pal.substmodel
Class SaturatedSingleSplitDistribution

java.lang.Object
  extended by pal.substmodel.SaturatedSingleSplitDistribution
All Implemented Interfaces:
NeoParameterized, SingleSplitDistribution

public class SaturatedSingleSplitDistribution
extends java.lang.Object
implements SingleSplitDistribution

Title: SaturatedSingleSplitDistribution

Description: A model

Copyright: Copyright (c) 2003

Company:

Version:
1.0
Author:
not attributable

Constructor Summary
SaturatedSingleSplitDistribution(int numberOfBaseTransitionCategories)
           
SaturatedSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)
           
 
Method Summary
 void getDefaultValues(double[] store, int startIndex)
          get default value parameter values
 double[] getDistribution()
           
 double[][] getDistributionInfo()
          Obtain the distribution information stored in the following format: [beforeclass][afterclass] For example, the probability of evolving in class 0 before the split, and class 1 after the split - [0][1]
 double getLowerLimit(int n)
          get lower parameter limit
 int getNumberOfBaseTransitionCategories()
           
 int getNumberOfParameters()
          get number of parameters
 void getParameters(double[] store, int startIndex)
          get model parameter
 double getUpperLimit(int n)
          get upper parameter limit
 void setParameters(double[] store, int startIndex)
          set model parameter
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SaturatedSingleSplitDistribution

public SaturatedSingleSplitDistribution(int numberOfBaseTransitionCategories)

SaturatedSingleSplitDistribution

public SaturatedSingleSplitDistribution(int numberOfBaseTransitionCategories,
                                        double[] initialParameters)
Method Detail

getDistribution

public double[] getDistribution()

getNumberOfBaseTransitionCategories

public int getNumberOfBaseTransitionCategories()
Specified by:
getNumberOfBaseTransitionCategories in interface SingleSplitDistribution

getDistributionInfo

public double[][] getDistributionInfo()
Description copied from interface: SingleSplitDistribution
Obtain the distribution information stored in the following format: [beforeclass][afterclass] For example, the probability of evolving in class 0 before the split, and class 1 after the split - [0][1]

Specified by:
getDistributionInfo in interface SingleSplitDistribution
Returns:
an appropriate matrix representing the probability of evolving in the different combinations of before and after classes

getNumberOfParameters

public int getNumberOfParameters()
Description copied from interface: NeoParameterized
get number of parameters

Specified by:
getNumberOfParameters in interface NeoParameterized
Returns:
number of parameters

setParameters

public void setParameters(double[] store,
                          int startIndex)
Description copied from interface: NeoParameterized
set model parameter

Specified by:
setParameters in interface NeoParameterized
Parameters:
store - the array holding the parameters
startIndex - the index into the array that the related parameters start at

getParameters

public void getParameters(double[] store,
                          int startIndex)
Description copied from interface: NeoParameterized
get model parameter

Specified by:
getParameters in interface NeoParameterized
startIndex - the index into the array that the related parameters start at

getLowerLimit

public double getLowerLimit(int n)
Description copied from interface: NeoParameterized
get lower parameter limit

Specified by:
getLowerLimit in interface NeoParameterized
Parameters:
n - parameter number
Returns:
lower bound

getUpperLimit

public double getUpperLimit(int n)
Description copied from interface: NeoParameterized
get upper parameter limit

Specified by:
getUpperLimit in interface NeoParameterized
Parameters:
n - parameter number
Returns:
upper bound

getDefaultValues

public void getDefaultValues(double[] store,
                             int startIndex)
Description copied from interface: NeoParameterized
get default value parameter values

Specified by:
getDefaultValues in interface NeoParameterized

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object