baseCode.dataFilter
Class AffymetrixProbeNameFilter

java.lang.Object
  baseCode.dataFilter.AbstractFilter
      baseCode.dataFilter.AffymetrixProbeNameFilter

All Implemented Interfaces:

Filter

public class AffymetrixProbeNameFilter

extends AbstractFilter

implements Filter

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.

Copyright (c) 2004

Institution:: Columbia University

Version:

$Id: AffymetrixProbeNameFilter.java,v 1.12 2004/08/17 21:17:40 pavlidis Exp $

Author:

Paul Pavlidis

Field Summary

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 baseCode.dataFilter.AbstractFilter

log

Constructor Summary

AffymetrixProbeNameFilter()
Filter probes with all criteria switched on.

AffymetrixProbeNameFilter(int[] criteria)

Method Summary

NamedMatrix

filter(NamedMatrix data) Filter the data

Methods inherited from class baseCode.dataFilter.AbstractFilter

getOutputMatrix

Methods inherited from class java.lang.Object

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

Field Detail

ST

public static final int ST

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

See Also:

Constant Field Values

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

X

public static final int X

Filter probes that have the "_x_at" 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

Constructor Detail

AffymetrixProbeNameFilter

public AffymetrixProbeNameFilter(int[] criteria)

Parameters:

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

AffymetrixProbeNameFilter

public AffymetrixProbeNameFilter()

Filter probes with all criteria switched on.

Method Detail

filter

public NamedMatrix filter(NamedMatrix data)

Description copied from interface: Filter

Filter the data

Specified by:

filter in interface Filter

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