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, 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

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

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

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

getAdvocate, getAminoAcidScores, getDeltaMass, getIdentificationCharge, getIdentificationFile, getIsotopeNumber, getPrecursorMatch, getRank, getRawScore, getScore, getTheoreticMz, setAminoAcidScores, setIdentificationCharge, setRank, setRawScore, 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

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