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
Method Summary |
abstract java.lang.Object |
clone()
|
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. |
abstract double |
getMutationRate(double t)
Gets the mutation rate, value of mu(t) at time t. |
abstract 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. |
void |
setUnits(int u)
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 |
fo
protected FormattedOutput fo
MutationRateModel
public MutationRateModel()
clone
public abstract java.lang.Object clone()
- Overrides:
clone
in class java.lang.Object
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 abstract double getTime(double expectedSubs)
- Return the time at which expected substitutions has occurred.
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.
setUnits
public void setUnits(int u)
- sets units of measurement.
- Parameters:
u
- units
getUnits
public int getUnits()
- returns units of measurement.
toSingleLine
public abstract java.lang.String toSingleLine()