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	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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Class WindowedMutationRate

Nested Class Summary

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

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

Field Summary

Fields inherited from class pal.mep.MutationRateModel

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class pal.mep.MutationRateModel

Methods inherited from class java.lang.Object

Constructor Detail

WindowedMutationRate

WindowedMutationRate

WindowedMutationRate

WindowedMutationRate

WindowedMutationRate

Method Detail

clone

getCopy

getSummaryTypes

getSummaryValue

getMu

getMutationRate

getExpectedSubstitutions

getEndTime

scale

getNumParameters

getParameter

getUpperLimit

getLowerLimit

getDefaultValue

setParameter

setParameterSE

toString

report

toSingleLine

generateFactory

getFactory