public class PeptideAssumption extends SpectrumIdentificationAssumption
advocate, aminoAcidScores, identificationCharge, identificationFile, rank, rawScore, score
NO_KEY
Constructor and Description |
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PeptideAssumption()
Default constructor for the purpose of instantiation.
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PeptideAssumption(Peptide peptide,
int identificationCharge)
Constructor for a simple peptide assumption containing only the
information necessary for spectrum annotation.
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PeptideAssumption(Peptide peptide,
int rank,
int advocate,
int identificationCharge,
double rawScore,
double score)
Constructor for a peptide assumption.
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PeptideAssumption(Peptide peptide,
int rank,
int advocate,
int identificationCharge,
double rawScore,
double score,
String identificationFile)
Constructor for a peptide assumption.
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Modifier and Type | Method and Description |
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Peptide |
getPeptide()
Get the theoretic peptide.
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double |
getTheoreticMass()
Returns the theoretic mass of the given assumption.
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void |
setPeptide(Peptide peptide)
Returns the peptides.
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getAdvocate, getAminoAcidScores, getDeltaMass, getIdentificationCharge, getIdentificationFile, getIsotopeNumber, getPrecursorMatch, getRank, getRawScore, getScore, getTheoreticMz, setAdvocate, setAminoAcidScores, setIdentificationCharge, setIdentificationFile, setRank, setRawScore, setScore
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public PeptideAssumption()
public PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score, String identificationFile)
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 filepublic PeptideAssumption(Peptide peptide, int rank, int advocate, int identificationCharge, double rawScore, double score)
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)public PeptideAssumption(Peptide peptide, int identificationCharge)
peptide
- the theoretic peptideidentificationCharge
- the charge used by the search engine for
identificationpublic Peptide getPeptide()
public void setPeptide(Peptide peptide)
peptide
- the peptidepublic double getTheoreticMass()
SpectrumIdentificationAssumption
getTheoreticMass
in class SpectrumIdentificationAssumption
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