QtClustering API qtclustering-163 (20111029234107)
C D E G I M Q S

C

cluster(SimilarityDistanceCalculator, double) - Method in interface edu.cornell.med.icb.clustering.Clusterer
Groups instances into clusters.
cluster(SimilarityDistanceCalculator, double) - Method in class edu.cornell.med.icb.clustering.MCLClusterer
Groups instances into clusters.
cluster(SimilarityDistanceCalculator, double) - Method in class edu.cornell.med.icb.clustering.QTClusterer
Groups instances into clusters.
Clusterer - Interface in edu.cornell.med.icb.clustering
Common interface definition for clustering algorithms.
ClusteringException - Exception in edu.cornell.med.icb.clustering
Indicates a problem while clustering objects.
ClusteringException() - Constructor for exception edu.cornell.med.icb.clustering.ClusteringException
Constructs a new runtime exception with null as its detail message.
ClusteringException(String) - Constructor for exception edu.cornell.med.icb.clustering.ClusteringException
Constructs a new runtime exception with the specified detail message.
ClusteringException(String, Throwable) - Constructor for exception edu.cornell.med.icb.clustering.ClusteringException
Constructs a new runtime exception with the specified detail message and cause.
ClusteringException(Throwable) - Constructor for exception edu.cornell.med.icb.clustering.ClusteringException
Constructs a new runtime exception with the specified cause and a detail message of (cause==null ? null : cause.toString()) (which typically contains the class and detail message of cause).

D

distance(int, int) - Method in interface edu.cornell.med.icb.clustering.SimilarityDistanceCalculator
Returns the distance between two instances.

E

edu.cornell.med.icb.clustering - package edu.cornell.med.icb.clustering
Contains classes to aid in the classification of objects into different groups, or more precisely, the partitioning of a data set into subsets (clusters), so that the data in each subset (ideally) share some common trait - often proximity according to some defined distance measure.

G

getClusters() - Method in interface edu.cornell.med.icb.clustering.Clusterer
Returns the list of clusters produced by clustering.
getClusters() - Method in class edu.cornell.med.icb.clustering.MCLClusterer
Returns the list of clusters produced by clustering.
getClusters() - Method in class edu.cornell.med.icb.clustering.QTClusterer
Returns the list of clusters produced by clustering.
getIgnoreDistance() - Method in class edu.cornell.med.icb.clustering.MaxLinkageDistanceCalculator
When some distances between instance pairs are missing/unknown the ignoreDistance is returned.
getIgnoreDistance() - Method in interface edu.cornell.med.icb.clustering.SimilarityDistanceCalculator
When some distances between instance pairs are missing/unknown the ignoreDistance is returned.
getLogInterval() - Method in class edu.cornell.med.icb.clustering.QTClusterer
Get the the progress logging interval.

I

ignoreDistance - Variable in class edu.cornell.med.icb.clustering.MaxLinkageDistanceCalculator
Default value to use when pairs are missing or unknown.
isLogClusterProgress() - Method in class edu.cornell.med.icb.clustering.QTClusterer
Is progress on clusters being logged?
isLogInnerLoopProgress() - Method in class edu.cornell.med.icb.clustering.QTClusterer
Is progress on the inner loop being logged?
isLogOuterLoopProgress() - Method in class edu.cornell.med.icb.clustering.QTClusterer
Is progress on the outer loop being logged?

M

MaxLinkageDistanceCalculator - Class in edu.cornell.med.icb.clustering
Maximum distance linkage calculator.
MaxLinkageDistanceCalculator() - Constructor for class edu.cornell.med.icb.clustering.MaxLinkageDistanceCalculator
Create a new SimilarityDistanceCalculator.
MCLClusterer - Class in edu.cornell.med.icb.clustering
http://micans.org/mcl/
MCLClusterer(int) - Constructor for class edu.cornell.med.icb.clustering.MCLClusterer
Construct a new quality threshold clusterer.
MCLClusterer(int, String) - Constructor for class edu.cornell.med.icb.clustering.MCLClusterer
 
MCLClusterer(Reader) - Constructor for class edu.cornell.med.icb.clustering.MCLClusterer
Creates clusters that are read directly from an MCL output file.

Q

QTClusterer - Class in edu.cornell.med.icb.clustering
Implements the QT Clustering algorithm.
QTClusterer(int) - Constructor for class edu.cornell.med.icb.clustering.QTClusterer
Construct a new quality threshold clusterer.
QTClusterer(int, int) - Constructor for class edu.cornell.med.icb.clustering.QTClusterer
Construct a new quality threshold clusterer.
QTClusterer(int, ParallelTeam) - Constructor for class edu.cornell.med.icb.clustering.QTClusterer
Construct a new quality threshold clusterer.

S

setLogClusterProgress(boolean) - Method in class edu.cornell.med.icb.clustering.QTClusterer
Should progress on the clusters be logged?
setLogInnerLoopProgress(boolean) - Method in class edu.cornell.med.icb.clustering.QTClusterer
Should progress on the inner loop be logged?
setLogInterval(long) - Method in class edu.cornell.med.icb.clustering.QTClusterer
Set the the progress logging interval.
setLogOuterLoopProgress(boolean) - Method in class edu.cornell.med.icb.clustering.QTClusterer
Should progress on the outer loop be logged?
SimilarityDistanceCalculator - Interface in edu.cornell.med.icb.clustering
Calculates a similarity measure between two instances available to the clustering algorithm, or between one instance and a cluster.

C D E G I M Q S
QtClustering API qtclustering-163 (20111029234107)

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