Serialized Form
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Package jebl.evolution.distances
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Class jebl.evolution.distances.CannotBuildDistanceMatrixException extends java.lang.IllegalArgumentException implements Serializable
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Package jebl.evolution.graphs
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Class jebl.evolution.graphs.Graph.NoEdgeException extends java.lang.Exception implements Serializable
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Package jebl.evolution.io
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Class jebl.evolution.io.ImportException extends java.lang.Exception implements Serializable
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Class jebl.evolution.io.ImportException.BadFormatException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.DuplicateFieldException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.DuplicateTaxaException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.MissingFieldException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.ShortSequenceException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.TooFewTaxaException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.UnknownTaxonException extends ImportException implements Serializable
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Class jebl.evolution.io.ImportException.UnparsableDataException extends ImportException implements Serializable
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Class jebl.evolution.io.NexusImporter.MissingBlockException extends ImportException implements Serializable
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Package jebl.evolution.sequences
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Class jebl.evolution.sequences.SequenceStateException extends java.lang.Exception implements Serializable
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Package jebl.evolution.substmodel
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Class jebl.evolution.substmodel.AbstractRateMatrix extends java.lang.Object implements Serializable
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Serialized Fields
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dimension
int dimension
dimension -
frequency
double[] frequency
stationary frequencies (sum = 1.0) -
parameterStore_
double[] parameterStore_
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rate
double[][] rate
rate matrix (transition: from 1st index to 2nd index) -
sequenceType
SequenceType sequenceType
data type
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Class jebl.evolution.substmodel.AminoAcidModel extends AbstractRateMatrix implements Serializable
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Class jebl.evolution.substmodel.MatrixExponential extends java.lang.Object implements Serializable
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Serialized Fields
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amat
double[][] amat
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ci
double ci
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cr
double cr
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dimension_
int dimension_
dimension of rate matrix -
Eval
double[] Eval
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evali
double[] evali
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Evec
double[][] Evec
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Ievc
double[][] Ievc
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iexp
double[][] iexp
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ordr
int[] ordr
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transProb
double[][] transProb
transition probability matrix
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Class jebl.evolution.substmodel.WAG extends AminoAcidModel implements Serializable
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Package jebl.evolution.taxa
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Class jebl.evolution.taxa.MissingTaxonException extends java.lang.Throwable implements Serializable
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Package jebl.math
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Class jebl.math.MatrixCalcException extends java.lang.Exception implements Serializable
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Class jebl.math.MatrixCalcException.NotSquareMatrixException extends MatrixCalcException implements Serializable
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Class jebl.math.MatrixCalcException.PositiveDefiniteException extends MatrixCalcException implements Serializable
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