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java.lang.Objectpal.mep.MutationRateModel
pal.mep.WindowedMutationRate
public class WindowedMutationRate
This class models a windowed mutation rate
(parameter: mu = mutation rate).
Nested Class Summary |
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Nested classes/interfaces inherited from class pal.mep.MutationRateModel |
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MutationRateModel.Factory |
Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary |
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Fields inherited from class pal.mep.MutationRateModel |
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fo |
Fields inherited from interface pal.misc.Units |
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DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS |
Constructor Summary | |
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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. |
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WindowedMutationRate(double muWindow,
double muBackground,
double windowCenter,
double windowWidth,
int units,
double maximumMutationRate)
Construct mutation rate model of a give rate in given units. |
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WindowedMutationRate(double muBackground,
double windowCenter,
double windowWidth,
int units,
double maximumMutationRate)
Construct mutation rate model of a give rate in given units. |
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WindowedMutationRate(double windowCenter,
double windowWidth,
int units,
double maximumMutationRate)
Construct mutation model with default settings |
protected |
WindowedMutationRate(WindowedMutationRate toCopy)
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Method Summary | |
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java.lang.Object |
clone()
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MutationRateModel.Factory |
generateFactory()
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MutationRateModel |
getCopy()
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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()
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double |
getSummaryValue(int summaryType)
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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()
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java.lang.String |
toString()
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Methods inherited from class pal.mep.MutationRateModel |
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getExpectedSubstitutions, getMaximumMutationRate, getOrthogonalHints, getTime, getUnits, scale, setUnits |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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protected WindowedMutationRate(WindowedMutationRate toCopy)
public WindowedMutationRate(double windowCenter, double windowWidth, int units, double maximumMutationRate)
public WindowedMutationRate(double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate)
public WindowedMutationRate(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, boolean fixedb, double maximumMutationRate)
public WindowedMutationRate(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate)
Method Detail |
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public java.lang.Object clone()
clone
in class MutationRateModel
public MutationRateModel getCopy()
getCopy
in class MutationRateModel
public java.lang.String[] getSummaryTypes()
getSummaryTypes
in interface Summarizable
public double getSummaryValue(int summaryType)
getSummaryValue
in interface Summarizable
public double getMu()
public final double getMutationRate(double t)
MutationRateModel
getMutationRate
in class MutationRateModel
public final double getExpectedSubstitutions(double time)
getExpectedSubstitutions
in class MutationRateModel
public final double getEndTime(double expectedSubs, double startTime)
getEndTime
in class MutationRateModel
public final void scale(double scale)
scale
in class MutationRateModel
scale
- getExpectedSubstitutions should return scale instead of 1.0 at time t.public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public double getParameter(int k)
Parameterized
getParameter
in interface Parameterized
k
- parameter number
public double getUpperLimit(int k)
Parameterized
getUpperLimit
in interface Parameterized
k
- parameter number
public double getLowerLimit(int k)
Parameterized
getLowerLimit
in interface Parameterized
k
- parameter number
public double getDefaultValue(int k)
Parameterized
getDefaultValue
in interface Parameterized
k
- parameter number
public void setParameter(double value, int k)
Parameterized
setParameter
in interface Parameterized
value
- parameter valuek
- parameter numberpublic void setParameterSE(double value, int k)
Parameterized
setParameterSE
in interface Parameterized
value
- standard error of parameter valuek
- parameter numberpublic java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic java.lang.String toSingleLine()
toSingleLine
in class MutationRateModel
public MutationRateModel.Factory generateFactory()
generateFactory
in class MutationRateModel
public static final MutationRateModel.Factory getFactory(double muWindow, double muBackground, double windowCenter, double windowWidth, int units, double maximumMutationRate)
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