pal.treesearch
public class GeneralLikelihoodSearcher extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
NO_OPTIMISE |
static int |
OPTIMISE_ALL |
static int |
OPTIMISE_PRIMARY |
static int |
OPTIMISE_SECONDARY |
Constructor and Description |
---|
GeneralLikelihoodSearcher(Node baseTopology,
Alignment baseAlignment,
ConstraintModel constraintModel) |
Modifier and Type | Method and Description |
---|---|
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() |
public static final int OPTIMISE_ALL
public static final int OPTIMISE_PRIMARY
public static final int OPTIMISE_SECONDARY
public static final int NO_OPTIMISE
public GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback)
public double optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor)
public double optimiseConstraintRateModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor)
public double optimiseSubstitutionModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback)
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
public double optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType)
public double optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
public double optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
public double optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor)
public Node buildPALNodeBase()
public Tree buildPALTreeBase()
public Node buildPALNodeES()
public Tree buildPALTreeES()
public double calculatedLogLikelihood()
public void testLikelihood()