Uses of Interface
jebl.evolution.distances.DistanceMatrix
-
Packages that use DistanceMatrix Package Description 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 Modifier and Type Class Description class
SequenceAlignmentsDistanceMatrix
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 DistanceMatrix Modifier and Type Field Description DistanceMatrix
AlignmentTreeBuilderFactory.Result. distance
-
Uses of DistanceMatrix in jebl.evolution.distances
Classes in jebl.evolution.distances that implement DistanceMatrix Modifier and Type Class Description class
BasicDistanceMatrix
class
F84DistanceMatrix
class
HKYDistanceMatrix
Compute HKY corrected distance matrixclass
JukesCantorDistanceMatrix
Compute jukes-cantor corrected distance matrix for a set of aligned sequences.class
TamuraNeiDistanceMatrix
Date: 22/01/2006 Time: 17:28:59Methods in jebl.evolution.distances that return DistanceMatrix Modifier and Type Method Description DistanceMatrix
BasicDistanceMatrix. getSubmatrix(java.util.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(java.util.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 Modifier and Type Method Description DistanceMatrix
NexusImporter. parseDistancesBlock(java.util.List<Taxon> taxonList)
Parse the next 'DISTANCES' block encountered in the input.Methods in jebl.evolution.io that return types with arguments of type DistanceMatrix Modifier and Type Method Description java.util.List<DistanceMatrix>
DistanceMatrixImporter. importDistanceMatrices()
importDistances.java.util.List<DistanceMatrix>
NexusImporter. importDistanceMatrices()
Import all distance matrices from all DISTANCES blocks in the input form the current position.java.util.List<DistanceMatrix>
TabDelimitedImporter. importDistanceMatrices()
importDistances.Methods in jebl.evolution.io with parameters of type DistanceMatrix Modifier and Type Method Description void
NexusExporter. exportMatrix(DistanceMatrix distanceMatrix)
-
Uses of DistanceMatrix in jebl.evolution.trees
Methods in jebl.evolution.trees with parameters of type DistanceMatrix Modifier and Type Method Description static 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 DistanceMatrix Constructor Description NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix)
construct NJ tree
-