Serialized Form
-
Package jebl.evolution.distances
-
Exception jebl.evolution.distances.CannotBuildDistanceMatrixException
class CannotBuildDistanceMatrixException extends IllegalArgumentException implements Serializable
-
-
Package jebl.evolution.graphs
-
Exception jebl.evolution.graphs.Graph.NoEdgeException
class NoEdgeException extends Exception implements Serializable
-
-
Package jebl.evolution.io
-
Exception jebl.evolution.io.ImportException
class ImportException extends Exception implements Serializable -
Exception jebl.evolution.io.ImportException.BadFormatException
class BadFormatException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.DuplicateFieldException
class DuplicateFieldException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.DuplicateTaxaException
class DuplicateTaxaException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.MissingFieldException
class MissingFieldException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.ShortSequenceException
class ShortSequenceException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.TooFewTaxaException
class TooFewTaxaException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.UnknownTaxonException
class UnknownTaxonException extends ImportException implements Serializable -
Exception jebl.evolution.io.ImportException.UnparsableDataException
class UnparsableDataException extends ImportException implements Serializable -
Exception jebl.evolution.io.NexusImporter.MissingBlockException
class MissingBlockException extends ImportException implements Serializable
-
-
Package jebl.evolution.sequences
-
Exception 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
-
Class jebl.evolution.taxa.MissingTaxonException
class MissingTaxonException extends Throwable implements Serializable
-
-
Package jebl.math
-
Exception jebl.math.MatrixCalcException
class MatrixCalcException extends Exception implements Serializable -
Exception jebl.math.MatrixCalcException.NotSquareMatrixException
class NotSquareMatrixException extends MatrixCalcException implements Serializable -
Exception jebl.math.MatrixCalcException.PositiveDefiniteException
class PositiveDefiniteException extends MatrixCalcException implements Serializable
-