java.lang.Object
com.compomics.util.experiment.identification.protein_sequences.digestion.IteratorFactory

public class IteratorFactory
extends Object
The iterator goes through a sequence and lists possible peptides with their fixed modifications.
Author:
Marc Vaudel
  • Constructor Details

    • IteratorFactory

      public IteratorFactory()
      Empty default constructor
    • IteratorFactory

      public IteratorFactory​(ArrayList<String> fixedModifications, Integer maxX)
      Constructor.
      Parameters:
      fixedModifications - a list of fixed modifications to consider when iterating the protein sequences.
      maxX - The maximal number of Xs allowed in a sequence to derive the possible peptides
    • IteratorFactory

      public IteratorFactory​(ArrayList<String> fixedModifications)
      Constructor with 2 Xs allowed.
      Parameters:
      fixedModifications - a list of fixed modifications to consider when iterating the protein sequences.
  • Method Details

    • getSequenceIterator

      public SequenceIterator getSequenceIterator​(String sequence, DigestionParameters digestionPreferences, double massMin, double massMax) throws InterruptedException
      Returns a sequence iterator for the given protein sequence and digestion preferences.
      Parameters:
      sequence - the sequence to iterate
      digestionPreferences - the digestion preferences to use
      massMin - the minimal mass of a peptide
      massMax - the maximal mass of a peptide
      Returns:
      a sequence iterator
      Throws:
      InterruptedException - exception thrown if a thread is interrupted