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java.lang.ObjectLikelihood.Probabilities
public class Probabilities
Stores the values of each transition, frequency etc for one set of parameters.
Constructor Summary | |
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Probabilities(Model m,
Tree t,
Parameters p)
Constructor |
Method Summary | |
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java.util.Set<java.lang.String> |
getAllStates()
Gets the set of all possible states |
double |
getFreq(RateCategory r,
java.lang.String state)
Gets the root frequency for a specified state under a specified RateClass |
double |
getP(RateCategory r,
Branch b,
java.lang.String startState,
java.lang.String endState)
Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass |
java.util.Set<RateCategory> |
getRateCategory()
Gets the set of RateClasses that we have calculated probailities for |
double |
getRateP(RateCategory r)
Gets the probability of a rate class |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Probabilities(Model m, Tree t, Parameters p) throws TreeException, RateCategory.RateException, Model.ModelException, Parameters.ParameterException
m
- The modelt
- The treep
- The parameters
TreeException
- Thrown if there is a problem with the tree.
RateCategory.RateException
- Thrown if there is an issue with
a rate category in the model (e.g. a badly formatted rate).
Model.ModelException
- Thrown if there is a problem with the
model (e.g. the rate categories differ in their states)
Parameters.ParameterException
- Thrown if there is a problem
with the parameters (e.g. a requied parameter is not present)Method Detail |
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public java.util.Set<RateCategory> getRateCategory()
public java.util.Set<java.lang.String> getAllStates()
public double getP(RateCategory r, Branch b, java.lang.String startState, java.lang.String endState)
r
- The rate classb
- The branchstartState
- The start stateendState
- The end state
public double getFreq(RateCategory r, java.lang.String state)
r
- The rate classstate
- The state
public double getRateP(RateCategory r)
r
- the rate class
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