Uses of Class
eu.isas.peptideshaker.ptm.ModificationLocalizationScorer

Packages that use ModificationLocalizationScorer

Package	Description
eu.isas.peptideshaker.processing	Classes used to create PeptideShaker projects.

Uses of ModificationLocalizationScorer in eu.isas.peptideshaker.processing

Methods in eu.isas.peptideshaker.processing with parameters of type ModificationLocalizationScorer

Modifier and Type	Method	Description
void	ProteinProcessor.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.
void	PsmProcessor.processPsms(InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

Constructors in eu.isas.peptideshaker.processing with parameters of type ModificationLocalizationScorer

Modifier	Constructor	Description
	PsmProcessorRunnable(ConcurrentLinkedQueue<Long> spectrumMatchKeysIterator, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Constructor.