Uses of Interface
jebl.evolution.distances.DistanceMatrix
Packages that use DistanceMatrix
Package
Description
Provides classes and interfaces for pairwise alignment of two sequences.
-
Uses of DistanceMatrix in jebl.evolution.align
Classes in jebl.evolution.align that implement DistanceMatrixModifier and TypeClassDescriptionclass
Builds a distance matrix by performing a series of pairwise alignments between the specified sequences (unlike the methods in jebl.evolution.distances, which extract the pairwise distances from a multiple sequence alignment).Fields in jebl.evolution.align declared as DistanceMatrixModifier and TypeFieldDescriptionfinal DistanceMatrix
AlignmentTreeBuilderFactory.Result.distance
-
Uses of DistanceMatrix in jebl.evolution.distances
Classes in jebl.evolution.distances that implement DistanceMatrixModifier and TypeClassDescriptionclass
class
class
Compute HKY corrected distance matrixclass
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.class
Date: 22/01/2006 Time: 17:28:59Methods in jebl.evolution.distances that return DistanceMatrixModifier and TypeMethodDescriptionBasicDistanceMatrix.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.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 DistanceMatrixModifier and TypeMethodDescriptionNexusImporter.parseDistancesBlock
(List<Taxon> taxonList) Parse the next 'DISTANCES' block encountered in the input.Methods in jebl.evolution.io that return types with arguments of type DistanceMatrixModifier and TypeMethodDescriptionDistanceMatrixImporter.importDistanceMatrices()
importDistances.NexusImporter.importDistanceMatrices()
Import all distance matrices from all DISTANCES blocks in the input form the current position.TabDelimitedImporter.importDistanceMatrices()
importDistances.Methods in jebl.evolution.io with parameters of type DistanceMatrix -
Uses of DistanceMatrix in jebl.evolution.trees
Methods in jebl.evolution.trees with parameters of type DistanceMatrixModifier and TypeMethodDescriptionstatic ClusteringTreeBuilder
ClusteringTreeBuilder.getBuilder
(TreeBuilderFactory.Method method, DistanceMatrix distances) A factory method to create a ClusteringTreeBuilderstatic ClusteringTreeBuilder
TreeBuilderFactory.getBuilder
(TreeBuilderFactory.Method method, DistanceMatrix distances) Constructors in jebl.evolution.trees with parameters of type DistanceMatrixModifierConstructorDescriptionNeighborJoiningTreeBuilder
(DistanceMatrix distanceMatrix) construct NJ tree