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java.lang.Object | +--pal.substmodel.AbstractRateMatrix | +--pal.substmodel.NucleotideModel | +--pal.substmodel.GTR
GTR (general time reversible) model of nucleotide evolution
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 | |
GTR(double[] params,
double[] freq)
constructor 2 |
|
GTR(double a,
double b,
double c,
double d,
double e,
double[] freq)
constructor 1 |
Method Summary | |
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 |
double |
getParameter(int n)
get model parameter |
java.lang.String |
getParameterName(int i)
|
java.lang.String |
getUniqueName()
|
double |
getUpperLimit(int n)
get upper parameter limit |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
Methods inherited from class pal.substmodel.NucleotideModel |
getInstance, printFrequencies, printRatios |
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, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance |
Constructor Detail |
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 frequenciesMethod Detail |
public java.lang.Object clone()
clone
in class AbstractRateMatrix
public int getModelID()
RateMatrix
getModelID
in class AbstractRateMatrix
pal.substmodel.RateMatrix
public void report(java.io.PrintWriter out)
Report
pal.misc.Report
out
- output streampublic int getNumParameters()
Parameterized
pal.misc.Parameterized
public void setParameter(double param, int n)
Parameterized
pal.misc.Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic java.lang.String getUniqueName()
public java.lang.String getParameterName(int i)
pal.misc.NamedParameterized
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