pal.substmodel
Interface SubstitutionModel

All Superinterfaces:
Parameterized, Report, java.io.Serializable
All Known Implementing Classes:
SimpleSubstitutionModel

public interface SubstitutionModel
extends Parameterized, Report, java.io.Serializable

model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities


Method Summary
 void addPalObjectListener(PalObjectListener pol)
          Add a PalObjectListener to be notified of changes to the model.
 java.lang.Object clone()
          A non shallow implementation of clone()
 DataType getDataType()
           
 int getDimension()
          Deprecated.  
 RateDistribution getRateDistribution()
           
 RateMatrix getRateMatrix()
           
 void removePalObjectListener(PalObjectListener pol)
           
 void setDistance(double k)
          set distance and corresponding computation transition probabilities
 double transProb(int r, int i, int j)
          get transition probability for the preselected model and the previously specified distance
 
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
 
Methods inherited from interface pal.misc.Report
report
 

Method Detail

getRateMatrix

public RateMatrix getRateMatrix()
Returns:
the rate matrix

getRateDistribution

public RateDistribution getRateDistribution()
Returns:
the rate distribution of this substitution model.

setDistance

public void setDistance(double k)
set distance and corresponding computation transition probabilities
Parameters:
k - distance

transProb

public double transProb(int r,
                        int i,
                        int j)
get transition probability for the preselected model and the previously specified distance
Parameters:
r - rate category
i - start state
j - end state
Returns:
transition probability

getDimension

public int getDimension()
Deprecated.  

Returns the dimension of this model.

getDataType

public DataType getDataType()

addPalObjectListener

public void addPalObjectListener(PalObjectListener pol)
Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called

removePalObjectListener

public void removePalObjectListener(PalObjectListener pol)

clone

public java.lang.Object clone()
A non shallow implementation of clone()
Overrides:
clone in class java.lang.Object