Uses of Interface
org.forester.pccx.CoverageCalculationOptions
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Packages that use CoverageCalculationOptions Package Description org.forester.pccx -
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Uses of CoverageCalculationOptions in org.forester.pccx
Classes in org.forester.pccx that implement CoverageCalculationOptions Modifier and Type Class Description class
ExternalNodeBasedCoverageMethodOptions
Methods in org.forester.pccx with parameters of type CoverageCalculationOptions Modifier and Type Method Description Coverage
CoverageCalculationMethod. calculateCoverage(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> names, CoverageCalculationOptions options, boolean annotate_phylogenies)
Coverage
ExternalNodeBasedCoverageMethod. calculateCoverage(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> names, CoverageCalculationOptions options, boolean annotate_phylogenies)
void
BranchCountingBasedScoringMethod. calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
void
ScoringMethodForExternalNode. calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
This calculates the coverage score for one external node.java.util.List<java.lang.String>
BasicExternalNodeBasedCoverageExtender. find(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> already_covered, int number_names_to_find, CoverageCalculationOptions options, java.io.PrintStream out)
java.util.List<java.lang.String>
CoverageExtender. find(java.util.List<Phylogeny> phylogenies, java.util.List<java.lang.String> already_covered, int number_names_to_find, CoverageCalculationOptions options, java.io.PrintStream out)
static CoverageCalculator
CoverageCalculator. getInstance(CoverageCalculationMethod method, CoverageCalculationOptions options)
Constructors in org.forester.pccx with parameters of type CoverageCalculationOptions Constructor Description ExternalNodeBasedCoverage(DescriptiveStatistics stats, double average_raw_score, CoverageCalculationOptions options)
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