Package com.compomics.util.experiment.identification.protein_inference

Interface FastaMapper

All Known Implementing Classes:
FMIndex
public interface FastaMapper
Interface for a class mapping peptides and tags to a protein.
Author:
Marc Vaudel, Dominik Kopczynski

  • Method Details

    • getProteinMapping

      ArrayList<PeptideProteinMapping> getProteinMapping(String peptideSequence, SequenceMatchingParameters proteinInferencePreferences)
      Returns the protein mapping in the FASTA file loaded in the sequence factory for the given peptide sequence in a map: peptide sequence found in the FASTA file | protein accession | list of indexes of the peptide sequence on the protein sequence. 0 is the first amino acid.
      Parameters:
      peptideSequence - the peptide sequence
      proteinInferencePreferences - the sequence matching preferences
      Returns:
      the peptide to protein mapping: peptide sequence > protein accession > index in the protein An empty map if not

    • getProteinMapping

      ArrayList<PeptideProteinMapping> getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)
      Returns the protein mappings for the given peptide sequence. Peptide sequence | Protein accession | Index in the protein. An empty map if not found.
      Parameters:
      tag - the tag to look for in the tree. Must contain a consecutive amino acid sequence of longer or equal size than the initialTagSize of the tree
      sequenceMatchingPreferences - the sequence matching preferences
      Returns:
      the protein mapping for the given peptide sequence