com.compomics.util.experiment.quantification.reporterion

Class ReporterIonQuantification

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.quantification.Quantification

com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification

All Implemented Interfaces:

Serializable, Cloneable

public class ReporterIonQuantification
extends Quantification

This class contains quantification parameters.

Author:

Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class com.compomics.util.experiment.quantification.Quantification

Quantification.QuantificationMethod

Field Summary

Fields inherited from class com.compomics.util.experiment.quantification.Quantification

methodUsed

Constructor Summary

Constructors

Constructor and Description
ReporterIonQuantification(Quantification.QuantificationMethod methodUsed) Constructor for the reporter ion quantification.

Method Summary

Methods

Modifier and Type	Method and Description
void	addNormalisationFactor(String reporterIonName, double normalisationFactor) Adds a normalisation factor.
void	assignSample(String reporterName, Sample sample) Assign a sample to an ion referenced by its static index.
ArrayList<String>	getControlSamples() Returns the indexes of the samples labelled as control.
static String	getDefaultReference(String experimentReference, String sampleReference, int replicateNumber) Returns the default reference for an identification.
double	getNormalisationFactor(String reporterIonName) Returns the normalisation factor for the given sample.
String	getReporterIndex(Sample aSample) This method returns the reporter ion name associated to the given sample.
ReporterMethod	getReporterMethod() returns the reporter method used.
Sample	getSample(String reporterIonName) This method returns the sample associated to the given ion.
Set<String>	getSampleIndexes() Returns a set containing the indexes of every sample.
boolean	hasNormalisationFactors() Indicates whether the normalisation factors are set.
void	resetNormalisationFactors() Resets the normalisation factors.
void	setControlSamples(ArrayList<String> controlSamples) Sets the indexes of the samples labelled as control.
void	setMethod(ReporterMethod reporterMethod) Sets the reporter method used.

Methods inherited from class com.compomics.util.experiment.quantification.Quantification

getMethodUsed, setMethodUsed

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

Constructor Detail

ReporterIonQuantification

public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)

Constructor for the reporter ion quantification.

Parameters:

methodUsed - the method used for this quantification

Method Detail

assignSample

public void assignSample(String reporterName,
                Sample sample)

Assign a sample to an ion referenced by its static index.

Parameters:

reporterName - the name of the reporter ion

sample - the sample

getSample

public Sample getSample(String reporterIonName)

This method returns the sample associated to the given ion.

Parameters:

reporterIonName - the static index of the reporter ion

Returns:

the corresponding sample

getReporterIndex

public String getReporterIndex(Sample aSample)

This method returns the reporter ion name associated to the given sample. Null if not found.

Parameters:

aSample - the sample

Returns:

the static index of the associated ion

getReporterMethod

public ReporterMethod getReporterMethod()

returns the reporter method used.

Returns:

the method used

setMethod

public void setMethod(ReporterMethod reporterMethod)

Sets the reporter method used.

Parameters:

reporterMethod - the reporter method used

getDefaultReference

public static String getDefaultReference(String experimentReference,
                         String sampleReference,
                         int replicateNumber)

Returns the default reference for an identification.

Parameters:

experimentReference - the experiment reference

sampleReference - the sample reference

replicateNumber - the replicate number

Returns:

the default reference

getControlSamples

public ArrayList<String> getControlSamples()

Returns the indexes of the samples labelled as control.

Returns:

the indexes of the samples labelled as control

setControlSamples

public void setControlSamples(ArrayList<String> controlSamples)

Sets the indexes of the samples labelled as control.

Parameters:

controlSamples - the indexes of the samples to label as control

hasNormalisationFactors

public boolean hasNormalisationFactors()

Indicates whether the normalisation factors are set.

Returns:

a boolean indicating whether the normalisation factors are set

resetNormalisationFactors

public void resetNormalisationFactors()

Resets the normalisation factors.

addNormalisationFactor

public void addNormalisationFactor(String reporterIonName,
                          double normalisationFactor)

Adds a normalisation factor.

Parameters:

reporterIonName - the index of the sample

normalisationFactor - the normalisation factor

getNormalisationFactor

public double getNormalisationFactor(String reporterIonName)

Returns the normalisation factor for the given sample.

Parameters:

reporterIonName - the index of the sample

Returns:

the normalisation factor, 1.0 if not set.

getSampleIndexes

public Set<String> getSampleIndexes()

Returns a set containing the indexes of every sample.

Returns:

a set containing the indexes of every sample