Package org.snpeff.geneSets.algorithm

Class EnrichmentAlgorithm

java.lang.Object

org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

Direct Known Subclasses:

EnrichmentAlgorithmGreedy, FisherPValueAlgorithm, NoneAlgorithm, RankSumPValueAlgorithm

public abstract class EnrichmentAlgorithm
extends java.lang.Object

A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets

Author:

pcingola

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	EnrichmentAlgorithm.EnrichmentAlgorithmType

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String[]	HTML_BG_COLOR
static java.lang.String	HTML_BG_COLOR_TITLE
static int	HTML_TD_GENES_MAX_LEN
static long	PRINT_SOMETHING_TIME

Constructor Summary

Constructors

Constructor	Description
EnrichmentAlgorithm(GeneSets geneSets, int numberToSelect)

Method Summary

Modifier and Type	Method	Description
double	getMaxPvalueAdjusted()
java.lang.StringBuilder	getOutput()
protected boolean	isShow(Result result)	Showld we show this result or should the output be filtered?
protected void	print(java.lang.String str)
Result	select()	Select the 'best' gene sets
void	setDebug(boolean debug)
void	setFilterOutputGeneSets(java.util.Set<java.lang.String> filterOutputGeneSets)
void	setHtmlTable(boolean htmlTable)
void	setMaxGeneSetSize(int maxGeneSetSize)
void	setMaxPValue(double maxPValue)
void	setMaxPvalueAdjusted(double maxPvalueAdjusted)
void	setMinGeneSetSize(int minGeneSetSize)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Field Detail

HTML_TD_GENES_MAX_LEN

public static final int HTML_TD_GENES_MAX_LEN

See Also:

Constant Field Values

HTML_BG_COLOR

public static final java.lang.String[] HTML_BG_COLOR

HTML_BG_COLOR_TITLE

public static final java.lang.String HTML_BG_COLOR_TITLE

See Also:

Constant Field Values

PRINT_SOMETHING_TIME

public static long PRINT_SOMETHING_TIME

Constructor Detail

EnrichmentAlgorithm

public EnrichmentAlgorithm(GeneSets geneSets,
                           int numberToSelect)

Method Detail

getMaxPvalueAdjusted

public double getMaxPvalueAdjusted()

getOutput

public java.lang.StringBuilder getOutput()

isShow

protected boolean isShow(Result result)

Showld we show this result or should the output be filtered?

Parameters:

result -

Returns:

print

protected void print(java.lang.String str)

select

public Result select()

Select the 'best' gene sets

Returns:

setDebug

public void setDebug(boolean debug)

setFilterOutputGeneSets

public void setFilterOutputGeneSets(java.util.Set<java.lang.String> filterOutputGeneSets)

setHtmlTable

public void setHtmlTable(boolean htmlTable)

setMaxGeneSetSize

public void setMaxGeneSetSize(int maxGeneSetSize)

setMaxPValue

public void setMaxPValue(double maxPValue)

setMaxPvalueAdjusted

public void setMaxPvalueAdjusted(double maxPvalueAdjusted)

setMinGeneSetSize

public void setMinGeneSetSize(int minGeneSetSize)

setVerbose

public void setVerbose(boolean verbose)