java.lang.Object
- pal.mep.MutationRateModel

All Implemented Interfaces:

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

Direct Known Subclasses:

ConstantMutationRate, SteppedMutationRate, WindowedMutationRate
```
public abstract class MutationRateModel
extends java.lang.Object
implements Units, Parameterized, Report, java.lang.Cloneable, java.io.Serializable, Summarizable
```
This abstract class contains methods that are of general use for modelling mutation rate changes over time.

Version:

$Id: MutationRateModel.java,v 1.12 2004/08/02 05:22:04 matt Exp $

Author:

Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static interface MutationRateModel.Factory
An interface for objects which generate fresh MutationRAteModels
- Nested classes/interfaces inherited from interface pal.misc.Parameterized
  Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Field Summary

Fields
Modifier and Type Field Description

protected FormattedOutput 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
`protected`	`MutationRateModel(int units, double maximumMutationRate)`
`protected`	`MutationRateModel(MutationRateModel toCopy)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`abstract java.lang.Object`	`clone()`
`abstract MutationRateModel.Factory`	`generateFactory()`
`abstract MutationRateModel`	`getCopy()`
`abstract double`	`getEndTime(double expectedSubs, double startTime)`	Return the end time at which expected substitutions has occurred, given we start at start time
`abstract double`	`getExpectedSubstitutions(double t)`	Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
`double`	`getExpectedSubstitutions(double start, double finish)`	Calculates the integral 1/mu(x) dx between start and finish.
`protected double`	`getMaximumMutationRate()`
`abstract double`	`getMutationRate(double t)`	Gets the mutation rate, value of mu(t) at time t.
`OrthogonalHints`	`getOrthogonalHints()`	Overide if there is any orthogonal hint information available
`double`	`getTime(double expectedSubs)`	Return the time at which expected substitutions has occurred.
`int`	`getUnits()`	returns units of measurement.
`abstract void`	`scale(double scale)`	Linearly scales this mutation rate model.
`TimeOrderCharacterData`	`scale(TimeOrderCharacterData toScale)`
`void`	`setUnits(int u, double maximumMutationRate)`	sets units of measurement.
`abstract java.lang.String`	`toSingleLine()`

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE

Methods inherited from interface pal.misc.Report
report

Methods inherited from interface pal.misc.Summarizable
getSummaryTypes, getSummaryValue

- Field Detail
  - fo
```
protected FormattedOutput fo
```
- Constructor Detail
  - MutationRateModel
```
protected MutationRateModel(int units,
                            double maximumMutationRate)
```
  - MutationRateModel
```
protected MutationRateModel(MutationRateModel toCopy)
```
- Method Detail
  - clone
```
public abstract java.lang.Object clone()
```
    Overrides:
    
    clone in class java.lang.Object
  - getCopy
```
public abstract MutationRateModel getCopy()
```
  - getMutationRate
```
public abstract double getMutationRate(double t)
```
    Gets the mutation rate, value of mu(t) at time t.
  - getExpectedSubstitutions
```
public abstract double getExpectedSubstitutions(double t)
```
    Returns integral of mutation rate function (= integral mu(x) dx from 0 to t).
  - getTime
```
public double getTime(double expectedSubs)
```
    Return the time at which expected substitutions has occurred.
  - getEndTime
```
public abstract double getEndTime(double expectedSubs,
                                  double startTime)
```
    Return the end time at which expected substitutions has occurred, given we start at start time
  - scale
```
public abstract void scale(double scale)
```
    Linearly scales this mutation rate model.
    
    Parameters:
    
    scale - getExpectedSubstitutions should return scale instead of 1.0 at time t.
  - getExpectedSubstitutions
```
public double getExpectedSubstitutions(double start,
                                       double finish)
```
    Calculates the integral 1/mu(x) dx between start and finish.
  - scale
```
public TimeOrderCharacterData scale(TimeOrderCharacterData toScale)
```
    Returns:
    
    a TimeOrderCharacterData scaled to use EXPECTED_SUBSTITUTIONS based on this MutationRateModel
    
    Throws:
    
    java.lang.IllegalArgumentException - if units of this Model doenot match the units of the TimeOrderCharacterData object (toScale).
  - setUnits
```
public final void setUnits(int u,
                           double maximumMutationRate)
```
    sets units of measurement.
    
    Parameters:
    
    u - units
    
    the - maximumMutationRate that is allowable, given the units. This needs to be given intelligently.
    
    Throws:
    
    java.lang.IllegalArgumentException - if units are ExpectedSubstitutions
  - getMaximumMutationRate
```
protected final double getMaximumMutationRate()
```
    Returns:
    
    the maximum mutation rate as indicated by the user
  - getUnits
```
public int getUnits()
```
    returns units of measurement.
  - getOrthogonalHints
```
public OrthogonalHints getOrthogonalHints()
```
    Overide if there is any orthogonal hint information available
    
    Returns:
    
    null
  - toSingleLine
```
public abstract java.lang.String toSingleLine()
```
  - generateFactory
```
public abstract MutationRateModel.Factory generateFactory()
```

Class MutationRateModel

Nested Class Summary

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

Field Summary

Fields inherited from interface pal.misc.Units

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.Parameterized

Methods inherited from interface pal.misc.Report

Methods inherited from interface pal.misc.Summarizable

Field Detail

fo

Constructor Detail

MutationRateModel

MutationRateModel

Method Detail

clone

getCopy

getMutationRate

getExpectedSubstitutions

getTime

getEndTime

scale

getExpectedSubstitutions

scale

setUnits

getMaximumMutationRate

getUnits

getOrthogonalHints

toSingleLine

generateFactory