public abstract class IntermediatePeptideSpectrumMatch extends Object implements FDRComputableByDecoys
Constructor and Description |
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IntermediatePeptideSpectrumMatch() |
Modifier and Type | Method and Description |
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boolean |
equals(Object obj) |
abstract List<String> |
getBaseScoreAccessions()
Returns the basic scores of this PSM.
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abstract Integer |
getCharge()
Getter for the charge.
|
abstract Comparable |
getControllerID()
Returns the ID of the used controller for importing.
|
abstract Double |
getDeltaMass()
Getter for the mass-delta (NOT m/z) between measured and theoretical
mass value (measured - theoretical)
|
abstract Double |
getExperimentalMassToCharge()
Getter for the PSM's measured experimental m/z
|
Double |
getFDR()
Gets the local FDR value.
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Double |
getFDRScore()
Gets the smoothed FDRScore value.
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abstract Comparable |
getID()
Returns an ID of the peptideSpectrumMatch
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Boolean |
getIsDecoy()
Getter for the isDecoy flag.
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Boolean |
getIsUnique()
Returns whether the PSM is unique for only one protein (given the
database)
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abstract Integer |
getMissedCleavages()
Getter for the number of missed cleavages
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abstract List<uk.ac.ebi.jmzidml.model.mzidml.Modification> |
getModifications()
Getter for the modifications
|
abstract List<uk.ac.ebi.jmzidml.model.mzidml.AbstractParam> |
getParams()
Getter for additional CV and user params (like sourceID, spectrum
title...)
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IntermediatePeptide |
getPeptide()
Getter for the peptide.
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Double |
getQValue()
Getter for the qValue.
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abstract Double |
getRetentionTime()
Getter for the PSMs' retention time.
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abstract Double |
getScore(String scoreAccession)
Returns the score value of the score with the given accession.
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List<String> |
getScoreAccessions()
Returns the accessions of the available scores of this PSM, including
calculated scores.
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abstract String |
getSequence()
Getter for the sequence.
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abstract String |
getSpectrumId()
Getter for the spectrum id (as in mzIdentML's SpectrumIdentificationResult)
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int |
hashCode() |
void |
setFDR(Double fdr)
Sets the local FDR value.
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void |
setFDRScore(Double fdrScore)
Sets the smoothed FDRScore value.
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void |
setIsDecoy(Boolean isDecoy)
Deprecated.
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void |
setIsUnique(Boolean isUnique)
Sets the isUnique flag, should only be done by importers.
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void |
setPeptide(IntermediatePeptide peptide)
Setter for the peptide (called while parsing the PIA XML file).
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void |
setQValue(Double value)
Setter for the qValue.
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public abstract Comparable getID()
public abstract Comparable getControllerID()
public abstract Double getScore(String scoreAccession)
getScore
in interface FDRComputableByDecoys
public final List<String> getScoreAccessions()
public abstract List<String> getBaseScoreAccessions()
public abstract String getSpectrumId()
public abstract Double getExperimentalMassToCharge()
public abstract Double getDeltaMass()
public abstract Double getRetentionTime()
null, if not available
public abstract Integer getCharge()
public abstract Integer getMissedCleavages()
public abstract String getSequence()
public abstract List<uk.ac.ebi.jmzidml.model.mzidml.Modification> getModifications()
public abstract List<uk.ac.ebi.jmzidml.model.mzidml.AbstractParam> getParams()
public Boolean getIsUnique()
public void setIsUnique(Boolean isUnique)
isUnique
- public Boolean getIsDecoy()
If the decoy was not set by setIsDecoy, the decoy status of the original PSM is returned. The original spectrumIdentification is a decoy, if it is connected to peptideEvidences / proteins which are only decoys.
getIsDecoy
in interface FDRComputableByDecoys
@Deprecated public void setIsDecoy(Boolean isDecoy)
This overwrites any decoy settings from the original spectrumIdentification. This is only for legacy usage of older PIA intermediate files, now the decoy state is encoded in the protein.
public void setPeptide(IntermediatePeptide peptide)
pep
- public IntermediatePeptide getPeptide()
public void setFDR(Double fdr)
FDRComputableByDecoys
setFDR
in interface FDRComputableByDecoys
public Double getFDR()
FDRComputableByDecoys
getFDR
in interface FDRComputableByDecoys
public void setQValue(Double value)
FDRComputableByDecoys
setQValue
in interface FDRComputableByDecoys
public Double getQValue()
FDRComputableByDecoys
getQValue
in interface FDRComputableByDecoys
public void setFDRScore(Double fdrScore)
FDRComputableByDecoys
setFDRScore
in interface FDRComputableByDecoys
public Double getFDRScore()
FDRComputableByDecoys
getFDRScore
in interface FDRComputableByDecoys
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