AFFX

public static final int AFFX

Filter probes that have the AFFX prefix.

See Also:

Constant Field Values

F

public static final int F

Filter probes that have the "_f_at" (family) tag.

See Also:

Constant Field Values

G

public static final int G

Filter probes that have the "_g_at" (group) tag.

See Also:

Constant Field Values

ST

public static final int ST

Filter probes that contain the '_st' (sense strand) tag

See Also:

Constant Field Values

X

public static final int X

Filter probes that have the "_x_at" tag.

See Also:

Constant Field Values

Constructor Detail

AffymetrixProbeNameFilter

public AffymetrixProbeNameFilter()

Filter probes with all criteria switched on.

AffymetrixProbeNameFilter

public AffymetrixProbeNameFilter(int[] criteria)

Parameters:

criteria - int[] of constants indicating the criteria to use.

Method Detail

filter

public M filter(M data)

Description copied from interface: Filter

Filter the data

Parameters:

data - a NamedMatrix. Some types of filters require that this be of a particular type of implementation of the Filter interface.

Returns:

The resulting filtered matrix