java.lang.Object
com.compomics.util.experiment.identification.utils.ProteinUtils

public class ProteinUtils
extends Object
Convenience functions for the handling of proteins.
Author:
Marc Vaudel
  • Constructor Details

    • ProteinUtils

      public ProteinUtils()
      Empty default constructor.
  • Method Details

    • isDecoy

      public static boolean isDecoy​(String accession, FastaParameters fastaParameters)
      Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given FASTA parameters.
      Parameters:
      accession - the protein accession
      fastaParameters - the FASTA parameters
      Returns:
      a boolean indicating whether the given accession corresponds to a decoy sequence
    • isDecoy

      public static boolean isDecoy​(String accession, SequenceProvider sequenceProvider)
      Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.
      Parameters:
      accession - the protein accession
      sequenceProvider - the sequence provider
      Returns:
      a boolean indicating whether the given accession corresponds to a decoy sequence
    • getObservableAminoAcids

      public static int[] getObservableAminoAcids​(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)
      Returns the observable amino acids in the sequence when using the given enzymes with the given maximal peptide length.
      Parameters:
      sequence - the protein sequence
      enzymes - the enzymes to use
      pepMaxLength - the max peptide length
      Returns:
      the number of observable amino acids of the sequence
    • getObservableLength

      public static int getObservableLength​(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)
      Returns the number of observable amino acids in the sequence.
      Parameters:
      sequence - the protein sequence
      enzymes - the enzymes to use
      pepMaxLength - the max peptide length
      Returns:
      the number of observable amino acids of the sequence
    • getNCleavageSites

      public static int getNCleavageSites​(String sequence, ArrayList<Enzyme> enzymes)
      Returns the number of cleavage sites.
      Parameters:
      sequence - the protein sequence
      enzymes - the enzymes to use
      Returns:
      the number of possible peptides
    • computeMolecularWeight

      public static double computeMolecularWeight​(String sequence)
      Returns the protein's molecular weight.
      Parameters:
      sequence - the protein sequence
      Returns:
      the protein's molecular weight in kDa