Uses of Interface
org.expasy.mzjava.core.ms.cluster.SimilarityGraph

Packages that use SimilarityGraph

Package	Description
org.expasy.mzjava.core.ms.cluster

Uses of SimilarityGraph in org.expasy.mzjava.core.ms.cluster

Classes in org.expasy.mzjava.core.ms.cluster with type parameters of type SimilarityGraph

Modifier and Type	Class and Description
protected static class	DenseSimilarityGraph.AbstractBuilder<V,G extends SimilarityGraph<V>>
interface	SimilarityGraphBuilder<V,G extends SimilarityGraph<V>> Common interface for similarity graph builders.

Classes in org.expasy.mzjava.core.ms.cluster that implement SimilarityGraph

Modifier and Type	Class and Description
class	DenseSimilarityGraph<V> A similarity graph that is backed by a matrix
class	SparseSimilarityGraph<V>

Methods in org.expasy.mzjava.core.ms.cluster with type parameters of type SimilarityGraph

Modifier and Type	Method and Description
static <A extends PeakAnnotation,S extends PeakList<A>,G extends SimilarityGraph<S>> G	PeakListSimGraphFactory.build(List<S> spectra, SimilarityGraphBuilder<S,G> builder, SimFunc<A,A> simFunc, Tolerance precursorTolerance, double scoreThreshold) Build a new SimilarityGraph

Methods in org.expasy.mzjava.core.ms.cluster that return SimilarityGraph

Modifier and Type	Method and Description
static <A extends PeakAnnotation,S extends PeakList<A>> SimilarityGraph<S>	PeakListSimGraphFactory.build(List<S> spectra, SimFunc<A,A> simFunc, Tolerance precursorTolerance, double scoreThreshold) Build a new DenseSimilarityGraph

Methods in org.expasy.mzjava.core.ms.cluster with parameters of type SimilarityGraph

Modifier and Type	Method and Description
Collection<Set<V>>	ClusterBuilder.cluster(SimilarityGraph<V> graph) Cluster the vertices given a SimilarityGraph
Collection<Set<V>>	GlobalThresholdClusterBuilder.cluster(SimilarityGraph<V> graph)
Collection<Set<V>>	CompoundClusterBuilder.cluster(SimilarityGraph<V> graph)
Collection<Set<V>>	MSTClusterBuilder.cluster(SimilarityGraph<V> graph)
Collection<Set<V>>	KMeansPlusPlusClusterBuilder.cluster(SimilarityGraph<V> graph)
Collection<Set<V>>	ClusterBuilder.cluster(SimilarityGraph<V> graph, Collection<Set<V>> startingClusters) Cluster the vertices in graph using the startingClusters as a starting point.
Collection<Set<V>>	GlobalThresholdClusterBuilder.cluster(SimilarityGraph<V> graph, Collection<Set<V>> startingClusters)
Collection<Set<V>>	CompoundClusterBuilder.cluster(SimilarityGraph<V> graph, Collection<Set<V>> startingClusters)
Collection<Set<V>>	MSTClusterBuilder.cluster(SimilarityGraph<V> graph, Collection<Set<V>> startingClusters)
Collection<Set<V>>	KMeansPlusPlusClusterBuilder.cluster(SimilarityGraph<V> graph, Collection<Set<V>> startingClusters)

Constructors in org.expasy.mzjava.core.ms.cluster with parameters of type SimilarityGraph

Constructor and Description
JungSimGraphWrapper(SimilarityGraph<V> simGraph)