PairwiseDistanceCalculator

java.lang.Object

org.forester.evoinference.distance.PairwiseDistanceCalculator

public final class PairwiseDistanceCalculator extends Object

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static enum

PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
Field Summary

Fields

Modifier and Type

Field

Description

static final double

DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA
Method Summary

Modifier and Type

Method

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)

Object

clone()

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- 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 Details
- clone
  
  public Object clone() throws CloneNotSupportedException
  
  Overrides:
  
  clone in class Object
  
  Throws:
  
  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)