Package eu.isas.peptideshaker.utils

Class DeepLcUtils

java.lang.Object
eu.isas.peptideshaker.utils.DeepLcUtils
public class DeepLcUtils extends Object
Utils for the export and import of ms2pip results.
Author:
Marc Vaudel, Dafni Skiadopoulou

  • Constructor Summary

    Constructors
    Constructor
    Description
    DeepLcUtils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static String
    getModifications(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)
    Returns the modifications of the peptides encoded as required by DeepLc.
    static String
    getPeptideData(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, double retentionTime, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)
    Gets the peptide data to provide to ms2pip.
    static long
    getPeptideKey(String peptideData)
    Returns a unique key corresponding to the given peptide.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • DeepLcUtils

      public DeepLcUtils()

  • Method Details

    • getPeptideData

      public static String getPeptideData(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, double retentionTime, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)
      Gets the peptide data to provide to ms2pip.
      Parameters:
      peptideAssumption - The peptide assumption.
      retentionTime - The retention time when the peptide was measured.
      modificationParameters - The modification parameters of the search.
      sequenceProvider - The sequence provider.
      sequenceMatchingParameters - The sequence matching parameters.
      modificationFactory - The factory containing the modification details
      Returns:
      The peptide data as string.

    • getModifications

      public static String getModifications(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)
      Returns the modifications of the peptides encoded as required by DeepLc.
      Parameters:
      peptide - The pepitde.
      modificationParameters - The modification parameters of the search.
      sequenceProvider - The sequence provider.
      sequenceMatchingParameters - The sequence matching parameters.
      modificationFactory - The factory containing the modification details
      Returns:
      the modifications of the peptides encoded as required by DeepLc.

    • getPeptideKey

      public static long getPeptideKey(String peptideData)
      Returns a unique key corresponding to the given peptide.
      Parameters:
      peptideData - The peptide data as string.
      Returns:
      The unique key corresponding to the peptide data.