Uses of Class
de.jstacs.clustering.hierachical.ClusterTree

Packages that use ClusterTree

Package	Description
de.jstacs.clustering.distances
de.jstacs.clustering.hierachical

Uses of ClusterTree in de.jstacs.clustering.distances

Methods in de.jstacs.clustering.distances with parameters of type ClusterTree

Modifier and Type	Method and Description
static Pair<double[][],int[][]>	DeBruijnMotifComparison.getClusterRepresentative(ClusterTree<StatisticalModel> tree, int n) Returns a position weight matrix (PWM) representation of the root node of the given cluster tree and also computed the relative shifts of the motifs such that they align best with the consensus motif at the root.

Uses of ClusterTree in de.jstacs.clustering.hierachical

Methods in de.jstacs.clustering.hierachical that return ClusterTree

Modifier and Type	Method and Description
ClusterTree<Integer>	Hclust.cluster(double[][] distMat, LinkedList<ClusterTree<Integer>> list, int indexOff) Further clusters the supplied cluster trees using the given distance matrix and creating original indexes for the inner node starting at -indexOff-1 in descending order
ClusterTree<T>	Hclust.cluster(double[][] distMat, T... objects) Clusters the given objects using the supplied distance matrix, which must be in the same order as the elements provided in objects.
ClusterTree<T>	Hclust.cluster(int indexOff, double[][] distMat, ClusterTree<T>[] leaves) Clusters the given leaf trees using the supplied distance matrix
ClusterTree<T>	Hclust.cluster(T... objects) Clusters the supplied objects and return the resulting cluster tree.
ClusterTree<T>	Hclust.createTree(ClusterTree<Integer> intTree, T... objects) Creates a cluster tree given an index tree using the original indexes refering to the indexes of elements in objects.
static <T> ClusterTree<T>[]	Hclust.cutTree(double distance, ClusterTree<T> tree) Cuts the cluster tree at the given distance and returns the sub-trees below the cut.
<S> ClusterTree<S>	ClusterTree.dropBelow(IntList rootOriginalIndexes, S[] newElements) Removes all sub-trees below the inner nodes identified by the original indexes supplied and creates new leaf nodes instead, which obtain the supplied leaf elements.
ClusterTree<Integer>	ClusterTree.getIndexTree() Returns a cluster tree with identical structure as this cluster tree but with all leaves replaced by integer leaves holding the corresponding original indices.
ClusterTree<T>[]	ClusterTree.getLeaves() Returns all leaves of this cluster tree as ClusterTree objects comprising just the corresponding leaf element
ClusterTree<T>[]	ClusterTree.getSubTrees() Returns the sub-trees of this cluster tree root node

Methods in de.jstacs.clustering.hierachical with parameters of type ClusterTree

Modifier and Type	Method and Description
ClusterTree<T>	Hclust.cluster(int indexOff, double[][] distMat, ClusterTree<T>[] leaves) Clusters the given leaf trees using the supplied distance matrix
ClusterTree<T>	Hclust.createTree(ClusterTree<Integer> intTree, T... objects) Creates a cluster tree given an index tree using the original indexes refering to the indexes of elements in objects.
static <T> T[][]	Hclust.cutTree(ClusterTree<T> tree, double distance) Cuts the cluster tree at the specified distance and returns the leaf elements grouped by their origin in the sub-trees below the cut
static <T> ClusterTree<T>[]	Hclust.cutTree(double distance, ClusterTree<T> tree) Cuts the cluster tree at the given distance and returns the sub-trees below the cut.
double	Hclust.getDistance(double[][] distMat, ClusterTree<Integer> tree, ClusterTree<Integer> tree2) Returns the distance between the two supplied trees using the linkage method of this Hclust object and the given distance matrix.
double	Hclust.getDistance(double[][] distMat, ClusterTree<Integer> tree, ClusterTree<Integer> tree2) Returns the distance between the two supplied trees using the linkage method of this Hclust object and the given distance matrix.

Method parameters in de.jstacs.clustering.hierachical with type arguments of type ClusterTree

Modifier and Type	Method and Description
ClusterTree<Integer>	Hclust.cluster(double[][] distMat, LinkedList<ClusterTree<Integer>> list, int indexOff) Further clusters the supplied cluster trees using the given distance matrix and creating original indexes for the inner node starting at -indexOff-1 in descending order

Constructors in de.jstacs.clustering.hierachical with parameters of type ClusterTree

Constructor and Description
ClusterTree(double distance, int originalIndex, ClusterTree<T>... subTrees) Creates a new cluster tree with supplied sub-trees and given distance.