com.compomics.util.experiment.identification

Class SpectrumIdentificationAssumption

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

All Implemented Interfaces:

Serializable, Cloneable

Direct Known Subclasses:

PeptideAssumption, TagAssumption

public abstract class SpectrumIdentificationAssumption
extends ExperimentObject

Spectrum identification assumption made by an identification algorithm.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected int	advocate The advocate supporting this assumption.
protected Charge	identificationCharge The charge used for identification.
protected String	identificationFile The identification file.
protected int	rank The rank of the peptide assumption for the concerned spectrum.
protected double	score The (advocate specific) score used to rank this assumption.

Constructor Summary

Constructors

Constructor and Description
SpectrumIdentificationAssumption()

Method Summary

Methods

Modifier and Type	Method and Description
int	getAdvocate() Get the used advocate.
double	getDeltaMass(double measuredMZ, boolean ppm) Returns the precursor mass error (in ppm or Da).
double	getDeltaMass(double measuredMZ, boolean ppm, boolean subtractIsotope) Returns the precursor mass error (in ppm or Da).
Charge	getIdentificationCharge() Returns the charge used for identification.
String	getIdentificationFile() Returns the identification file.
int	getIsotopeNumber(double measuredMZ) Returns the precursor isotope number according to the number of protons.
IonMatch	getPrecursorMatch(Peak precursorPeak) Returns the ion match.
int	getRank() Get the identification rank.
double	getScore() Returns the score assigned by the advocate.
abstract double	getTheoreticMass() Returns the theoretic mass of the given assumption.
double	getTheoreticMz() Returns the theoretic m/z.
void	setIdentificationCharge(Charge identificationCharge) Sets the identification charge.
void	setRank(int aRank) Set the rank of the PeptideAssumption.
void	setScore(double score) Sets the score.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Field Detail

rank

protected int rank

The rank of the peptide assumption for the concerned spectrum.

advocate

protected int advocate

The advocate supporting this assumption.

identificationCharge

protected Charge identificationCharge

The charge used for identification.

score

protected double score

The (advocate specific) score used to rank this assumption.

identificationFile

protected String identificationFile

The identification file.

Constructor Detail

SpectrumIdentificationAssumption

public SpectrumIdentificationAssumption()

Method Detail

getRank

public int getRank()

Get the identification rank.

Returns:

the identification rank

setRank

public void setRank(int aRank)

Set the rank of the PeptideAssumption.

Parameters:

aRank - the rank of the PeptideAssumptio

getAdvocate

public int getAdvocate()

Get the used advocate.

Returns:

the advocate index

getScore

public double getScore()

Returns the score assigned by the advocate.

Returns:

the score

setScore

public void setScore(double score)

Sets the score.

Parameters:

score - the score

getIdentificationFile

public String getIdentificationFile()

Returns the identification file.

Returns:

the identification file

getIdentificationCharge

public Charge getIdentificationCharge()

Returns the charge used for identification.

Returns:

the charge used for identification

setIdentificationCharge

public void setIdentificationCharge(Charge identificationCharge)

Sets the identification charge.

Parameters:

identificationCharge - the identification charge

getTheoreticMass

public abstract double getTheoreticMass()

Returns the theoretic mass of the given assumption.

Returns:

the theoretic mass of the given assumption

getTheoreticMz

public double getTheoreticMz()

Returns the theoretic m/z.

Returns:

the theoretic m/z

getDeltaMass

public double getDeltaMass(double measuredMZ,
                  boolean ppm,
                  boolean subtractIsotope)

Returns the precursor mass error (in ppm or Da). Note that the value is returns as (experimental mass - theoretical mass) and that negative values thus can occur. The isotopic error can subtracted and retrieved by the function getIsotopeNumber().

Parameters:

measuredMZ - the precursor m/z

ppm - if true the error is returns in ppm, false returns the error in Da

subtractIsotope - if true the isotope number will be subtracted from the theoretic mass

Returns:

the precursor mass error (in ppm or Da)

getDeltaMass

public double getDeltaMass(double measuredMZ,
                  boolean ppm)

Returns the precursor mass error (in ppm or Da). Note that the value is returns as (experimental mass - theoretical mass) and that negative values thus can occur. The isotopic error is subtracted and can be retrieved by the function getIsotopeNumber().

Parameters:

measuredMZ - the precursor m/z

ppm - if true the error is returns in ppm, false returns the error in Da

Returns:

the precursor mass error (in ppm or Da)

getIsotopeNumber

public int getIsotopeNumber(double measuredMZ)

Returns the precursor isotope number according to the number of protons.

Parameters:

measuredMZ -

Returns:

the precursor isotope number according to the number of protons

getPrecursorMatch

public IonMatch getPrecursorMatch(Peak precursorPeak)

Returns the ion match.

Parameters:

precursorPeak -

Returns:

the ion match