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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.substmodel.SimpleSubstitutionModel
model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
Constructor Summary | |
SimpleSubstitutionModel(RateMatrix rmat)
constructor 1 (uniform rate distribution) |
|
SimpleSubstitutionModel(RateMatrix rmat,
int n,
double a)
constructor 2 (gamma rate distribution) |
|
SimpleSubstitutionModel(RateMatrix rmat,
RateDistribution rdist)
constructor 3 (arbitrary rate distribution) |
|
SimpleSubstitutionModel(SubstitutionModel model)
Return a copy of this substitution model. |
Method Summary | |
void |
addPalObjectListener(PalObjectListener pol)
Add a PalObjectListener to be notified of changes to the model. |
java.lang.Object |
clone()
A non shallow implementation of clone() |
DataType |
getDataType()
|
double |
getDefaultValue(int n)
get default value of parameter |
int |
getDimension()
Returns the dimension of this model. |
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumParameters()
get number of parameters |
double |
getParameter(int n)
get model parameter |
RateDistribution |
getRateDistribution()
|
RateMatrix |
getRateMatrix()
|
double |
getUpperLimit(int n)
get upper parameter limit |
boolean |
isSimpleJukesCantor()
|
void |
removePalObjectListener(PalObjectListener pol)
Currently passes request on to rateMatrix |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setDistance(double k)
set distance and corresponding computation transition probabilities |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
void |
setTime(double start,
double end)
|
java.lang.String |
toString()
Return string representation of substitution model. |
double |
transProb(int r,
int i,
int j)
get transition probability for the preselected model and the previously specified distance |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public SimpleSubstitutionModel(RateMatrix rmat)
rmat
- rate matrixpublic SimpleSubstitutionModel(RateMatrix rmat, int n, double a)
rmat
- rate matrixn
- number of rate categoriesa
- shape parameterpublic SimpleSubstitutionModel(RateMatrix rmat, RateDistribution rdist)
rmat
- rate matrixrdist
- rate distributionpublic SimpleSubstitutionModel(SubstitutionModel model)
Method Detail |
public DataType getDataType()
getDataType
in interface SubstitutionModel
public void report(java.io.PrintWriter out)
Report
report
in interface Report
pal.misc.Report
out
- output streampublic java.lang.String toString()
toString
in class java.lang.Object
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
pal.misc.Parameterized
public void setParameter(double param, int n)
Parameterized
setParameter
in interface Parameterized
pal.misc.Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
getParameter
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setTime(double start, double end)
public void setDistance(double k)
setDistance
in interface SubstitutionModel
k
- distancepublic double transProb(int r, int i, int j)
transProb
in interface SubstitutionModel
r
- rate categoryi
- start statej
- end statepublic boolean isSimpleJukesCantor()
public java.lang.Object clone()
clone
in interface SubstitutionModel
clone
in class java.lang.Object
public RateMatrix getRateMatrix()
getRateMatrix
in interface SubstitutionModel
pal.substmodel.SubstitutionModel
public RateDistribution getRateDistribution()
getRateDistribution
in interface SubstitutionModel
pal.substmodel.SubstitutionModel
public int getDimension()
SubstitutionModel
getDimension
in interface SubstitutionModel
public void addPalObjectListener(PalObjectListener pol)
addPalObjectListener
in interface SubstitutionModel
public void removePalObjectListener(PalObjectListener pol)
removePalObjectListener
in interface SubstitutionModel
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