Uses of Interface
jebl.evolution.distances.DistanceMatrix

Packages that use DistanceMatrix

jebl.evolution.align	Provides classes and interfaces for pairwise alignment of two sequences.
jebl.evolution.distances
jebl.evolution.io
jebl.evolution.trees

Uses of DistanceMatrix in jebl.evolution.align

Classes in jebl.evolution.align that implement DistanceMatrix

class

SequenceAlignmentsDistanceMatrix

Fields in jebl.evolution.align declared as DistanceMatrix

DistanceMatrix

AlignmentTreeBuilderFactory.Result.distance

Uses of DistanceMatrix in jebl.evolution.distances

Classes in jebl.evolution.distances that implement DistanceMatrix

class	BasicDistanceMatrix
class	F84DistanceMatrix
class	HKYDistanceMatrix Compute HKY corrected distance matrix
class	JukesCantorDistanceMatrix Compute jukes-cantor corrected distance matrix for a set of aligned sequences.
class	TamuraNeiDistanceMatrix Date: 22/01/2006 Time: 17:28:59

Methods in jebl.evolution.distances that return DistanceMatrix

DistanceMatrix	BasicDistanceMatrix.getSubmatrix(Collection<Taxon> taxonSubset) Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).
DistanceMatrix	DistanceMatrix.getSubmatrix(Collection<Taxon> taxa) Gets a sub-matrix for only those taxa in the collection (all of which should be present in this matrix).

Uses of DistanceMatrix in jebl.evolution.io

Methods in jebl.evolution.io that return DistanceMatrix

DistanceMatrix

NexusImporter.parseDistancesBlock(List<Taxon> taxonList)

Methods in jebl.evolution.io that return types with arguments of type DistanceMatrix

List<DistanceMatrix>	DistanceMatrixImporter.importDistanceMatrices() importDistances.
List<DistanceMatrix>	NexusImporter.importDistanceMatrices() importDistances.
List<DistanceMatrix>	TabDelimitedImporter.importDistanceMatrices() importDistances.

Methods in jebl.evolution.io with parameters of type DistanceMatrix

void	NexusExporter.exportMatrix(DistanceMatrix distanceMatrix)

Uses of DistanceMatrix in jebl.evolution.trees

Fields in jebl.evolution.trees declared as DistanceMatrix

protected DistanceMatrix

ClusteringTreeBuilder.distanceMatrix

Methods in jebl.evolution.trees with parameters of type DistanceMatrix

static ClusteringTreeBuilder	ClusteringTreeBuilder.getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances) A factory method to create a ClusteringTreeBuilder
static ClusteringTreeBuilder	TreeBuilderFactory.getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances)
protected void	ClusteringTreeBuilder.init(DistanceMatrix distanceMatrix)

Constructors in jebl.evolution.trees with parameters of type DistanceMatrix

ClusteringTreeBuilder(DistanceMatrix distanceMatrix, int minimumTaxa)
Constructor

NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix)
construct NJ tree