Package pal.substmodel
Class BLOSUM62
java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
pal.substmodel.BLOSUM62
- All Implemented Interfaces:
Serializable
,Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
,XMLConstants
BLOSUM62 model of amino acid evolution
- Version:
- $Id: BLOSUM62.java,v 1.7 2003/11/13 04:05:39 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
get numerical code describing the model typestatic double[]
static void
getOriginalFrequencies
(double[] f) get the frequencies of the original data set that formed the basis for the estimation of the rate matrixprotected void
rebuildRateMatrix
(double[][] rate, double[] parameters) void
report
(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
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Constructor Details
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BLOSUM62
public BLOSUM62(double[] f) constructor- Parameters:
f
- amino acid frequencies
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Method Details
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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
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report
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
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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
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getOriginalFrequencies
public static double[] getOriginalFrequencies()- Returns:
- the frequencies of the original data set that formed the basis for the estimation of the rate matrix
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getUniqueName
- Specified by:
getUniqueName
in interfaceRateMatrix
- Returns:
- a short unique human-readable identifier for this rate matrix.
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rebuildRateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters) - Specified by:
rebuildRateMatrix
in classAbstractRateMatrix
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