statalign.model.subst.plugins
Class NucleotideModel

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

Direct Known Subclasses:

Felsenstein81, Felsenstein84, HKY85, JukesCantor, Kimura3, ReversibleNucleotide, Tamura92, TamuraNei

public abstract class NucleotideModel
extends SubstitutionModel

This is the abstract class for nucleotide models.

Author:

lyngsoe

Field Summary

static java.lang.String

type

Fields inherited from class statalign.model.subst.SubstitutionModel

alphabet, attachedScoringScheme, d, e, menuName, params, v, w

Method Summary

double	acceptable(RawSequences r) This function decides if this model can analyze input sequences.
java.awt.Color	getColor(char c) This function assigns colors to characters.
char	mostLikely(double[] seq) Returns with the most likely character, given a Felsentein likelihood array.
java.lang.String	print() returns the description of the current parameters of the model
void	restoreParameter() restore the parameters to the old values when a parameter-changing proposal is not accepted.
void	setPrintRNA(boolean printRNA) Selects whether to print RNA nucleotides (U for T) or default DNA ones.

Methods inherited from class statalign.model.subst.SubstitutionModel

getMenuName, getMenuName, getPrior, getType, getType, sampleParameter, updateSpan, updateTransitionMatrix

Methods inherited from class java.lang.Object

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

Field Detail

type

public static java.lang.String type

Method Detail

acceptable

public double acceptable(RawSequences r)

This function decides if this model can analyze input sequences. accepted characters are 'acgutryswmkbdhvn'. Our program is case insensitive.

Specified by:

acceptable in class SubstitutionModel

Parameters:

r - raw sequences

Returns:

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

getColor

public java.awt.Color getColor(char c)

This function assigns colors to characters. 'A' is red, 'C' is blue, 'G' is orange, 'T' or 'U' is green, the remaining characters (ambiguous characters and the gap symbol) are grey

Specified by:

getColor in class SubstitutionModel

Parameters:

c - character whose background colour is to be returned

print

public java.lang.String print()

returns the description of the current parameters of the model

Specified by:

print in class SubstitutionModel

Returns:

the resulting String

restoreParameter

public void restoreParameter()

restore the parameters to the old values when a parameter-changing proposal is not accepted.

Specified by:

restoreParameter in class SubstitutionModel

mostLikely

public char mostLikely(double[] seq)

Returns with the most likely character, given a Felsentein likelihood array. It can handle ambiguous characters. If the probabilities in the Felsentein array are all zero, returns '*'.

Specified by:

mostLikely in class SubstitutionModel

setPrintRNA

public void setPrintRNA(boolean printRNA)

Selects whether to print RNA nucleotides (U for T) or default DNA ones. Affects the beviour of mostLikely(double[]).