Package com.compomics.util.experiment.quantification.spectrumcounting

Class ScalingFactorsEstimators

java.lang.Object

com.compomics.util.experiment.quantification.spectrumcounting.ScalingFactorsEstimators

public class ScalingFactorsEstimators
extends Object

This class estimates spectrum counting scaling factors.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
ScalingFactorsEstimators()	Empty default constructor
ScalingFactorsEstimators(SpectrumCountingParameters spectrumCountingParameters)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	estimateScalingFactors(Identification identification, Metrics metrics, SequenceProvider sequenceProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters)	Estimates the scaling factors and stores them in the given metrics.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ScalingFactorsEstimators

public ScalingFactorsEstimators()

Empty default constructor

ScalingFactorsEstimators

public ScalingFactorsEstimators(SpectrumCountingParameters spectrumCountingParameters)

Constructor.

Parameters:

spectrumCountingParameters - the spectrum counting parameters

Method Details

estimateScalingFactors

public void estimateScalingFactors(Identification identification,
 Metrics metrics,
 SequenceProvider sequenceProvider,
 IdentificationFeaturesGenerator identificationFeaturesGenerator,
 WaitingHandler waitingHandler,
 ExceptionHandler exceptionHandler,
 ProcessingParameters processingParameters)
                            throws InterruptedException,
TimeoutException

Estimates the scaling factors and stores them in the given metrics.

Parameters:

identification - the identification

metrics - the metrics where to save the results

sequenceProvider - a sequence provider

identificationFeaturesGenerator - the identification features generator

waitingHandler - a waiting handler

exceptionHandler - an exception handler

processingParameters - the processing parameters

Throws:

InterruptedException - exception thrown if a thread gets interrupted

TimeoutException - exception thrown if the operation times out