eu.isas.peptideshaker.processing

Class ProteinProcessor

java.lang.Object

eu.isas.peptideshaker.processing.ProteinProcessor

public class ProteinProcessor
extends Object

Scores modification localization on proteins, estimates spectrum counting and summary statistics values.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description

ProteinProcessor(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider) Constructor.

Method Summary

Modifier and Type

Method and Description

void

processProteins(ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.parameters.tools.ProcessingParameters processingParameters) Scores the PTMs of all protein matches contained in an identification object, estimates spectrum counting and summary statistics.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinProcessor

public ProteinProcessor(com.compomics.util.experiment.identification.Identification identification,
                        com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                        com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator,
                        com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)

Constructor.

Parameters:

identification - the identification

identificationParameters - the identification parameters

identificationFeaturesGenerator - the identification features generator

sequenceProvider - the sequence provider

Method Detail

processProteins

public void processProteins(ModificationLocalizationScorer modificationLocalizationScorer,
                            com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics,
                            com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider,
                            com.compomics.util.waiting.WaitingHandler waitingHandler,
                            com.compomics.util.exceptions.ExceptionHandler exceptionHandler,
                            com.compomics.util.parameters.tools.ProcessingParameters processingParameters)
                     throws InterruptedException,
                            TimeoutException

Scores the PTMs of all protein matches contained in an identification object, estimates spectrum counting and summary statistics.

Parameters:

modificationLocalizationScorer - The modification localization scorer to use.

metrics - If provided, metrics on proteins will be saved while iterating the matches.

modificationProvider - The modification provider to use.

waitingHandler - The handler displaying feedback to the user.

exceptionHandler - The exception handler to use.

processingParameters - The processing parameters.

Throws:

InterruptedException - exception thrown if a thread gets interrupted

TimeoutException - exception thrown if the operation times out