Package com.compomics.util.experiment.identification.spectrum_assumptions

Class PeptideAssumption

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.identification.SpectrumIdentificationAssumption

com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption

All Implemented Interfaces:

Serializable

public class PeptideAssumption
extends SpectrumIdentificationAssumption

This object 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

advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score

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

NO_KEY

Constructor Summary

Constructors

Constructor	Description
PeptideAssumption()	Default constructor for the purpose of instantiation.
PeptideAssumption(Peptide peptide, int identificationCharge)	Constructor for a simple peptide assumption containing only the information necessary for spectrum annotation.
PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score)	Constructor for a peptide assumption.
PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score, String identificationFile)	Constructor for a peptide assumption.

Method Summary

Modifier and Type	Method	Description
Peptide	getPeptide()	Get the theoretic peptide.
double	getTheoreticMass()	Returns the theoretic mass of the given assumption.
void	setPeptide(Peptide peptide)	Returns the peptides.

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

getAdvocate, getAminoAcidScores, getDeltaMz, getIdentificationCharge, getIdentificationFile, getIsotopeNumber, getPrecursorMatch, getRank, getRawScore, getScore, getTheoreticMz, setAdvocate, setAminoAcidScores, setIdentificationCharge, setIdentificationFile, setRank, setRawScore, setScore

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

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Constructor Details

PeptideAssumption

public PeptideAssumption()

Default constructor for the purpose of instantiation.

PeptideAssumption

public PeptideAssumption(Peptide peptide,
 int rank,
 int advocate,
 int identificationCharge,
 double rawScore,
 double score,
 String identificationFile)

Constructor for a peptide assumption.

Parameters:

peptide - the theoretic peptide

rank - the identification rank

advocate - the advocate used

identificationCharge - the charge used by the search engine for identification

rawScore - the raw score, i.e. the untransformed score given by the search engine

score - the (potentially transformed) 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 peptide,
 int rank,
 int advocate,
 int identificationCharge,
 double rawScore,
 double score)

Constructor for a peptide assumption.

Parameters:

peptide - the theoretic peptide

rank - the identification rank

advocate - the advocate used

identificationCharge - the charge used by the search engine for identification

rawScore - the raw score, i.e. the untransformed score given by the search engine

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

PeptideAssumption

public PeptideAssumption(Peptide peptide,
 int identificationCharge)

Constructor for a simple peptide assumption containing only the information necessary for spectrum annotation.

Parameters:

peptide - the theoretic peptide

identificationCharge - the charge used by the search engine for identification

Method Details

getPeptide

public Peptide getPeptide()

Get the theoretic peptide.

Returns:

the peptide

setPeptide

public void setPeptide(Peptide peptide)

Returns the peptides.

Parameters:

peptide - the peptide

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