Uses of Interface
org.graffiti.plugin.algorithm.Algorithm

Packages that use Algorithm

Package	Description
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.data_mapping
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance	Provides the HammingDistancePlugin, a plugin for computing the hamming distances between graphs.
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.lines_as_substances
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder	Provides the NaivePatternFinderPlugin, a plugin for finding given patterns within a given graph.
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths
de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som
de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.commands
de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.alt_id_statistics
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.hierarchies
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.hierarchy
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color
de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.startlayout
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_no_overlapp
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fd_edge_routing
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid	Provides the GridLayouterPlugin, a plugin for placing nodes on a grid.
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.no_overlapp_as_tim
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout	Provides the GridLayouterPlugin, a plugin for placing nodes on a grid.
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.springembedder_1
de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.ppt_exporter
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.scripting
de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter
de.ipk_gatersleben.ag_nw.graffiti.services
de.ipk_gatersleben.ag_nw.graffiti.services.algorithms
org.graffiti.editor	Contains classes for the famous graffiti editor.
org.graffiti.editor.actions	Contains the editor's action classes.
org.graffiti.managers
org.graffiti.plugin	Contains an interface and an adapter class for a generic plugin.
org.graffiti.plugin.algorithm
org.graffiti.session	Contains classes, which are needed for the session handling.
org.graffiti.util	Contains utility classes for frequently needed functionality.
org.vanted.plugins.layout.adaptagrams.edgerouting
org.vanted.plugins.layout.multilevelframework	A layout algorithm to Vanted that implements the multi-level graph layout framework.
org.vanted.plugins.layout.stressminimization	A layout algorithm to Vanted that implements stress minimization.
scenario
vanted_feature

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.circle_search that implement Algorithm

Modifier and Type	Class	Description
class	CircleSearchAndLayoutAlgorithm	Searches for circular sub-graphs and optionally applies a CircleLayouter.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.data_mapping

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.data_mapping that implement Algorithm

Modifier and Type	Class	Description
class	DataMapping

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.davidtest that implement Algorithm

Modifier and Type	Class	Description
class	ColorizeAlgorithm
class	DavidTestAlgorithm	Executes the David et.
class	GrubbsTestAlgorithm	Executes the Grubbs' statistical test to detect outliers.
class	ShowStatisticsTab

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.graph_generation that implement Algorithm

Modifier and Type	Class	Description
class	BarabasiAlbertGraphGenerator	Needs implementation
class	ErdosRenyiGraphGenerator	Algorithm to generate an Erdos Renyi random network of n nodes, using p edge probability.
class	WattsStrogatzGraphGenerator	Algorithm for generation of a random small-world network.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.hamming_distance that implement Algorithm

Modifier and Type	Class	Description
class	HammingDistanceAlgorithm	This algorithm computes the hamming distances between directed graphs.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.inverse_graph that implement Algorithm

Modifier and Type	Class	Description
class	InverseGraphPluginAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.lines_as_substances

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.lines_as_substances that implement Algorithm

Modifier and Type	Class	Description
class	LinesToSubstancesAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder that implement Algorithm

Modifier and Type	Class	Description
class	NaivePatternFinderAlgorithm	Finds pattern within a given target graph.

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder with parameters of type Algorithm

Modifier and Type	Method	Description
static void	NaivePatternFinderAlgorithm.searchPatterns(Graph graph, List<Graph> patterns, Algorithm optLayoutAlgorithm, boolean ignoreEdgeDirection, boolean startWithLargestCircle, boolean allowOverlap, BackgroundTaskStatusProviderSupportingExternalCall status)	Search a number of pattern graphs in the target graph, beginning with the largest pattern (determined by number of nodes)

Constructors in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.naive_pattern_finder with parameters of type Algorithm

Constructor	Description
PatternVistorLayouter(Algorithm layoutAlgorithm)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.ratioview that implement Algorithm

Modifier and Type	Class	Description
class	ExchangeNodePositionsAlgorithm
class	RatioViewAlgorithm
class	SubstanceRatioCalculationAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.shortest_paths that implement Algorithm

Modifier and Type	Class	Description
class	AllPathsSelectionAlgorithm
class	ShortestPathSelectionAlgorithm
class	WeightedShortestPathSelectionAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som that implement Algorithm

Modifier and Type	Class	Description
class	MultiDataView
class	SOManalysis
class	SOMclusterAnalysis
class	SOMclusterAnalysisDoCluster
class	SOMprintDataset

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.algorithms.som with parameters of type Algorithm

Modifier and Type	Method	Description
boolean	SOManalysis.closeDialogBeforeExecution(Algorithm algorithm)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.commands

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.transpath.commands that implement Algorithm

Modifier and Type	Class	Description
class	TranspathPathwayLoader

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.editcomponents.compound_image that implement Algorithm

Modifier and Type	Class	Description
class	ImageAssignmentCommand	Algorithm to assign an image to a node.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe that implement Algorithm

Modifier and Type	Class	Description
class	ApplyAlternativeIdentifiersTo
class	CombineMappingData
class	CreateFuncatGraphAlgorithm
class	MergeNodes	Merges nodes within the same network, while considering connecting edges and data mapping information.
class	ReplaceDiagramTitleFromAlternativeSubstanceNames
class	ShowOrHideImageAttributesAlgorithm
class	SplitNodeForSingleMappingData
class	UserMappingAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.algorithms that implement Algorithm

Modifier and Type	Class	Description
class	AddDiagramLegendAlgorithm
class	ColorScaleLegendAlgorithm
class	CreateDistanceMatrixAlgorithm
class	ExtractMappingDataAlgorithm
class	RecolorEdgesAlgorithm
class	RemoveMappingDataAlgorithm
class	SetNumericAttributeFromDataAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.alt_id_statistics

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.alt_id_statistics that implement Algorithm

Modifier and Type	Class	Description
class	AlternativeIDannotationStatistics

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go that implement Algorithm

Modifier and Type	Class	Description
class	CreateGOtreeAlgorithm
class	InterpreteGOtermsAlgorithm
class	InterpreteParentGOtermsAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.go_cluster_histogram that implement Algorithm

Modifier and Type	Class	Description
class	ClusterHistogramFisherTest
class	CreateDirectChildrenClustersHistogramAlgorithm
class	CreateGOchildrenAverageDataDiagramAlgorithm
class	CreateGOchildrenClustersHistogramAlgorithm
class	CreateGOchildrenTtestHistogramAlgorithm
class	ProcessHierarchynodesDepOnLeafNodes
class	PruneTreeAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.hierarchies

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.hierarchies that implement Algorithm

Modifier and Type	Class	Description
class	CreateKEGGOrthologyGraphAlgorithm	This class replaces the CreateFuncatGraphAlgorithm, The first class created KEGG hierarchies based on direct given hierarchies (using alternative labels in the nodes), or

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.database_processing.kegg_reaction that implement Algorithm

Modifier and Type	Class	Description
class	CreateKeggReactionNetworkAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.hierarchy

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.hierarchy that implement Algorithm

Modifier and Type	Class	Description
class	HierarchyAlgorithms	Deprecated.
class	HierarchyWizard

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.dbe.selectCommands that implement Algorithm

Modifier and Type	Class	Description
class	SelectCompoundsAlgorithm
class	SelectEdgesAlgorithm
class	SelectEnzymesAlgorithm
class	SelectGenesAlgorithm
class	SelectMapNodesAlgorithm
class	SelectMapTitleNodesAlgorithm
class	SelectNodesWithExperimentalDataAlgorithm
class	SelectReactionsAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools that implement Algorithm

Modifier and Type	Class	Description
class	CloseAllWindows
class	EvaluateKGML
class	RecreateView

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.kegg_bar that implement Algorithm

Modifier and Type	Class	Description
class	ColorizeSuperGraphAlgorithm
class	CreateOrgSpecificSuperGraphsAlgorithm
class	MergeWindowsAlgorithm
class	SelectWindowsAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui that implement Algorithm

Modifier and Type	Class	Description
class	LaunchGui

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui that return types with arguments of type Algorithm

Modifier and Type	Method	Description
Collection<Algorithm>	LaunchGui.getAlgorithmList()

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.launch_gui with parameters of type Algorithm

Modifier and Type	Method	Description
boolean	LaunchGui.closeDialogBeforeExecution(Algorithm algorithm)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.dbe that implement Algorithm

Modifier and Type	Class	Description
class	AbstractExperimentDataProcessor	Management of action commands for data mapping.
class	PutIntoSidePanel

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.layout_control.workflow with parameters of type Algorithm

Modifier and Type	Method	Description
void	WorkflowHelper.postWorkflowStep(Algorithm algorithm, Parameter[] params)	Deprecated.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.plugin_settings with parameters of type Algorithm

Modifier and Type	Method	Description
void	PreferencesDialog.initAlgorithmPreferencesPanel(JDialog thisDialog, Algorithm alg, Graph graph, Selection sele, HandlesAlgorithmData setAlgorithmDataObject, boolean executeMoveToTopAfterwards)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.rotate that implement Algorithm

Modifier and Type	Class	Description
class	RotateAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.set_background_color that implement Algorithm

Modifier and Type	Class	Description
class	SetBackgroundColorAlgorithm	DOCUMENT ME!
class	WindowSettings	DOCTODO: Include class header

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.startlayout

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.startlayout that implement Algorithm

Modifier and Type	Class	Description
class	StartLayoutAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.apply_from_graph that implement Algorithm

Modifier and Type	Class	Description
class	ApplyGraphLayout
class	ShowLayoutTab

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.circle that implement Algorithm

Modifier and Type	Class	Description
class	CircleLayouterAlgorithm	Places all nodes on a circle with a user specified radius.
class	CircleLayouterWithMinimumCrossingsAlgorithm	Places all nodes on a circle with a user specified radius.
class	CountCircularCrossingsAlgorithm
class	DotLayoutAlgorithm
class	NullLayoutAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.connected_components that implement Algorithm

Modifier and Type	Class	Description
class	ConnectedComponentLayout

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.copy_pattern_layout that implement Algorithm

Modifier and Type	Class	Description
class	CopyPatternLayoutAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_no_overlapp

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_no_overlapp that implement Algorithm

Modifier and Type	Class	Description
class	NoOverlappLayoutAlgorithm	Epands the layout to remove any overlapping of nodes.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.expand_reduce_space that implement Algorithm

Modifier and Type	Class	Description
class	ExpandReduceLayouterAlgorithm	Transforms the layout by doing a calculation like x=x*1.4 and y=y*1.4 for the nodes and bends positions.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fd_edge_routing

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fd_edge_routing that implement Algorithm

Modifier and Type	Class	Description
class	ForceDirectedEdgeLayout

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.fish_eye that implement Algorithm

Modifier and Type	Class	Description
class	FishEyeLayout	An implementation of a fish eye layout algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.graph_to_origin_mover that implement Algorithm

Modifier and Type	Class	Description
class	CenterLayouterAlgorithm	DOCTODO: Include class header
class	NoOverlappOfClustersAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid that implement Algorithm

Modifier and Type	Class	Description
class	GridLayouterAlgorithm	Gridlayouter algorithm: Performs a layout where every node is placed on a position of a grid.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.grid_placement that implement Algorithm

Modifier and Type	Class	Description
class	GridPlacementAlgorithm
class	IterateGridPlacementLayout

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.no_overlapp_as_tim

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.no_overlapp_as_tim that implement Algorithm

Modifier and Type	Class	Description
class	NoOverlappLayoutAlgorithmAS	Epands the layout to remove any overlapping of nodes.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder that implement Algorithm

Modifier and Type	Class	Description
class	PatternSpringembedder	Spring Embedder Algorithm.
class	PatternSpringembedder3d	Spring Embedder Algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder_no_cache that implement Algorithm

Modifier and Type	Class	Description
class	PatternSpringembedder	Spring Embedder Algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands that implement Algorithm

Modifier and Type	Class	Description
class	AddRandomClusterInformationAlgorithm
class	BendsLaunchGUI	Deprecated.
class	BringToFrontOrBackAlgorithm
class	BundleParallelEdges
class	ClusterGraphLayout
class	ClusterIndividualLayout
class	ClusterOverviewNetworkLaunchGui
class	CreateClusterGraphAlgorithm
class	CreateHierarchyTree	Deprecated.
class	DuplicateEdge
class	IntroduceBendsAlgorithm
class	IntroduceParallelEdgeBends
class	IntroduceSelfEdgeBends
class	PajekClusterColor
class	RemoveBendsAlgorithm
class	RemoveParallelEdges	The following algorithm deletes additional parallel edges, leaving only a single edge.
class	ResetEdgeSourceOrTarget
class	ResizeNodesDepDegreeAlgorithm
class	SelectClusterAlgorithm
class	SetClusterInfoAlgorithm
class	SetClusterInfoFromLabelAlgorithm
class	SetClusterInfoFromSubgraphAlgorithm
class	SetClusterLaunchGui
class	ShowClusterGraphAlgorithm
class	SortIntoCluster	Sorts graph elements into cluster.

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.pattern_springembedder.clusterCommands with parameters of type Algorithm

Modifier and Type	Method	Description
boolean	ClusterOverviewNetworkLaunchGui.closeDialogBeforeExecution(Algorithm algorithm)
boolean	SetClusterLaunchGui.closeDialogBeforeExecution(Algorithm algorithm)
void	MyClusterGraphBasedReLayoutService.setAlgorithm(Algorithm algorithm, Algorithm optAlgorithm2)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.radial_tree that implement Algorithm

Modifier and Type	Class	Description
class	RadialTreeLayout	An implementation of a radial tree layout algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.random that implement Algorithm

Modifier and Type	Class	Description
class	RandomLayouterAlgorithm	This algorithm performs a random placement of the nodes on the visible area.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.resize_and_grid_layout that implement Algorithm

Modifier and Type	Class	Description
class	ArrayLayout
class	GridLayoutAlgorithm	Resize+Gridlayout: Resizes all nodes and places them on a grid.
class	ResizeFromMappingCountLayoutAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.rt_tree that implement Algorithm

Modifier and Type	Class	Description
class	MultiTreeLayout
class	RTTreeLayout	An implementation of a tree layout algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.springembedder_1

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.springembedder_1 that implement Algorithm

Modifier and Type	Class	Description
class	SpringEmbedderAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.layouters.tree_simple that implement Algorithm

Modifier and Type	Class	Description
class	GraphTreeLayout	An implementation of a tree layout algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.add_attributes that implement Algorithm

Modifier and Type	Class	Description
class	AddInterestingAttributes
class	CalculateAttribute
class	ComputeAttributesAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.graph_cleanup that implement Algorithm

Modifier and Type	Class	Description
class	DeleteNodesAlgorithm	Labels all selected nodes with unique numbers.
class	NumberNodesAndEdgesAlgorithm	Labels all selected nodes with unique numbers.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.hierarchy that implement Algorithm

Modifier and Type	Class	Description
class	HideOrShowChildNodes
class	HierarchyAlgorithm
class	SelectLeafNodesAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.invert_selection that implement Algorithm

Modifier and Type	Class	Description
class	ChangeEdgeStyle
class	ChangeElementStyle
class	ChangeNodeStyle
class	ClearSelection
class	CopyDataTableAlgorithm
class	ExpandSelectionAlgorithm	Labels all selected nodes with unique numbers.
class	ExportDataTableAlgorithm
class	FindReplaceDialog	Labels all selected nodes with unique numbers.
class	InvertSelectionAlgorithm	Labels all selected nodes with unique numbers.
class	RemoveSelectedNodesPreserveEdgesAlgorithm	Labels all selected nodes with unique numbers.
class	SearchAndSelecAlgorithm	Labels all selected nodes with unique numbers.
class	SetToolTipAlgorithm
class	SetURLAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.label_editing that implement Algorithm

Modifier and Type	Class	Description
class	ChangeLabelsAlgorithm	Deprecated.
class	EnrichHiddenLabelsAlgorithm
class	RemoveHiddenLabelsAlgorithm
class	RemoveParenthesisLabels
class	ReplaceLabelAlgorithm
class	RestoreLabelAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.pathway_references that implement Algorithm

Modifier and Type	Class	Description
class	LinkSelection
class	PathwayReferenceAlgorithm
class	PathwayReferenceAutoCreationAlgorithm

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.ppt_exporter

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.ppt_exporter that implement Algorithm

Modifier and Type	Class	Description
class	PPTAlgorithm	Provides a PPT writer.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.print.printer that implement Algorithm

Modifier and Type	Class	Description
class	PrintAlgorithm	The print algorithm.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.process_alternative_ids that implement Algorithm

Modifier and Type	Class	Description
class	AdditionalIdentifiersAlgorithm
class	ReplaceLabelFromAlternativeSubstanceNames

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.scripting

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.scripting that implement Algorithm

Modifier and Type	Class	Description
class	BeanShellDesktopAlgorithm	Provides a Bean Shell Desktop for the execution of Bean Shell Scripts.

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter

Classes in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter that implement Algorithm

Modifier and Type	Class	Description
class	GraphicExport
class	PDFAlgorithm	The print algorithm.
class	PDFSVGAlgorithm
class	PngJpegAlgorithm
class	SVGAlgorithm	The print algorithm.
class	WebsiteGeneration

Methods in de.ipk_gatersleben.ag_nw.graffiti.plugins.misc.svg_exporter with parameters of type Algorithm

Modifier and Type	Method	Description
static String	PngJpegAlgorithm.getCachedFileName(String extension, Graph graph, Algorithm algorithm, ObjectRef lastEvent, ObjectRef lastFolder)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.services

Methods in de.ipk_gatersleben.ag_nw.graffiti.services that return Algorithm

Modifier and Type	Method	Description
Algorithm	HandlesAlgorithmData.getAlgorithm()
Algorithm	RunAlgorithmDialog.getAlgorithm()

Methods in de.ipk_gatersleben.ag_nw.graffiti.services with parameters of type Algorithm

Modifier and Type	Method	Description
void	HandlesAlgorithmData.setAlgorithm(Algorithm algorithm)
void	RunAlgorithmDialog.setAlgorithm(Algorithm algorithm)

Uses of Algorithm in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms

Methods in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms that return types with arguments of type Algorithm

Modifier and Type	Method	Description
static List<Algorithm>	SearchAlgorithms.searchAlgorithms(SearchAlgorithms.OperatorOnCategories[] operatorSearchSet)	Searches Algorithms listed in Vanted, given an array of operators on categories.
static List<Algorithm>	SearchAlgorithms.searchAlgorithms(Category[] categories)	Searches Algorithms listed in Vanted, given an array of categories that this algorithm needs to be a member of The categories are combined with an AND operator

Methods in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms with parameters of type Algorithm

Modifier and Type	Method	Description
Component	AlgorithmListCellRenderer.getListCellRendererComponent(JList<? extends Algorithm> list, Algorithm value, int index, boolean isSelected, boolean cellHasFocus)
void	AlgorithmPanelFactory.initializeGUIforGivenContainer(boolean vertical, Algorithm[] algorithms)

Method parameters in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms with type arguments of type Algorithm

Modifier and Type	Method	Description
static JPanel	AlgorithmPanelFactory.createForAlgorithms(boolean vertical, List<Algorithm> algorithms)
Component	AlgorithmListCellRenderer.getListCellRendererComponent(JList<? extends Algorithm> list, Algorithm value, int index, boolean isSelected, boolean cellHasFocus)

Constructor parameters in de.ipk_gatersleben.ag_nw.graffiti.services.algorithms with type arguments of type Algorithm

Constructor	Description
AlgorithmPanelFactory(boolean vertical, List<Algorithm> algorithms)

Uses of Algorithm in org.graffiti.editor

Methods in org.graffiti.editor that return Algorithm

Modifier and Type	Method	Description
Algorithm	GravistoService.getAlgorithmInstanceFromFriendlyName(String name)	Returns a algorithm instance, defined by its name (e.g.

Methods in org.graffiti.editor with parameters of type Algorithm

Modifier and Type	Method	Description
void	GravistoService.algorithmAttachData(Algorithm algorithm)
static void	GravistoService.attachData(Algorithm algorithm)
static void	GravistoService.processUndoableAlgorithm(Algorithm algorithm)	Process undoable edits for AbstractAlgorithm instances.
void	GravistoService.runAlgorithm(Algorithm algorithm, boolean enableMultipleSessionProcessing, ActionEvent event)
void	GravistoService.runAlgorithm(Algorithm algorithm, ActionEvent event)
void	GravistoService.runAlgorithm(Algorithm algorithm, Graph graph, Selection selection, boolean enableMultipleSessionProcessing, ActionEvent event)
void	GravistoService.runAlgorithm(Algorithm algorithm, Graph graph, Selection selection, ActionEvent event)

Uses of Algorithm in org.graffiti.editor.actions

Constructors in org.graffiti.editor.actions with parameters of type Algorithm

Constructor	Description
RunAlgorithm(String algorithmClassName, String name, MainFrame mainFrame, EditComponentManager editComponentManager, Algorithm instance)	Constructor for RunAlgorithm.

Uses of Algorithm in org.graffiti.managers

Methods in org.graffiti.managers that return types with arguments of type Algorithm

Modifier and Type	Method	Description
List<Algorithm>	DefaultAlgorithmManager.getAlgorithms()

Methods in org.graffiti.managers with parameters of type Algorithm

Modifier and Type	Method	Description
void	AlgorithmManager.addAlgorithm(Algorithm algorithm)	Adds the given algorithm to the list of algorithms.
void	DefaultAlgorithmManager.addAlgorithm(Algorithm algorithm)

Uses of Algorithm in org.graffiti.plugin

Methods in org.graffiti.plugin that return Algorithm

Modifier and Type	Method	Description
Algorithm[]	GenericPlugin.getAlgorithms()	Returns the array of org.graffiti.algorithm.Algorithms the plugin contains.
Algorithm[]	GenericPluginAdapter.getAlgorithms()	Returns the array of org.graffiti.algorithm.Algorithms the plugin contains.

Uses of Algorithm in org.graffiti.plugin.algorithm

Subinterfaces of Algorithm in org.graffiti.plugin.algorithm

Modifier and Type	Interface	Description
interface	AnimatedAlgorithm	An AnimatedAlgorithm provides the possibility to execute the underlying algorithm in steps, so that the intermediate results can be seen.
interface	CalculatingAlgorithm	After its execution a CalculatingAlgorithm has computed an AlgorithmResult, that can be obtained through the getResult() method.
interface	EditorAlgorithm

Classes in org.graffiti.plugin.algorithm that implement Algorithm

Modifier and Type	Class	Description
class	AbstractAlgorithm	Implements some empty versions of non-obligatory methods.
class	AbstractAnimatedAlgorithm	Gives a standard implementation for the execute() method.
class	AbstractEditorAlgorithm
class	AbstractThreadSaveLayoutAlgorithm	Basis for Thread Safe (layout) Plugins and communication to the MainFrame
class	ThreadSafeAlgorithm	DOCUMENT ME!

Methods in org.graffiti.plugin.algorithm that return types with arguments of type Algorithm

Modifier and Type	Method	Description
Collection<Algorithm>	ProvidesAccessToOtherAlgorithms.getAlgorithmList()

Methods in org.graffiti.plugin.algorithm with parameters of type Algorithm

Modifier and Type	Method	Description
boolean	ProvidesAccessToOtherAlgorithms.closeDialogBeforeExecution(Algorithm algorithm)

Uses of Algorithm in org.graffiti.session

Methods in org.graffiti.session with parameters of type Algorithm

Modifier and Type	Method	Description
String	Session.getClassName(Algorithm algorithm)	Returns the class name of the specified algorithm.

Uses of Algorithm in org.graffiti.util

Methods in org.graffiti.util that return types with arguments of type Algorithm

Modifier and Type	Method	Description
static List<? extends Algorithm>	PluginHelper.getAvailableAlgorithms()

Uses of Algorithm in org.vanted.plugins.layout.adaptagrams.edgerouting

Classes in org.vanted.plugins.layout.adaptagrams.edgerouting that implement Algorithm

Modifier and Type	Class	Description
class	EdgeRoutingAlgorithm

Uses of Algorithm in org.vanted.plugins.layout.multilevelframework

Classes in org.vanted.plugins.layout.multilevelframework that implement Algorithm

Modifier and Type	Class	Description
class	ForceDirectedLayoutWrapper	Wrapper class to enable usage of the PatternspringEmbedder (a.k.a.
class	MultilevelFrameworkLayout	Main class of the MLF add-on that contains the method that actually performs the layout.

Methods in org.vanted.plugins.layout.multilevelframework that return Algorithm

Modifier and Type	Method	Description
Algorithm	LayoutAlgorithmWrapper.getAlgorithm()

Uses of Algorithm in org.vanted.plugins.layout.stressminimization

Classes in org.vanted.plugins.layout.stressminimization that implement Algorithm

Modifier and Type	Class	Description
class	BackgroundAlgorithm	Algorithm which runs in the background and able to notify other classes about state of the algorithm or the layout change of the graph.
class	BackgroundExecutionAlgorithm	This class handles the execution of a given BackgroundAlgorithm in the background, i.e.
class	StressMinimizationLayout	Layout algorithm performing a stress minimization layout process.

Uses of Algorithm in scenario

Methods in scenario with parameters of type Algorithm

Modifier and Type	Method	Description
void	ScenarioGui.postWorkflowStep(Algorithm algorithm, Parameter[] params)
static void	ScenarioService.postWorkflowStep(Algorithm algorithm, Parameter[] params)

Uses of Algorithm in vanted_feature

Classes in vanted_feature that implement Algorithm

Modifier and Type	Class	Description
class	SelectAlgorithm	Deprecated.

Methods in vanted_feature that return Algorithm

Modifier and Type	Method	Description
static Algorithm	PluginFeatureClusterCommands.getSelectClusterAlgorithm()
static Algorithm[]	PluginFeatureHierarchyCommands.getSelectionAlgorithms()

Methods in vanted_feature with parameters of type Algorithm

Modifier and Type	Method	Description
boolean	SelectAlgorithm.closeDialogBeforeExecution(Algorithm algorithm)	Deprecated.