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 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
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

addProteinMatch

public void addProteinMatch(ProteinMatch proteinMatch)
                     throws Exception
Add a protein identification to the identification results

Parameters:
proteinMatch - the protein identification match
Throws:
Exception

addProteinMatch

public void addProteinMatch(ArrayList<ProteinMatch> proteinMatches)
                     throws Exception
Add protein identifications to the identification results

Parameters:
proteinMatches - the list of protein identification matches
Throws:
Exception

addSpectrumMatch

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

Parameters:
newMatch - the new spectrum match

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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