statalign.model.subst.plugins
Class AminoAcidModel

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

Direct Known Subclasses:

Blosum, CpRev, Dayhoff, Jones, MtMam, MtREV, RtREV, Vt, Wag

public abstract class AminoAcidModel
extends SubstitutionModel

Common superclass for amino acid substitution models.

Author:

novak

Field Summary

static java.lang.String

type

Fields inherited from class statalign.model.subst.SubstitutionModel

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

Constructor Summary

AminoAcidModel()

Method Summary

double	acceptable(RawSequences r) This function decides if the model can accept the input sequences.
java.awt.Color	getColor(char c) Returns the color of a character.
char	mostLikely(double[] seq) Returns the most likely character given the Felsentein likelihood array.
java.lang.String	print() Dummy function with the possibility of further developments.
void	restoreParameter() Empty method provided for models with no parameters (the evolutionary time is represented in the edge lengths).
double	sampleParameter() It does nothing and returns 0, i.e log-probability 1.

Methods inherited from class statalign.model.subst.SubstitutionModel

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

Methods inherited from class java.lang.Object

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

Field Detail

type

public static final java.lang.String type

See Also:

Constant Field Values

Constructor Detail

AminoAcidModel

public AminoAcidModel()

Method Detail

getColor

public java.awt.Color getColor(char c)

Returns the color of a character. Magenta characters are 'RHK', red characters are 'AVFPMILW', blue characters are 'DE' and green characters are 'STYCNGQ'.

Specified by:

getColor in class SubstitutionModel

Parameters:

c - character whose background colour is to be returned

print

public java.lang.String print()

Dummy function with the possibility of further developments.

Specified by:

print in class SubstitutionModel

Returns:

the resulting String

restoreParameter

public void restoreParameter()

Empty method provided for models with no parameters (the evolutionary time is represented in the edge lengths).

Specified by:

restoreParameter in class SubstitutionModel

sampleParameter

public double sampleParameter()

It does nothing and returns 0, i.e log-probability 1.

Specified by:

sampleParameter in class SubstitutionModel

Returns:

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

acceptable

public double acceptable(RawSequences r)

This function decides if the model can accept the input sequences.

Specified by:

acceptable in class SubstitutionModel

Parameters:

r - raw sequences

Returns:

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

mostLikely

public char mostLikely(double[] seq)

Returns the most likely character given the Felsentein likelihood array.

Specified by:

mostLikely in class SubstitutionModel