statalign.model.subst.plugins
Class TamuraNei

java.lang.Object
  extended by statalign.model.subst.SubstitutionModel
      extended by statalign.model.subst.plugins.NucleotideModel
          extended by statalign.model.subst.plugins.TamuraNei

public class TamuraNei
extends NucleotideModel

This class implements the Tamura-Nei parameter model.

Author:
lyngsoe

Field Summary
static java.lang.String menuName
           
 
Fields inherited from class statalign.model.subst.plugins.NucleotideModel
type
 
Fields inherited from class statalign.model.subst.SubstitutionModel
alphabet, attachedScoringScheme, d, e, params, v, w
 
Constructor Summary
TamuraNei()
          This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.
 
Method Summary
 java.lang.String print()
          Prints the parameters of the model
 double sampleParameter()
          This function implements a proposal for new parameter values.
 
Methods inherited from class statalign.model.subst.plugins.NucleotideModel
acceptable, getColor, mostLikely, restoreParameter, setPrintRNA
 
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

menuName

public static final java.lang.String menuName
See Also:
Constant Field Values
Constructor Detail

TamuraNei

public TamuraNei()
          throws java.io.IOException
This constructor uses numerical methods to diagonalise the rate matrix and to set diagonalising matrices.

Throws:
java.io.IOException
Method Detail

print

public java.lang.String print()
Prints the parameters of the model

Overrides:
print in class NucleotideModel
Returns:
the resulting String

sampleParameter

public double sampleParameter()
This function implements a proposal for new parameter values. Returns with the logarithm of the Metropolis-Hastings ratio.

Specified by:
sampleParameter in class SubstitutionModel
Returns:
log(fwd proposal probability/bwd proposal probability) [i.e. inverse Hastings ratio]