Package gorsat.gtgen

Class GPParser

  • public class GPParser
extends java.lang.Object
    Utility functions for parsing genotype probability triplets.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static double[] glCcToGp​(int gl, char cc)  
      static double[] glToGp​(java.lang.CharSequence glTriplet, char sep)  
      static double parseDouble​(java.lang.CharSequence cs, int begin, int end)
      Parses a double from a subsequence of a character sequence.
      static double[] parseDoubleTriplet​(java.lang.CharSequence cs, char sep)
      The method does not do any validations so the the functionality is undefined if the input is bad.
      static int parseInt​(java.lang.CharSequence cs, int begin, int end)
      Parses an integer from a subsequence of a character sequence.
      static int[] parseIntTriplet​(java.lang.CharSequence cs, char sep)
      The method does not do any validations so the the functionality is undefined if the input is bad.
      static double[] plToGp​(java.lang.CharSequence plTriplet, char sep)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Method Detail

      • plToGp

        public static double[] plToGp​(java.lang.CharSequence plTriplet,
                              char sep)

      • glToGp

        public static double[] glToGp​(java.lang.CharSequence glTriplet,
                              char sep)

      • glCcToGp

        public static double[] glCcToGp​(int gl,
                                char cc)
        Parameters:
        gl - An integer representing the difference of log of probability of most likely genotype and the log of second most likely genotype.
        cc - The called genotype, '0', '1', '2'.
        Returns:
        An estimated triplet.

      • parseDoubleTriplet

        public static double[] parseDoubleTriplet​(java.lang.CharSequence cs,
                                          char sep)
        The method does not do any validations so the the functionality is undefined if the input is bad.
        Parameters:
        cs - A triplet of doubles, separated by sep.
        sep - The separator.
        Returns:
        The triplet as double array.

      • parseDouble

        public static double parseDouble​(java.lang.CharSequence cs,
                                 int begin,
                                 int end)
        Parses a double from a subsequence of a character sequence. The method does not do any validations so the the functionality is undefined if the input is bad.
        Parameters:
        cs - The character sequence to parse from.
        begin - The beginning of the subsequence.
        end - The end of the subsequence (exclusive).
        Returns:
        The parsed double.

      • parseIntTriplet

        public static int[] parseIntTriplet​(java.lang.CharSequence cs,
                                    char sep)
        The method does not do any validations so the the functionality is undefined if the input is bad.
        Parameters:
        cs - A triplet of integers, separated by sep.
        sep - The separator.
        Returns:
        The triplet as int array.

      • parseInt

        public static int parseInt​(java.lang.CharSequence cs,
                           int begin,
                           int end)
        Parses an integer from a subsequence of a character sequence. The method does not do any validations so the the functionality is undefined if the input is bad.
        Parameters:
        cs - The sequence to parse from.
        begin - The beginning of the subsequence.
        end - The end of the subsequence (exclusive).
        Returns:
        The parsed integer.