pal.substmodel

Class VT

java.lang.Object

pal.substmodel.AbstractRateMatrix

pal.substmodel.AminoAcidModel

pal.substmodel.VT

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

public class VT
extends AminoAcidModel
implements XMLConstants

VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T. and Vingron, M., 2000. Journal of Computational Biology, 7(6):761-776.

Version:

$Id: VT.java,v 1.7 2003/11/13 04:05:39 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields inherited from class pal.substmodel.AbstractRateMatrix

format

Fields inherited from interface pal.util.XMLConstants

A_TO_C, A_TO_G, A_TO_T, ALIGNMENT, ALPHA, ANCESTRAL_MU_RATE, ANCESTRAL_POP_SIZE, ATTRIBUTE, BACKWARDS, BLOSUM62, C_TO_G, C_TO_T, COALESCENT, CONST_EXP_CONST, CONST_EXP_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, CURRENT_POP_SIZE_DURATION, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPANDING_POPULATION, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GAMMA_ALPHA, GAMMA_DISTRIBUTION, GENERATIONS, GROWTH_PHASE_DURATION, GROWTH_RATE, GTR, HEIGHT, HKY, ID, JC, JTT, KAPPA, LENGTH, MISSING, MODEL, MONTHS, MTREV24, MU_STEP_TIME, MUTATION_RATE, MUTATION_RATE_MODEL, MUTATIONS, NAME, NODE, NUMBER_CATEGORIES, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_DISTRIBUTION, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNIFORM_RATE_DISTRIBUTION, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS

Constructor Summary

Constructors

Constructor and Description
VT(double[] f) constructor

Method Summary

Methods

Modifier and Type	Method and Description
int	getModelID() get numerical code describing the model type
static double[]	getOriginalFrequencies()
static void	getOriginalFrequencies(double[] f) get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
java.lang.String	getUniqueName()
protected void	rebuildRateMatrix(double[][] rate, double[] parameters)
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)

Methods inherited from class pal.substmodel.AminoAcidModel

getDefaultValue, getInstance, getLowerLimit, getNumParameters, getParameterName, getSuitableModelID, getUpperLimit, printFrequencies, setParameterSE

Methods inherited from class pal.substmodel.AbstractRateMatrix

addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getOrthogonalHints, getParameter, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, parameterChanged, rebuild, removePalObjectListener, scale, setDataType, setDistance, setDistanceTranspose, setFrequencies, setParameter, setParameters, setParametersNoScale, updateMatrixExp

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface pal.substmodel.RateMatrix

addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from interface pal.misc.Parameterized

getParameter, setParameter

Constructor Detail

VT

public VT(double[] f)

constructor

Parameters:

f - amino acid frequencies

Method Detail

getModelID

public int getModelID()

Description copied from class: AbstractRateMatrix

get numerical code describing the model type

Specified by:

getModelID in interface RateMatrix

Specified by:

getModelID in class AbstractRateMatrix

Returns:

integer code identifying a substitution model

report

public void report(java.io.PrintWriter out)

Description copied from interface: Report

print human readable report (e.g., on parameters and associated model)

Specified by:

report in interface Report

Specified by:

report in class AminoAcidModel

Parameters:

out - output stream

getOriginalFrequencies

public static void getOriginalFrequencies(double[] f)

get the frequencies of the original data set that formed the basis for the estimation of the rate matrix

Parameters:

f - array where amino acid frequencies will be stored

getOriginalFrequencies

public static double[] getOriginalFrequencies()

Returns:

the frequencies of the original data set that formed the basis for the estimation of the rate matrix

getUniqueName

public java.lang.String getUniqueName()

Specified by:

getUniqueName in interface RateMatrix

Returns:

a short unique human-readable identifier for this rate matrix.

rebuildRateMatrix

protected void rebuildRateMatrix(double[][] rate,
                     double[] parameters)

Specified by:

rebuildRateMatrix in class AbstractRateMatrix