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
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Field Summary
Fields inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score
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Constructor Summary
Constructors Constructor Description PeptideAssumption()
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 score)
Constructor for a peptide assumption.PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, 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)
Methods inherited from class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
getAdvocate, getAminoAcidScores, getDeltaMass, 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
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Constructor Details
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PeptideAssumption
public PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double score, String identificationFile)Constructor for a peptide assumption.- Parameters:
peptide
- the theoretic peptiderank
- the identification rankadvocate
- the advocate usedidentificationCharge
- the charge used by the search engine for identificationscore
- 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
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PeptideAssumption
public PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double score)Constructor for a peptide assumption.- Parameters:
peptide
- the theoretic peptiderank
- the identification rankadvocate
- the advocate usedidentificationCharge
- the charge used by the search engine for identificationscore
- the score (whether the score is ascending or descending can be known from the SearchEngine class)
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PeptideAssumption
Constructor for a simple peptide assumption containing only the information necessary for spectrum annotation.- Parameters:
peptide
- the theoretic peptideidentificationCharge
- the charge used by the search engine for identification
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PeptideAssumption
public PeptideAssumption()
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Method Details
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getPeptide
Get the theoretic peptide.- Returns:
- the peptide
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setPeptide
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getTheoreticMass
public double getTheoreticMass()Description copied from class:SpectrumIdentificationAssumption
Returns the theoretic mass of the given assumption.- Specified by:
getTheoreticMass
in classSpectrumIdentificationAssumption
- Returns:
- the theoretic mass of the given assumption
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