com.chemaxon.clustering.util

Class Util

java.lang.Object

com.chemaxon.clustering.util.Util

@Beta
 @PublicAPI
public final class Util
extends Object

Clustering related utility methods.

Please note that this class is marked with Beta annotation, so it can be subject of incompatible changes or removal in later releases.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Util.StringScatterPlot ASCII scatter plot.

Method Summary

Modifier and Type	Method and Description
static int	countNumberOfClusters(HierarchicClustering<?,? extends HierarchicCluster<?>> c) Count the number of clusters in a clustering.
static <T> String	hierarchicIndexOf(T member, HierarchicClustering<T,? extends HierarchicCluster<T>> clustering) Consruct a hierarchic index for a given member of a clustering.
static String	hierarchyToString(IDBasedHierarchicClustering clustering, IDBasedAssigner levels, List<String> labels, int cols) Render a minimalist dendrogram from a String.
static DissimilarityInput	linearEuclideanDissimilarityInput(double[] values) Construct a DissimilarityInput over a set of 1D values.
static int	maxDepth(HierarchicClustering<?,? extends HierarchicCluster<?>> c) Find max depth.
static String	toJsonMixed(IDBasedHierarchicClustering clustering) Provide a JSON-like representation for Web GUI widget display.
static String	toMultilineString(IDBasedHierarchicClustering clustering, String prefix)
static <T> List<T>	traversePostOrderDFS(PostOrderDfsVisitor<T> visitor, IDBasedHierarchicClustering clustering) Invoke recursive DFS post order traversal on a hierarchy.
static void	traverseSimpleDfs(IDBasedHierarchicClustering h, SimpleDfsVisitor preorderVisitorOrNull, SimpleDfsVisitor postorderVisitorOrNull) Simple DFS traversal.
static void	traverseSimplePostOrderDfs(IDBasedHierarchicClustering h, SimpleDfsVisitor postOrderVisitor) Simple postorder DFS traversal.
static void	traverseSimplePreOrderDfs(IDBasedHierarchicClustering h, SimpleDfsVisitor preOrderVisitor) Simple preorder DFS traversal.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

toMultilineString

public static String toMultilineString(IDBasedHierarchicClustering clustering,
                                       String prefix)

toJsonMixed

public static String toJsonMixed(IDBasedHierarchicClustering clustering)

Provide a JSON-like representation for Web GUI widget display.

Please note that the provided representation is not defined, it can be changed in future releases.

Parameters:

clustering - Clustering to JSonify

Returns:

JSON representation

countNumberOfClusters

public static int countNumberOfClusters(HierarchicClustering<?,? extends HierarchicCluster<?>> c)

Count the number of clusters in a clustering.

Parameters:

c - A clustering

Returns:

Total number of clusters, including singletons

maxDepth

public static int maxDepth(HierarchicClustering<?,? extends HierarchicCluster<?>> c)

Find max depth.

Parameters:

c - A clustering

Returns:

Max parent-children steps required to reach every leaf

hierarchicIndexOf

public static <T> String hierarchicIndexOf(T member,
                                           HierarchicClustering<T,? extends HierarchicCluster<T>> clustering)

Consruct a hierarchic index for a given member of a clustering.

Hierarchic index is a comma (,) separated list of 1-based indexes of the path leading to the given member from the roots. In a clustering, hierarchic index "2,3,4" means that the given member is accessible from the second root's third child cluster, as its fourth element. The previous elements can be further clusters or leaf nodes.

This implementation orders child clusters before immediate leaves.

Type Parameters:

T - Type of clustered members

Parameters:

member - A member

clustering - Associated clustering

Returns:

1-based, comma separated compact (no whitespaces) hierarchic index string of the given member

Throws:

IllegalArgumentException - when the given member is not part of the given clustering

traverseSimplePreOrderDfs

public static void traverseSimplePreOrderDfs(IDBasedHierarchicClustering h,
                                             SimpleDfsVisitor preOrderVisitor)

Simple preorder DFS traversal. This is a convenience method delegating to traverseSimpleDfs(com.chemaxon.clustering.common.IDBasedHierarchicClustering, com.chemaxon.clustering.util.SimpleDfsVisitor, com.chemaxon.clustering.util.SimpleDfsVisitor).

Parameters:

h - Hierarchy to traverse

preOrderVisitor - A non-null visitor to invoke

traverseSimplePostOrderDfs

public static void traverseSimplePostOrderDfs(IDBasedHierarchicClustering h,
                                              SimpleDfsVisitor postOrderVisitor)

Simple postorder DFS traversal. This is a convenience method delegating to traverseSimpleDfs(com.chemaxon.clustering.common.IDBasedHierarchicClustering, com.chemaxon.clustering.util.SimpleDfsVisitor, com.chemaxon.clustering.util.SimpleDfsVisitor).

Parameters:

h - Hierarchy to traverse

postOrderVisitor - A non-null visitor to invoke

traverseSimpleDfs

public static void traverseSimpleDfs(IDBasedHierarchicClustering h,
                                     SimpleDfsVisitor preorderVisitorOrNull,
                                     SimpleDfsVisitor postorderVisitorOrNull)

Simple DFS traversal. Non recursive DFS traversal of all (intermediate included) clusters with a List based stack. Leaves and members must be handled by the visitor implementation.

For the following tree (only clusters shown, no leaves/members considered)

   C-0
   C-1 -+- C-2 --- C-3
        +- C-4
   C-5
   C-6 --- C-7 --- C-8
 

The following invocation order is expected (<PATH> / <VISITED>) for the preorder callback:

 "C-0"               / "C-0"
 "C-1"               / "C-1"
 "C-1", "C-2"        / "C-2"
 "C-1", "C-2", "C-3" / "C-3"
 "C-1", "C-4"        / "C-4"
 "C-5"               / "C-5"
 "C-6"               / "C-6"
 "C-6", "C-7"        / "C-7"
 "C-6", "C-7", "C-8" / "C-8"
 

The following invocation order is expected (<PATH> / <VISITED>) for the postorder callback:

 "C-0"               / "C-0"
 "C-1", "C-2", "C-3" / "C-3"
 "C-1", "C-2"        / "C-2"
 "C-1", "C-4"        / "C-4"
 "C-1"               / "C-1"
 "C-5"               / "C-5"
 "C-6", "C-7", "C-8" / "C-8"
 "C-6", "C-7"        / "C-7"
 "C-6"               / "C-6"
 

Parameters:

h - Clustering

preorderVisitorOrNull - Visitor to be invoked before a descend step or null

postorderVisitorOrNull - Visitor to be invoked after an ascend or side step or null

linearEuclideanDissimilarityInput

public static DissimilarityInput linearEuclideanDissimilarityInput(double[] values)

Construct a DissimilarityInput over a set of 1D values.

Parameters:

values - Values to consider

Returns:

Dissimilarity input representing their euclidean distances

traversePostOrderDFS

public static <T> List<T> traversePostOrderDFS(PostOrderDfsVisitor<T> visitor,
                                               IDBasedHierarchicClustering clustering)

Invoke recursive DFS post order traversal on a hierarchy.

Type Parameters:

T - Traversal result type

Parameters:

visitor - Callback interface for traversal/skipping

clustering - Clustering to traverse

Returns:

Result list of traversal associated to roots

hierarchyToString

public static String hierarchyToString(IDBasedHierarchicClustering clustering,
                                       IDBasedAssigner levels,
                                       List<String> labels,
                                       int cols)

Render a minimalist dendrogram from a String.

Parameters:

clustering - Source clustering to use

levels - Level assignemnt to use

labels - Leaf labels for leaf IDs

cols - Total columns

Returns:

String representation of the given clustering