Uses of Interface
org.forester.pccx.CoverageCalculationOptions
Packages that use CoverageCalculationOptions
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Uses of CoverageCalculationOptions in org.forester.pccx
Classes in org.forester.pccx that implement CoverageCalculationOptionsMethods in org.forester.pccx with parameters of type CoverageCalculationOptionsModifier and TypeMethodDescriptionCoverageCalculationMethod.calculateCoverage
(List<Phylogeny> phylogenies, List<String> names, CoverageCalculationOptions options, boolean annotate_phylogenies) ExternalNodeBasedCoverageMethod.calculateCoverage
(List<Phylogeny> phylogenies, List<String> names, CoverageCalculationOptions options, boolean annotate_phylogenies) void
BranchCountingBasedScoringMethod.calculateScoreForExternalNode
(SortedMap<PhylogenyNode, Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) void
ScoringMethodForExternalNode.calculateScoreForExternalNode
(SortedMap<PhylogenyNode, Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) This calculates the coverage score for one external node.BasicExternalNodeBasedCoverageExtender.find
(List<Phylogeny> phylogenies, List<String> already_covered, int number_names_to_find, CoverageCalculationOptions options, PrintStream out) CoverageExtender.find
(List<Phylogeny> phylogenies, List<String> already_covered, int number_names_to_find, CoverageCalculationOptions options, PrintStream out) static CoverageCalculator
CoverageCalculator.getInstance
(CoverageCalculationMethod method, CoverageCalculationOptions options) Constructors in org.forester.pccx with parameters of type CoverageCalculationOptionsModifierConstructorDescriptionExternalNodeBasedCoverage
(DescriptiveStatistics stats, double average_raw_score, CoverageCalculationOptions options)