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()
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, 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()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 peptiderank
- the identification rankadvocate
- the advocate usedidentificationCharge
- the charge used by the search engine for identificationrawScore
- the raw score, i.e. the untransformed score given by the search enginescore
- 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
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PeptideAssumption
public PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, 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 identificationrawScore
- the raw score, i.e. the untransformed score given by the search enginescore
- the (potentially transformed) score, typically a search engine e-value (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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Method Details
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getPeptide
Get the theoretic peptide.- Returns:
- the peptide
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setPeptide
Returns the peptides.- Parameters:
peptide
- the peptide
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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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