Class PairwiseDistanceCalculator
- java.lang.Object
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- org.forester.evoinference.distance.PairwiseDistanceCalculator
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public final class PairwiseDistanceCalculator extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
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Field Summary
Fields Modifier and Type Field Description static double
DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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)
java.lang.Object
clone()
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Field Detail
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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
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Method Detail
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clone
public java.lang.Object clone() throws java.lang.CloneNotSupportedException
- Overrides:
clone
in classjava.lang.Object
- Throws:
java.lang.CloneNotSupportedException
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calcFractionalDissimilarities
public static BasicSymmetricalDistanceMatrix calcFractionalDissimilarities(Msa msa)
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calcPoissonDistances
public static BasicSymmetricalDistanceMatrix calcPoissonDistances(Msa msa)
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calcKimuraDistances
public static BasicSymmetricalDistanceMatrix calcKimuraDistances(Msa msa)
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calcKimuraDistances
public static BasicSymmetricalDistanceMatrix calcKimuraDistances(Msa msa, double value_for_too_large_distance_for_kimura_formula)
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