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 ArrayList<double[]> |
aminoAcidScores
The individual amino acid scores.
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protected int |
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 |
rawScore
The raw score as provided by the identification algorithm.
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protected double |
score
The (advocate specific) score used to rank this assumption.
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NO_KEY
Constructor and Description |
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SpectrumIdentificationAssumption()
Empty default constructor.
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Modifier and Type | Method and Description |
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int |
getAdvocate()
Get the used advocate.
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ArrayList<double[]> |
getAminoAcidScores()
Returns the amino acid scores.
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double |
getDeltaMass(double measuredMZ,
boolean ppm,
int minIsotope,
int maxIsotope)
Returns the precursor mass error (in ppm or Da).
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int |
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,
int minIsotope,
int maxIsotope)
Returns the precursor isotope number according to the number of protons.
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IonMatch |
getPrecursorMatch(double precursorMz,
double precursorIntensity)
Returns the ion match.
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int |
getRank()
Get the identification rank.
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double |
getRawScore()
Returns the raw score as provided by the identification algorithm.
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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 |
setAdvocate(int advocate)
Sets the advocate id.
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void |
setAminoAcidScores(ArrayList<double[]> aminoAcidScores)
Set the amino acid scores.
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void |
setIdentificationCharge(int identificationCharge)
Sets the identification charge.
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void |
setIdentificationFile(String identificationFile)
Sets the identification file.
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void |
setRank(int rank)
Set the rank of the PeptideAssumption.
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void |
setRawScore(double rawScore)
Sets the raw score as provided by the identification algorithm.
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void |
setScore(double score)
Sets the score.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
protected int rank
protected int advocate
protected int identificationCharge
protected double score
protected String identificationFile
protected double rawScore
protected ArrayList<double[]> aminoAcidScores
public SpectrumIdentificationAssumption()
public int getRank()
public void setRank(int rank)
rank
- the rank of the PeptideAssumptiopublic int getAdvocate()
public void setAdvocate(int advocate)
advocate
- The advocate id.public double getScore()
public void setScore(double score)
score
- the scorepublic String getIdentificationFile()
public void setIdentificationFile(String identificationFile)
identificationFile
- The identification file.public int getIdentificationCharge()
public void setIdentificationCharge(int identificationCharge)
identificationCharge
- the identification chargepublic abstract double getTheoreticMass()
public double getTheoreticMz()
public double getDeltaMass(double measuredMZ, boolean ppm, int minIsotope, int maxIsotope)
measuredMZ
- the precursor m/zppm
- if true the error is returns in ppm, false returns the error
in DaminIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic int getIsotopeNumber(double measuredMZ, int minIsotope, int maxIsotope)
measuredMZ
- the measured m/z valueminIsotope
- the minimal isotopemaxIsotope
- the maximal isotopepublic IonMatch getPrecursorMatch(double precursorMz, double precursorIntensity)
precursorMz
- The precursor measured m/z.precursorIntensity
- The precursor measured intensity.public double getRawScore()
public void setRawScore(double rawScore)
rawScore
- the raw score as provided by the identification algorithmpublic ArrayList<double[]> getAminoAcidScores()
public void setAminoAcidScores(ArrayList<double[]> aminoAcidScores)
aminoAcidScores
- the amino acid scoresCopyright © 2021. All rights reserved.