com.compomics.util.experiment.identification
Class Identification

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.identification.Identification
All Implemented Interfaces:
Serializable, Cloneable
Direct Known Subclasses:
Ms2Identification

public abstract class Identification
extends ExperimentObject

This class contains identification results. User: Marc Date: Nov 11, 2010 Time: 3:56:15 PM

See Also:
Serialized Form

Field Summary
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
Identification()
           
 
Method Summary
 void addSpectrumMatch(Set<SpectrumMatch> spectrumMatches)
          Add a set of spectrumMatches to the model
 void addSpectrumMatch(SpectrumMatch newMatch)
          Add a spectrum match to the spectrum matches map.
 void buildPeptidesAndProteins()
          Creates the peptides and protein instances based on the spectrum matches.
 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
addUrParam, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

proteinIdentification

protected HashMap<String,ProteinMatch> proteinIdentification
The identification results as a proteine match map, indexed by protein accession.


peptideIdentification

protected HashMap<String,PeptideMatch> peptideIdentification
The identification results as a peptide match map, indexed by peptide index


spectrumIdentification

protected HashMap<String,SpectrumMatch> spectrumIdentification
The identification results as a spectrum match map, indexed by spectrum id: FILE_TITLE


proteinMap

protected HashMap<String,ArrayList<ProteinMatch>> proteinMap
a map linking protein accessions to all their protein matches


methodUsed

protected int methodUsed
The method used.

Constructor Detail

Identification

public Identification()
Method Detail

getProteinIdentification

public HashMap<String,ProteinMatch> getProteinIdentification()
Returns the identification results associated to the corresponding method in a protein identification map (accession -> protein match).

Returns:
the corresponding identification results

getPeptideIdentification

public HashMap<String,PeptideMatch> getPeptideIdentification()
Returns the identification results in a peptide identification map (peptide index -> peptideMatch)

Returns:
the corresponding identification results

getSpectrumIdentification

public HashMap<String,SpectrumMatch> getSpectrumIdentification()
Returns the identification results in a spectrum identification map (spectrumMatch id -> spectrumMatch)

Returns:
the corresponding identification resutls

addSpectrumMatch

public void addSpectrumMatch(SpectrumMatch newMatch)
Add a spectrum match to the spectrum matches map.

Parameters:
newMatch - the new spectrum match

buildPeptidesAndProteins

public void buildPeptidesAndProteins()
Creates the peptides and protein instances based on the spectrum matches. Note that the attribute bestAssumption should be set for every spectrum match at this point.


addSpectrumMatch

public void addSpectrumMatch(Set<SpectrumMatch> spectrumMatches)
                      throws Exception
Add a set of spectrumMatches to the model

Parameters:
spectrumMatches - The spectrum matches
Throws:
Exception - exception thrown when one tries to assign more than one identification per advocate to the same spectrum

getMethodUsed

public int getMethodUsed()
Getter for the identification method used

Returns:
the identification method used

getProteinMap

public HashMap<String,ArrayList<ProteinMatch>> getProteinMap()
Returns a map of all the protein matches which can be ascribed to a protein indexed by its accession.

Returns:
a map of all the protein matches which can be ascribed to a protein indexed by its accession.


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