pal.substmodel
Class InvariableSites

java.lang.Object
  extended by pal.misc.PalObjectListener.EventGenerator
      extended by pal.substmodel.RateDistribution
          extended by pal.substmodel.InvariableSites
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, Parameterized, Report

public class InvariableSites
extends RateDistribution
implements java.io.Serializable

invariable sites model (two-rate model with mean rate = 1.0)

Version:
$Id: InvariableSites.java,v 1.4 2003/06/11 05:26:46 matt Exp $
Author:
Korbinian Strimmer
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
 
Field Summary
 
Fields inherited from class pal.substmodel.RateDistribution
format, numRates, probability, rate
 
Constructor Summary
InvariableSites(double f)
          construct discrete rate distribution with two rates (one invariable and one variable)
 
Method Summary
 double getDefaultValue(int n)
          get default value of parameter
 double getLowerLimit(int n)
          get lower parameter limit
 int getNumParameters()
          get number of parameters
 double getParameter(int n)
          get model parameter
 double getUpperLimit(int n)
          get upper parameter limit
 boolean isDistributionIndependentlyMutable()
           
 void report(java.io.PrintWriter out)
          print human readable report (e.g., on parameters and associated model)
 void setParameter(double param, int n)
          set model parameter
 void setParameterSE(double paramSE, int n)
          set standard errors for model parameter
 
Methods inherited from class pal.substmodel.RateDistribution
clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates
 
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

InvariableSites

public InvariableSites(double f)
construct discrete rate distribution with two rates (one invariable and one variable)

Parameters:
f - fraction of invariable sites
Method Detail

report

public void report(java.io.PrintWriter out)
Description copied from interface: Report
print human readable report (e.g., on parameters and associated model)

Specified by:
report in interface Report
Parameters:
out - output stream

getNumParameters

public int getNumParameters()
Description copied from interface: Parameterized
get number of parameters

Specified by:
getNumParameters in interface Parameterized
Returns:
number of parameters

setParameter

public void setParameter(double param,
                         int n)
Description copied from interface: Parameterized
set model parameter

Specified by:
setParameter in interface Parameterized
Parameters:
param - parameter value
n - parameter number

getParameter

public double getParameter(int n)
Description copied from interface: Parameterized
get model parameter

Specified by:
getParameter in interface Parameterized
Parameters:
n - parameter number
Returns:
parameter value

setParameterSE

public void setParameterSE(double paramSE,
                           int n)
Description copied from interface: Parameterized
set standard errors for model parameter

Specified by:
setParameterSE in interface Parameterized
Parameters:
paramSE - standard error of parameter value
n - parameter number

getLowerLimit

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

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

getUpperLimit

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

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

getDefaultValue

public double getDefaultValue(int n)
Description copied from interface: Parameterized
get default value of parameter

Specified by:
getDefaultValue in interface Parameterized
Parameters:
n - parameter number
Returns:
default value

isDistributionIndependentlyMutable

public boolean isDistributionIndependentlyMutable()