Package com.compomics.util.experiment.io.biology.protein

Interface ProteinDetailsProvider

All Known Implementing Classes:
FMIndex
public interface ProteinDetailsProvider
Interface for a class able to provide metadata on proteins.
Author:
Marc Vaudel

  • Method Details

    • getDescription

      String getDescription(String accession)
      Returns the description of the protein with the given accession.
      Parameters:
      accession - the accession of the protein
      Returns:
      the description of the protein with the given accession

    • getSimpleDescription

      String getSimpleDescription(String accession)
      Returns the simple description of the protein with the given accession.
      Parameters:
      accession - the accession of the protein
      Returns:
      the description of the protein with the given accession

    • getProteinDatabase

      ProteinDatabase getProteinDatabase(String accession)
      Returns the the protein database for the given protein.
      Parameters:
      accession - the accession of the protein
      Returns:
      the name of the protein database

    • getGeneName

      String getGeneName(String accession)
      Returns the gene name for the given protein.
      Parameters:
      accession - the accession of the protein
      Returns:
      the gene name for the given protein

    • getTaxonomy

      String getTaxonomy(String accession)
      Returns the taxonomy for the given protein.
      Parameters:
      accession - the accession of the protein
      Returns:
      the taxonomy for the given protein

    • getOrganismIdentifier

      String getOrganismIdentifier(String accession)
      Returns the organism identifier for the given protein.
      Parameters:
      accession - the accession of the protein
      Returns:
      the organism name for the given protein

    • getProteinEvidence

      Integer getProteinEvidence(String accession)
      Returns an integer representing the protein evidence level as indexed by UniProt.
      Parameters:
      accession - the protein accession
      Returns:
      an integer representing the protein evidence level as indexed by UniProt