Uses of Interface
jebl.evolution.distances.DistanceMatrix
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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 -
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Uses of DistanceMatrix in jebl.evolution.align
Classes in jebl.evolution.align that implement DistanceMatrix Modifier and Type Class Description classSequenceAlignmentsDistanceMatrixBuilds 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 DistanceMatrixAlignmentTreeBuilderFactory.Result. distance -
Uses of DistanceMatrix in jebl.evolution.distances
Classes in jebl.evolution.distances that implement DistanceMatrix Modifier and Type Class Description classBasicDistanceMatrixclassF84DistanceMatrixclassHKYDistanceMatrixCompute HKY corrected distance matrixclassJukesCantorDistanceMatrixCompute jukes-cantor corrected distance matrix for a set of aligned sequences.classTamuraNeiDistanceMatrixDate: 22/01/2006 Time: 17:28:59Methods in jebl.evolution.distances that return DistanceMatrix Modifier and Type Method Description DistanceMatrixBasicDistanceMatrix. 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).DistanceMatrixDistanceMatrix. 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 DistanceMatrixNexusImporter. 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 voidNexusExporter. 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 ClusteringTreeBuilderClusteringTreeBuilder. getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances)A factory method to create a ClusteringTreeBuilderstatic ClusteringTreeBuilderTreeBuilderFactory. getBuilder(TreeBuilderFactory.Method method, DistanceMatrix distances)Constructors in jebl.evolution.trees with parameters of type DistanceMatrix Constructor Description NeighborJoiningTreeBuilder(DistanceMatrix distanceMatrix)construct NJ tree
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