pal.treesearch
Class GeneralLikelihoodSearcher
java.lang.Object
pal.treesearch.GeneralLikelihoodSearcher
public class GeneralLikelihoodSearcher
- extends java.lang.Object
Method Summary |
Node |
buildPALNodeBase()
|
Node |
buildPALNodeES()
|
Tree |
buildPALTreeBase()
|
Tree |
buildPALTreeES()
|
double |
calculatedLogLikelihood()
|
double |
optimiseAllFullHeirarchy(StoppingCriteria mainStopper,
StoppingCriteria subStopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor)
|
double |
optimiseAllPlusSubstitutionModel(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
MultivariateMinimum substitutionModelMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
int substitutionModelOptimiseFrequency,
MinimiserMonitor substitutionModelMonitor,
MinimiserMonitor rateMonitor)
|
double |
optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback)
|
double |
optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor)
|
double |
optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor,
int groupOptimistionType)
|
double |
optimiseAllSimpleHeirarchy(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor)
|
double |
optimiseConstraintRateModels(MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor rateMonitor)
|
double |
optimiseGeneral(StoppingCriteria stopper,
int fracDigits,
AlgorithmCallback callback)
|
double |
optimiseGeneral(StoppingCriteria stopper,
int fracDigits,
AlgorithmCallback callback,
SearchMonitor monitor)
|
double |
optimiseSubstitutionModels(MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
|
void |
testLikelihood()
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
OPTIMISE_ALL
public static final int OPTIMISE_ALL
- See Also:
- Constant Field Values
OPTIMISE_PRIMARY
public static final int OPTIMISE_PRIMARY
- See Also:
- Constant Field Values
OPTIMISE_SECONDARY
public static final int OPTIMISE_SECONDARY
- See Also:
- Constant Field Values
NO_OPTIMISE
public static final int NO_OPTIMISE
- See Also:
- Constant Field Values
GeneralLikelihoodSearcher
public GeneralLikelihoodSearcher(Node baseTopology,
Alignment baseAlignment,
ConstraintModel constraintModel)
optimiseGeneral
public double optimiseGeneral(StoppingCriteria stopper,
int fracDigits,
AlgorithmCallback callback)
optimiseGeneral
public double optimiseGeneral(StoppingCriteria stopper,
int fracDigits,
AlgorithmCallback callback,
SearchMonitor monitor)
optimiseConstraintRateModels
public double optimiseConstraintRateModels(MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor rateMonitor)
optimiseSubstitutionModels
public double optimiseSubstitutionModels(MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback)
optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor)
optimiseAllSimple
public double optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor,
int groupOptimistionType)
optimiseAllSimpleHeirarchy
public double optimiseAllSimpleHeirarchy(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor)
optimiseAllFullHeirarchy
public double optimiseAllFullHeirarchy(StoppingCriteria mainStopper,
StoppingCriteria subStopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor)
optimiseAllPlusSubstitutionModel
public double optimiseAllPlusSubstitutionModel(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
MultivariateMinimum substitutionModelMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
int substitutionModelOptimiseFrequency,
MinimiserMonitor substitutionModelMonitor,
MinimiserMonitor rateMonitor)
buildPALNodeBase
public Node buildPALNodeBase()
buildPALTreeBase
public Tree buildPALTreeBase()
buildPALNodeES
public Node buildPALNodeES()
buildPALTreeES
public Tree buildPALTreeES()
calculatedLogLikelihood
public double calculatedLogLikelihood()
testLikelihood
public void testLikelihood()