statalign.model.subst
Class SubstitutionModel

java.lang.Object
  statalign.model.subst.SubstitutionModel

Direct Known Subclasses:

AminoAcidModel, NucleotideModel

public abstract class SubstitutionModel
extends java.lang.Object

Superclass of the substitution models.

Author:

miklos, novak

Field Summary

char[]	alphabet This array contains the potential characters of the alphabet.
SubstitutionScore	attachedScoringScheme This scoring scheme is used for constructing an initial tree.
double[]	d The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix.
double[]	e This array tells the equilibrium distribution
static java.lang.String	menuName Sets the name of the model plugin that will appear in the menu when declared with the same name and type.
double[]	params Model parameters.
static java.lang.String	type Tells whether your plugin is a nucleotide or protein model (or something else) when declared with the same name and type.
double[][]	v The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix
double[][]	w The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix

Constructor Summary

SubstitutionModel()

Method Summary

abstract double	acceptable(RawSequences r) If a model cannot accept the currently loaded sequences (for example, because the sequences contains a character that is not part of the model) then it returns a negative number.
abstract java.awt.Color	getColor(char c) Returns the colour associated with the character.
java.lang.String	getMenuName() Retrieves the static field menuName of the class of the object the method is called on.
static java.lang.String	getMenuName(java.lang.Class<? extends SubstitutionModel> cl) Retrieves menuName static field of a SubstitutionModel plug-in class.
double	getPrior() Returns the prior for the substitution parameters.
java.lang.String	getType() Retrieves the static field type of the class of the object the method is called on.
static java.lang.String	getType(java.lang.Class<? extends SubstitutionModel> cl) Retrieves the static field type of a SubstitutionModel plug-in class.
abstract char	mostLikely(double[] seq)
abstract java.lang.String	print() Represents model state as a String (usually parameter values concatenated)
abstract void	restoreParameter() Restores state just before the call of sampleParameter
abstract double	sampleParameter() Abstract method to sample a new model parameter and update v,w,d,e accordingly.
void	updateSpan(double newSpan)
double[][]	updateTransitionMatrix(double[][] transitionMatrix, double edgeLength) Updates externally stored transition matrix using current values of v, w, d, e and current edge length.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

v

public double[][] v

The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix

w

public double[][] w

The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix

d

public double[] d

The rate matrix must be diagonalized and represented in a v d w product, where d is a diagonal matrix. Only the diagonal elements must be put into the one dimensional array d.

e

public double[] e

This array tells the equilibrium distribution

alphabet

public char[] alphabet

This array contains the potential characters of the alphabet.

params

public double[] params

Model parameters.

type

public static java.lang.String type

Tells whether your plugin is a nucleotide or protein model (or something else) when declared with the same name and type. Affects grouping of models in the menu.

menuName

public static java.lang.String menuName

Sets the name of the model plugin that will appear in the menu when declared with the same name and type.

attachedScoringScheme

public SubstitutionScore attachedScoringScheme

This scoring scheme is used for constructing an initial tree.

Constructor Detail

SubstitutionModel

public SubstitutionModel()

Method Detail

updateSpan

public void updateSpan(double newSpan)

acceptable

public abstract double acceptable(RawSequences r)

If a model cannot accept the currently loaded sequences (for example, because the sequences contains a character that is not part of the model) then it returns a negative number. Otherwise it returns a double value between 0 and 1, the better likes the model the sequences the greater the return number is.

Parameters:

r - raw sequences

Returns:

the value telling how well the substitution model likes the sequences.

updateTransitionMatrix

public double[][] updateTransitionMatrix(double[][] transitionMatrix,
                                         double edgeLength)

Updates externally stored transition matrix using current values of v, w, d, e and current edge length. Must always be called in the form m = updateTransitionMatrix(m, len) where m can be null as well.

Parameters:

transitionMatrix - reference to matrix to store results, null to create new

edgeLength - evolutionary time

Returns:

updated (or newly created) transition matrix

sampleParameter

public abstract double sampleParameter()

Abstract method to sample a new model parameter and update v,w,d,e accordingly.

Returns:

log(fwd proposal probability/bwd proposal probability) [i.e. inverse Hastings ratio]

restoreParameter

public abstract void restoreParameter()

Restores state just before the call of sampleParameter

print

public abstract java.lang.String print()

Represents model state as a String (usually parameter values concatenated)

Returns:

the resulting String

getColor

public abstract java.awt.Color getColor(char c)

Returns the colour associated with the character. This colour will be the background colour of the character in the printed alignments.

Parameters:

c - character whose background colour is to be returned

mostLikely

public abstract char mostLikely(double[] seq)

getType

public java.lang.String getType()

Retrieves the static field type of the class of the object the method is called on. See getType(Class cl) for details.

getType

public static java.lang.String getType(java.lang.Class<? extends SubstitutionModel> cl)

Retrieves the static field type of a SubstitutionModel plug-in class. In the class it must be declared public static String. Searches the class hierarchy upwards until a class with the field declared is found.

Parameters:

cl - class extending SubstitutionModel

Returns:

value of the static field type or "unknown" if the field is null or empty

getMenuName

public java.lang.String getMenuName()

Retrieves the static field menuName of the class of the object the method is called on. See getMenuName(Class cl) for details.

getMenuName

public static java.lang.String getMenuName(java.lang.Class<? extends SubstitutionModel> cl)

Retrieves menuName static field of a SubstitutionModel plug-in class. In the class it must be declared public static String.

Parameters:

cl - class extending SubstitutionModel

Returns:

value of the static field menuName or the simple name of cl if the field doesn't exist or is null

getPrior

public double getPrior()

Returns the prior for the substitution parameters. By default the prior is uniform and this function returns 1.

Returns:

prior for the parameters of the substitution model.