A B C D E F G H I K L M N O P Q R S T U V W _

A

actionPerformed(ActionEvent) - Method in class de.uni_leipzig.cvk.gui.Application
 
actionPerformed(ActionEvent) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.AddButtonActionListener
 
actionPerformed(ActionEvent) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.AlgoActionListener
 
actionPerformed(ActionEvent) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.ClusterActionListener
 
actionPerformed(ActionEvent) - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.MeasureButtonAction
 
add(TreeSet<Integer>) - Method in class de.uni_leipzig.bf.cluster.ClusterCache
Adds new final cluster elements to m_cache and all logged elements in m_log for this cluster to m_cacheHistory.
add(int, int, double) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
adds a to the specified element, growing the matrix if necessary.
add(String, String, double) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
Add an edge to matrix and index
add(SparseVector) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable add
add(int, double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable add
addAggregate(Table) - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Adds the sorted data of column ClusterTableSettings.CLUSTER_COLUMN_NAME from clusterTable parameter to the AggregateTable instance AggregatePanel.m_aTable, sets a Decorator with the AggregatePanel.setDecorators() method.
addAlgorithm(String, ClusterAlgorithm) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Adds a new instance of a ClusterAlgorithm.
addd(Comparable) - Method in class de.uni_leipzig.bf.util.AlphaList
add elements in alphabetic order
addd(Comparable) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
addGraph(Graph) - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Adds a Graph, refreshes search items and removes aggregates.
addNode(Integer) - Method in class de.uni_leipzig.bf.cluster.Cluster
 
addObject(String) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
addToSchema() - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
adjustMaxIndex(int, int) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
adjusts the size of the matrix.
AGGR_DECORATORS - Static variable in class de.uni_leipzig.cvk.visual.AggregatePanel
decorator id
AggregateDragControl - Class in de.uni_leipzig.cvk.visual
Interactive drag control that is "aggregate-aware"
AggregateDragControl(String) - Constructor for class de.uni_leipzig.cvk.visual.AggregateDragControl
Creates a new drag control that issues repaint requests as an item is dragged.
AggregateLayout - Class in de.uni_leipzig.cvk.visual
Layout algorithm that computes a convex hull surrounding aggregate items and saves it in the "_polygon" field.
AggregateLayout(String) - Constructor for class de.uni_leipzig.cvk.visual.AggregateLayout
 
AggregatePanel - Class in de.uni_leipzig.cvk.visual
Is a JPanel class and uses a Visualization instance AggregatePanel.m_vis and a Display instance AggregatePanel.m_display.
AggregatePanel(int, int) - Constructor for class de.uni_leipzig.cvk.visual.AggregatePanel
Constructs a new AggregatePanel.
AggregatePanel.Actions - Enum in de.uni_leipzig.cvk.visual
Action group names for Visualization.
AGGRS - Static variable in class de.uni_leipzig.cvk.visual.AggregatePanel
prefuse default id
AGGRS_ID - Static variable in class de.uni_leipzig.cvk.visual.AggregatePanel
visual aggr id
ALL - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
allNodesInCluster(Graph, Table) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
 
AlphaList - Class in de.uni_leipzig.bf.util
Implements an alphabetically sorted set.
AlphaList() - Constructor for class de.uni_leipzig.bf.util.AlphaList
 
analyze(String) - Static method in class de.uni_leipzig.bf.util.Distribution
 
Application - Class in de.uni_leipzig.cvk.gui
The Application class is used to build all Swing components with all other classes in this package and with a Model instance to get all necessary data.
Application(Model) - Constructor for class de.uni_leipzig.cvk.gui.Application
Constructs a new Application by initializing a AggregatePanel, ClusterPanel and a GraphStatisticPanel Observer instance and some other Swing components with data of the given Model instance data.
Application.MenuArrowIcon - Class in de.uni_leipzig.cvk.gui
Adding an arrow to Icon
Application.MenuArrowIcon() - Constructor for class de.uni_leipzig.cvk.gui.Application.MenuArrowIcon
 
Application.MenuToggleButton - Class in de.uni_leipzig.cvk.gui
Adding JPopupMenu to JToolBar-Button
Application.MenuToggleButton() - Constructor for class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
Application.MenuToggleButton(Icon) - Constructor for class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
Application.MenuToggleButton(String) - Constructor for class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
Application.MenuToggleButton(String, Icon) - Constructor for class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
ATTRNAME - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
ATTRTYPE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 

B

BACKGROUND - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
 
BALANCED_TREE - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method
bigSmall - Variable in class de.uni_leipzig.bf.util.GraphFold
 
blue - Variable in class de.uni_leipzig.cvk.visual.NodeColorAction
 
BOOLEAN - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
border - Variable in class de.uni_leipzig.bf.cluster.Cluster
 
BorderFlow - Class in de.uni_leipzig.bf.cluster
 
BorderFlow(String, String, Harden) - Constructor for class de.uni_leipzig.bf.cluster.BorderFlow
Constructs new instance.
BorderFlow(String, Harden) - Constructor for class de.uni_leipzig.bf.cluster.BorderFlow
Constructs new instance for tabulator separated files.
borderFlowDemo(String, String, double, boolean, boolean, boolean, Main.HardenStrategy, Main.MeasureStrategy) - Static method in class de.uni_leipzig.bf.cluster.Main
A demo of BorderFlow CLI version.
buildContingencyTable(String, String) - Method in class de.uni_leipzig.bf.eval.DataReader
public double computeComplexwiseSeparation() { } /** Compute contingency table from cluster2protMap and complex2protMap

C

cache - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
cache(TreeSet<Integer>) - Method in class de.uni_leipzig.bf.cluster.ClusterCache
Checks for cached elements in m_cacheHistory or adds elements to m_log.
changeColor() - Method in class de.uni_leipzig.cvk.data.Model
 
changeDirection() - Method in class de.uni_leipzig.cvk.data.Model
 
changeDistanceFilter() - Method in class de.uni_leipzig.cvk.data.Model
 
changePause() - Method in class de.uni_leipzig.cvk.data.Model
 
changeQuality() - Method in class de.uni_leipzig.cvk.data.Model
 
characters(char[], int, int) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
checkClusterSize(Table) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
checks all cluster size > 1
checkClusterSize(Table, int) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
checks the size of all cluster
clean(Connection, String, String, String, double) - Static method in class de.uni_leipzig.bf.util.DBOps
Removes the n*100% most frequent word from the similarity database
clean(String, String) - Static method in class de.uni_leipzig.bf.util.SilhouetteCleaner
 
cleanGraph(String, String, String) - Static method in class de.uni_leipzig.bf.eval.DataReader
Cleans graph from unclassified proteins
clique(int, int) - Static method in class de.uni_leipzig.cvk.data.GraphGenerator
Generates a (n,k)-partite-clique.
CLIQUE - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method
close() - Method in class de.uni_leipzig.cvk.gui.LogPanelHandler
 
closeConnection() - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Close connection to database.
cluster(double, boolean, boolean, boolean) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Starts Borderflow with the given configuration to write in String.
cluster(String[], boolean, boolean, boolean) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Starts Borderflow with the given configuration to write in String.
Cluster - Class in de.uni_leipzig.bf.cluster
 
Cluster(ClusterGraph, Integer) - Constructor for class de.uni_leipzig.bf.cluster.Cluster
 
cluster(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
A template method to call the concrete clustering method.
cluster(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
The cluster method gets the cluster back in a table.
CLUSTER - Static variable in class de.uni_leipzig.cvk.data.Model
argument for view
cluster(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.Model
 
cluster2protMap - Variable in class de.uni_leipzig.bf.eval.DataReader
 
CLUSTER_COLUMN_ID - Static variable in interface de.uni_leipzig.cvk.data.cluster.ClusterTableSettings
Id to show and identify cluster for decorator
CLUSTER_COLUMN_ID_TYPE - Static variable in interface de.uni_leipzig.cvk.data.cluster.ClusterTableSettings
Identifier for data type (int) of id column.
CLUSTER_COLUMN_NAME - Static variable in interface de.uni_leipzig.cvk.data.cluster.ClusterTableSettings
Identifier for the column in cluster table given back from ClusterAlgorithm.clustering(String[], double, String, String, String, String) method.
CLUSTER_COLUMN_NAME_TYPE - Static variable in interface de.uni_leipzig.cvk.data.cluster.ClusterTableSettings
Identifier for data type (TreeSet)of column in cluster table given back from ClusterAlgorithm.clustering(String[], double, String, String, String, String) method.
CLUSTER_COLUMN_SIZE - Static variable in interface de.uni_leipzig.cvk.data.cluster.ClusterTableSettings
Identifier for size of cluster table, is used to sort the clusters for a non overlapping painting.
CLUSTER_COLUMN_SIZE_TYPE - Static variable in interface de.uni_leipzig.cvk.data.cluster.ClusterTableSettings
Identifier for data type (int) of size column.
ClusterAlgorithm - Class in de.uni_leipzig.cvk.data.cluster
Is an abstract base class for a concrete cluster algorithm implementation.
ClusterAlgorithm() - Constructor for class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
 
clusterAlgorithm - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterContext
an instance of the current ClusterAlgorithm
ClusterAlgorithmBorderFlow - Class in de.uni_leipzig.cvk.data.cluster
Is a ClusterAlgorithm and an adapt for BorderFlow algorithm of BorderFlow class.
ClusterAlgorithmBorderFlow() - Constructor for class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithmBorderFlow
new available settings
ClusterAlgorithmKNN - Class in de.uni_leipzig.cvk.data.cluster
Is a ClusterAlgorithm and an adapt for knn algorithm of BorderFlow class.
ClusterAlgorithmKNN() - Constructor for class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithmKNN
Builds new available settings.
clusterAlgorithmMap - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterContext
all added algorithms
ClusterAlgorithmMCL - Class in de.uni_leipzig.cvk.data.cluster
Is a ClusterAlgorithm and an adapt for mcl algorithm of MarkovClustering class.
ClusterAlgorithmMCL() - Constructor for class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithmMCL
 
ClusterCache - Class in de.uni_leipzig.bf.cluster
ClusterCache implements a very simple caching strategy.
ClusterCache() - Constructor for class de.uni_leipzig.bf.cluster.ClusterCache
ClusterCache enabled.
ClusterCache(boolean) - Constructor for class de.uni_leipzig.bf.cluster.ClusterCache
 
ClusterContext - Class in de.uni_leipzig.cvk.data.cluster
This class represents the clients context interface and holds a concrete ClusterAlgorithm instance, clients can select, add and use an available cluster algorithm instance.
ClusterContext() - Constructor for class de.uni_leipzig.cvk.data.cluster.ClusterContext
Initializes the all available algorithms and sets the LogPanelHandler Handler to the Logger.
ClusterGraph - Class in de.uni_leipzig.bf.cluster
 
ClusterGraph() - Constructor for class de.uni_leipzig.bf.cluster.ClusterGraph
 
clustering(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
An abstract method for a concrete clustering algorithm implementation or adaption.
clustering(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithmBorderFlow
implemented abstract method
clustering(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithmKNN
implemented abstract method
clustering(String[], double, String, String, String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithmMCL
 
ClusterPanel - Class in de.uni_leipzig.cvk.gui
It's an Observer JPanel for settings and configurations of a ClusterAlgorithm.
ClusterPanel() - Constructor for class de.uni_leipzig.cvk.gui.ClusterPanel
Default constructor.
ClusterPanel.AddButtonActionListener - Class in de.uni_leipzig.cvk.gui
ActionListener implementation for a JButton to add a node to a inner TableModel instance.
ClusterPanel.AddButtonActionListener(JPanel, TableModel) - Constructor for class de.uni_leipzig.cvk.gui.ClusterPanel.AddButtonActionListener
 
ClusterPanel.AlgoActionListener - Class in de.uni_leipzig.cvk.gui
ActionListener implementation for a JComboBox to choose an algorithm.
ClusterPanel.AlgoActionListener(Observable) - Constructor for class de.uni_leipzig.cvk.gui.ClusterPanel.AlgoActionListener
 
ClusterPanel.ClusterActionListener - Class in de.uni_leipzig.cvk.gui
ActionListener implementation for a JButton to start clustering.
ClusterPanel.ClusterActionListener(Observable, JPanel) - Constructor for class de.uni_leipzig.cvk.gui.ClusterPanel.ClusterActionListener
 
ClusterPanel.SeedTableModel - Class in de.uni_leipzig.cvk.gui
 
ClusterPanel.SeedTableModel() - Constructor for class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
ClusterTableSettings - Interface in de.uni_leipzig.cvk.data.cluster
Settings for column labels and column types of a Table which holds the cluster data.
clusterToDatabase(double) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Clusters to the database found under connection
clusterToFile(String, double, boolean, boolean, boolean) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Starts Borderflow with the given configuration to write in file.
clusterVisualizationKitDemo() - Static method in class de.uni_leipzig.cvk.gui.Main
A demo of BorderFlow GUI version.
compareSet(Set<Integer>, Set<Integer>) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
 
compareSet(Set<Integer>, Set<Integer>) - Method in class de.uni_leipzig.bf.cluster.harden.Harden
Method for a concrete harden implementation.
compareTo(Object) - Method in class de.uni_leipzig.bf.util.WeightedKeyword
 
complex2protMap - Variable in class de.uni_leipzig.bf.eval.DataReader
 
complexIds - Variable in class de.uni_leipzig.bf.eval.DataReader
 
complexList - Variable in class de.uni_leipzig.bf.eval.DataReader
 
complexWiseSensitivity(HashMap<String, TreeSet<String>>, ArrayList<TreeSet<String>>) - Static method in class de.uni_leipzig.bf.eval.DataReader
Computes complex-wise sensitivity of a clustering
computeAccuracy() - Method in class de.uni_leipzig.bf.eval.DataReader
Accuracy is the geometric mean of PPV and sensitivity
computeComplexwiseSperation() - Method in class de.uni_leipzig.bf.eval.DataReader
 
computePPV() - Method in class de.uni_leipzig.bf.eval.DataReader
Compute PPV of a clustering
computePPVDebug() - Method in class de.uni_leipzig.bf.eval.DataReader
Compute PPV (and print debug informations) of a clustering
computePurity(String, String, String, int) - Static method in class de.uni_leipzig.bf.eval.Evaluator
 
computeSensitivity() - Method in class de.uni_leipzig.bf.eval.DataReader
Compute sensitivity of a clustering
computeSensitivityDebug() - Method in class de.uni_leipzig.bf.eval.DataReader
Compute sensitivity (and print debug informations) of a clustering
computeSeparationByColumn() - Method in class de.uni_leipzig.bf.eval.DataReader
Computes separation by column
computeSeparationMatrix() - Method in class de.uni_leipzig.bf.eval.DataReader
Computes separation by row
computeSeparations() - Method in class de.uni_leipzig.bf.eval.DataReader
 
con - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
config_A - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
An array of default available settings, override this array for a concrete configuration.
config_B - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
An array of default available settings, override this array for a concrete configuration.
config_C - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
An array of default available settings, override this array for a concrete configuration.
config_D - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
An array of default available settings, override this array for a concrete configuration.
containss(Comparable) - Method in class de.uni_leipzig.bf.util.AlphaList
 
contingencyMatrix - Variable in class de.uni_leipzig.bf.eval.DataReader
 
convert(Comparable) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
copy() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
copy the matrix and its elements
copy() - Method in class de.uni_leipzig.mcl.cluster.SparseVector
copy the contents of the sparse vector
countAndFilter() - Method in class de.uni_leipzig.bf.util.GraphFold
 

D

DATA - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
database - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
DataReader - Class in de.uni_leipzig.bf.eval
 
DataReader(double[][], HashMap<String, Integer>) - Constructor for class de.uni_leipzig.bf.eval.DataReader
Creates a new instance of DataReader
DataReader(String, String) - Constructor for class de.uni_leipzig.bf.eval.DataReader
 
DATE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
DBOps - Class in de.uni_leipzig.bf.util
 
DBOps() - Constructor for class de.uni_leipzig.bf.util.DBOps
Creates a new instance of DBOps
de.uni_leipzig.bf.cluster.harden - package de.uni_leipzig.bf.cluster.harden
Provides the classes which implement hardening versions for BorderFlow.
de.uni_leipzig.bf.eval - package de.uni_leipzig.bf.eval
Provides the classes which implement evaluation methods.
de.uni_leipzig.bf.util - package de.uni_leipzig.bf.util
Provides the classes which implement utility methods.
de.uni_leipzig.cvk.data - package de.uni_leipzig.cvk.data
Provides the classes which implement methods for input/output and methods to get access to all adapted algorithms e.g.BorderFlow.
de.uni_leipzig.cvk.data.cluster - package de.uni_leipzig.cvk.data.cluster
Provides the classes which implement a strategy for extended ClusterAlgorithm classes.
de.uni_leipzig.cvk.gui - package de.uni_leipzig.cvk.gui
Provides the classes which implement the Swing components for the Application.
de.uni_leipzig.cvk.visual - package de.uni_leipzig.cvk.visual
Provides the classes which implement the visualization with the top-level Visualization and Display classes of prefuse toolkit.
de.uni_leipzig.mcl.cluster - package de.uni_leipzig.mcl.cluster
Provides the classes which implement the Markov clustering algorithm.
DEFAULT - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
DEFAULT_HOPS - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
default filter values
DEFAULT_SEED_TEXT - Variable in class de.uni_leipzig.cvk.gui.ClusterPanel
default table text
deleteRows(int[]) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
deleteRows() - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
DIAMOND_TREE - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method
DIRECTED - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
Distribution - Class in de.uni_leipzig.bf.util
 
Distribution() - Constructor for class de.uni_leipzig.bf.util.Distribution
Creates a new instance of Distribution
DOUBLE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
down - Variable in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
downloadClusters(Connection, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
Downloads the clusters from the database
downloadClustersErroneous(Connection, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
Downloads the clusters from the database
dragged - Variable in class de.uni_leipzig.cvk.visual.AggregateDragControl
 

E

EDGE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
EDGE_WEIGHT - Static variable in interface de.uni_leipzig.cvk.data.GraphReaderSettings
Inner id for edge weights
EDGEDEF - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
EdgeListGraphReader - Class in de.uni_leipzig.cvk.data
Reads a given edge list to a Graph instance.
EdgeListGraphReader(String) - Constructor for class de.uni_leipzig.cvk.data.EdgeListGraphReader
 
EDGES - Static variable in class de.uni_leipzig.cvk.visual.AggregatePanel
prefuse default id
elements - Variable in class de.uni_leipzig.bf.cluster.Cluster
 
endDocument() - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
endElement(String, String, String) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
erdosRenyi(int, double, long) - Static method in class de.uni_leipzig.cvk.data.GraphGenerator
Generates a graph with the Erdos-Renyi binomial model.
ERDOSRENYI - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method
error(String) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
error(Exception) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
Eval - Class in de.uni_leipzig.cvk.data.cluster
Only undirected supported.
Eval() - Constructor for class de.uni_leipzig.cvk.data.cluster.Eval
 
Evaluator - Class in de.uni_leipzig.bf.eval
 
Evaluator() - Constructor for class de.uni_leipzig.bf.eval.Evaluator
Creates a new instance of Evaluator
expand(SparseMatrix) - Method in class de.uni_leipzig.mcl.cluster.MarkovClustering
expand stochastic quadratic matrix by sqaring it with itself: result = m * m.
expSum(int) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
exponential sum, i.e., sum (elements^p)
extractHardClusters(ArrayList<TreeSet<Integer>>) - Method in class de.uni_leipzig.bf.cluster.harden.HardenMaxQuality
Gets an ArrayList of TreeSet with different Integers in every TreeSet.

F

factor(double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable factorisation
filename - Variable in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
path to file
filterSimFile(String, double, String) - Static method in class de.uni_leipzig.bf.eval.FilterSimilarityFile
Filters similarity files and allows only values above a given threshold
FilterSimilarityFile - Class in de.uni_leipzig.bf.eval
 
FilterSimilarityFile() - Constructor for class de.uni_leipzig.bf.eval.FilterSimilarityFile
Creates a new instance of FilterSimilarityFile
FitOverviewListener - Class in de.uni_leipzig.cvk.visual
 
FitOverviewListener() - Constructor for class de.uni_leipzig.cvk.visual.FitOverviewListener
 
FLOAT - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
flow(Graph, TreeSet<String>) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
gets the total weight of edges with nodes in cluster and neighbors aren't in cluster
flush() - Method in class de.uni_leipzig.cvk.gui.LogPanelHandler
 
foldGraph(String, String, int) - Method in class de.uni_leipzig.bf.util.GraphFold
 
FOR - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 

G

get(int, int) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
get number at index or 0.
get(Object) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
get ensures it returns 0 for empty hash values or if index exceeds length.
getA() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
gets available configuration
getA() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Available settings of current cluster algorithm.
getAbsoluteFlow(Cluster, Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Computes the inverse relative flow to make sure that no division by zero is carried out
getAlgorithmNames() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Gets all available algorithm names.
getB() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
gets available configuration
getB() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Available settings of current cluster algorithm.
getC() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
gets available configuration
getC() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Available settings of current cluster algorithm.
getClickedTableNode() - Method in class de.uni_leipzig.cvk.data.Model
 
getCluster() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
gets all cluster in a List of TreeSet
getClusterContext() - Method in class de.uni_leipzig.cvk.data.Model
 
getClusterTable() - Method in class de.uni_leipzig.cvk.data.Model
 
getColor() - Method in class de.uni_leipzig.cvk.data.Model
 
getColorImg() - Method in class de.uni_leipzig.cvk.data.Model
 
getColum(int) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
get a column of the sparse matrix (expensive).
getColumnClass(int) - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableModel
 
getColumnCount() - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
getColumnCount() - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableModel
 
getColumnName(int) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
getColumnName(int) - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableModel
 
getConnection() - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Get connection to database
getConnection(String, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
 
getCopy() - Method in class de.uni_leipzig.bf.cluster.Cluster
Generate a copy of this clusters
getCpuTime() - Static method in class de.uni_leipzig.bf.eval.Timer
Get CPU time in nanoseconds.
getCurrentAlgorithmName() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
 
getD() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
gets available configuration
getD() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Available settings of current cluster algorithm.
getDense() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
create dense representation
getDense() - Method in class de.uni_leipzig.mcl.cluster.SparseVector
get dense represenation
getDirection() - Method in class de.uni_leipzig.cvk.data.Model
 
getDisplay() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Gets the Display to export an image in File.
getDistanceFilter() - Method in class de.uni_leipzig.cvk.data.Model
 
getDistanceFilterImg() - Method in class de.uni_leipzig.cvk.data.Model
 
getEdgeListToTable() - Method in class de.uni_leipzig.cvk.data.Model
reads a delimited file to table
getEdgeWeight(Integer, Integer) - Method in class de.uni_leipzig.bf.cluster.ClusterGraph
 
getElements() - Method in class de.uni_leipzig.bf.cluster.Cluster
 
getFlowFromNodeToSet(TreeSet<Integer>, Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Compute flow from node to set of nodes
getFlowFromNodeToSet(TreeSet<Integer>, Integer) - Method in class de.uni_leipzig.bf.cluster.harden.Harden
Method for a concrete harden implementation.
getForceTab() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Builds a JPanel with elements for force settings, an overview and a distance filter.
getGraph() - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
getGraph() - Method in class de.uni_leipzig.cvk.data.Model
 
getIconHeight() - Method in class de.uni_leipzig.cvk.gui.Application.MenuArrowIcon
 
getIconWidth() - Method in class de.uni_leipzig.cvk.gui.Application.MenuArrowIcon
 
getInverseRelativeFlow(Cluster, Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Computes the inverse relative flow to make sure that no division by zero is carried out
getJContentPane() - Method in class de.uni_leipzig.cvk.gui.Application
This method initializes jContentPane
getKey(int) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
getKeyOne(int) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
getKeyTwo(int) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
getKeyword() - Method in class de.uni_leipzig.bf.util.WeightedKeyword
Get the actual value of keyword
getLength() - Method in class de.uni_leipzig.mcl.cluster.SparseVector
get the length of the vector
getLogPanel() - Static method in class de.uni_leipzig.cvk.gui.LogPanelHandler
Gets one instance of LogPanel
getMatrix() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
 
getMostFrequent(String, double) - Static method in class de.uni_leipzig.bf.util.DBOps
 
getMySQLConnection(String, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
Get connection to database
getNeighbours(int) - Method in class de.uni_leipzig.bf.cluster.ClusterGraph
 
getNumberOfNeighbours(Integer) - Method in class de.uni_leipzig.bf.cluster.ClusterGraph
 
getOpenChooser() - Method in class de.uni_leipzig.cvk.gui.Application
 
getPause() - Method in class de.uni_leipzig.cvk.data.Model
 
getPauseImg() - Method in class de.uni_leipzig.cvk.data.Model
 
getPurity(HashMap<String, TreeSet<String>>, TreeSet<String>) - Static method in class de.uni_leipzig.bf.eval.Evaluator
Evaluates one cluster against a given map
getQuality(TreeSet<Integer>, TreeSet<Integer>, ClusterGraph) - Method in class de.uni_leipzig.bf.cluster.harden.QualityMeasure
Implement this abstract method for your concrete QualityMeasure class.
getQuality(Set<TreeSet<Integer>>, TreeSet<Integer>, ClusterGraph) - Method in class de.uni_leipzig.bf.cluster.harden.QualityMeasure
Gets the quality for a Set with the overloaded method QualityMeasure.getQuality(TreeSet, TreeSet, ClusterGraph), and ignores null and empty TreeSets in clusters.
getQuality(TreeSet<Integer>, TreeSet<Integer>, ClusterGraph) - Method in class de.uni_leipzig.bf.cluster.harden.QualityMeasureRelativeFlow
Same as in Cluster.getRelativeFlow(), but ignore Integers of blackList.
getQuality(TreeSet<Integer>, TreeSet<Integer>, ClusterGraph) - Method in class de.uni_leipzig.bf.cluster.harden.QualityMeasureSilhouette
Same as in Cluster.getSilhouette()
getQuality() - Method in class de.uni_leipzig.cvk.data.Model
 
getQualityImg() - Method in class de.uni_leipzig.cvk.data.Model
 
getRelativeFlow() - Method in class de.uni_leipzig.bf.cluster.Cluster
 
getRelativeFlow(Graph, Table) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
 
getRelativeFlow(Graph, TreeSet<String>) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
 
getRelativerFlow(TreeSet<Integer>) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
 
getRowCount() - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
getRowCount() - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableModel
 
getSaveChooser() - Method in class de.uni_leipzig.cvk.gui.Application
 
getSeedJLabel() - Method in class de.uni_leipzig.cvk.gui.ClusterPanel
Gets the JLabel for clicked nodes.
getSeparator() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
gets the separator of ClusterAlgorithm.filename depends on the file extension
getSilhouette() - Method in class de.uni_leipzig.bf.cluster.Cluster
Computes the silhouette value of the clusters at hand
getSilhouetteAndRelativeFlow(TreeSet<Integer>) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Computes the silhouette for a set of nodes
getSilhouetteFull() - Method in class de.uni_leipzig.bf.cluster.Cluster
Computes the silhouette value of the clusters at hand
getSize() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
get the size of the matrix
getState() - Method in class de.uni_leipzig.bf.cluster.Cluster
Get current state of cluster
getSystemTime() - Static method in class de.uni_leipzig.bf.eval.Timer
Get system time in nanoseconds.
getTable() - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
gets a valid Table, that means with a column of ClusterTableSettings.CLUSTER_COLUMN_NAME and a type of ClusterTableSettings.CLUSTER_COLUMN_NAME_TYPE for the cluster data
getUserTime() - Static method in class de.uni_leipzig.bf.eval.Timer
Get user time in nanoseconds.
getValue(int) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
getValueAt(int, int) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel.SeedTableModel
 
getValueAt(int, int) - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableModel
 
getWeight() - Method in class de.uni_leipzig.bf.util.WeightedKeyword
Get the actual value of the weight
graph - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
graph - Variable in class de.uni_leipzig.bf.cluster.Cluster
 
GRAPH - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
GRAPH - Static variable in class de.uni_leipzig.cvk.visual.AggregatePanel
prefuse default id
GraphFold - Class in de.uni_leipzig.bf.util
 
GraphFold() - Constructor for class de.uni_leipzig.bf.util.GraphFold
Creates a new instance of GraphFold
GraphGenerator - Class in de.uni_leipzig.cvk.data
Generates graphs.
GraphGenerator() - Constructor for class de.uni_leipzig.cvk.data.GraphGenerator
 
GraphMLReaderMod - Class in de.uni_leipzig.cvk.data
GraphReader instance that reads in graph file formatted using the GraphML file format.
GraphMLReaderMod() - Constructor for class de.uni_leipzig.cvk.data.GraphMLReaderMod
 
GraphMLReaderMod.GraphMLHandler - Class in de.uni_leipzig.cvk.data
A SAX Parser for GraphML data files.
GraphMLReaderMod.GraphMLHandler() - Constructor for class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
GraphMLReaderMod.Tokens - Interface in de.uni_leipzig.cvk.data
String tokens used in the GraphML format.
GraphReaderSettings - Interface in de.uni_leipzig.cvk.data
Settings for all GraphReaders.
GraphStatisticPanel - Class in de.uni_leipzig.cvk.gui
It's an Observer JPanel to show graph statistics.
GraphStatisticPanel() - Constructor for class de.uni_leipzig.cvk.gui.GraphStatisticPanel
This is the default constructor
GraphStatisticPanel.MeasureButtonAction - Class in de.uni_leipzig.cvk.gui
ActionListener to perform measureButton actions.
GraphStatisticPanel.MeasureButtonAction(Observable) - Constructor for class de.uni_leipzig.cvk.gui.GraphStatisticPanel.MeasureButtonAction
 
GraphStatisticPanel.TableModel - Class in de.uni_leipzig.cvk.gui
A new TableModel to hold the data.
GraphStatisticPanel.TableModel(Table) - Constructor for class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableModel
 
GraphStatisticPanel.TableMouseListener - Class in de.uni_leipzig.cvk.gui
MouseListener for nodeTable
GraphStatisticPanel.TableMouseListener(Model) - Constructor for class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableMouseListener
 
green - Variable in class de.uni_leipzig.cvk.visual.NodeColorAction
 
GRID_GRAPH - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method

H

hadamardPower(double) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
mutable m2 = m .^ s
hadamardPower(double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable Hadamard power
hadamardProduct(SparseMatrix) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
mutable Hadamard product
hadamardProduct(SparseVector) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable Hadamard product (elementwise multiplication)
harden - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
harden(HashMap<TreeSet<Integer>, TreeSet<Integer>>) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Harden method used a Harden instance.
Harden - Class in de.uni_leipzig.bf.cluster.harden
Is an abstract base class for a concrete Harden implementation.
Harden() - Constructor for class de.uni_leipzig.bf.cluster.harden.Harden
Empty constructor.
Harden(QualityMeasure) - Constructor for class de.uni_leipzig.bf.cluster.harden.Harden
Initializes m_qualityMeasure and calls setDefaultQualityMeasure method.
harden(HashMap<TreeSet<Integer>, TreeSet<Integer>>, ClusterGraph) - Method in class de.uni_leipzig.bf.cluster.harden.Harden
Method for hardening.
harden(HashMap<TreeSet<Integer>, TreeSet<Integer>>) - Method in class de.uni_leipzig.bf.cluster.harden.Harden
Implement this abstract method for your concrete Harden class.
harden(HashMap<TreeSet<Integer>, TreeSet<Integer>>) - Method in class de.uni_leipzig.bf.cluster.harden.HardenMaxQuality
 
harden(HashMap<TreeSet<Integer>, TreeSet<Integer>>) - Method in class de.uni_leipzig.bf.cluster.harden.HardenSuperset
 
HardenMaxQuality - Class in de.uni_leipzig.bf.cluster.harden
Is a Harden class and uses a QualityMeasure instance to find the best clusters.
HardenMaxQuality() - Constructor for class de.uni_leipzig.bf.cluster.harden.HardenMaxQuality
 
HardenMaxQuality(QualityMeasure) - Constructor for class de.uni_leipzig.bf.cluster.harden.HardenMaxQuality
 
HardenSuperset - Class in de.uni_leipzig.bf.cluster.harden
Is a Harden class.
HardenSuperset() - Constructor for class de.uni_leipzig.bf.cluster.harden.HardenSuperset
 
HEIGHT - Static variable in class de.uni_leipzig.cvk.gui.Application
 
heuristicGetCluster(Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Compute cluster for a given seed using heuristic version of BorderFlow.
heuristicGetClusterTestOne(Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Compute cluster for a given seed using heuristic and test one version of BorderFlow.
HONEYCOMB - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method

I

ID - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
idxOf(Comparable) - Method in class de.uni_leipzig.bf.util.AlphaList
Implements a binary search to find objects in the list.
idxOf(Comparable) - Method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
IMG_FOLDER - Variable in class de.uni_leipzig.cvk.data.Model
resource path
IMG_INFO - Variable in class de.uni_leipzig.cvk.data.Model
resource path
IMG_QUALITY_OFF - Variable in class de.uni_leipzig.cvk.data.Model
resource path
IMG_QUALITY_ON - Variable in class de.uni_leipzig.cvk.data.Model
resource path
importBioResults(Connection, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
Import biology results
importIDs(Connection, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
Reads in an n-gram file and writes it in the specified database
importNGram(Connection, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
 
importNGramV2(Connection, String, String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
Works only for folded graphs
index - Variable in class de.uni_leipzig.bf.cluster.ClusterGraph
 
indexes - Variable in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
 
inflate(SparseMatrix, double, double) - Method in class de.uni_leipzig.mcl.cluster.MarkovClustering
inflate stochastic matrix by Hadamard (elementwise) exponentiation, pruning and normalisation :
init() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
This is a template method and used by constructors to initializes some data.
INIT_ID - Variable in class de.uni_leipzig.cvk.gui.ClusterPanel
 
INIT_ID - Variable in class de.uni_leipzig.cvk.gui.GraphStatisticPanel
 
INIT_ID - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
 
initClusterIds(String) - Method in class de.uni_leipzig.bf.eval.DataReader
Read results of BorderFlow and write them in cluster2protMap
initComplexIds(String) - Method in class de.uni_leipzig.bf.eval.DataReader
 
initialize(String, String) - Method in class de.uni_leipzig.bf.cluster.ClusterGraph
We ignore edges with the same node as source and target.
innerBorder - Variable in class de.uni_leipzig.bf.cluster.Cluster
 
insert(int, Comparable) - Method in class de.uni_leipzig.bf.util.AlphaList
Insert an element at a given position
instance() - Static method in class de.uni_leipzig.cvk.gui.LogPanelHandler
Gets the instance of LogPanelHandler
INT - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
INTEGER - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
intersection(TreeSet<String>, TreeSet<String>) - Static method in class de.uni_leipzig.bf.eval.DataReader
Computes the intersection of two TreeSet
ip - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
isHarden(Table) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
gets true if a disjoint sets of clusters is given in clusterTable
itemBoundsChanged(Display) - Method in class de.uni_leipzig.cvk.visual.FitOverviewListener
 
itemDragged(VisualItem, MouseEvent) - Method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
itemEntered(VisualItem, MouseEvent) - Method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
itemExited(VisualItem, MouseEvent) - Method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
itemPressed(VisualItem, MouseEvent) - Method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
itemReleased(VisualItem, MouseEvent) - Method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 

K

KEY - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
keyPressed(KeyEvent) - Method in class de.uni_leipzig.cvk.gui.Application
keyPressed(KeyEvent e) to actionPerformed(ActionEvent e)
keyReleased(KeyEvent) - Method in class de.uni_leipzig.cvk.gui.Application
Empty
keyTyped(KeyEvent) - Method in class de.uni_leipzig.cvk.gui.Application
Empty
knnCluster(Integer, int) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Compute cluster for a given seed.
knnToFile(String, double, int) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Starts knn with the given configuration to write in file.
knnToString(String[], int) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Starts knn with the given configuration to write in String.
knnToString(double, int) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Starts knn with the given configuration to write in String.

L

LabelLayout - Class in de.uni_leipzig.cvk.visual
Set label positions.
LabelLayout(String) - Constructor for class de.uni_leipzig.cvk.visual.LabelLayout
 
loadMatrix(String, String) - Static method in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
reads in a file.
LOGO - Static variable in class de.uni_leipzig.cvk.gui.Application
 
LogPanel - Class in de.uni_leipzig.cvk.gui
It's an Observer JPanel to show logs to the application with LogPanel.showLog(String) method.
LogPanel() - Constructor for class de.uni_leipzig.cvk.gui.LogPanel
This is the default constructor
LogPanelHandler - Class in de.uni_leipzig.cvk.gui
The singleton LogPanelHandler class is a Handler to log to a LogPanel member instance.
LONG - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 

M

m_aggregateLayout - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
Layout for aggregates
m_cache - Variable in class de.uni_leipzig.bf.cluster.ClusterCache
 
m_cacheHistory - Variable in class de.uni_leipzig.bf.cluster.ClusterCache
 
m_clusterContext - Variable in class de.uni_leipzig.cvk.data.Model
access to all algorithm
m_clusterGraph - Variable in class de.uni_leipzig.bf.cluster.harden.Harden
 
m_clusterTable - Variable in class de.uni_leipzig.cvk.data.Model
table to hold cluster data
m_dflt - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_display - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
Display instance
m_edges - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_enabled - Variable in class de.uni_leipzig.bf.cluster.ClusterCache
 
m_esch - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_for - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_graph - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_graph - Variable in class de.uni_leipzig.cvk.data.Model
current graph data
m_graphid - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_group - Variable in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
m_id - Variable in class de.uni_leipzig.bf.cluster.ClusterCache
 
m_id - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_idMap - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_log - Variable in class de.uni_leipzig.bf.cluster.ClusterCache
 
m_m - Variable in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableMouseListener
 
m_name - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_nodeBlackList - Variable in class de.uni_leipzig.bf.cluster.harden.HardenMaxQuality
all used nodes
m_nodeMap - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_nodes - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_nsch - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_o - Variable in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.MeasureButtonAction
 
m_pf - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_qualityMeasure - Variable in class de.uni_leipzig.bf.cluster.harden.Harden
 
m_sbuf - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_type - Variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
m_vis - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
Visualization instance
main(String[]) - Static method in class de.uni_leipzig.bf.cluster.Cluster
 
main(String[]) - Static method in class de.uni_leipzig.bf.cluster.ClusterGraph
 
Main - Class in de.uni_leipzig.bf.cluster
 
Main() - Constructor for class de.uni_leipzig.bf.cluster.Main
 
main(String[]) - Static method in class de.uni_leipzig.bf.cluster.Main
Entry point.
main(String[]) - Static method in class de.uni_leipzig.bf.eval.DataReader
 
main(String[]) - Static method in class de.uni_leipzig.bf.eval.Evaluator
 
main(String[]) - Static method in class de.uni_leipzig.bf.eval.FilterSimilarityFile
 
main(String[]) - Static method in class de.uni_leipzig.bf.eval.MeshEval
 
main(String[]) - Static method in class de.uni_leipzig.bf.eval.Timer
 
main(String[]) - Static method in class de.uni_leipzig.bf.util.DBOps
 
main(String[]) - Static method in class de.uni_leipzig.bf.util.Distribution
 
main(String[]) - Static method in class de.uni_leipzig.bf.util.GraphFold
 
main(String[]) - Static method in class de.uni_leipzig.bf.util.QuickSort
 
main(String[]) - Static method in class de.uni_leipzig.bf.util.SilhouetteCleaner
 
main(String[]) - Static method in class de.uni_leipzig.bf.util.ValuedAlphaList
 
Main - Class in de.uni_leipzig.cvk.gui
 
Main() - Constructor for class de.uni_leipzig.cvk.gui.Main
 
main(String[]) - Static method in class de.uni_leipzig.cvk.gui.Main
Entry point.
main(String[]) - Static method in class de.uni_leipzig.mcl.cluster.MarkovClustering
 
Main.HardenStrategy - Enum in de.uni_leipzig.bf.cluster
 
Main.MeasureStrategy - Enum in de.uni_leipzig.bf.cluster
 
MarkovClustering - Class in de.uni_leipzig.mcl.cluster
MarkovClustering implements the Markov clustering (MCL) algorithm for graphs, using a HashMap-based sparse representation of a Markov matrix, i.e., an adjacency matrix m that is normalised to one.
MarkovClustering() - Constructor for class de.uni_leipzig.mcl.cluster.MarkovClustering
 
matrix - Variable in class de.uni_leipzig.bf.cluster.ClusterGraph
 
matrixTimes(SparseMatrix) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
immutable multiply matrix M with this (A) : M * A
max() - Method in class de.uni_leipzig.mcl.cluster.SparseVector
maximum element value
MAX_EDGE_WEIGHT - Static variable in interface de.uni_leipzig.cvk.data.GraphReaderSettings
The max.
MAX_HOPS - Variable in class de.uni_leipzig.cvk.visual.AggregatePanel
default filter values
mergeAddMap(Map<TreeSet<Integer>, TreeSet<Integer>>, TreeSet<Integer>, TreeSet<Integer>) - Method in class de.uni_leipzig.bf.cluster.harden.Harden
Method for a concrete harden implementation.
mergeAndWrite(String) - Method in class de.uni_leipzig.bf.util.GraphFold
 
MeshEval - Class in de.uni_leipzig.bf.eval
 
MeshEval() - Constructor for class de.uni_leipzig.bf.eval.MeshEval
Creates a new instance of MeshEval
Model - Class in de.uni_leipzig.cvk.data
This class represents an Observable Model to hold, load and save data with an instances of EdgeListGraphReader and GraphMLReaderMod class, to give access to all supported algorithm with an instance of ClusterContext class and to notify all registered views by arguments.
Model() - Constructor for class de.uni_leipzig.cvk.data.Model
Constructs a new Model instance.
mouseClicked(MouseEvent) - Method in class de.uni_leipzig.cvk.gui.Application
Sets focus to clicked Component
mouseClicked(MouseEvent) - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel.TableMouseListener
 
move(VisualItem, double, double) - Static method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
mult(int, double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable mult

N

NAME - Static variable in class de.uni_leipzig.cvk.gui.Application
 
ncut(Graph, Table) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
 
NODE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
NODE_NAME - Static variable in interface de.uni_leipzig.cvk.data.GraphReaderSettings
Inner id for nodes, should different form any id field in xml file
NODE_TABLE_EVENT - Static variable in class de.uni_leipzig.cvk.data.Model
argument for view
NodeColorAction - Class in de.uni_leipzig.cvk.visual
A new ColorAction for all nodes.
NodeColorAction(String) - Constructor for class de.uni_leipzig.cvk.visual.NodeColorAction
 
NODES - Static variable in class de.uni_leipzig.cvk.visual.AggregatePanel
prefuse default id
normalise(double) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
normalise rows to rowsum
normalise() - Method in class de.uni_leipzig.mcl.cluster.SparseVector
normalises the vector to 1.
normalise(double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
normalises the vector to newsum
normaliseCols() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
normalise by minor dimension (columns), expensive.
normaliseRows() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
normalise by major dimension (rows)
notifyGui(String) - Method in class de.uni_leipzig.cvk.data.Model
 

O

OPENFILE - Static variable in class de.uni_leipzig.cvk.data.Model
argument for view
openFile(File) - Method in class de.uni_leipzig.cvk.data.Model
Reads a graph to m_graph with EdgeListGraphReader or GraphMLReaderMod class depends on the extension of given file.
openGraph(String) - Method in class de.uni_leipzig.cvk.data.Model
Reads or generates a graph to m_graph with GraphLib or GraphGenerator class depends on argument name.
optimalGetCluster(Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Compute cluster for a given seed using optimal version of BorderFlow.
optimalGetClusterTestOne(Integer) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Compute cluster for a given seed using optimal and test one version of BorderFlow.
orange - Variable in class de.uni_leipzig.cvk.visual.NodeColorAction
 
outerBorder - Variable in class de.uni_leipzig.bf.cluster.Cluster
 

P

paintComponent(Graphics) - Method in class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
paintIcon(Component, Graphics, int, int) - Method in class de.uni_leipzig.cvk.gui.Application.MenuArrowIcon
 
parse(String, Class) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
parseType(String) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
password - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 
PAUSE - Static variable in class de.uni_leipzig.cvk.data.Model
argument for view
pop - Variable in class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
prune(double) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
prune all values whose magnitude is below threshold
prune(double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
remove all elements whose magnitude is < threshold
publish(LogRecord) - Method in class de.uni_leipzig.cvk.gui.LogPanelHandler
 
put(Integer, Double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
put increases the matrix size if the index exceeds the current size.

Q

qsort(ArrayList, int, int) - Static method in class de.uni_leipzig.bf.util.QuickSort
eigentlicher Quicksort-Algorithmus.
QUALITY - Static variable in class de.uni_leipzig.cvk.data.Model
argument for view
qualityMeasure() - Method in class de.uni_leipzig.bf.cluster.harden.Harden
 
QualityMeasure - Class in de.uni_leipzig.bf.cluster.harden
Is an abstract base class for a concrete QualityMeasure implementation.
QualityMeasure() - Constructor for class de.uni_leipzig.bf.cluster.harden.QualityMeasure
 
QualityMeasureRelativeFlow - Class in de.uni_leipzig.bf.cluster.harden
Is a QualityMeasure class.
QualityMeasureRelativeFlow() - Constructor for class de.uni_leipzig.bf.cluster.harden.QualityMeasureRelativeFlow
 
QualityMeasureSilhouette - Class in de.uni_leipzig.bf.cluster.harden
Is a QualityMeasure class.
QualityMeasureSilhouette() - Constructor for class de.uni_leipzig.bf.cluster.harden.QualityMeasureSilhouette
 
QuickSort - Class in de.uni_leipzig.bf.util
 
QuickSort() - Constructor for class de.uni_leipzig.bf.util.QuickSort
 
quickSort(ArrayList) - Static method in class de.uni_leipzig.bf.util.QuickSort
Sorts a list of WeightedKeywords

R

readComplexes(String) - Static method in class de.uni_leipzig.bf.eval.DataReader
 
readGraph(File, boolean) - Method in class de.uni_leipzig.cvk.data.EdgeListGraphReader
Reads an edge list to a Graph instance.
readGraph(String, boolean) - Method in class de.uni_leipzig.cvk.data.EdgeListGraphReader
Reads an edge list to a Graph instance.
readGraph(InputStream) - Method in class de.uni_leipzig.cvk.data.EdgeListGraphReader
 
readGraph(InputStream) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod
 
readMesh(String, int) - Static method in class de.uni_leipzig.bf.eval.MeshEval
Read in the mesh mapping
REAL - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
red - Variable in class de.uni_leipzig.cvk.visual.NodeColorAction
 
reverseIndex - Variable in class de.uni_leipzig.bf.cluster.ClusterGraph
 
run(double) - Method in class de.uni_leipzig.cvk.visual.AggregateLayout
Computes convex hull if aggregates are visible.
run(double) - Method in class de.uni_leipzig.cvk.visual.LabelLayout
 
run(SparseMatrix, double, double, double, double) - Method in class de.uni_leipzig.mcl.cluster.MarkovClustering
run the MCL process.
runs - Variable in class de.uni_leipzig.cvk.visual.AggregateLayout
Flag that indicates the state of AggregateLayout.run(double) member method.
runtest() - Static method in class de.uni_leipzig.bf.eval.DataReader
 

S

saveFile(File) - Method in class de.uni_leipzig.cvk.data.Model
clusters to file
schemaCheck() - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
seed - Variable in class de.uni_leipzig.bf.cluster.Cluster
 
separationMatrix - Variable in class de.uni_leipzig.bf.eval.DataReader
 
set(int, SparseVector) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
set the sparse vector at index i.
set(int, int, double) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
set the value at the index i,j, returning the old value or 0.
SET_ALGO - Static variable in class de.uni_leipzig.cvk.data.Model
argument for view
setActions() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Initializes colors, force, ...
setAlgorithm(String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
select an available algorithm by the given unique name, to get access of the concrete configurations.
setAlgorithm(String, String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterContext
Select an available algorithm by the given unique name.
setClickedTableNode(String) - Method in class de.uni_leipzig.cvk.data.Model
sets the chosen node from table
setDatabaseVariables(String, String, String, String) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Set database variables.
setDecorators() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Refreshes AggregatePanel.AGGR_DECORATORS for every new AggregatePanel.AGGRS
setFilename(String) - Method in class de.uni_leipzig.cvk.data.cluster.ClusterAlgorithm
sets ClusterAlgorithm.filename, the path to file
setFixed(VisualItem, boolean) - Static method in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
setJSliderVisible(boolean) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel
 
setLength(int) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
set the new length of the vector (regardless of the maximum index).
setListeners() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Adds ControlAdapter instances to AggregatePanel.m_display
setMatrix(SparseMatrix) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
 
setPopupMenu(JPopupMenu) - Method in class de.uni_leipzig.cvk.gui.Application.MenuToggleButton
 
setRendererFactory() - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
Sets renderers for AggregatePanel.NODES,AggregatePanel.EDGES, AggregatePanel.AGGRS and AggregatePanel.AGGR_DECORATORS group.
setSeedLabel(JLabel) - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
This method is used to set a JLabel instance for clicked nodes.
setSignum(int, double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
mutable mult
setSignum(double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
Change signum
setWeight(double) - Method in class de.uni_leipzig.bf.util.WeightedKeyword
Sets the weight of the keyword.
showLog(String) - Method in class de.uni_leipzig.cvk.gui.LogPanel
Adds a String to the JTextArea instance to show the log.
SilhouetteCleaner - Class in de.uni_leipzig.bf.util
 
SilhouetteCleaner() - Constructor for class de.uni_leipzig.bf.util.SilhouetteCleaner
Creates a new instance of SilhouetteCleaner
silhouetteMean(Graph, Table) - Static method in class de.uni_leipzig.cvk.data.cluster.Eval
computes average of average silhouette for all clusters
size - Variable in class de.uni_leipzig.bf.cluster.ClusterGraph
 
smallBig - Variable in class de.uni_leipzig.bf.util.GraphFold
 
SOURCE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
SparseMatrix - Class in de.uni_leipzig.mcl.cluster
SparseMatrix is a sparse matrix with row-major format.
SparseMatrix() - Constructor for class de.uni_leipzig.mcl.cluster.SparseMatrix
empty sparse matrix
SparseMatrix(int, int) - Constructor for class de.uni_leipzig.mcl.cluster.SparseMatrix
empty sparse matrix with allocated number of rows
SparseMatrix(double[][]) - Constructor for class de.uni_leipzig.mcl.cluster.SparseMatrix
create sparse matrix from full matrix
SparseMatrix(SparseMatrix) - Constructor for class de.uni_leipzig.mcl.cluster.SparseMatrix
copy contructor
SparseMatrixLabeled - Class in de.uni_leipzig.mcl.cluster
 
SparseMatrixLabeled() - Constructor for class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
Creates a new instance of SparseMatrixLabeled
SparseVector - Class in de.uni_leipzig.mcl.cluster
SparseVector represents a sparse vector.
SparseVector() - Constructor for class de.uni_leipzig.mcl.cluster.SparseVector
create empty vector
SparseVector(int) - Constructor for class de.uni_leipzig.mcl.cluster.SparseVector
create empty vector with length
SparseVector(double[]) - Constructor for class de.uni_leipzig.mcl.cluster.SparseVector
create vector from dense vector
SparseVector(SparseVector) - Constructor for class de.uni_leipzig.mcl.cluster.SparseVector
copy constructor
split(String, int) - Method in class de.uni_leipzig.bf.util.GraphFold
Splits a list contained in a file in 2 list and sorts it.
SRC - Static variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
SRCID - Static variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
startDocument() - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
startElement(String, String, String, Attributes) - Method in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
STRING - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
string2treeSet(String) - Method in class de.uni_leipzig.bf.eval.DataReader
Transforms strings of the form [X(, Y)*] to TreeSet
sum(double) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
power sum of the elements
symmetrify(String, String) - Static method in class de.uni_leipzig.bf.util.DBOps
 
symV2(String, String, int) - Static method in class de.uni_leipzig.bf.util.DBOps
 

T

TARGET - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
temp - Variable in class de.uni_leipzig.cvk.visual.AggregateDragControl
 
Timer - Class in de.uni_leipzig.bf.eval
 
Timer() - Constructor for class de.uni_leipzig.bf.eval.Timer
 
times(SparseVector) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
immutable multiply this times the vector: A * x, i.e., rowwise.
times(SparseMatrix) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
immutable multiply this matrix (A) with M : A * M
times(SparseVector) - Method in class de.uni_leipzig.mcl.cluster.SparseVector
immutable scalar product
timesTransposed(SparseMatrix) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
mutable multiply this matrix (A) with M : A * M'
topped() - Static method in class de.uni_leipzig.cvk.data.GraphGenerator
Generates a topped tetrahedron.
TOPPED - Static variable in class de.uni_leipzig.cvk.data.Model
argument for openGraph method
toString() - Method in class de.uni_leipzig.bf.cluster.Cluster
 
toString() - Method in class de.uni_leipzig.bf.cluster.ClusterGraph
 
toString() - Method in class de.uni_leipzig.bf.cluster.harden.Harden
gets this class name
toString() - Method in class de.uni_leipzig.bf.cluster.harden.QualityMeasure
Gets this class name.
toString() - Method in class de.uni_leipzig.bf.util.WeightedKeyword
Writes the keyword and the associated weight in a String
toString() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
 
toString() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
 
toString() - Method in class de.uni_leipzig.mcl.cluster.SparseVector
 
transpose() - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
immutable transpose.
TRG - Static variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
TRGID - Static variable in class de.uni_leipzig.cvk.data.GraphMLReaderMod.GraphMLHandler
 
TYPE - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 

U

UNDIRECTED - Static variable in interface de.uni_leipzig.cvk.data.GraphMLReaderMod.Tokens
 
update(Observable, Object) - Method in class de.uni_leipzig.cvk.gui.ClusterPanel
Sets configurations for an algorithm.
update(Observable, Object) - Method in class de.uni_leipzig.cvk.gui.GraphStatisticPanel
Updates this view.
update(Observable, Object) - Method in class de.uni_leipzig.cvk.visual.AggregatePanel
This method updates this Observer by arguments and data from Model instance.
usage() - Static method in class de.uni_leipzig.bf.cluster.Main
Main method arguments information.
user - Variable in class de.uni_leipzig.bf.cluster.BorderFlow
 

V

ValuedAlphaList - Class in de.uni_leipzig.bf.util
All elements are treated as strings A?B?Value
ValuedAlphaList() - Constructor for class de.uni_leipzig.bf.util.ValuedAlphaList
 
valueOf(String) - Static method in enum de.uni_leipzig.bf.cluster.Main.HardenStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.uni_leipzig.bf.cluster.Main.MeasureStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.uni_leipzig.cvk.visual.AggregatePanel.Actions
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.uni_leipzig.bf.cluster.Main.HardenStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.uni_leipzig.bf.cluster.Main.MeasureStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.uni_leipzig.cvk.visual.AggregatePanel.Actions
Returns an array containing the constants of this enum type, in the order they are declared.
vectorTimes(SparseVector) - Method in class de.uni_leipzig.mcl.cluster.SparseMatrix
immutable multiply the vector times this: x' * A, i.e., colwise.
VERBOSE - Static variable in class de.uni_leipzig.bf.cluster.harden.Harden
 

W

WeightedKeyword - Class in de.uni_leipzig.bf.util
This class is a help class with objects composed of keyword and its weight for later retrieval.
WeightedKeyword(String, double) - Constructor for class de.uni_leipzig.bf.util.WeightedKeyword
Creates a new instance of WeightedKeyword
WIDTH - Static variable in class de.uni_leipzig.cvk.gui.Application
 
writeToString(HashMap<TreeSet<Integer>, TreeSet<Integer>>) - Method in class de.uni_leipzig.bf.cluster.BorderFlow
Writes clusterSeedMap to String.

_

_mat - Variable in class de.uni_leipzig.mcl.cluster.SparseMatrixLabeled
 

A B C D E F G H I K L M N O P Q R S T U V W _