org.expasy.mzjava.core.ms.cluster

Class SpectrumClusterEvaluator<A extends PeakAnnotation,S extends PeakList<A>>

java.lang.Object

org.expasy.mzjava.core.ms.cluster.SpectrumClusterEvaluator<A,S>

public class SpectrumClusterEvaluator<A extends PeakAnnotation,S extends PeakList<A>>
extends Object

Class to evaluate whether a set of spectra cluster together. If the set contains alien spectra, the SpectrumClusterEvaluator.evaluate method tries to find the largest subset of similar spectra. If no such subset can be found, it returns the spectrum with the largest similarity to the other set members.

Version:

0.0

Author:

Markus Muller

Field Summary

Fields

Modifier and Type	Field and Description
protected double	maxSimScore
protected double	meanSimScore
protected double	minSimScore
protected int	nrMembersCleaned
protected int	nrMembersOrg
protected double	sdSimScore

Constructor Summary

Constructors

Constructor and Description
SpectrumClusterEvaluator(Tolerance tolerance, SimFunc<A,A> simFunc, ClusterBuilder<S> clusterBuilder)

Method Summary

Methods

Modifier and Type	Method and Description
Set<S>	evaluate(Collection<S> spectra)
double	getMaxSimScore()
double	getMeanSimScore()
double	getMinSimScore()
int	getNrMembersCleaned()
int	getNrMembersOrg()
double	getSdSimScore()

Methods inherited from class java.lang.Object

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

Field Detail

minSimScore

protected double minSimScore

maxSimScore

protected double maxSimScore

meanSimScore

protected double meanSimScore

sdSimScore

protected double sdSimScore

nrMembersOrg

protected int nrMembersOrg

nrMembersCleaned

protected int nrMembersCleaned

Constructor Detail

SpectrumClusterEvaluator

public SpectrumClusterEvaluator(Tolerance tolerance,
                        SimFunc<A,A> simFunc,
                        ClusterBuilder<S> clusterBuilder)

Method Detail

evaluate

public Set<S> evaluate(Collection<S> spectra)

getMinSimScore

public double getMinSimScore()

getMaxSimScore

public double getMaxSimScore()

getMeanSimScore

public double getMeanSimScore()

getSdSimScore

public double getSdSimScore()

getNrMembersOrg

public int getNrMembersOrg()

getNrMembersCleaned

public int getNrMembersCleaned()