org.fhcrc.cpl.viewer.amt
Class AmtPeptideEntry

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

public class AmtPeptideEntry
extends java.lang.Object

Encapsulates everything we need to retrieve from / store into an AMT database. Awfully redundant with the XmlBeans amtXml representation. It's worth it to have a separate class so that we have complete control over the code and can do things like calculate predicted hydrophobicities.

Nested Class Summary

static class	AmtPeptideEntry.AmtPeptideModificationStateEntry Represents an entry for a specific modification state
static class	AmtPeptideEntry.AmtPeptideObservation Represents a single peptide observation.

Field Summary

protected static double	MEAN_HYDRO_UNCALCULATED_SENTINEL
protected double	mHydrophobicityStandardDeviation
protected double	mMassUsingMonoisotopicMassTable
protected double	mMeanObservedHydrophobicity
protected double	mMedianObservedHydrophobicity
protected double	mMedianPeptideProphet
protected java.util.HashMap<java.lang.String,AmtPeptideEntry.AmtPeptideModificationStateEntry>	mModificationStateEntryMap
protected org.fhcrc.cpl.toolbox.proteomics.Peptide	mPeptide
protected java.lang.String	mPeptideSequence
protected double	mPredictedHydrophobicity

Constructor Summary

AmtPeptideEntry()

Method Summary

void	addModificationStateEntry(AmtPeptideEntry.AmtPeptideModificationStateEntry newModificationStateEntry) Add a modification state entry.
AmtPeptideEntry.AmtPeptideModificationStateEntry	addModificationStateEntry(java.lang.String modifiedPeptideSequence, double modifiedMass, java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications)
void	addObservation(java.lang.String peptide, java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications, AmtPeptideEntry.AmtPeptideObservation observation) Add an observation for this peptide and recalculate the stats
protected void	addObservationNoRecalc(java.lang.String peptide, java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications, AmtPeptideEntry.AmtPeptideObservation observation) Add an observation for this peptide.
void	addObservations(java.lang.String peptide, java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications, AmtPeptideEntry.AmtPeptideObservation[] observations, double modificationMassRoundingFactor) Add a bunch of observations for this peptide, without recalculating stats, then recalculate once.
float	calculateIDProbability() Calculate the probability that the ID for this peptide entry is correct.
static AmtPeptideEntry	createEntryFromObservation(java.lang.String peptideSequence, java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications, AmtPeptideEntry.AmtPeptideObservation observation)
static AmtPeptideEntry	createEntryFromObservation(java.lang.String peptideSequence, java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications, double predictedHydrophobicity, AmtPeptideEntry.AmtPeptideObservation observation) Create a new entry with one observation based on a calculated hydrophobicity and that observation
double	getHydrophobicityStandardDeviation()
double	getMass() Calculate this on demand only
double	getMass(double[] massTable) Assume this is a table other than monoisotopic mass table, actually calculate
double	getMeanObservedHydrophobicity() This is not a cost-free getter.
double	getMedianObservedHydrophobicity()
double	getMedianPeptideProphet()
AmtPeptideEntry.AmtPeptideModificationStateEntry[]	getModificationStateEntries()
AmtPeptideEntry.AmtPeptideModificationStateEntry	getModificationStateEntry(java.lang.String modifiedSequence)
int	getNumModificationStates() how many observations for this peptide entry?
int	getNumObservations() how many observations for this peptide entry?
AmtPeptideEntry.AmtPeptideObservation	getObservationForRun(AmtRunEntry runEntry) Quick and dirty method to find which observation, if any, came from this run entry.
AmtPeptideEntry.AmtPeptideObservation[]	getObservations() This getter is computationally intensive, since observations are stored one level down
org.fhcrc.cpl.toolbox.proteomics.Peptide	getPeptide() Build this on demand only
static org.fhcrc.cpl.toolbox.proteomics.Peptide	getPeptideForPeptideSequence(java.lang.String peptideSequence)
java.lang.String	getPeptideSequence()
double	getPredictedHydrophobicity()
int	getSpectralCount()
static double	predictHydrophobicityForPeptideSequence(java.lang.String peptideSequence) predict hydrophobicity based on a peptide sequence.
void	recalculateStats()
void	recalculateStats(int precision) Recalculate the mean observed hydrophobicity and other stats, munging together all observations, giving them equal weight.
boolean	removeObservation(AmtPeptideEntry.AmtPeptideObservation observationToRemove) Removes an observation
protected static double	roundModifiedMass(double inputMass) Round to the nearest multiple of modificationMassRoundingFactor.
void	setHydrophobicityStandardDeviation(double newValue)
void	setPeptideSequence(java.lang.String peptideSequence)
void	setPredictedHydrophobicity(double predictedHydrophobicity)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

mPeptideSequence

protected java.lang.String mPeptideSequence

mPeptide

protected org.fhcrc.cpl.toolbox.proteomics.Peptide mPeptide

mPredictedHydrophobicity

protected double mPredictedHydrophobicity

mMedianObservedHydrophobicity

protected double mMedianObservedHydrophobicity

mMedianPeptideProphet

protected double mMedianPeptideProphet

mHydrophobicityStandardDeviation

protected double mHydrophobicityStandardDeviation

mMassUsingMonoisotopicMassTable

protected double mMassUsingMonoisotopicMassTable

mMeanObservedHydrophobicity

protected double mMeanObservedHydrophobicity

MEAN_HYDRO_UNCALCULATED_SENTINEL

protected static final double MEAN_HYDRO_UNCALCULATED_SENTINEL

See Also:

Constant Field Values

mModificationStateEntryMap

protected java.util.HashMap<java.lang.String,AmtPeptideEntry.AmtPeptideModificationStateEntry> mModificationStateEntryMap

Constructor Detail

AmtPeptideEntry

public AmtPeptideEntry()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

createEntryFromObservation

public static AmtPeptideEntry createEntryFromObservation(java.lang.String peptideSequence,
                                                         java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications,
                                                         AmtPeptideEntry.AmtPeptideObservation observation)

createEntryFromObservation

public static AmtPeptideEntry createEntryFromObservation(java.lang.String peptideSequence,
                                                         java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications,
                                                         double predictedHydrophobicity,
                                                         AmtPeptideEntry.AmtPeptideObservation observation)

Create a new entry with one observation based on a calculated hydrophobicity and that observation

Parameters:

predictedHydrophobicity -

observation -

Returns:

roundModifiedMass

protected static double roundModifiedMass(double inputMass)

Round to the nearest multiple of modificationMassRoundingFactor. Do it by dividing by the factor, rounding to nearest 1, then multiplying by the factor

Parameters:

inputMass -

Returns:

addObservations

public void addObservations(java.lang.String peptide,
                            java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications,
                            AmtPeptideEntry.AmtPeptideObservation[] observations,
                            double modificationMassRoundingFactor)

Add a bunch of observations for this peptide, without recalculating stats, then recalculate once. Because recalculation is expensive

Parameters:

observations -

addObservation

public void addObservation(java.lang.String peptide,
                           java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications,
                           AmtPeptideEntry.AmtPeptideObservation observation)

Add an observation for this peptide and recalculate the stats

Parameters:

observation -

addObservationNoRecalc

protected void addObservationNoRecalc(java.lang.String peptide,
                                      java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications,
                                      AmtPeptideEntry.AmtPeptideObservation observation)

Add an observation for this peptide. Don't recalculate stats

Parameters:

observation -

getPeptide

public org.fhcrc.cpl.toolbox.proteomics.Peptide getPeptide()

Build this on demand only

Returns:

getMass

public double getMass()

Calculate this on demand only

Returns:

getMass

public double getMass(double[] massTable)

Assume this is a table other than monoisotopic mass table, actually calculate

Parameters:

massTable -

Returns:

getPeptideForPeptideSequence

public static org.fhcrc.cpl.toolbox.proteomics.Peptide getPeptideForPeptideSequence(java.lang.String peptideSequence)

predictHydrophobicityForPeptideSequence

public static double predictHydrophobicityForPeptideSequence(java.lang.String peptideSequence)

predict hydrophobicity based on a peptide sequence. This isn't free, so we want to avoid doing it too often, which explains the structure of some of this code

Parameters:

peptideSequence -

Returns:

recalculateStats

public void recalculateStats(int precision)

Recalculate the mean observed hydrophobicity and other stats, munging together all observations, giving them equal weight. Possibly, in the future, if we store probability on observations, weight them

recalculateStats

public void recalculateStats()

calculateIDProbability

public float calculateIDProbability()

Calculate the probability that the ID for this peptide entry is correct. This is calculated simply as: 1 - the product of (1 - each peptide observation's probability)

Returns:

getObservationForRun

public AmtPeptideEntry.AmtPeptideObservation getObservationForRun(AmtRunEntry runEntry)

Quick and dirty method to find which observation, if any, came from this run entry. If nothing, return null. TODO: If this is something we do often, I should build a datastructure for this. TODO: This is totally broken with respect to multiple modification states

Parameters:

runEntry -

Returns:

getNumObservations

public int getNumObservations()

how many observations for this peptide entry?

Returns:

getNumModificationStates

public int getNumModificationStates()

how many observations for this peptide entry?

Returns:

getHydrophobicityStandardDeviation

public double getHydrophobicityStandardDeviation()

setHydrophobicityStandardDeviation

public void setHydrophobicityStandardDeviation(double newValue)

getObservations

public AmtPeptideEntry.AmtPeptideObservation[] getObservations()

This getter is computationally intensive, since observations are stored one level down

Returns:

removeObservation

public boolean removeObservation(AmtPeptideEntry.AmtPeptideObservation observationToRemove)

Removes an observation

Returns:

true if the observation was in this entry already

getModificationStateEntry

public AmtPeptideEntry.AmtPeptideModificationStateEntry getModificationStateEntry(java.lang.String modifiedSequence)

getModificationStateEntries

public AmtPeptideEntry.AmtPeptideModificationStateEntry[] getModificationStateEntries()

addModificationStateEntry

public AmtPeptideEntry.AmtPeptideModificationStateEntry addModificationStateEntry(java.lang.String modifiedPeptideSequence,
                                                                                  double modifiedMass,
                                                                                  java.util.List<org.fhcrc.cpl.toolbox.proteomics.MS2Modification>[] modifications)

addModificationStateEntry

public void addModificationStateEntry(AmtPeptideEntry.AmtPeptideModificationStateEntry newModificationStateEntry)

Add a modification state entry. If we've already got one for this modified peptide (after re-rounding), add all of the new entry's observations to the old entry

Parameters:

newModificationStateEntry -

getPeptideSequence

public java.lang.String getPeptideSequence()

setPeptideSequence

public void setPeptideSequence(java.lang.String peptideSequence)

getPredictedHydrophobicity

public double getPredictedHydrophobicity()

setPredictedHydrophobicity

public void setPredictedHydrophobicity(double predictedHydrophobicity)

getMedianObservedHydrophobicity

public double getMedianObservedHydrophobicity()

getMedianPeptideProphet

public double getMedianPeptideProphet()

getMeanObservedHydrophobicity

public double getMeanObservedHydrophobicity()

This is not a cost-free getter. We store median, not mean, at this level, so if we need the mean we have to calculate it. Once calculated, store it.

Returns:

getSpectralCount

public int getSpectralCount()