public class PrideIntermediatePeptideSpectrumMatch extends IntermediatePeptideSpectrumMatch
Constructor and Description |
---|
PrideIntermediatePeptideSpectrumMatch(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller,
Comparable proteinID,
Comparable peptideID) |
PrideIntermediatePeptideSpectrumMatch(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller,
Comparable proteinID,
Comparable peptideID,
String cacheScoreAccession)
creates a new PRIDE intermediate PSM and caches the score given by the
accession (this requires some mor memory, but is much faster)
|
Modifier and Type | Method and Description |
---|---|
List<String> |
getBaseScoreAccessions()
Returns the basic scores of this PSM.
|
Integer |
getCharge()
Getter for the charge.
|
String |
getControllerID()
Returns the ID of the used controller for importing.
|
Double |
getDeltaMass()
Getter for the mass-delta (NOT m/z) between measured and theoretical
mass value (measured - theoretical)
|
Double |
getExperimentalMassToCharge()
Getter for the PSM's measured experimental m/z
|
String |
getID()
Returns an ID of the peptideSpectrumMatch
|
Integer |
getMissedCleavages()
Getter for the number of missed cleavages
|
List<uk.ac.ebi.jmzidml.model.mzidml.Modification> |
getModifications()
Getter for the modifications
|
List<uk.ac.ebi.jmzidml.model.mzidml.AbstractParam> |
getParams()
Getter for additional CV and user params (like sourceID, spectrum
title...)
|
Double |
getRetentionTime()
Getter for the PSMs' retention time.
|
Double |
getScore(String scoreAccession)
Returns the score value of the score with the given accession.
|
String |
getSequence()
Getter for the sequence.
|
String |
getSpectrumId()
Getter for the spectrum id (as in mzIdentML's SpectrumIdentificationResult)
|
equals, getFDR, getFDRScore, getIsDecoy, getIsUnique, getPeptide, getQValue, getScoreAccessions, hashCode, setFDR, setFDRScore, setIsDecoy, setIsUnique, setPeptide, setQValue
public PrideIntermediatePeptideSpectrumMatch(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller, Comparable proteinID, Comparable peptideID)
public PrideIntermediatePeptideSpectrumMatch(uk.ac.ebi.pride.utilities.data.controller.DataAccessController controller, Comparable proteinID, Comparable peptideID, String cacheScoreAccession)
controller
- proteinID
- peptideID
- cacheScoreAccession
- public String getID()
IntermediatePeptideSpectrumMatch
getID
in class IntermediatePeptideSpectrumMatch
public String getControllerID()
IntermediatePeptideSpectrumMatch
getControllerID
in class IntermediatePeptideSpectrumMatch
public Double getScore(String scoreAccession)
IntermediatePeptideSpectrumMatch
getScore
in interface FDRComputableByDecoys
getScore
in class IntermediatePeptideSpectrumMatch
public List<String> getBaseScoreAccessions()
IntermediatePeptideSpectrumMatch
getBaseScoreAccessions
in class IntermediatePeptideSpectrumMatch
public String getSpectrumId()
IntermediatePeptideSpectrumMatch
getSpectrumId
in class IntermediatePeptideSpectrumMatch
public Double getExperimentalMassToCharge()
IntermediatePeptideSpectrumMatch
getExperimentalMassToCharge
in class IntermediatePeptideSpectrumMatch
public Double getDeltaMass()
IntermediatePeptideSpectrumMatch
getDeltaMass
in class IntermediatePeptideSpectrumMatch
public Double getRetentionTime()
IntermediatePeptideSpectrumMatch
null, if not available
getRetentionTime
in class IntermediatePeptideSpectrumMatch
public Integer getCharge()
IntermediatePeptideSpectrumMatch
getCharge
in class IntermediatePeptideSpectrumMatch
public Integer getMissedCleavages()
IntermediatePeptideSpectrumMatch
getMissedCleavages
in class IntermediatePeptideSpectrumMatch
public String getSequence()
IntermediatePeptideSpectrumMatch
getSequence
in class IntermediatePeptideSpectrumMatch
public List<uk.ac.ebi.jmzidml.model.mzidml.Modification> getModifications()
IntermediatePeptideSpectrumMatch
getModifications
in class IntermediatePeptideSpectrumMatch
public List<uk.ac.ebi.jmzidml.model.mzidml.AbstractParam> getParams()
IntermediatePeptideSpectrumMatch
getParams
in class IntermediatePeptideSpectrumMatch
Copyright © 2015. All Rights Reserved.