java.io.Serializable
, java.lang.Cloneable
, ExternalParameterListener
, NamedParameterized
, Parameterized
, Report
, RateMatrix
, XMLConstants
public class GTR extends NucleotideModel implements java.io.Serializable, XMLConstants
Parameters
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
format
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 | Description |
---|---|
GTR(double[] params,
double[] freq) |
constructor 2
|
GTR(double a,
double b,
double c,
double d,
double e,
double[] freq) |
constructor 1
|
Modifier and Type | Method | Description |
---|---|---|
java.lang.Object |
clone() |
|
double |
getDefaultValue(int n) |
get default value of parameter
|
double |
getLowerLimit(int n) |
get lower parameter limit
|
int |
getModelID() |
get numerical code describing the model type
|
int |
getNumParameters() |
get number of parameters
|
java.lang.String |
getParameterName(int i) |
|
java.lang.String |
getUniqueName() |
|
double |
getUpperLimit(int n) |
get upper parameter limit
|
protected void |
rebuildRateMatrix(double[][] rate,
double[] parameters) |
|
void |
report(java.io.PrintWriter out) |
print human readable report (e.g., on parameters and associated model)
|
void |
setParameterSE(double paramSE,
int n) |
set standard errors for model parameter
|
addPalObjectListener, 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
getInstance, printFrequencies, printRatios
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getParameter, setParameter
addPalObjectListener, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
public GTR(double a, double b, double c, double d, double e, double[] freq)
a
- entry in rate matrixb
- entry in rate matrixc
- entry in rate matrixd
- entry in rate matrixe
- entry in rate matrixfreq
- nucleotide frequenciespublic GTR(double[] params, double[] freq)
params
- parameter listfreq
- nucleotide frequenciespublic java.lang.Object clone()
clone
in interface RateMatrix
clone
in class AbstractRateMatrix
public int getModelID()
AbstractRateMatrix
getModelID
in interface RateMatrix
getModelID
in class AbstractRateMatrix
public void report(java.io.PrintWriter out)
Report
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter numberpublic java.lang.String getUniqueName()
getUniqueName
in interface RateMatrix
public java.lang.String getParameterName(int i)
getParameterName
in interface NamedParameterized
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
rebuildRateMatrix
in class AbstractRateMatrix