org.forester.evoinference.distance

Class PairwiseDistanceCalculator

java.lang.Object

org.forester.evoinference.distance.PairwiseDistanceCalculator

public final class PairwiseDistanceCalculator
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PairwiseDistanceCalculator.PWD_DISTANCE_METHOD

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA

Method Summary

Methods

Modifier and Type	Method and Description
static BasicSymmetricalDistanceMatrix	calcFractionalDissimilarities(Msa msa)
static BasicSymmetricalDistanceMatrix	calcKimuraDistances(Msa msa)
static BasicSymmetricalDistanceMatrix	calcKimuraDistances(Msa msa, double value_for_too_large_distance_for_kimura_formula)
static BasicSymmetricalDistanceMatrix	calcPoissonDistances(Msa msa)
java.lang.Object	clone()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA

public static final double DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA

See Also:

Constant Field Values

Method Detail

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

calcFractionalDissimilarities

public static BasicSymmetricalDistanceMatrix calcFractionalDissimilarities(Msa msa)

calcPoissonDistances

public static BasicSymmetricalDistanceMatrix calcPoissonDistances(Msa msa)

calcKimuraDistances

public static BasicSymmetricalDistanceMatrix calcKimuraDistances(Msa msa)

calcKimuraDistances

public static BasicSymmetricalDistanceMatrix calcKimuraDistances(Msa msa,
                                                 double value_for_too_large_distance_for_kimura_formula)