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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.Identification
public abstract class Identification
This class contains identification results. User: Marc Date: Nov 11, 2010 Time: 3:56:15 PM
Field Summary | |
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protected int |
methodUsed
The method used. |
protected HashMap<String,PeptideMatch> |
peptideIdentification
The identification results as a peptide match map, indexed by peptide index |
protected HashMap<String,ProteinMatch> |
proteinIdentification
The identification results as a proteine match map, indexed by protein accession. |
protected HashMap<String,ArrayList<ProteinMatch>> |
proteinMap
a map linking protein accessions to all their protein matches |
protected HashMap<String,SpectrumMatch> |
spectrumIdentification
The identification results as a spectrum match map, indexed by spectrum id: FILE_TITLE |
Constructor Summary | |
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Identification()
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Method Summary | |
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void |
addProteinMatch(ArrayList<ProteinMatch> proteinMatches)
Add protein identifications to the identification results |
void |
addProteinMatch(ProteinMatch proteinMatch)
Add a protein identification to the identification results |
void |
addSpectrumMatch(Set<SpectrumMatch> spectrumMatches)
Add a set of spectrumMatches to the model |
void |
addSpectrumMatch(SpectrumMatch newMatch)
Add a spectrum match to the model. |
int |
getMethodUsed()
Getter for the identification method used |
HashMap<String,PeptideMatch> |
getPeptideIdentification()
Returns the identification results in a peptide identification map (peptide index -> peptideMatch) |
HashMap<String,ProteinMatch> |
getProteinIdentification()
Returns the identification results associated to the corresponding method in a protein identification map (accession -> protein match). |
HashMap<String,ArrayList<ProteinMatch>> |
getProteinMap()
Returns a map of all the protein matches which can be ascribed to a protein indexed by its accession. |
HashMap<String,SpectrumMatch> |
getSpectrumIdentification()
Returns the identification results in a spectrum identification map (spectrumMatch id -> spectrumMatch) |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected HashMap<String,ProteinMatch> proteinIdentification
protected HashMap<String,PeptideMatch> peptideIdentification
protected HashMap<String,SpectrumMatch> spectrumIdentification
protected HashMap<String,ArrayList<ProteinMatch>> proteinMap
protected int methodUsed
Constructor Detail |
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public Identification()
Method Detail |
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public HashMap<String,ProteinMatch> getProteinIdentification()
public HashMap<String,PeptideMatch> getPeptideIdentification()
public HashMap<String,SpectrumMatch> getSpectrumIdentification()
public void addProteinMatch(ProteinMatch proteinMatch) throws Exception
proteinMatch
- the protein identification match
Exception
public void addProteinMatch(ArrayList<ProteinMatch> proteinMatches) throws Exception
proteinMatches
- the list of protein identification matches
Exception
public void addSpectrumMatch(SpectrumMatch newMatch)
newMatch
- the new spectrum matchpublic void addSpectrumMatch(Set<SpectrumMatch> spectrumMatches) throws Exception
spectrumMatches
- The spectrum matches
Exception
- exception thrown when one tries to assign more than one identification per advocate to the same spectrumpublic int getMethodUsed()
public HashMap<String,ArrayList<ProteinMatch>> getProteinMap()
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