Class SpectrumIdentificationAssumption
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.SpectrumIdentificationAssumption
- All Implemented Interfaces:
Serializable
- Direct Known Subclasses:
PeptideAssumption
,TagAssumption
public abstract class SpectrumIdentificationAssumption extends ExperimentObject
Spectrum identification assumption made by an identification algorithm.
- Author:
- Marc Vaudel, Dominik Kopczynski
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description protected int
advocate
The advocate supporting this assumption.protected ArrayList<double[]>
aminoAcidScores
The individual amino acid scores.protected int
identificationCharge
The charge used for identification.protected String
identificationFile
The identification file.protected int
rank
The rank of the peptide assumption for the concerned spectrum.protected double
rawScore
The raw score as provided by the identification algorithm.protected double
score
The (advocate specific) score used to rank this assumption. -
Constructor Summary
Constructors Constructor Description SpectrumIdentificationAssumption()
Empty default constructor. -
Method Summary
Modifier and Type Method Description int
getAdvocate()
Get the used advocate.ArrayList<double[]>
getAminoAcidScores()
Returns the amino acid scores.double
getDeltaMass(double measuredMZ, boolean ppm, int minIsotope, int maxIsotope)
Returns the precursor mass error (in ppm or Da).int
getIdentificationCharge()
Returns the charge used for identification.String
getIdentificationFile()
Returns the identification file.int
getIsotopeNumber(double measuredMZ, int minIsotope, int maxIsotope)
Returns the precursor isotope number according to the number of protons.IonMatch
getPrecursorMatch(double precursorMz, double precursorIntensity)
Returns the ion match.int
getRank()
Get the identification rank.double
getRawScore()
Returns the raw score as provided by the identification algorithm.double
getScore()
Returns the score assigned by the advocate.abstract double
getTheoreticMass()
Returns the theoretic mass of the given assumption.double
getTheoreticMz()
Returns the theoretic m/z.void
setAdvocate(int advocate)
Sets the advocate id.void
setAminoAcidScores(ArrayList<double[]> aminoAcidScores)
Set the amino acid scores.void
setIdentificationCharge(int identificationCharge)
Sets the identification charge.void
setIdentificationFile(String identificationFile)
Sets the identification file.void
setRank(int rank)
Set the rank of the PeptideAssumption.void
setRawScore(double rawScore)
Sets the raw score as provided by the identification algorithm.void
setScore(double score)
Sets the score.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Field Details
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rank
protected int rankThe rank of the peptide assumption for the concerned spectrum. -
advocate
protected int advocateThe advocate supporting this assumption. -
identificationCharge
protected int identificationChargeThe charge used for identification. -
score
protected double scoreThe (advocate specific) score used to rank this assumption. -
identificationFile
The identification file. -
rawScore
protected double rawScoreThe raw score as provided by the identification algorithm. -
aminoAcidScores
The individual amino acid scores. Null if not set.
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Constructor Details
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SpectrumIdentificationAssumption
public SpectrumIdentificationAssumption()Empty default constructor.
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Method Details
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getRank
public int getRank()Get the identification rank.- Returns:
- the identification rank
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setRank
public void setRank(int rank)Set the rank of the PeptideAssumption.- Parameters:
rank
- the rank of the PeptideAssumptio
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getAdvocate
public int getAdvocate()Get the used advocate.- Returns:
- the advocate index
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setAdvocate
public void setAdvocate(int advocate)Sets the advocate id.- Parameters:
advocate
- The advocate id.
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getScore
public double getScore()Returns the score assigned by the advocate.- Returns:
- the score
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setScore
public void setScore(double score)Sets the score. Note: if PsmScores.scoreRoundingDecimal is not null the scored will be floored accordingly.- Parameters:
score
- the score
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getIdentificationFile
Returns the identification file.- Returns:
- the identification file
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setIdentificationFile
Sets the identification file.- Parameters:
identificationFile
- The identification file.
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getIdentificationCharge
public int getIdentificationCharge()Returns the charge used for identification.- Returns:
- the charge used for identification
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setIdentificationCharge
public void setIdentificationCharge(int identificationCharge)Sets the identification charge.- Parameters:
identificationCharge
- the identification charge
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getTheoreticMass
public abstract double getTheoreticMass()Returns the theoretic mass of the given assumption.- Returns:
- the theoretic mass of the given assumption
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getTheoreticMz
public double getTheoreticMz()Returns the theoretic m/z.- Returns:
- the theoretic m/z
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getDeltaMass
public double getDeltaMass(double measuredMZ, boolean ppm, int minIsotope, int maxIsotope)Returns the precursor mass error (in ppm or Da). Note that the value is returns as (experimental mass - theoretical mass) and that negative values thus can occur. The isotopic error can subtracted and retrieved by the function getIsotopeNumber().- Parameters:
measuredMZ
- the precursor m/zppm
- if true the error is returns in ppm, false returns the error in DaminIsotope
- the minimal isotopemaxIsotope
- the maximal isotope- Returns:
- the precursor mass error (in ppm or Da)
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getIsotopeNumber
public int getIsotopeNumber(double measuredMZ, int minIsotope, int maxIsotope)Returns the precursor isotope number according to the number of protons.- Parameters:
measuredMZ
- the measured m/z valueminIsotope
- the minimal isotopemaxIsotope
- the maximal isotope- Returns:
- the precursor isotope number according to the number of protons
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getPrecursorMatch
Returns the ion match.- Parameters:
precursorMz
- The precursor measured m/z.precursorIntensity
- The precursor measured intensity.- Returns:
- the ion match
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getRawScore
public double getRawScore()Returns the raw score as provided by the identification algorithm.- Returns:
- the raw score as provided by the identification algorithm
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setRawScore
public void setRawScore(double rawScore)Sets the raw score as provided by the identification algorithm.- Parameters:
rawScore
- the raw score as provided by the identification algorithm
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getAminoAcidScores
Returns the amino acid scores. Null of not set. For Peptide objects the list only contains one element, while for Tag objects the list will be indexed in identically to the TagComponent list.- Returns:
- the amino acid scores
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setAminoAcidScores
Set the amino acid scores. For Peptide objects the list should only contain one element, while for Tag objects the list should be indexed in identical to the TagComponent list.- Parameters:
aminoAcidScores
- the amino acid scores
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