pal.substmodel
public class BLOSUM62 extends AminoAcidModel implements XMLConstants
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 and Description |
---|
BLOSUM62(double[] f)
constructor
|
Modifier and Type | Method and Description |
---|---|
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)
|
getDefaultValue, getInstance, getLowerLimit, getNumParameters, getParameterName, getSuitableModelID, getUpperLimit, printFrequencies, setParameterSE
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 BLOSUM62(double[] f)
f
- amino acid frequenciespublic int getModelID()
AbstractRateMatrix
getModelID
in interface RateMatrix
getModelID
in class AbstractRateMatrix
public void report(java.io.PrintWriter out)
Report
report
in interface Report
report
in class AminoAcidModel
out
- output streampublic static void getOriginalFrequencies(double[] f)
f
- array where amino acid frequencies will be storedpublic static double[] getOriginalFrequencies()
public java.lang.String getUniqueName()
getUniqueName
in interface RateMatrix
protected void rebuildRateMatrix(double[][] rate, double[] parameters)
rebuildRateMatrix
in class AbstractRateMatrix