public class PeptideAssumption extends ExperimentObject
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 eValue,
String identificationFile)
Constructor for a peptide assumption.
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Modifier and Type | Method and Description |
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int |
getAdvocate()
Get the used advocate.
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double |
getDeltaMass(double measuredMZ,
boolean ppm)
Returns the precursor mass error (in ppm or Da).
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double |
getDeltaMass(double measuredMZ,
boolean ppm,
boolean subtractIsotope)
Returns the precursor mass error (in ppm or Da).
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double |
getEValue()
Returns the e-value assigned by the advocate.
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String |
getFile()
Returns the file.
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Charge |
getIdentificationCharge()
Returns the charge used for identification.
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int |
getIsotopeNumber(double measuredMZ)
Returns the precursor isotope number according to the number of protons.
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Peptide |
getPeptide()
Get the theoretic peptide.
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IonMatch |
getPrecursorMatch(Peak precursorPeak)
Returns the ion match.
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int |
getRank()
Get the identification rank.
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boolean |
isDecoy()
Is the identification decoy?
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void |
setRank(int aRank)
Set the rank of the PeptideAssumption.
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addUrParam, getParameterKey, getUrParam
public PeptideAssumption(Peptide aPeptide, int rank, int advocate, Charge identificationCharge, double eValue, String identificationFile)
aPeptide
- the theoretic peptiderank
- the identification rankadvocate
- the advocate usedidentificationCharge
- the charge used by the search engine for
identificationeValue
- the e-valueidentificationFile
- 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 (the lower, the better)public int getRank()
public Peptide getPeptide()
public int getAdvocate()
public double getDeltaMass(double measuredMZ, boolean ppm, boolean subtractIsotope)
measuredMZ
- the precursor m/zppm
- if true the error is returns in ppm, false returns the error
in DasubtractIsotope
- if true the isotope number will be subtracted from
the theoretic masspublic double getDeltaMass(double measuredMZ, boolean ppm)
measuredMZ
- the precursor m/zppm
- if true the error is returns in ppm, false returns the error
in Dapublic int getIsotopeNumber(double measuredMZ)
measuredMZ
- public double getEValue()
public String getFile()
public boolean isDecoy()
public Charge getIdentificationCharge()
public void setRank(int aRank)
aRank
- the rank of the PeptideAssumptioCopyright © 2013. All Rights Reserved.