pal.treesearch
Class GeneralLikelihoodSearcher

java.lang.Object
  extended by pal.treesearch.GeneralLikelihoodSearcher

public class GeneralLikelihoodSearcher
extends java.lang.Object


Field Summary
static int NO_OPTIMISE
           
static int OPTIMISE_ALL
           
static int OPTIMISE_PRIMARY
           
static int OPTIMISE_SECONDARY
           
 
Constructor Summary
GeneralLikelihoodSearcher(Node baseTopology, Alignment baseAlignment, ConstraintModel constraintModel)
           
 
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
 

Field Detail

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
Constructor Detail

GeneralLikelihoodSearcher

public GeneralLikelihoodSearcher(Node baseTopology,
                                 Alignment baseAlignment,
                                 ConstraintModel constraintModel)
Method Detail

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()