public class SpectrumIdentification extends IdentifiableParamGroup
Constructor and Description |
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SpectrumIdentification(Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
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SpectrumIdentification(ParamGroup params,
Comparable id,
String name,
int chargeState,
double experimentalMassToCharge,
double calculatedMassToCharge,
double calculatedPI,
PeptideSequence peptideSequence,
int rank,
boolean passThreshold,
MassTable massTable,
Sample sample,
List<PeptideEvidence> peptideEvidenceList,
List<FragmentIon> fragmentation,
Score score,
Spectrum spectrum,
SpectraData spectraData)
Spectrum Identification Item
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getId, getName, setId, setName, toString
addCvParam, addCvParams, addUserParam, addUserParams, getCvParams, getUserParams, isEmpty, removeCvParam, removeCvParams, removeUserParam, removeUserParams, setCvParams, setUserParams
public SpectrumIdentification(Comparable id, String name, int chargeState, double experimentalMassToCharge, double calculatedMassToCharge, double calculatedPI, PeptideSequence peptideSequence, int rank, boolean passThreshold, MassTable massTable, Sample sample, List<PeptideEvidence> peptideEvidenceList, List<FragmentIon> fragmentation, Score score, Spectrum spectrum, SpectraData spectraData)
id
- Idname
- namechargeState
- Charge stateexperimentalMassToCharge
- Experimental ChargecalculatedMassToCharge
- Calculated MasscalculatedPI
- Calculated PIpeptideSequence
- Peptide Sequencerank
- Peptide RankpassThreshold
- If Pass the thresholdmassTable
- Mass table used to identified the peptidesample
- Sample in which this peptide appearpeptideEvidenceList
- List of peptide evidences.fragmentation
- Fragmentation assignedscore
- Identification Scorespectrum
- Spectrum use to identified the peptidespectraData
- The reference to SpectraDatapublic SpectrumIdentification(ParamGroup params, Comparable id, String name, int chargeState, double experimentalMassToCharge, double calculatedMassToCharge, double calculatedPI, PeptideSequence peptideSequence, int rank, boolean passThreshold, MassTable massTable, Sample sample, List<PeptideEvidence> peptideEvidenceList, List<FragmentIon> fragmentation, Score score, Spectrum spectrum, SpectraData spectraData)
params
- CvParams associated with the scoreid
- Idname
- namechargeState
- Charge stateexperimentalMassToCharge
- Experimental ChargecalculatedMassToCharge
- Calculated MasscalculatedPI
- Calculated PIpeptideSequence
- Peptide Sequencerank
- Peptide RankpassThreshold
- If Pass the thresholdmassTable
- Mass table used to identified the peptidesample
- Sample in which this peptide appearpeptideEvidenceList
- List of peptide evidences.fragmentation
- Fragmentation assignedscore
- Identification Scorespectrum
- Spectrum use to identified the peptidespectraData
- The reference to SpectraDatapublic int getChargeState()
public void setChargeState(int chargeState)
public double getExperimentalMassToCharge()
public void setExperimentalMassToCharge(double experimentalMassToCharge)
public double getCalculatedMassToCharge()
public void setCalculatedMassToCharge(double calculatedMassToCharge)
public double getCalculatedPI()
public void setCalculatedPI(double calculatedPI)
public PeptideSequence getPeptideSequence()
public void setPeptideSequence(PeptideSequence peptideSequence)
public int getRank()
public void setRank(int rank)
public boolean isPassThreshold()
public void setPassThreshold(boolean passThreshold)
public MassTable getMassTable()
public void setMassTable(MassTable massTable)
public Sample getSample()
public void setSample(Sample sample)
public List<PeptideEvidence> getPeptideEvidenceList()
public void setPeptideEvidenceList(List<PeptideEvidence> peptideEvidenceList)
public List<FragmentIon> getFragmentation()
public void setFragmentation(List<FragmentIon> fragmentation)
public Score getScore()
public void setScore(Score score)
public Spectrum getSpectrum()
public void setSpectrum(Spectrum spectrum)
public SpectraData getSpectraData()
public void setSpectraData(SpectraData spectraData)
public boolean hasModification()
public int getSequenceLength()
public List<Modification> getModifications()
public String getSequence()
public String getRetentionTime()
public void setRetentionTime(String retentionTime)
public boolean equals(Object o)
equals
in class IdentifiableParamGroup
public int hashCode()
hashCode
in class IdentifiableParamGroup
Copyright © 2015 European Bioinformatics Institute. All Rights Reserved.