pal.substmodel
Class Dayhoff
java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
pal.substmodel.Dayhoff
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants
public class Dayhoff
- extends AminoAcidModel
- implements XMLConstants
Dayhoff model for amino acid evolution
Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978)
A model of evolutionary change in proteins.
Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3,
National Biomedical Research Foundation, Washington DC, pp. 345-352.
- Version:
- $Id: Dayhoff.java,v 1.7 2003/11/13 04:05:39 matt Exp $
- Author:
- Korbinian Strimmer
- See Also:
- Serialized Form
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_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 Summary |
Dayhoff(double[] f)
constructor |
Method Summary |
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) |
Methods inherited from class pal.substmodel.AbstractRateMatrix |
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 |
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, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale |
Dayhoff
public Dayhoff(double[] f)
- constructor
- Parameters:
f
- amino acid frequencies
getModelID
public int getModelID()
- Description copied from class:
AbstractRateMatrix
- get numerical code describing the model type
- Specified by:
getModelID
in interface RateMatrix
- Specified by:
getModelID
in class AbstractRateMatrix
- 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)
- Specified by:
report
in interface Report
- Specified by:
report
in class AminoAcidModel
- 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
getOriginalFrequencies
public static double[] getOriginalFrequencies()
- Returns:
- the frequencies of the original data set that
formed the basis for the estimation of the rate matrix
getUniqueName
public java.lang.String getUniqueName()
- Specified by:
getUniqueName
in interface RateMatrix
- Returns:
- a short unique human-readable identifier for this rate matrix.
rebuildRateMatrix
protected void rebuildRateMatrix(double[][] rate,
double[] parameters)
- Specified by:
rebuildRateMatrix
in class AbstractRateMatrix