maltcms.datastructures.peak

Class Clique<T extends IBipacePeak>

java.lang.Object

maltcms.datastructures.peak.Clique<T>

public class Clique<T extends IBipacePeak>
extends Object

Author:

Nils Hoffmann

Constructor Summary

Constructors

Constructor and Description
Clique()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addPeak(T p) Returns false, if a peak did not meet the criteria to be added to the clique.
boolean	addPeak(T p, boolean force)
boolean	addPeak2(T p)
void	clear()
org.jfree.data.statistics.BoxAndWhiskerItem	createApexTicBoxAndWhisker()
org.jfree.data.statistics.BoxAndWhiskerItem	createRTBoxAndWhisker()
boolean	equals(Object obj)
int	getBBHs()
IPeak	getCliqueCentroid()
double	getCliqueMean()
double	getCliqueRTMean()
double	getCliqueRTVariance()
double	getCliqueVar()
int	getExpectedBBHs()
int	getExpectedBBHs(int groupSize)
long	getID()
int	getMaxBBHErrors()
double	getMinBbhFraction()
List<T>	getPeakList()
double	getRatioOfRTDistanceToCentroidAndCliqueVariance(IPeak p)
double	getRTDistanceToCentroid(IPeak p)
double	getSimilarityForPeaks(String a, String b)
int	hashCode()
boolean	removePeak(T p)
void	setMaxBBHErrors(int maxBBHErrors)
void	setMinBbhFraction(double fraction)
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Clique

public Clique()

Method Detail

getID

public long getID()

addPeak

public boolean addPeak(T p,
              boolean force)

addPeak

public boolean addPeak(T p)
                throws IllegalArgumentException

Returns false, if a peak did not meet the criteria to be added to the clique. Returns true, if a peak is either already contained in the clique, or if it has been successfully added, due to satisfaction of all required criteria.

Parameters:

p -

Returns:

Throws:

IllegalArgumentException

addPeak2

public boolean addPeak2(T p)
                 throws IllegalArgumentException

Throws:

IllegalArgumentException

removePeak

public boolean removePeak(T p)

clear

public void clear()

getBBHs

public int getBBHs()

getExpectedBBHs

public int getExpectedBBHs()

getExpectedBBHs

public int getExpectedBBHs(int groupSize)

createRTBoxAndWhisker

public org.jfree.data.statistics.BoxAndWhiskerItem createRTBoxAndWhisker()

createApexTicBoxAndWhisker

public org.jfree.data.statistics.BoxAndWhiskerItem createApexTicBoxAndWhisker()

getRTDistanceToCentroid

public double getRTDistanceToCentroid(IPeak p)

getRatioOfRTDistanceToCentroidAndCliqueVariance

public double getRatioOfRTDistanceToCentroidAndCliqueVariance(IPeak p)

getCliqueRTVariance

public double getCliqueRTVariance()

getCliqueRTMean

public double getCliqueRTMean()

getCliqueCentroid

public IPeak getCliqueCentroid()

toString

public String toString()

Overrides:

toString in class Object

getPeakList

public List<T> getPeakList()

getSimilarityForPeaks

public double getSimilarityForPeaks(String a,
                           String b)

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

getCliqueMean

public double getCliqueMean()

getCliqueVar

public double getCliqueVar()

getMaxBBHErrors

public int getMaxBBHErrors()

setMaxBBHErrors

public void setMaxBBHErrors(int maxBBHErrors)

setMinBbhFraction

public void setMinBbhFraction(double fraction)

getMinBbhFraction

public double getMinBbhFraction()