Package ubic.basecode.datafilter

Class AbstractLevelFilter<R,C>

java.lang.Object

ubic.basecode.datafilter.AbstractFilter<DoubleMatrix<R,C>,R,C,Double>

ubic.basecode.datafilter.AbstractLevelFilter<R,C>

All Implemented Interfaces:

Filter<DoubleMatrix<R,C>,R,C,Double>

Direct Known Subclasses:

ItemLevelFilter, RowLevelFilter

public abstract class AbstractLevelFilter<R,C>
extends AbstractFilter<DoubleMatrix<R,C>,R,C,Double>

Abstract class representing a filter that removes things from DoubleMatrixNamed matrices based on the values themselves.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected double	highCut
protected double	lowCut
protected boolean	useHighAsFraction
protected boolean	useLowAsFraction

Fields inherited from class ubic.basecode.datafilter.AbstractFilter

log

Constructor Summary

Constructors

Constructor	Description
AbstractLevelFilter()

Method Summary

Modifier and Type	Method	Description
void	setHighCut(double h)	Set the high threshold for removal.
void	setHighCut(double highCut, boolean isFraction)
void	setLowCut(double lowCut)	Set the low threshold for removal.
void	setLowCut(double lowCut, boolean isFraction)
void	setUseAsFraction(boolean setting)	Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of the rows with the lowest values.
void	setUseHighCutAsFraction(boolean setting)
void	setUseLowCutAsFraction(boolean setting)

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

Methods inherited from interface ubic.basecode.datafilter.Filter

filter

Field Detail

highCut

protected double highCut

lowCut

protected double lowCut

useHighAsFraction

protected boolean useHighAsFraction

useLowAsFraction

protected boolean useLowAsFraction

Constructor Detail

AbstractLevelFilter

public AbstractLevelFilter()

Method Detail

setHighCut

public void setHighCut(double h)

Set the high threshold for removal. If not set, no filtering will occur.

Parameters:

h - the threshold

setHighCut

public void setHighCut(double highCut,
                       boolean isFraction)

Parameters:

highCut -

isFraction -

setLowCut

public void setLowCut(double lowCut)

Set the low threshold for removal.

Parameters:

lowCut - the threshold

setLowCut

public void setLowCut(double lowCut,
                      boolean isFraction)

Parameters:

lowCut -

isFraction -

setUseAsFraction

public void setUseAsFraction(boolean setting)

Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of the rows with the lowest values. Otherwise the cuts are interpeted as actual values. Default = false.

Parameters:

setting - boolean

setUseHighCutAsFraction

public void setUseHighCutAsFraction(boolean setting)

Parameters:

setting -

setUseLowCutAsFraction

public void setUseLowCutAsFraction(boolean setting)

Parameters:

setting -