pal.mep
Class MutationRateModel

java.lang.Object
  pal.mep.MutationRateModel

All Implemented Interfaces:

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

See Also:

Serialized Form

Nested Class Summary

static interface

MutationRateModel.Factory An interface for objects which generate fresh MutationRAteModels

Nested classes inherited from class pal.misc.Parameterized

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

Field Summary

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

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

Method Summary

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()

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

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()