Serialized Form

Package jebl.evolution.distances

Class jebl.evolution.distances.CannotBuildDistanceMatrixException extends java.lang.IllegalArgumentException implements Serializable

Package jebl.evolution.graphs

Class jebl.evolution.graphs.Graph.NoEdgeException extends java.lang.Exception implements Serializable

Package jebl.evolution.io

Class jebl.evolution.io.ImportException extends java.lang.Exception implements Serializable

Class jebl.evolution.io.ImportException.BadFormatException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.DuplicateFieldException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.DuplicateTaxaException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.MissingFieldException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.ShortSequenceException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.TooFewTaxaException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.UnknownTaxonException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.UnparsableDataException extends ImportException implements Serializable

Class jebl.evolution.io.NexusImporter.MissingBlockException extends ImportException implements Serializable

Package jebl.evolution.sequences

Class jebl.evolution.sequences.SequenceStateException extends java.lang.Exception implements Serializable

Package jebl.evolution.substmodel

Class jebl.evolution.substmodel.AbstractRateMatrix extends java.lang.Object implements Serializable

Serialized Fields

dimension

int dimension

dimension

frequency

double[] frequency

stationary frequencies (sum = 1.0)

rate

double[][] rate

rate matrix (transition: from 1st index to 2nd index)

sequenceType

SequenceType sequenceType

data type

parameterStore_

double[] parameterStore_

Class jebl.evolution.substmodel.AminoAcidModel extends AbstractRateMatrix implements Serializable

Class jebl.evolution.substmodel.MatrixExponential extends java.lang.Object implements Serializable

Serialized Fields

Eval

double[] Eval

Evec

double[][] Evec

Ievc

double[][] Ievc

iexp

double[][] iexp

ordr

int[] ordr

evali

double[] evali

amat

double[][] amat

dimension_

int dimension_

dimension of rate matrix

transProb

double[][] transProb

transition probability matrix

cr

double cr

ci

double ci

Class jebl.evolution.substmodel.WAG extends AminoAcidModel implements Serializable

Package jebl.evolution.taxa

Class jebl.evolution.taxa.MissingTaxonException extends java.lang.Throwable implements Serializable

Package jebl.math

Class jebl.math.MatrixCalcException extends java.lang.Exception implements Serializable

Class jebl.math.MatrixCalcException.NotSquareMatrixException extends MatrixCalcException implements Serializable

Class jebl.math.MatrixCalcException.PositiveDefiniteException extends MatrixCalcException implements Serializable