Uses of Interface
pal.util.AlgorithmCallback
Packages that use AlgorithmCallback
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes to model population genetic processes using the coalescent.
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
Utility classes for sorting etc.
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Uses of AlgorithmCallback in pal.algorithmics
Methods in pal.algorithmics with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionvoid
StoppingCriteria.newIteration
(double currentScore, double bestScore, boolean maximising, boolean externalStablized, AlgorithmCallback callback) void
SearchEngine.run
(AlgorithmCallback callback, double initialScore, ObjectState subject, StoppingCriteria.Factory stoppingCriteria, Ranker ranker) -
Uses of AlgorithmCallback in pal.alignment
Methods in pal.alignment with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionAlignmentGenerator.getNextAlignment
(AlgorithmCallback callback) -
Uses of AlgorithmCallback in pal.coalescent
Methods in pal.coalescent with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionSerialCoalescentGenerator.generateResults
(AlgorithmCallback callback) final Tree[]
SerialCoalescentGenerator.generateTrees
(AlgorithmCallback callback) If callback request stop then returns trees creating thus far -
Uses of AlgorithmCallback in pal.distance
Methods in pal.distance with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionDistanceMatrixGenerator.generateNextMatrix
(AlgorithmCallback callback) DistanceMatrixAccess.obtainMatrix
(AlgorithmCallback callback) void
AlignmentDistanceMatrix.recompute
(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback) recompute maximum-likelihood distances under new site patternvoid
AlignmentDistanceMatrix.recompute
(SitePattern sp, AlgorithmCallback callback) recompute observed distances under new site patternConstructors in pal.distance with parameters of type AlgorithmCallbackModifierConstructorDescriptionAlignmentDistanceMatrix
(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback) compute maximum-likelihood distancesAlignmentDistanceMatrix
(SitePattern sp, AlgorithmCallback callback) compute observed distances -
Uses of AlgorithmCallback in pal.statistics
Methods in pal.statistics with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionLikelihoodEvaluator.getMLOptimised
(Tree tree, Alignment alignment, AlgorithmCallback callback) double[]
GeneralTopologyPool.getNewReplicateLogLikelihoods
(AlgorithmCallback callback) double[]
RELLTopologyPool.getNewReplicateLogLikelihoods
(AlgorithmCallback callback) double[]
TopologyTestEngine.TopologyPool.getNewReplicateLogLikelihoods
(AlgorithmCallback callback) void
GeneralTopologyPool.optimiseOriginalTopologies
(AlgorithmCallback callback) TopologyTestEngine.performTest
(TopologyTestEngine.TopologyPool topologyPool, int numberOfReplicates, AlgorithmCallback callback) -
Uses of AlgorithmCallback in pal.supgma
Methods in pal.supgma with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionSUPGMABase.generateAlignmentBootstrappedSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.generateSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver) SUPGMABase.PopulationParameters.inferCI
(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver) SUPGMABase.process
(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.process
(AlgorithmCallback callback, LMSSolver solver) Tree[]
SUPGMABase.PopulationParameters.simulateTrees
(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver) SUPGMABase.solve
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver) -
Uses of AlgorithmCallback in pal.tree
Methods in pal.tree with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionfinal SimulatedAlignment[]
SimulatedAlignment.Factory.generateAlignments
(Tree[] trees, AlgorithmCallback callback) Generate an array of simulated alignments based on an array of input treesTreeGenerator.getNextTree
(AlgorithmCallback callback) static final Tree
TreeUtils.getReplicateCladeSupport
(String attributeName, Tree baseTree, TreeGenerator treeGenerator, int numberOfReplicates, AlgorithmCallback callback) Generates a tree which is identical to baseTree but has attributes (defined by attributeName) at all internal nodes excluding the root node signifying (as a value between 0 and 100) the replicate support by clade (that is the proportion of replicates that produce the sub clade under that node) -
Uses of AlgorithmCallback in pal.treesearch
Methods in pal.treesearch with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionTreeSearchTool.basicUnrootedTreeMLSearch
(Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback) Do a basic tree search using maximum likelihood on an unrooted tree space, without a given starting treeTreeSearchTool.basicUnrootedTreeMLSearch
(Tree baseTree, Alignment a, SubstitutionModel sm, boolean optimiseModel, AlgorithmCallback callback) Do a basic tree search using maximum likelihood on an unrooted tree space, with a given starting treedouble
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) static final Tree
TreeSearchTool.optimiseClockConstrainedFixed
(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback) Optimise the branches of a tree with regard to maximum likelihood, with the contraints of a global molecular clock - that is, all the tips terminate at the same point.double
GeneralLikelihoodSearcher.optimiseGeneral
(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback) double
GeneralLikelihoodSearcher.optimiseGeneral
(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor) static final Tree
TreeSearchTool.optimiseUnrootedFixed
(Tree tree, Alignment alignment, SubstitutionModel model, boolean optimiseModel, AlgorithmCallback callback) Optimise the branches of a tree with regard to maximum likelihood, with no constraints on the branchlengths (as for an unrooted tree).double
UnrootedMLSearcher.simpleOptimiseLikelihood
(double epsilon, AlgorithmCallback callback) Optimise the branch lengths of the tree to obtain the maximum likelihood.double
UnrootedMLSearcher.simpleOptimiseLikelihood
(StoppingCriteria stopper, AlgorithmCallback callback) Optimise the branch lengths of the tree to obtain the maximum likelihood. -
Uses of AlgorithmCallback in pal.util
Methods in pal.util that return AlgorithmCallbackModifier and TypeMethodDescriptionstatic final AlgorithmCallback
AlgorithmCallback.Utils.getNullCallback()
static final AlgorithmCallback
AlgorithmCallback.Utils.getPrintWriterCallback
(PrintWriter pw) Construct an algorithm callback that redirects status reports to a print writerstatic final AlgorithmCallback
AlgorithmCallback.Utils.getSubCallback
(AlgorithmCallback parent, String id, double minProgress, double maxProgress) static final AlgorithmCallback
AlgorithmCallback.Utils.getSystemOutCallback()
Methods in pal.util with parameters of type AlgorithmCallbackModifier and TypeMethodDescriptionstatic final AlgorithmCallback
AlgorithmCallback.Utils.getSubCallback
(AlgorithmCallback parent, String id, double minProgress, double maxProgress)