# Serialized Form

## Package jebl.evolution.distances

### Exception Class jebl.evolution.distances.CannotBuildDistanceMatrixException

class CannotBuildDistanceMatrixException extends IllegalArgumentException implements Serializable

## Package jebl.evolution.graphs

### Exception Class jebl.evolution.graphs.Graph.NoEdgeException

class NoEdgeException extends Exception implements Serializable

## Package jebl.evolution.io

### Exception Class jebl.evolution.io.ImportException

class ImportException extends Exception implements Serializable

### Exception Class jebl.evolution.io.ImportException.BadFormatException

class BadFormatException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.DuplicateFieldException

class DuplicateFieldException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.DuplicateTaxaException

class DuplicateTaxaException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.MissingFieldException

class MissingFieldException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.ShortSequenceException

class ShortSequenceException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.TooFewTaxaException

class TooFewTaxaException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.UnknownTaxonException

class UnknownTaxonException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.ImportException.UnparsableDataException

class UnparsableDataException extends ImportException implements Serializable

### Exception Class jebl.evolution.io.NexusImporter.MissingBlockException

class MissingBlockException extends ImportException implements Serializable

## Package jebl.evolution.sequences

### Exception Class jebl.evolution.sequences.SequenceStateException

class SequenceStateException extends Exception implements Serializable

## Package jebl.evolution.substmodel

### Class jebl.evolution.substmodel.AbstractRateMatrix

class AbstractRateMatrix extends Object implements Serializable

#### Serialized Fields

##### dimension

    int dimension

dimension

##### frequency

    double[] frequency

stationary frequencies (sum = 1.0)

##### parameterStore_

    double[] parameterStore_

##### rate

    double[][] rate

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

##### sequenceType

    SequenceType sequenceType

data type

### Class jebl.evolution.substmodel.AminoAcidModel

class AminoAcidModel extends AbstractRateMatrix implements Serializable

### Class jebl.evolution.substmodel.MatrixExponential

class MatrixExponential extends Object implements Serializable

#### Serialized Fields

##### amat

    double[][] amat

##### ci

    double ci

##### cr

    double cr

##### dimension_

    int dimension_

dimension of rate matrix

##### Eval

    double[] Eval

##### evali

    double[] evali

##### Evec

    double[][] Evec

##### Ievc

    double[][] Ievc

##### iexp

    double[][] iexp

##### ordr

    int[] ordr

##### transProb

    double[][] transProb

transition probability matrix

### Class jebl.evolution.substmodel.WAG

class WAG extends AminoAcidModel implements Serializable

## Package jebl.evolution.taxa

### Exception Class jebl.evolution.taxa.MissingTaxonException

class MissingTaxonException extends Throwable implements Serializable

## Package jebl.math

### Exception Class jebl.math.MatrixCalcException

class MatrixCalcException extends Exception implements Serializable

### Exception Class jebl.math.MatrixCalcException.NotSquareMatrixException

class NotSquareMatrixException extends MatrixCalcException implements Serializable

### Exception Class jebl.math.MatrixCalcException.PositiveDefiniteException

class PositiveDefiniteException extends MatrixCalcException implements Serializable