Uses of Class
ffx.numerics.clustering.Cluster

Packages that use Cluster

Package	Description
ffx.numerics.clustering	The clustering package provides hierarchical agglomerative clustering utilities, including linkage strategies (single, complete, average, weighted), distance map management, and supporting data structures and algorithms.
ffx.numerics.clustering.visualization	Visualization components for clustering results, including Swing-based classes to render dendrograms and related views of hierarchical clusters.

Uses of Cluster in ffx.numerics.clustering

Methods in ffx.numerics.clustering that return Cluster

Modifier and Type	Method	Description
Cluster	ClusterPair.agglomerate(int clusterIdx)	Agglomerates left and right clusters under an auto-generated name.
Cluster	ClusterPair.agglomerate(String name)	Agglomerates left and right clusters into a new parent with the given name.
Cluster	ClusterPair.getlCluster()	Gets the left cluster.
Cluster	ClusterPair.getOtherCluster(Cluster c)	Returns the opposite cluster of the provided one in this pair.
Cluster	Cluster.getParent()	Gets the parent cluster of this node, or null if this is the root.
Cluster	ClusterPair.getrCluster()	Gets the right cluster.
Cluster	HierarchyBuilder.getRootCluster()	Returns the root cluster if the hierarchy is complete.
Cluster	ClusteringAlgorithm.performClustering(double[][] distances, String[] clusterNames, LinkageStrategy linkageStrategy)	Performs hierarchical agglomerative clustering on a square distance matrix.
Cluster	DefaultClusteringAlgorithm.performClustering(double[][] distances, String[] clusterNames, LinkageStrategy linkageStrategy)	Performs hierarchical agglomerative clustering using a full N x N distance matrix.
Cluster	PDistClusteringAlgorithm.performClustering(double[][] distances, String[] clusterNames, LinkageStrategy linkageStrategy)	Performs hierarchical agglomerative clustering using a condensed pdist-like matrix.
Cluster	ClusteringAlgorithm.performWeightedClustering(double[][] distances, String[] clusterNames, double[] weights, LinkageStrategy linkageStrategy)	Performs hierarchical clustering when each initial element has an associated weight.
Cluster	DefaultClusteringAlgorithm.performWeightedClustering(double[][] distances, String[] clusterNames, double[] weights, LinkageStrategy linkageStrategy)	Performs hierarchical clustering when each element has an associated weight.
Cluster	PDistClusteringAlgorithm.performWeightedClustering(double[][] distances, String[] clusterNames, double[] weights, LinkageStrategy linkageStrategy)	Weighted variant for condensed inputs; currently delegates to unweighted clustering as weights are not applied with condensed input in this implementation.

Methods in ffx.numerics.clustering that return types with arguments of type Cluster

Modifier and Type	Method	Description
List<Cluster>	HierarchyBuilder.flatAgg(LinkageStrategy linkageStrategy, Double threshold)	Performs agglomeration until the minimal inter-cluster distance exceeds the threshold, and returns the remaining clusters (flat clustering at that cut).
List<Cluster>	Cluster.getChildren()	Returns the list of child clusters, creating it lazily if needed.
List<Cluster>	HierarchyBuilder.getClusters()	Returns the current working list of clusters (not necessarily a single root).
List<Cluster>	ClusteringAlgorithm.performFlatClustering(double[][] distances, String[] clusterNames, LinkageStrategy linkageStrategy, Double threshold)	Performs a flat clustering by agglomerating until the next linkage distance would exceed the provided threshold, and returns the list of clusters at that cut.
List<Cluster>	DefaultClusteringAlgorithm.performFlatClustering(double[][] distances, String[] clusterNames, LinkageStrategy linkageStrategy, Double threshold)	Produces a flat clustering by agglomerating until the next merge would exceed the threshold.
List<Cluster>	PDistClusteringAlgorithm.performFlatClustering(double[][] distances, String[] clusterNames, LinkageStrategy linkageStrategy, Double threshold)	Produces a flat clustering from a condensed distance matrix by agglomerating until the threshold is exceeded.

Methods in ffx.numerics.clustering with parameters of type Cluster

Modifier and Type	Method	Description
void	Cluster.addChild(Cluster cluster)	Adds a child cluster to this node.
boolean	Cluster.contains(Cluster cluster)	Tests whether this cluster has the specified child.
int	Cluster.countLeafs(Cluster node, int count)	Recursive helper to count leaves under the specified node.
ClusterPair	DistanceMap.findByCodePair(Cluster c1, Cluster c2)	Finds the ClusterPair for the two provided clusters.
Cluster	ClusterPair.getOtherCluster(Cluster c)	Returns the opposite cluster of the provided one in this pair.
void	ClusterPair.setlCluster(Cluster lCluster)	Sets the left cluster.
void	Cluster.setParent(Cluster parent)	Sets the parent cluster of this node.
void	ClusterPair.setrCluster(Cluster rCluster)	Sets the right cluster.

Method parameters in ffx.numerics.clustering with type arguments of type Cluster

Modifier and Type	Method	Description
void	Cluster.setChildren(List<Cluster> children)	Sets the list of child clusters for this node.

Constructors in ffx.numerics.clustering with parameters of type Cluster

Modifier	Constructor	Description
	ClusterPair(Cluster left, Cluster right, Double distance)	Creates a ClusterPair linking two clusters at a given distance.

Constructor parameters in ffx.numerics.clustering with type arguments of type Cluster

Modifier	Constructor	Description
	HierarchyBuilder(List<Cluster> clusters, DistanceMap distances)	Constructs a HierarchyBuilder with an initial set of clusters and inter-cluster distances.

Uses of Cluster in ffx.numerics.clustering.visualization

Methods in ffx.numerics.clustering.visualization that return Cluster

Modifier and Type	Method	Description
Cluster	ClusterComponent.getCluster()	Gets the Cluster model represented by this component.
Cluster	DendrogramPanel.getModel()

Methods in ffx.numerics.clustering.visualization with parameters of type Cluster

Modifier and Type	Method	Description
void	ClusterComponent.setCluster(Cluster cluster)	Sets the Cluster model represented by this component.
void	DendrogramPanel.setModel(Cluster model)

Constructors in ffx.numerics.clustering.visualization with parameters of type Cluster

Modifier	Constructor	Description
	ClusterComponent(Cluster cluster, boolean printName, VCoord initPoint)	Constructs a visual node component for a Cluster.
	DendrogramFrame(Cluster cluster)	Creates a frame displaying a dendrogram for the provided clustering result.