ubic.erminej.analysis

Class AbstractResamplingGeneSetScore

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractResamplingGeneSetScore

All Implemented Interfaces:

NullDistributionGenerator

Direct Known Subclasses:

GeneSetResamplingBackgroundDistributionGenerator, ResamplingCorrelationGeneSetScore

public abstract class AbstractResamplingGeneSetScore
extends AbstractLongTask
implements NullDistributionGenerator

Version:

$Id: AbstractResamplingGeneSetScore.java,v 1.3 2012/03/02 20:15:45 paul Exp $

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected int	classMaxSize
protected int	classMinSize
protected Histogram	hist
protected double	histogramMax
protected double	histogramMin
protected static org.apache.commons.logging.Log	log
protected static int	NORMAL_APPROX_SAMPLE_FREQUENCY Check for fit to a normal distribution every n trials.
protected int	numClasses
protected int	numRuns
protected static double	SPEDUPSIZEEXTRASTEP
protected static int	SPEEDUPSIZECUT The size we use to start skipping sizes for resampling.
protected static double	TOLERANCE Used to control interations.
protected boolean	useNormalApprox
protected boolean	useSpeedUp

Constructor Summary

Constructors

Constructor and Description
AbstractResamplingGeneSetScore()

Method Summary

Methods

Modifier and Type	Method and Description
Histogram	getHist()
void	setClassMaxSize(int value)
void	setUseNormalApprox(boolean useNormalApprox)
void	setUseSpeedUp(boolean useSpeedUp) If you set this to true, when large class sizes are analyzed, not every size is measured directly.

Methods inherited from class ubic.erminej.analysis.AbstractLongTask

ifInterruptedStop

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.erminej.analysis.NullDistributionGenerator

generateNullDistribution, setRandomSeed

Field Detail

log

protected static final org.apache.commons.logging.Log log

TOLERANCE

protected static final double TOLERANCE

Used to control interations.

See Also:

Constant Field Values

NORMAL_APPROX_SAMPLE_FREQUENCY

protected static final int NORMAL_APPROX_SAMPLE_FREQUENCY

Check for fit to a normal distribution every n trials. This sets n.

See Also:

Constant Field Values

SPEEDUPSIZECUT

protected static final int SPEEDUPSIZECUT

The size we use to start skipping sizes for resampling.

See Also:

Constant Field Values

SPEDUPSIZEEXTRASTEP

protected static final double SPEDUPSIZEEXTRASTEP

See Also:

Constant Field Values

useSpeedUp

protected boolean useSpeedUp

useNormalApprox

protected boolean useNormalApprox

classMaxSize

protected int classMaxSize

numRuns

protected int numRuns

numClasses

protected int numClasses

histogramMax

protected double histogramMax

histogramMin

protected double histogramMin

classMinSize

protected int classMinSize

hist

protected Histogram hist

Constructor Detail

AbstractResamplingGeneSetScore

public AbstractResamplingGeneSetScore()

Method Detail

getHist

public Histogram getHist()

setClassMaxSize

public void setClassMaxSize(int value)

Parameters:

value - int

setUseSpeedUp

public void setUseSpeedUp(boolean useSpeedUp)

If you set this to true, when large class sizes are analyzed, not every size is measured directly.

Parameters:

useSpeedUp -

setUseNormalApprox

public void setUseNormalApprox(boolean useNormalApprox)