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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
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()
|
int |
getDimension()
Deprecated. |
RateDistribution |
getRateDistribution()
|
RateMatrix |
getRateMatrix()
|
void |
removePalObjectListener(PalObjectListener pol)
|
void |
setDistance(double k)
set distance and corresponding computation transition probabilities |
double |
transProb(int r,
int i,
int j)
get transition probability for the preselected model and the previously specified distance |
Methods inherited from interface pal.misc.Parameterized |
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE |
Methods inherited from interface pal.misc.Report |
report |
Method Detail |
public RateMatrix getRateMatrix()
public RateDistribution getRateDistribution()
public void setDistance(double k)
k
- distancepublic double transProb(int r, int i, int j)
r
- rate categoryi
- start statej
- end statepublic int getDimension()
public DataType getDataType()
public void addPalObjectListener(PalObjectListener pol)
public void removePalObjectListener(PalObjectListener pol)
public java.lang.Object clone()
clone
in class java.lang.Object
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