org.expasy.mzjava.core.ms.spectrasim

Class PspcSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation>

java.lang.Object

org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc<X,Y>

org.expasy.mzjava.core.ms.spectrasim.PspcSimFunc<X,Y>

All Implemented Interfaces:

PeakPairSink<X,Y>, SimFunc<X,Y>

public class PspcSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation>
extends AbstractSimFunc<X,Y>

Poisson shared peak count similarity function. For each peak the counts from vector x are compared to the counts in vector y using Poisson comparison of two counts. If the two counts are significantly different the peak with the smaller count is set to zero.

The shared peak count is then calculated from 2*k/(m + n) Where k = the number of shared peaks, m = the number of peaks in x and n = the number of peaks in y

Version:

sqrt -1

Author:

Oliver Horlacher

Constructor Summary

Constructors

Constructor and Description
PspcSimFunc(int minPeakCount, PeakListAligner<X,Y> peakListAligner, PeakPairProcessor<X,Y>... chain)
PspcSimFunc(int minPeakCount, Tolerance tolerance)

Method Summary

Methods

Modifier and Type	Method and Description
double	calcSimilarity(PeakList<X> plX, PeakList<Y> plY) Calculate the similarity score of the two vectors.
double	getBestScore() Return the best score that can be returned by calls to calcSimilarity.
int	getTotalPeakCount() Returns the total number peaks in plX and plY from the last call to calcSimilarity
double	getWorstScore() Return the worst the score that can be returned by calls to calcSimilarity.
void	processPeakPair(double centroid, double x, double y, List<X> xAnnotations, List<Y> yAnnotations) Pushes the next peak pair to this sink

Methods inherited from class org.expasy.mzjava.core.ms.spectrasim.AbstractSimFunc

begin, end, vectorize

Methods inherited from class java.lang.Object

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

Constructor Detail

PspcSimFunc

public PspcSimFunc(int minPeakCount,
           Tolerance tolerance)

PspcSimFunc

public PspcSimFunc(int minPeakCount,
           PeakListAligner<X,Y> peakListAligner,
           PeakPairProcessor<X,Y>... chain)

Method Detail

calcSimilarity

public double calcSimilarity(PeakList<X> plX,
                    PeakList<Y> plY)

Description copied from interface: SimFunc

Calculate the similarity score of the two vectors. Returns the similarity score or NaN if the score cannot be calculated

Parameters:

plX - the fist peak list

plY - the second peak list

Returns:

the similarity score or NaN if the score cannot be calculated

getTotalPeakCount

public int getTotalPeakCount()

Description copied from interface: SimFunc

Returns the total number peaks in plX and plY from the last call to calcSimilarity

Returns:

the total number peaks in plX and plY from the last call to calcSimilarity

processPeakPair

public void processPeakPair(double centroid,
                   double x,
                   double y,
                   List<X> xAnnotations,
                   List<Y> yAnnotations)

Description copied from interface: PeakPairSink

Pushes the next peak pair to this sink

Parameters:

centroid - the m/z

x - the intensity of the first peak

y - the intensity of the second peak

xAnnotations - the annotations for the first peak

yAnnotations - the annotations for the second peak

getBestScore

public double getBestScore()

Description copied from interface: SimFunc

Return the best score that can be returned by calls to calcSimilarity. For similarity functions for which the best score has no upper limit Double.POSITIVE_INFINITY is returned and where the best score has no lower limit Double.NEGATIVE_INFINITY is returned.

Returns:

the best score that can be returned by calls to calcSimilarity

getWorstScore

public double getWorstScore()

Description copied from interface: SimFunc

Return the worst the score that can be returned by calls to calcSimilarity. For similarity functions for which the worst score has no upper limit Double.POSITIVE_INFINITY is returned and where the worst score has no lower limit Double.NEGATIVE_INFINITY is returned.

Returns:

the worst score that can be returned by calls to calcSimilarity