Uses of Interface
org.forester.pccx.CoverageCalculationOptions

Packages that use CoverageCalculationOptions

Package	Description
org.forester.pccx

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)