com.compomics.util.experiment.identification

Class PeptideAssumption

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

com.compomics.util.experiment.identification.PeptideAssumption

All Implemented Interfaces:

Serializable, Cloneable

public class PeptideAssumption
extends SpectrumIdentificationAssumption

This object will models the assumption made by an advocate.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

identificationFile, score

Constructor Summary

Constructors

Constructor and Description
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score) Constructor for a peptide assumption.
PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score, String identificationFile) Constructor for a peptide assumption.

Method Summary

Methods

Modifier and Type	Method and Description
int	getAdvocate() Get the used advocate.
double	getEValue() Deprecated. use getScore instead
Charge	getIdentificationCharge() Returns the charge used for identification.
String	getIdentificationFile() Returns the identification file.
Peptide	getPeptide() Get the theoretic peptide.
int	getRank() Get the identification rank.
double	getScore() Returns the score assigned by the advocate.
double	getTheoreticMass() Returns the theoretic mass of the given assumption.

Methods inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

getDeltaMass, getDeltaMass, getIsotopeNumber, getPrecursorMatch, getTheoreticMz, setIdentificationCharge, setRank, setScore

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

Constructor Detail

PeptideAssumption

public PeptideAssumption(Peptide aPeptide,
                 int rank,
                 int advocate,
                 Charge identificationCharge,
                 double score,
                 String identificationFile)

Constructor for a peptide assumption.

Parameters:

aPeptide - the theoretic peptide

rank - the identification rank

advocate - the advocate used

identificationCharge - the charge used by the search engine for identification

score - the score, typically a search engine e-value (whether the score is ascending or descending can be known from the SearchEngine class)

identificationFile - the identification file

PeptideAssumption

public PeptideAssumption(Peptide aPeptide,
                 int rank,
                 int advocate,
                 Charge identificationCharge,
                 double score)

Constructor for a peptide assumption.

Parameters:

aPeptide - the theoretic peptide

rank - the identification rank

advocate - the advocate used

identificationCharge - the charge used by the search engine for identification

score - the score (whether the score is ascending or descending can be known from the SearchEngine class)

Method Detail

getPeptide

public Peptide getPeptide()

Get the theoretic peptide.

Returns:

the peptide

getRank

public int getRank()

Description copied from class: SpectrumIdentificationAssumption

Get the identification rank.

Overrides:

getRank in class SpectrumIdentificationAssumption

Returns:

the identification rank

getAdvocate

public int getAdvocate()

Description copied from class: SpectrumIdentificationAssumption

Get the used advocate.

Overrides:

getAdvocate in class SpectrumIdentificationAssumption

Returns:

the advocate index

getEValue

public double getEValue()

Deprecated. use getScore instead

Returns the e-value assigned by the advocate.

Returns:

the e-value

getScore

public double getScore()

Description copied from class: SpectrumIdentificationAssumption

Returns the score assigned by the advocate.

Overrides:

getScore in class SpectrumIdentificationAssumption

Returns:

the score

getIdentificationFile

public String getIdentificationFile()

Description copied from class: SpectrumIdentificationAssumption

Returns the identification file.

Overrides:

getIdentificationFile in class SpectrumIdentificationAssumption

Returns:

the identification file

getIdentificationCharge

public Charge getIdentificationCharge()

Description copied from class: SpectrumIdentificationAssumption

Returns the charge used for identification.

Overrides:

getIdentificationCharge in class SpectrumIdentificationAssumption

Returns:

the charge used for identification

getTheoreticMass

public double getTheoreticMass()

Description copied from class: SpectrumIdentificationAssumption

Returns the theoretic mass of the given assumption.

Specified by:

getTheoreticMass in class SpectrumIdentificationAssumption

Returns:

the theoretic mass of the given assumption