org.expasy.mzjava.core.ms.spectrasim

Class AbstractSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation>

java.lang.Object

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

All Implemented Interfaces:

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

Direct Known Subclasses:

DpSimFunc, McNdpSimFunc, NdpSimFunc, PearsonsSimFunc, PspcSimFunc, SharedPeakSimFunc, WeightedPearsonsSimFunc

public abstract class AbstractSimFunc<X extends PeakAnnotation,Y extends PeakAnnotation>
extends Object
implements SimFunc<X,Y>, PeakPairSink<X,Y>

Abstract similarity function. This class takes care of vectorizing the PeakList pairs. Vectorizing aligns the two PeakLists and then processes the aligned peak pairs using the PeakPairProcessor chain.

Version:

1.0

Author:

Oliver Horlacher

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractSimFunc(PeakListAligner<X,Y> peakListAligner, PeakPairProcessor<X,Y>... chain) Creates a AbstractSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain.
protected	AbstractSimFunc(Tolerance tolerance) Creates a AbstractSimFunc that uses a DefaultPeakListAligner and clear processor chain.

Method Summary

Methods

Modifier and Type	Method and Description
void	begin(PeakList<X> xPeakList, PeakList<Y> yPeakList) Called before a new PeakList pair is processed
void	end() Called when all the peak pairs in the PeakList pair have been processed
void	vectorize(PeakList<X> peakListX, PeakList<Y> peakListY) Aligns the two PeakLists and then processes the aligned peak tupplets using the PeakPairProcessor chain.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.expasy.mzjava.core.ms.spectrasim.SimFunc

calcSimilarity, getBestScore, getTotalPeakCount, getWorstScore

Methods inherited from interface org.expasy.mzjava.core.ms.spectrasim.peakpairprocessor.PeakPairSink

processPeakPair

Constructor Detail

AbstractSimFunc

protected AbstractSimFunc(Tolerance tolerance)

Creates a AbstractSimFunc that uses a DefaultPeakListAligner and clear processor chain.

Parameters:

tolerance - the tolerance to use when aligning the two PeakLists

AbstractSimFunc

protected AbstractSimFunc(PeakListAligner<X,Y> peakListAligner,
               PeakPairProcessor<X,Y>... chain)

Creates a AbstractSimFunc that uses the supplied PeakListAligner and PeakPairProcessor chain.

Parameters:

peakListAligner - the object that is used to align the PeakList pairs

chain - PeakPairProcessor chain that is used to pre-process the aligned peaks before calculating the similarity

Method Detail

vectorize

public void vectorize(PeakList<X> peakListX,
             PeakList<Y> peakListY)

Aligns the two PeakLists and then processes the aligned peak tupplets using the PeakPairProcessor chain.

Parameters:

peakListX - the first peak list

peakListY - the second peak list

begin

public void begin(PeakList<X> xPeakList,
         PeakList<Y> yPeakList)

Description copied from interface: PeakPairSink

Called before a new PeakList pair is processed

Specified by:

begin in interface PeakPairSink<X extends PeakAnnotation,Y extends PeakAnnotation>

Parameters:

xPeakList - the first member of the peak pair that is going to be processed

yPeakList - the second member of the peak pair that is going to be processed

end

public void end()

Description copied from interface: PeakPairSink

Called when all the peak pairs in the PeakList pair have been processed

Specified by:

end in interface PeakPairSink<X extends PeakAnnotation,Y extends PeakAnnotation>