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 score,
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()
Deprecated.
use getScore instead
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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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double |
getScore()
Returns the score assigned by the advocate.
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double |
getTheoreticMz()
Returns the theoretic m/z expected for this assumption.
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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 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 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 double getTheoreticMz()
public int getIsotopeNumber(double measuredMZ)
measuredMZ
- public double getEValue()
public double getScore()
public String getFile()
public boolean isDecoy()
public Charge getIdentificationCharge()
public void setRank(int aRank)
aRank
- the rank of the PeptideAssumptioCopyright © 2013. All Rights Reserved.