public class PeptideAssumption extends SpectrumIdentificationAssumption
identificationFile, score
Constructor and Description |
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score)
Constructor for a peptide assumption.
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PeptideAssumption(Peptide aPeptide,
int rank,
int advocate,
Charge identificationCharge,
double score,
String identificationFile)
Constructor for a peptide assumption.
|
Modifier and Type | Method and Description |
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int |
getAdvocate()
Get the used advocate.
|
double |
getEValue()
Deprecated.
use getScore instead
|
Charge |
getIdentificationCharge()
Returns the charge used for identification.
|
String |
getIdentificationFile()
Returns the identification file.
|
Peptide |
getPeptide()
Get the theoretic peptide.
|
int |
getRank()
Get the identification rank.
|
double |
getScore()
Returns the score assigned by the advocate.
|
double |
getTheoreticMass()
Returns the theoretic mass of the given assumption.
|
getDeltaMass, getDeltaMass, getIsotopeNumber, getPrecursorMatch, getTheoreticMz, setIdentificationCharge, setRank, setScore
addUrParam, getParameterKey, getUrParam
public PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score, String identificationFile)
aPeptide
- 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 filepublic PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double score)
aPeptide
- 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)public Peptide getPeptide()
public int getRank()
SpectrumIdentificationAssumption
getRank
in class SpectrumIdentificationAssumption
public int getAdvocate()
SpectrumIdentificationAssumption
getAdvocate
in class SpectrumIdentificationAssumption
public double getEValue()
public double getScore()
SpectrumIdentificationAssumption
getScore
in class SpectrumIdentificationAssumption
public String getIdentificationFile()
SpectrumIdentificationAssumption
getIdentificationFile
in class SpectrumIdentificationAssumption
public Charge getIdentificationCharge()
SpectrumIdentificationAssumption
getIdentificationCharge
in class SpectrumIdentificationAssumption
public double getTheoreticMass()
SpectrumIdentificationAssumption
getTheoreticMass
in class SpectrumIdentificationAssumption
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