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Packages that use AlgorithmCallback | |
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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. |
Uses of AlgorithmCallback in pal.algorithmics |
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Methods in pal.algorithmics with parameters of type AlgorithmCallback | |
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void |
StoppingCriteria.newIteration(double currentScore,
double bestScore,
boolean maximising,
boolean externalStablized,
AlgorithmCallback callback)
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void |
SearchEngine.run(AlgorithmCallback callback,
double initialScore,
ObjectState subject,
StoppingCriteria.Factory stoppingCriteria,
Ranker ranker)
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Uses of AlgorithmCallback in pal.alignment |
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Methods in pal.alignment with parameters of type AlgorithmCallback | |
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Alignment |
AlignmentGenerator.getNextAlignment(AlgorithmCallback callback)
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Uses of AlgorithmCallback in pal.coalescent |
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Methods in pal.coalescent with parameters of type AlgorithmCallback | |
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SerialCoalescentGenerator.Results |
SerialCoalescentGenerator.generateResults(AlgorithmCallback callback)
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Tree[] |
SerialCoalescentGenerator.generateTrees(AlgorithmCallback callback)
If callback request stop then returns trees creating thus far |
Uses of AlgorithmCallback in pal.distance |
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Methods in pal.distance with parameters of type AlgorithmCallback | |
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DistanceMatrix |
DistanceMatrixGenerator.generateNextMatrix(AlgorithmCallback callback)
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DistanceMatrix |
DistanceMatrixAccess.obtainMatrix(AlgorithmCallback callback)
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void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
AlgorithmCallback callback)
recompute observed distances under new site pattern |
void |
AlignmentDistanceMatrix.recompute(SitePattern sp,
SubstitutionModel model,
AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern |
Constructors in pal.distance with parameters of type AlgorithmCallback | |
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AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback)
compute observed distances |
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AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback)
compute maximum-likelihood distances |
Uses of AlgorithmCallback in pal.statistics |
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Methods in pal.statistics with parameters of type AlgorithmCallback | |
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LikelihoodEvaluator.MLResult |
LikelihoodEvaluator.getMLOptimised(Tree tree,
Alignment alignment,
AlgorithmCallback callback)
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double[] |
GeneralTopologyPool.getNewReplicateLogLikelihoods(AlgorithmCallback callback)
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double[] |
TopologyTestEngine.TopologyPool.getNewReplicateLogLikelihoods(AlgorithmCallback callback)
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double[] |
RELLTopologyPool.getNewReplicateLogLikelihoods(AlgorithmCallback callback)
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void |
GeneralTopologyPool.optimiseOriginalTopologies(AlgorithmCallback callback)
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TopologyTestEngine.TestResult |
TopologyTestEngine.performTest(TopologyTestEngine.TopologyPool topologyPool,
int numberOfReplicates,
AlgorithmCallback callback)
|
Uses of AlgorithmCallback in pal.supgma |
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Uses of AlgorithmCallback in pal.tree |
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Methods in pal.tree with parameters of type AlgorithmCallback | |
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SimulatedAlignment[] |
SimulatedAlignment.Factory.generateAlignments(Tree[] trees,
AlgorithmCallback callback)
Generate an array of simulated alignments based on an array of input trees |
Tree |
TreeGenerator.getNextTree(AlgorithmCallback callback)
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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 |
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Methods in pal.treesearch with parameters of type AlgorithmCallback | |
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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 tree |
Tree |
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 tree |
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)
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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)
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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 |
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Methods in pal.util that return AlgorithmCallback | |
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static AlgorithmCallback |
AlgorithmCallback.Utils.getNullCallback()
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static AlgorithmCallback |
AlgorithmCallback.Utils.getPrintWriterCallback(java.io.PrintWriter pw)
Construct an algorithm callback that redirects status reports to a print writer |
static AlgorithmCallback |
AlgorithmCallback.Utils.getSubCallback(AlgorithmCallback parent,
java.lang.String id,
double minProgress,
double maxProgress)
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static AlgorithmCallback |
AlgorithmCallback.Utils.getSystemOutCallback()
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Methods in pal.util with parameters of type AlgorithmCallback | |
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static AlgorithmCallback |
AlgorithmCallback.Utils.getSubCallback(AlgorithmCallback parent,
java.lang.String id,
double minProgress,
double maxProgress)
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