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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.quantification.Quantification
public abstract class Quantification
This class contains quantification results. User: Marc Date: Nov 11, 2010 Time: 3:46:24 PM
Nested Class Summary | |
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static class |
Quantification.QuantificationMethod
The implemented quantification methods. |
Field Summary | |
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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 | |
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Quantification()
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Method Summary | |
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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 |
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addUrParam, getParameterKey, 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 Quantification.QuantificationMethod methodUsed
protected java.util.ArrayList<java.lang.String> proteinQuantification
protected java.util.ArrayList<java.lang.String> peptideQuantification
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> modifiedPeptidesQuantification
protected java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> psmIDentificationToQuantification
Constructor Detail |
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public Quantification()
Method Detail |
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public java.util.ArrayList<java.lang.String> getProteinQuantification()
public java.util.ArrayList<java.lang.String> getPeptideQuantification()
public java.util.ArrayList<java.lang.String> getModifiedPeptideQuantification(java.lang.String modificationName)
modificationName
- the name of the modification
public java.util.HashMap<java.lang.String,java.util.ArrayList<java.lang.String>> getPsmIDentificationToQuantification()
public Quantification.QuantificationMethod getMethodUsed()
public void setMethodUsed(Quantification.QuantificationMethod methodUsed)
methodUsed
- the method usedpublic java.util.ArrayList<PsmQuantification> getSpectrumMatches(java.lang.String identificationMatchKey) throws java.lang.Exception
identificationMatchKey
- the key of the identification match
java.lang.Exception
- exception thrown whenever an error occurred while
retrieving the matchpublic PsmQuantification getSpectrumMatch(java.lang.String spectrumKey) throws java.lang.Exception
spectrumKey
- the key of the spectrum match
java.lang.Exception
- exception thrown whenever an error occurred while
retrieving the matchpublic PeptideQuantification getPeptideMatch(java.lang.String peptideKey) throws java.lang.Exception
peptideKey
- the key of the match
java.lang.Exception
- exception thrown whenever an error occurred while
retrieving the matchpublic ProteinQuantification getProteinMatch(java.lang.String proteinKey) throws java.lang.Exception
proteinKey
- the key of the match
java.lang.Exception
- exception thrown whenever an error occurred while
retrieving the matchpublic void addPsmQuantification(PsmQuantification match) throws java.lang.Exception
match
- the new spectrum match
java.lang.Exception
public void addPeptideQuantification(PeptideQuantification match) throws java.lang.Exception
match
- the new spectrum match
java.lang.Exception
public void addProteinQuantification(ProteinQuantification match) throws java.lang.Exception
match
- the new spectrum match
java.lang.Exception
public void buildPeptidesAndProteinQuantifications(Identification identification, WaitingHandler waitingHandler) throws java.lang.Exception
identification
- waitingHandler
-
java.lang.Exception
public void setMatchChanged(QuantificationMatch match) throws java.lang.IllegalArgumentException, java.io.IOException, java.sql.SQLException
match
-
java.lang.IllegalArgumentException
java.io.IOException
java.sql.SQLException
public void establishConnection(java.lang.String dbFolder, java.lang.String name, boolean deleteOldDatabase, ObjectsCache objectsCache) throws java.sql.SQLException
dbFolder
- the absolute path to the folder where the database is
locatedname
- deleteOldDatabase
- if true, tries to delete the old databaseobjectsCache
-
java.sql.SQLException
- exception thrown whenever an error occurred while
establishing the connection
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