Package gorsat.gtgen

Class GPParser

java.lang.Object

gorsat.gtgen.GPParser

public class GPParser
extends Object

Utility functions for parsing genotype probability triplets.

Method Summary

Modifier and Type	Method	Description
static double[]	glCcToGp(int gl, char cc)
static double[]	glToGp(CharSequence glTriplet, char sep)
static double	parseDouble(CharSequence cs, int begin, int end)	Parses a double from a subsequence of a character sequence.
static double[]	parseDoubleTriplet(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(CharSequence cs, int begin, int end)	Parses an integer from a subsequence of a character sequence.
static int[]	parseIntTriplet(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(CharSequence plTriplet, char sep)

Methods inherited from class java.lang.Object

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

Method Details

plToGp

public static double[] plToGp(CharSequence plTriplet,
 char sep)

glToGp

public static double[] glToGp(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(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(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(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(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.