pal.substmodel
Class MTREV24

java.lang.Object
  |
  +--pal.substmodel.AbstractRateMatrix
        |
        +--pal.substmodel.AminoAcidModel
              |
              +--pal.substmodel.MTREV24
All Implemented Interfaces:
java.lang.Cloneable, NamedParameterized, Parameterized, RateMatrix, Report, java.io.Serializable, XMLConstants

public class MTREV24
extends AminoAcidModel
implements XMLConstants

MTREV24 model of amino acid evolution

See Also:
Serialized Form

Fields inherited from class pal.substmodel.AbstractRateMatrix
dataType, dimension, format, frequency, rate
 
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_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GENERATIONS, 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, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS
 
Constructor Summary
MTREV24(double[] f)
          constructor
 
Method Summary
 int getModelID()
          get numerical code describing the model type
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()
           
 void makeMTREV24()
           
 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, getParameter, getParameterName, getSuitableModelID, getUpperLimit, printFrequencies, setParameter, setParameterSE
 
Methods inherited from class pal.substmodel.AbstractRateMatrix
addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, fromQToR, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance, setFrequencies, 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, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance
 

Constructor Detail

MTREV24

public MTREV24(double[] f)
constructor
Parameters:
f - amino acid frequencies
Method Detail

getModelID

public int getModelID()
Description copied from interface: RateMatrix
get numerical code describing the model type
Overrides:
getModelID in class AbstractRateMatrix
Following copied from interface: pal.substmodel.RateMatrix
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)
Overrides:
report in class AminoAcidModel
Following copied from interface: pal.misc.Report
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

getUniqueName

public java.lang.String getUniqueName()
Following copied from interface: pal.substmodel.RateMatrix
Returns:
a short unique human-readable identifier for this rate matrix.

makeMTREV24

public void makeMTREV24()