uk.ac.ebi.pride.utilities.iongen.model

Class PeptideScore

java.lang.Object

uk.ac.ebi.pride.utilities.iongen.model.PeptideScore

public class PeptideScore
extends Object

Author:

qingwei Date: 10/12/12

Constructor Summary

Constructors

Constructor and Description
PeptideScore(PrecursorIon precursorIon, PeakSet peakSet)
PeptideScore(PrecursorIon precursorIon, PeakSet peakSet, ProductIonPair ionPair, double tolerance, boolean showWaterLoss, boolean showAmmoniaLoss)

Method Summary

Methods

Modifier and Type	Method and Description
List<PeakSet>	getDepthPeakSetList(int peakDepth, int splitSize) Peak set was first separated into windows of splitSize m/z units.
ProductIonPair	getIonPair()
ProductIonSet	getMatchedSet(ProductIonSet productIonSet, PeakSet peakSet) match the peak set to fragment ion list with an ion tolerance of [-tolerance, +tolerance]
double	getProbability(int peakDepth, int splitSize) probability of success.
ProductIonSet	getProductIonSet()
double	getScore(ProductIonSet productIonSet, int peakDepth, int splitSize) get a peptide score based on peakDepth.
double	getTolerance()
double	getWeightedAvgScore(ProductIonSet productIonSet, int splitSize, double[] weightList) get a weighted average peptide score.
boolean	isShowAmmoniaLoss()
boolean	isShowWaterLoss()
void	setIonPair(ProductIonPair ionPair)
void	setShowAmmoniaLoss(boolean showAmmoniaLoss)
void	setShowWaterLoss(boolean showWaterLoss)
void	setTolerance(double tolerance)

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideScore

public PeptideScore(PrecursorIon precursorIon,
            PeakSet peakSet,
            ProductIonPair ionPair,
            double tolerance,
            boolean showWaterLoss,
            boolean showAmmoniaLoss)

PeptideScore

public PeptideScore(PrecursorIon precursorIon,
            PeakSet peakSet)

Method Detail

getIonPair

public ProductIonPair getIonPair()

setIonPair

public void setIonPair(ProductIonPair ionPair)

isShowWaterLoss

public boolean isShowWaterLoss()

setShowWaterLoss

public void setShowWaterLoss(boolean showWaterLoss)

isShowAmmoniaLoss

public boolean isShowAmmoniaLoss()

setShowAmmoniaLoss

public void setShowAmmoniaLoss(boolean showAmmoniaLoss)

getTolerance

public double getTolerance()

setTolerance

public void setTolerance(double tolerance)

getProbability

public double getProbability(int peakDepth,
                    int splitSize)

probability of success.

getProductIonSet

public ProductIonSet getProductIonSet()

getMatchedSet

public ProductIonSet getMatchedSet(ProductIonSet productIonSet,
                          PeakSet peakSet)

match the peak set to fragment ion list with an ion tolerance of [-tolerance, +tolerance]

getDepthPeakSetList

public List<PeakSet> getDepthPeakSetList(int peakDepth,
                                int splitSize)

Peak set was first separated into windows of splitSize m/z units. Within each window, only the top peakDepth peaks were retained by intensity.

getScore

public double getScore(ProductIonSet productIonSet,
              int peakDepth,
              int splitSize)

get a peptide score based on peakDepth.

getWeightedAvgScore

public double getWeightedAvgScore(ProductIonSet productIonSet,
                         int splitSize,
                         double[] weightList)

get a weighted average peptide score.