Uses of Interface
pal.util.AlgorithmCallback
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Packages that use AlgorithmCallback Package Description pal.algorithmics pal.alignment Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating.pal.coalescent Classes to model population genetic processes using the coalescent.pal.distance Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).pal.statistics 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.)pal.supgma pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).pal.treesearch pal.util Utility classes for sorting etc. -
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Uses of AlgorithmCallback in pal.algorithmics
Methods in pal.algorithmics with parameters of type AlgorithmCallback Modifier and Type Method Description void
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)
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Uses of AlgorithmCallback in pal.alignment
Methods in pal.alignment with parameters of type AlgorithmCallback Modifier and Type Method Description Alignment
AlignmentGenerator. getNextAlignment(AlgorithmCallback callback)
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Uses of AlgorithmCallback in pal.coalescent
Methods in pal.coalescent with parameters of type AlgorithmCallback Modifier and Type Method Description SerialCoalescentGenerator.Results
SerialCoalescentGenerator. generateResults(AlgorithmCallback callback)
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 AlgorithmCallback Modifier and Type Method Description DistanceMatrix
DistanceMatrixGenerator. generateNextMatrix(AlgorithmCallback callback)
DistanceMatrix
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 AlgorithmCallback Constructor Description AlignmentDistanceMatrix(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 AlgorithmCallback Modifier and Type Method Description LikelihoodEvaluator.MLResult
LikelihoodEvaluator. 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.TestResult
TopologyTestEngine. performTest(TopologyTestEngine.TopologyPool topologyPool, int numberOfReplicates, AlgorithmCallback callback)
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Uses of AlgorithmCallback in pal.supgma
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Uses of AlgorithmCallback in pal.tree
Methods in pal.tree with parameters of type AlgorithmCallback Modifier and Type Method Description SimulatedAlignment[]
SimulatedAlignment.Factory. generateAlignments(Tree[] trees, AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input treesTree
TreeGenerator. getNextTree(AlgorithmCallback callback)
static Tree
TreeUtils. getReplicateCladeSupport(java.lang.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 AlgorithmCallback Modifier and Type Method Description Tree
TreeSearchTool. 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 treeTree
TreeSearchTool. 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 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 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 AlgorithmCallback Modifier and Type Method Description static AlgorithmCallback
AlgorithmCallback.Utils. getNullCallback()
static AlgorithmCallback
AlgorithmCallback.Utils. getPrintWriterCallback(java.io.PrintWriter pw)
Construct an algorithm callback that redirects status reports to a print writerstatic AlgorithmCallback
AlgorithmCallback.Utils. getSubCallback(AlgorithmCallback parent, java.lang.String id, double minProgress, double maxProgress)
static AlgorithmCallback
AlgorithmCallback.Utils. getSystemOutCallback()
Methods in pal.util with parameters of type AlgorithmCallback Modifier and Type Method Description static AlgorithmCallback
AlgorithmCallback.Utils. getSubCallback(AlgorithmCallback parent, java.lang.String id, double minProgress, double maxProgress)
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