pal.substmodel
public class TN extends NucleotideModel implements XMLConstants
Parameters
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Field and Description |
---|---|
static int |
KAPPA_PARAMETER_INDEX |
static int |
R_PARAMETER_INDEX |
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 and Description |
---|
TN(double[] params,
double[] freq)
constructor 2
|
TN(double kappa,
double r,
double[] freq)
constructor 1
|
Modifier and Type | Method and Description |
---|---|
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
|
getInstance, printFrequencies, printRatios
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
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
getParameter, setParameter
public static final int KAPPA_PARAMETER_INDEX
public static final int R_PARAMETER_INDEX
public TN(double kappa, double r, double[] freq)
kappa
- transition/transversion rate ratior
- pyrimidine/purin transition rate ratiofreq
- nucleotide frequenciespublic TN(double[] params, double[] freq)
params
- parameter listfreq
- nucleotode frequenciespublic 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