Package org.snpeff.geneSets

Class Result

java.lang.Object

org.snpeff.geneSets.Result

All Implemented Interfaces:

java.lang.Comparable<Result>

public class Result
extends java.lang.Object
implements java.lang.Comparable<Result>

Store a result form a greedy search algorithm

Author:

Pablo Cingolani

Constructor Summary

Constructors

Constructor	Description
Result()
Result(java.util.List<GeneSet> list, double pValue)
Result(GeneSet geneSet, org.apfloat.Apfloat pValue, int geneSetCount)
Result(Result res)

Method Summary

Modifier and Type	Method	Description
void	addGeneSetCount(int count)	Add an item to the list of counts
int	compareTo(Result res)
java.util.List<java.lang.Integer>	getGeneSetCount()
int	getGeneSetCountLast()
java.util.List<GeneSet>	getGeneSets()
GeneSet	getLatestGeneSet()
org.apfloat.Apfloat	getPvalue()
double	getPvalueAdjusted()	P-Value adjusted using
double	getPvalueDouble()
boolean	isEmpty()
void	set(java.util.List<GeneSet> geneSets, org.apfloat.Apfloat pValue)	Ser a new list and pvalue
void	setGeneSetCount(java.util.List<java.lang.Integer> geneSetCount)
void	setGeneSetCountLast(int count)
void	setGeneSets(java.util.List<GeneSet> newGeneSets)	Assign geneSets
void	setPvalue(double pValue)
void	setPvalue(org.apfloat.Apfloat pValue)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Result

public Result()

Result

public Result(GeneSet geneSet,
              org.apfloat.Apfloat pValue,
              int geneSetCount)

Result

public Result(java.util.List<GeneSet> list,
              double pValue)

Result

public Result(Result res)

Method Detail

addGeneSetCount

public void addGeneSetCount(int count)

Add an item to the list of counts

Parameters:

count -

compareTo

public int compareTo(Result res)

Specified by:

compareTo in interface java.lang.Comparable<Result>

getGeneSetCount

public java.util.List<java.lang.Integer> getGeneSetCount()

getGeneSetCountLast

public int getGeneSetCountLast()

getGeneSets

public java.util.List<GeneSet> getGeneSets()

getLatestGeneSet

public GeneSet getLatestGeneSet()

getPvalue

public org.apfloat.Apfloat getPvalue()

getPvalueAdjusted

public double getPvalueAdjusted()

P-Value adjusted using

Returns:

getPvalueDouble

public double getPvalueDouble()

isEmpty

public boolean isEmpty()

set

public void set(java.util.List<GeneSet> geneSets,
                org.apfloat.Apfloat pValue)

Ser a new list and pvalue

Parameters:

geneSets -

pvalue -

setGeneSetCount

public void setGeneSetCount(java.util.List<java.lang.Integer> geneSetCount)

setGeneSetCountLast

public void setGeneSetCountLast(int count)

setGeneSets

public void setGeneSets(java.util.List<GeneSet> newGeneSets)

Assign geneSets

Parameters:

newGeneSets -

setPvalue

public void setPvalue(org.apfloat.Apfloat pValue)

setPvalue

public void setPvalue(double pValue)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object