Package pal.substmodel
Class MTREV24
- java.lang.Object
-
- pal.substmodel.AbstractRateMatrix
-
- pal.substmodel.AminoAcidModel
-
- pal.substmodel.MTREV24
-
- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
,XMLConstants
public class MTREV24 extends AminoAcidModel implements XMLConstants
MTREV24 model of amino acid evolution- Version:
- $Id: MTREV24.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 Description MTREV24(double[] f)
constructor
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getModelID()
get numerical code describing the model typestatic 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 matrixjava.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.misc.Parameterized
getParameter, setParameter
-
Methods inherited from interface pal.substmodel.RateMatrix
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
-
-
-
-
Method Detail
-
getModelID
public int getModelID()
Description copied from class:AbstractRateMatrix
get numerical code describing the model type- Specified by:
getModelID
in interfaceRateMatrix
- Specified by:
getModelID
in classAbstractRateMatrix
- 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 interfaceReport
- Specified by:
report
in classAminoAcidModel
- 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 interfaceRateMatrix
- Returns:
- a short unique human-readable identifier for this rate matrix.
-
rebuildRateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
- Specified by:
rebuildRateMatrix
in classAbstractRateMatrix
-
-