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 
    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.