java.lang.Object
com.compomics.util.experiment.identification.protein_sequences.AaOccurrence

public class AaOccurrence
extends Object
This class gathers statistics on the occurrence of amino acids in a fasta file.
Author:
Marc Vaudel
  • Constructor Summary

    Constructors 
    Constructor Description
    AaOccurrence()
    Empty default constructor
    AaOccurrence​(int[] aaOccurrence)
    Constructor.
  • Method Summary

    Modifier and Type Method Description
    double getP​(char aa)
    Returns the log10 of the share of the given amino acid in the database.
    double getP​(char[] aas, int startIndex, int endIndex, double pMax)
    Returns the sum of the log10 of the share of the given amino acids in the database.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • AaOccurrence

      public AaOccurrence()
      Empty default constructor
    • AaOccurrence

      public AaOccurrence​(int[] aaOccurrence)
      Constructor.
      Parameters:
      aaOccurrence - the occurrence of all amino acids in the database indexed as in the AminoAcid clss.
  • Method Details

    • getP

      public double getP​(char aa)
      Returns the log10 of the share of the given amino acid in the database.
      Parameters:
      aa - the amino acid as single letter code
      Returns:
      the log10 of the share of the given amino acid in the database
    • getP

      public double getP​(char[] aas, int startIndex, int endIndex, double pMax)
      Returns the sum of the log10 of the share of the given amino acids in the database. Start and end indexes are 0 based, start is inclusive and end exclusive.
      Parameters:
      aas - the amino acids as char array of the single letter code
      startIndex - the index where to start in the sequence
      endIndex - the index where to start in the sequence
      pMax - the maximal value p can have
      Returns:
      the sum of the log10 of the share of the given amino acids in the database