public abstract class SpectrumIdentificationAssumption extends ExperimentObject
Modifier and Type | Field and Description |
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protected int |
advocate
The advocate supporting this assumption.
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protected Charge |
identificationCharge
The charge used for identification.
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protected String |
identificationFile
The identification file.
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protected int |
rank
The rank of the peptide assumption for the concerned spectrum.
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protected double |
score
The (advocate specific) score used to rank this assumption.
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Constructor and Description |
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SpectrumIdentificationAssumption() |
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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Charge |
getIdentificationCharge()
Returns the charge used for identification.
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String |
getIdentificationFile()
Returns the identification file.
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int |
getIsotopeNumber(double measuredMZ)
Returns the precursor isotope number according to the number of protons.
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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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abstract double |
getTheoreticMass()
Returns the theoretic mass of the given assumption.
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double |
getTheoreticMz()
Returns the theoretic m/z.
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void |
setRank(int aRank)
Set the rank of the PeptideAssumption.
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addUrParam, getParameterKey, getUrParam
protected int rank
protected int advocate
protected Charge identificationCharge
protected double score
protected String identificationFile
public int getRank()
public void setRank(int aRank)
aRank
- the rank of the PeptideAssumptiopublic int getAdvocate()
public double getScore()
public String getIdentificationFile()
public Charge getIdentificationCharge()
public abstract double getTheoreticMass()
public double getTheoreticMz()
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
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