com.compomics.util.experiment.quantification
Class Quantification

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.quantification.Quantification
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable
Direct Known Subclasses:
ReporterIonQuantification

public abstract class Quantification
extends ExperimentObject

This class contains quantification results. User: Marc Date: Nov 11, 2010 Time: 3:46:24 PM

See Also:
Serialized Form

Nested Class Summary
static class Quantification.QuantificationMethod
          The implemented quantification methods.
 
Field Summary
protected  Quantification.QuantificationMethod methodUsed
          The quantification method used
protected  java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> modifiedPeptidesQuantification
          The modified peptides quantification
protected  java.util.ArrayList<java.lang.String> peptideQuantification
          The peptide quantification
protected  java.util.ArrayList<java.lang.String> proteinQuantification
          The protein quantification
protected  java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> psmIDentificationToQuantification
          A convenience map indicating all psm quantifying an identified PSM
 
Constructor Summary
Quantification()
           
 
Method Summary
 void addPeptideQuantification(PeptideQuantification match)
          Add a peptide quantification match to the peptide quantification matches map if not already implemented.
 void addProteinQuantification(ProteinQuantification match)
          Add a protein quantification match to the peptide quantification matches map if not already implemented.
 void addPsmQuantification(PsmQuantification match)
          Add a spectrum quantification to the spectrum quantification matches map and overwrites if already implemented.
 void buildPeptidesAndProteinQuantifications(Identification identification, WaitingHandler waitingHandler)
          Creates the peptides and protein quantification instances based on the identification and the psm quantification.
 void establishConnection(java.lang.String dbFolder, java.lang.String name, boolean deleteOldDatabase, ObjectsCache objectsCache)
          Establishes connection to the database.
 Quantification.QuantificationMethod getMethodUsed()
          getter for the method used
 java.util.ArrayList<java.lang.String> getModifiedPeptideQuantification(java.lang.String modificationName)
          This method retrieves the quantification result at the modified peptides level
 PeptideQuantification getPeptideMatch(java.lang.String peptideKey)
          Returns a peptide quantification match.
 java.util.ArrayList<java.lang.String> getPeptideQuantification()
          This method retrieves the quantification result at the peptide level
 ProteinQuantification getProteinMatch(java.lang.String proteinKey)
          Returns a protein quantification match.
 java.util.ArrayList<java.lang.String> getProteinQuantification()
          This method retrieves the quantification result at the protein level
 java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> getPsmIDentificationToQuantification()
          This method retrieves the quantification result at the spectrum level
 PsmQuantification getSpectrumMatch(java.lang.String spectrumKey)
          Returns a spectrum quantification match.
 java.util.ArrayList<PsmQuantification> getSpectrumMatches(java.lang.String identificationMatchKey)
          Returns a list of PSM quantification matches corresponding to the given psm identification key.
 void setMatchChanged(QuantificationMatch match)
          Indicates that a match was changed, it will thus be serialized again if needed.
 void setMethodUsed(Quantification.QuantificationMethod methodUsed)
          setter for the method used
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

methodUsed

protected Quantification.QuantificationMethod methodUsed
The quantification method used


proteinQuantification

protected java.util.ArrayList<java.lang.String> proteinQuantification
The protein quantification


peptideQuantification

protected java.util.ArrayList<java.lang.String> peptideQuantification
The peptide quantification


modifiedPeptidesQuantification

protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> modifiedPeptidesQuantification
The modified peptides quantification


psmIDentificationToQuantification

protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> psmIDentificationToQuantification
A convenience map indicating all psm quantifying an identified PSM

Constructor Detail

Quantification

public Quantification()
Method Detail

getProteinQuantification

public java.util.ArrayList<java.lang.String> getProteinQuantification()
This method retrieves the quantification result at the protein level

Returns:
quantification at the protein level

getPeptideQuantification

public java.util.ArrayList<java.lang.String> getPeptideQuantification()
This method retrieves the quantification result at the peptide level

Returns:
quantification at the protein level

getModifiedPeptideQuantification

public java.util.ArrayList<java.lang.String> getModifiedPeptideQuantification(java.lang.String modificationName)
This method retrieves the quantification result at the modified peptides level

Parameters:
modificationName - the name of the modification
Returns:
quantification at the protein level

getPsmIDentificationToQuantification

public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> getPsmIDentificationToQuantification()
This method retrieves the quantification result at the spectrum level

Returns:
quantification at the protein level

getMethodUsed

public Quantification.QuantificationMethod getMethodUsed()
getter for the method used

Returns:
the method used

setMethodUsed

public void setMethodUsed(Quantification.QuantificationMethod methodUsed)
setter for the method used

Parameters:
methodUsed - the method used

getSpectrumMatches

public java.util.ArrayList<PsmQuantification> getSpectrumMatches(java.lang.String identificationMatchKey)
                                                          throws java.lang.Exception
Returns a list of PSM quantification matches corresponding to the given psm identification key.

Parameters:
identificationMatchKey - the key of the identification match
Returns:
the desired matches
Throws:
java.lang.Exception - exception thrown whenever an error occurred while retrieving the match

getSpectrumMatch

public PsmQuantification getSpectrumMatch(java.lang.String spectrumKey)
                                   throws java.lang.Exception
Returns a spectrum quantification match.

Parameters:
spectrumKey - the key of the spectrum match
Returns:
the desired match
Throws:
java.lang.Exception - exception thrown whenever an error occurred while retrieving the match

getPeptideMatch

public PeptideQuantification getPeptideMatch(java.lang.String peptideKey)
                                      throws java.lang.Exception
Returns a peptide quantification match.

Parameters:
peptideKey - the key of the match
Returns:
the desired match
Throws:
java.lang.Exception - exception thrown whenever an error occurred while retrieving the match

getProteinMatch

public ProteinQuantification getProteinMatch(java.lang.String proteinKey)
                                      throws java.lang.Exception
Returns a protein quantification match.

Parameters:
proteinKey - the key of the match
Returns:
the desired match
Throws:
java.lang.Exception - exception thrown whenever an error occurred while retrieving the match

addPsmQuantification

public void addPsmQuantification(PsmQuantification match)
                          throws java.lang.Exception
Add a spectrum quantification to the spectrum quantification matches map and overwrites if already implemented.

Parameters:
match - the new spectrum match
Throws:
java.lang.Exception

addPeptideQuantification

public void addPeptideQuantification(PeptideQuantification match)
                              throws java.lang.Exception
Add a peptide quantification match to the peptide quantification matches map if not already implemented.

Parameters:
match - the new spectrum match
Throws:
java.lang.Exception

addProteinQuantification

public void addProteinQuantification(ProteinQuantification match)
                              throws java.lang.Exception
Add a protein quantification match to the peptide quantification matches map if not already implemented.

Parameters:
match - the new spectrum match
Throws:
java.lang.Exception

buildPeptidesAndProteinQuantifications

public void buildPeptidesAndProteinQuantifications(Identification identification,
                                                   WaitingHandler waitingHandler)
                                            throws java.lang.Exception
Creates the peptides and protein quantification instances based on the identification and the psm quantification. This operation will be extremely slow if the cache is already full.

Parameters:
identification -
waitingHandler -
Throws:
java.lang.Exception

setMatchChanged

public void setMatchChanged(QuantificationMatch match)
                     throws java.lang.IllegalArgumentException,
                            java.io.IOException,
                            java.sql.SQLException
Indicates that a match was changed, it will thus be serialized again if needed.

Parameters:
match -
Throws:
java.lang.IllegalArgumentException
java.io.IOException
java.sql.SQLException

establishConnection

public void establishConnection(java.lang.String dbFolder,
                                java.lang.String name,
                                boolean deleteOldDatabase,
                                ObjectsCache objectsCache)
                         throws java.sql.SQLException
Establishes connection to the database.

Parameters:
dbFolder - the absolute path to the folder where the database is located
name -
deleteOldDatabase - if true, tries to delete the old database
objectsCache -
Throws:
java.sql.SQLException - exception thrown whenever an error occurred while establishing the connection


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