Package weka.clusterers

Class HierarchicalClusterer

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, Clusterer, CapabilitiesHandler, Drawable, OptionHandler, RevisionHandler
    public class HierarchicalClusterer
extends AbstractClusterer
implements OptionHandler, CapabilitiesHandler, Drawable
    Hierarchical clustering class. Implements a number of classic hierarchical clustering methods. Valid options are: 

     -N
  number of clusters
 
     -L
  Link type (Single, Complete, Average, Mean, Centroid, Ward, Adjusted complete, Neighbor Joining)
  [SINGLE|COMPLETE|AVERAGE|MEAN|CENTROID|WARD|ADJCOMLPETE|NEIGHBOR_JOINING]
 
     -A
 Distance function to use. (default: weka.core.EuclideanDistance)
 
     -P
 Print hierarchy in Newick format, which can be used for display in other programs.
 
     -D
 If set, classifier is run in debug mode and may output additional info to the console.
 
     -B
 \If set, distance is interpreted as branch length, otherwise it is node height.
    Version:
    $Revision: 11330 $
    Author:
    Remco Bouckaert (rrb@xm.co.nz, remco@cs.waikato.ac.nz), Eibe Frank (eibe@cs.waikato.ac.nz)
    See Also:
    Serialized Form

    • Field Detail

      • TAGS_LINK_TYPE

        public static final Tag[] TAGS_LINK_TYPE

    • Constructor Detail

      • HierarchicalClusterer

        public HierarchicalClusterer()

    • Method Detail

      • setNumClusters

        public void setNumClusters​(int nClusters)

      • getNumClusters

        public int getNumClusters()

      • setDistanceFunction

        public void setDistanceFunction​(DistanceFunction distanceFunction)

      • getPrintNewick

        public boolean getPrintNewick()

      • setPrintNewick

        public void setPrintNewick​(boolean bPrintNewick)

      • setLinkType

        public void setLinkType​(SelectedTag newLinkType)

      • buildClusterer

        public void buildClusterer​(Instances data)
                    throws java.lang.Exception
        Description copied from class: AbstractClusterer
        Generates a clusterer. Has to initialize all fields of the clusterer that are not being set via options.
        Specified by:
        buildClusterer in interface Clusterer
        Specified by:
        buildClusterer in class AbstractClusterer
        Parameters:
        data - set of instances serving as training data
        Throws:
        java.lang.Exception - if the clusterer has not been generated successfully

      • clusterInstance

        public int clusterInstance​(Instance instance)
                    throws java.lang.Exception
        Description copied from class: AbstractClusterer
        Classifies a given instance. Either this or distributionForInstance() needs to be implemented by subclasses.
        Specified by:
        clusterInstance in interface Clusterer
        Overrides:
        clusterInstance in class AbstractClusterer
        Parameters:
        instance - the instance to be assigned to a cluster
        Returns:
        the number of the assigned cluster as an integer
        Throws:
        java.lang.Exception - if instance could not be clustered successfully

      • distributionForInstance

        public double[] distributionForInstance​(Instance instance)
                                 throws java.lang.Exception
        Description copied from class: AbstractClusterer
        Predicts the cluster memberships for a given instance. Either this or clusterInstance() needs to be implemented by subclasses.
        Specified by:
        distributionForInstance in interface Clusterer
        Overrides:
        distributionForInstance in class AbstractClusterer
        Parameters:
        instance - the instance to be assigned a cluster.
        Returns:
        an array containing the estimated membership probabilities of the test instance in each cluster (this should sum to at most 1)
        Throws:
        java.lang.Exception - if distribution could not be computed successfully

      • numberOfClusters

        public int numberOfClusters()
                     throws java.lang.Exception
        Description copied from class: AbstractClusterer
        Returns the number of clusters.
        Specified by:
        numberOfClusters in interface Clusterer
        Specified by:
        numberOfClusters in class AbstractClusterer
        Returns:
        the number of clusters generated for a training dataset.
        Throws:
        java.lang.Exception - if number of clusters could not be returned successfully

      • listOptions

        public java.util.Enumeration listOptions()
        Returns an enumeration describing the available options.
        Specified by:
        listOptions in interface OptionHandler
        Returns:
        an enumeration of all the available options.

      • setOptions

        public void setOptions​(java.lang.String[] options)
                throws java.lang.Exception
        Parses a given list of options.

        Valid options are:

        Specified by:
        setOptions in interface OptionHandler
        Parameters:
        options - the list of options as an array of strings
        Throws:
        java.lang.Exception - if an option is not supported

      • getOptions

        public java.lang.String[] getOptions()
        Gets the current settings of the clusterer.
        Specified by:
        getOptions in interface OptionHandler
        Returns:
        an array of strings suitable for passing to setOptions()

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • setDebug

        public void setDebug​(boolean debug)
        Set debugging mode.
        Parameters:
        debug - true if debug output should be printed

      • getDebug

        public boolean getDebug()
        Get whether debugging is turned on.
        Returns:
        true if debugging output is on

      • getDistanceIsBranchLength

        public boolean getDistanceIsBranchLength()

      • setDistanceIsBranchLength

        public void setDistanceIsBranchLength​(boolean bDistanceIsHeight)

      • distanceIsBranchLengthTipText

        public java.lang.String distanceIsBranchLengthTipText()

      • debugTipText

        public java.lang.String debugTipText()
        Returns the tip text for this property
        Returns:
        tip text for this property suitable for displaying in the explorer/experimenter gui

      • numClustersTipText

        public java.lang.String numClustersTipText()
        Returns:
        a string to describe the NumClusters

      • printNewickTipText

        public java.lang.String printNewickTipText()
        Returns:
        a string to describe the print Newick flag

      • distanceFunctionTipText

        public java.lang.String distanceFunctionTipText()
        Returns:
        a string to describe the distance function

      • linkTypeTipText

        public java.lang.String linkTypeTipText()
        Returns:
        a string to describe the Link type

      • globalInfo

        public java.lang.String globalInfo()
        This will return a string describing the clusterer.
        Returns:
        The string.

      • main

        public static void main​(java.lang.String[] argv)

      • graph

        public java.lang.String graph()
                       throws java.lang.Exception
        Description copied from interface: Drawable
        Returns a string that describes a graph representing the object. The string should be in XMLBIF ver. 0.3 format if the graph is a BayesNet, otherwise it should be in dotty format.
        Specified by:
        graph in interface Drawable
        Returns:
        the graph described by a string
        Throws:
        java.lang.Exception - if the graph can't be computed

      • graphType

        public int graphType()
        Description copied from interface: Drawable
        Returns the type of graph representing the object.
        Specified by:
        graphType in interface Drawable
        Returns:
        the type of graph representing the object