pal.substmodel
Class BLOSUM62

java.lang.Object
  extended by pal.substmodel.AbstractRateMatrix
      extended by pal.substmodel.AminoAcidModel
          extended by pal.substmodel.BLOSUM62
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

public class BLOSUM62
extends AminoAcidModel
implements 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:
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
BLOSUM62(double[] f)
          constructor
 
Method Summary
 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

BLOSUM62

public BLOSUM62(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