Uses of Interface
pal.algorithmics.StoppingCriteria

Packages that use StoppingCriteria
pal.algorithmics   
pal.treesearch   
 

Uses of StoppingCriteria in pal.algorithmics
 

Methods in pal.algorithmics that return StoppingCriteria
 StoppingCriteria StoppingCriteria.Factory.newInstance()
           
 

Uses of StoppingCriteria in pal.treesearch
 

Methods in pal.treesearch with parameters of type StoppingCriteria
 double GeneralLikelihoodSearcher.optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
           
 double GeneralLikelihoodSearcher.optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor)
           
 double GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback)
           
 double GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
           
 double GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType)
           
 double GeneralLikelihoodSearcher.optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
           
 double GeneralLikelihoodSearcher.optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback)
           
 double GeneralLikelihoodSearcher.optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor)
           
 double UnrootedMLSearcher.simpleOptimiseLikelihood(StoppingCriteria stopper, AlgorithmCallback callback)
          Optimise the branch lengths of the tree to obtain the maximum likelihood.