pal.mep

Class WindowedMutationRate

java.lang.Object

pal.mep.MutationRateModel

pal.mep.WindowedMutationRate

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Parameterized, Report, Summarizable, Units

public class WindowedMutationRate
extends MutationRateModel
implements Report, Summarizable, Parameterized, java.io.Serializable

This class models a windowed mutation rate (parameter: mu = mutation rate).

Version:

$Id: WindowedMutationRate.java,v 1.8 2004/08/02 05:22:04 matt Exp $

Author:

Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class pal.mep.MutationRateModel

MutationRateModel.Factory

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields inherited from class pal.mep.MutationRateModel

fo

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors

Modifier	Constructor and Description
	WindowedMutationRate(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, boolean fixedb, double maximumMutationRate) Construct mutation rate model of a give rate in given units.
	WindowedMutationRate(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate) Construct mutation rate model of a give rate in given units.
	WindowedMutationRate(double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate) Construct mutation rate model of a give rate in given units.
	WindowedMutationRate(double windowCenter, double windowWidth, int units, double maximumMutationRate) Construct mutation model with default settings
protected	WindowedMutationRate(WindowedMutationRate toCopy)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone()
MutationRateModel.Factory	generateFactory()
MutationRateModel	getCopy()
double	getDefaultValue(int k) get default value of parameter
double	getEndTime(double expectedSubs, double startTime) Window must not span zero!
double	getExpectedSubstitutions(double time) Window must not span zero!
static MutationRateModel.Factory	getFactory(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate) Generate a MutationRateModel.Factory class for a WindowedMutationRate
double	getLowerLimit(int k) get lower parameter limit
double	getMu() returns current day mutation rate.
double	getMutationRate(double t) Gets the mutation rate, value of mu(t) at time t.
int	getNumParameters() get number of parameters
double	getParameter(int k) get model parameter
java.lang.String[]	getSummaryTypes()
double	getSummaryValue(int summaryType)
double	getUpperLimit(int k) get upper parameter limit
void	report(java.io.PrintWriter out) print human readable report (e.g., on parameters and associated model)
void	scale(double scale) Linearly scales this mutation rate model.
void	setParameter(double value, int k) set model parameter
void	setParameterSE(double value, int k) set standard errors for model parameter
java.lang.String	toSingleLine()
java.lang.String	toString()

Methods inherited from class pal.mep.MutationRateModel

getExpectedSubstitutions, getMaximumMutationRate, getOrthogonalHints, getTime, getUnits, scale, setUnits

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

WindowedMutationRate

protected WindowedMutationRate(WindowedMutationRate toCopy)

WindowedMutationRate

public WindowedMutationRate(double windowCenter,
                    double windowWidth,
                    int units,
                    double maximumMutationRate)

Construct mutation model with default settings

WindowedMutationRate

public WindowedMutationRate(double muBackground,
                    double windowCenter,
                    double windowWidth,
                    int units,
                    double maximumMutationRate)

Construct mutation rate model of a give rate in given units.

WindowedMutationRate

public WindowedMutationRate(double muWindow,
                    double muBackground,
                    double windowCenter,
                    double windowWidth,
                    int units,
                    boolean fixedb,
                    double maximumMutationRate)

Construct mutation rate model of a give rate in given units.

WindowedMutationRate

public WindowedMutationRate(double muWindow,
                    double muBackground,
                    double windowCenter,
                    double windowWidth,
                    int units,
                    double maximumMutationRate)

Construct mutation rate model of a give rate in given units.

Method Detail

clone

public java.lang.Object clone()

Specified by:

clone in class MutationRateModel

getCopy

public MutationRateModel getCopy()

Specified by:

getCopy in class MutationRateModel

getSummaryTypes

public java.lang.String[] getSummaryTypes()

Specified by:

getSummaryTypes in interface Summarizable

getSummaryValue

public double getSummaryValue(int summaryType)

Specified by:

getSummaryValue in interface Summarizable

getMu

public double getMu()

returns current day mutation rate.

getMutationRate

public final double getMutationRate(double t)

Description copied from class: MutationRateModel

Gets the mutation rate, value of mu(t) at time t.

Specified by:

getMutationRate in class MutationRateModel

getExpectedSubstitutions

public final double getExpectedSubstitutions(double time)

Window must not span zero!

Specified by:

getExpectedSubstitutions in class MutationRateModel

getEndTime

public final double getEndTime(double expectedSubs,
                double startTime)

Window must not span zero!

Specified by:

getEndTime in class MutationRateModel

scale

public final void scale(double scale)

Linearly scales this mutation rate model.

Specified by:

scale in class MutationRateModel

Parameters:

scale - getExpectedSubstitutions should return scale instead of 1.0 at time t.

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

getParameter

public double getParameter(int k)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

k - parameter number

Returns:

parameter value

getUpperLimit

public double getUpperLimit(int k)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

k - parameter number

Returns:

upper bound

getLowerLimit

public double getLowerLimit(int k)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

k - parameter number

Returns:

lower bound

getDefaultValue

public double getDefaultValue(int k)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

k - parameter number

Returns:

default value

setParameter

public void setParameter(double value,
                int k)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

value - parameter value

k - parameter number

setParameterSE

public void setParameterSE(double value,
                  int k)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

value - standard error of parameter value

k - parameter number

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

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

toSingleLine

public java.lang.String toSingleLine()

Specified by:

toSingleLine in class MutationRateModel

generateFactory

public MutationRateModel.Factory generateFactory()

Specified by:

generateFactory in class MutationRateModel

getFactory

public static final MutationRateModel.Factory getFactory(double muWindow,
                                   double muBackground,
                                   double windowCenter,
                                   double windowWidth,
                                   int units,
                                   double maximumMutationRate)

Generate a MutationRateModel.Factory class for a WindowedMutationRate