org.fhcrc.cpl.viewer.amt
Class AmtPeptideEntry.AmtPeptideObservation

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AmtPeptideEntry.AmtPeptideObservation

Enclosing class:

AmtPeptideEntry

public static class AmtPeptideEntry.AmtPeptideObservation
extends java.lang.Object

Represents a single peptide observation. Carries a reference to the AmtRunEntry that the observation came from

Field Summary

protected double	mObservedHydrophobicity
protected double	mPeptideProphet
protected int	mSpectralCount
protected double	mTimeInRun
protected AmtRunEntry	runEntry
static int	SPECTRAL_COUNT_UNKNOWN

Constructor Summary

AmtPeptideEntry.AmtPeptideObservation()

Method Summary

static AmtPeptideEntry.AmtPeptideObservation	createObservation(double observedHydrophobicity, double qualityScore, AmtRunEntry runEntry, double timeInRun) Given an observed hydrophobicity, create an observation
double	getObservedHydrophobicity()
double	getPeptideProphet()
AmtRunEntry	getRunEntry()
int	getSpectralCount()
double	getTimeInRun()
boolean	hasSpectralCount()
void	setObservedHydrophobicity(double observedHydrophobicity)
void	setPeptideProphet(double peptideProphet)
void	setRunEntry(AmtRunEntry runEntry)
void	setSpectralCount(int spectralCount)
void	setTimeInRun(double timeInRun)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

mObservedHydrophobicity

protected double mObservedHydrophobicity

mPeptideProphet

protected double mPeptideProphet

runEntry

protected AmtRunEntry runEntry

mTimeInRun

protected double mTimeInRun

mSpectralCount

protected int mSpectralCount

SPECTRAL_COUNT_UNKNOWN

public static final int SPECTRAL_COUNT_UNKNOWN

See Also:

Constant Field Values

Constructor Detail

AmtPeptideEntry.AmtPeptideObservation

public AmtPeptideEntry.AmtPeptideObservation()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

createObservation

public static AmtPeptideEntry.AmtPeptideObservation createObservation(double observedHydrophobicity,
                                                                      double qualityScore,
                                                                      AmtRunEntry runEntry,
                                                                      double timeInRun)

Given an observed hydrophobicity, create an observation

Parameters:

observedHydrophobicity -

Returns:

getObservedHydrophobicity

public double getObservedHydrophobicity()

setObservedHydrophobicity

public void setObservedHydrophobicity(double observedHydrophobicity)

getPeptideProphet

public double getPeptideProphet()

setPeptideProphet

public void setPeptideProphet(double peptideProphet)

getRunEntry

public AmtRunEntry getRunEntry()

setRunEntry

public void setRunEntry(AmtRunEntry runEntry)

getSpectralCount

public int getSpectralCount()

setSpectralCount

public void setSpectralCount(int spectralCount)

hasSpectralCount

public boolean hasSpectralCount()

getTimeInRun

public double getTimeInRun()

setTimeInRun

public void setTimeInRun(double timeInRun)