Uses of Package
org.cytoscape.model

Packages that use org.cytoscape.model

Package	Description
org.cytoscape.app	This is the Cytoscape App API, which supports development of Cytoscape 3.X apps in a manner similar to apps developed in Cytoscape 2.X.
org.cytoscape.application	This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
org.cytoscape.application.events	This package provides application events/listeners, including Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/ setSelectedNetwork.
org.cytoscape.application.swing	This package defines the various interfaces, abstract classes, and enums that represent the Cytoscape Swing Application API.
org.cytoscape.command	Interface to support execution of tasks as commands, including the ability to get a list of namespaces, commands, and arguments, and then execute those commands with a set of arguments.
org.cytoscape.command.util	Tunable classes useful for command applications
org.cytoscape.equations	Various types and utility methods relating to attribute equations.
org.cytoscape.group	This package provides an API for creating and managing groups in Cytoscape.
org.cytoscape.group.data	An api for configuring CyGroups.
org.cytoscape.group.events	This package contains the various events and listeners related to group management, creation, and destruction.
org.cytoscape.io.read	Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.io.write	This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
org.cytoscape.jobs	This package provides a mechanism for executing remote jobs from within Cytoscape.
org.cytoscape.model	This package has the core interfaces of network and table data structures that are foundational to Cytoscape.
org.cytoscape.model.events	This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
org.cytoscape.model.subnetwork	This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
org.cytoscape.session	This package contains the interfaces and classes necessary to capturing, storing, and retrieving the state of a Cytoscape session.
org.cytoscape.task	This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
org.cytoscape.task.create	This package provides a variety of task factory interfaces for creating new instances of network and other objects.
org.cytoscape.task.edit	This package include a set of task factory interfaces that allow the modification or editing of various objects within Cytoscape.
org.cytoscape.task.hide	This package includes a set of task factory interfaces showing and hiding nodes and edges within network views.
org.cytoscape.task.select	This package includes a set of task factory interfaces for selecting, de-selecting and inverting selections of nodes, edges, or combinations of both based on specific criteria.
org.cytoscape.task.write	This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
org.cytoscape.util.json
org.cytoscape.view.layout	This package provides access to the available layout algorithms, as well as provides abstract layout classes and layout information containers for the convenience of implementing other layout algorithms.
org.cytoscape.view.model	Module for View Models and Visual Properties.
org.cytoscape.view.model.events	Definitions for View-Model related events and their listeners.
org.cytoscape.view.presentation	API set for rendering engines (visualizers).
org.cytoscape.view.presentation.annotations	This package provides support for graphical annotations associated with a Cytoscape CyNetworkView.
org.cytoscape.view.presentation.customgraphics	This package provides an API for augmenting a RenderingEngines node rendering with custom graphics.
org.cytoscape.view.presentation.property	Implementations of basic VisualProperty objects and VisualLexicons.
org.cytoscape.view.presentation.property.values	Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShape
org.cytoscape.view.vizmap	Visual Mapping basic API module.
org.cytoscape.view.vizmap.gui	This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.
org.cytoscape.view.vizmap.gui.editor	Provides editors for Visual Properties and editor managers for VizMap GUI.
org.cytoscape.view.vizmap.mappings	APIs for different mapping functions -- continuous mapping, discrete mapping and pass through mapping.

Classes in org.cytoscape.model used by org.cytoscape.app

Class	Description
CyNetworkFactory	A singleton factory object used for instantiating CyNetwork objects.
CyNetworkManager	Basic access to networks and view in an instance of Cytoscape.
CyTableFactory	An interface describing a factory used for creating CyTable objects.
CyTableManager	A singleton object for managing registered CyTables.

Classes in org.cytoscape.model used by org.cytoscape.application

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.application.events

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.application.swing

Class	Description
CyColumn	This class describes a column in a CyTable.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.

Classes in org.cytoscape.model used by org.cytoscape.command

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.command.util

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.equations

Class	Description
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.group

Class	Description
CyColumn	This class describes a column in a CyTable.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.group.data

Class	Description
CyColumn	This class describes a column in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.group.events

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.io.read

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNetworkFactory	A singleton factory object used for instantiating CyNetwork objects.
CyNetworkManager	Basic access to networks and view in an instance of Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.io.write

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.jobs

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNetworkManager	Basic access to networks and view in an instance of Cytoscape.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.model

Class	Description
CyColumn	This class describes a column in a CyTable.
CyDisposable	An interface for objects that require an explicit clean up at the end of their lifecycle.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyEdge.Type	The Type enum is used by methods in CyNetwork to restrict the edges that match a query.
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.
CyTable.Mutability	Mutability of the table specifies whether or not it is able to be deleted..
CyTableFactory.InitialTableSize	A description of the initial size of the table.
SavePolicy	The SavePolicy of an object specifies whether or not it will be saved.
VirtualColumnInfo	Information object for columns that stores extra Virtual Column information if applicable.

Classes in org.cytoscape.model used by org.cytoscape.model.events

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNetworkManager	Basic access to networks and view in an instance of Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.
CyTableManager	A singleton object for managing registered CyTables.

Classes in org.cytoscape.model used by org.cytoscape.model.subnetwork

Class	Description
CyDisposable	An interface for objects that require an explicit clean up at the end of their lifecycle.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyTable	A simple representation of a table object consisting of rows and columns.
SavePolicy	The SavePolicy of an object specifies whether or not it will be saved.

Classes in org.cytoscape.model used by org.cytoscape.session

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyTableMetadata	A snapshot of information about a relationship shared between a CyTable instance and an associated CyNetworks.

Classes in org.cytoscape.model used by org.cytoscape.task

Class	Description
CyColumn	This class describes a column in a CyTable.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.task.create

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.

Classes in org.cytoscape.model used by org.cytoscape.task.edit

Class	Description
CyColumn	This class describes a column in a CyTable.
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.task.hide

Class	Description
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.task.select

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.

Classes in org.cytoscape.model used by org.cytoscape.task.write

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.util.json

Class	Description
CyColumn	This class describes a column in a CyTable.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.
CyTable	A simple representation of a table object consisting of rows and columns.

Classes in org.cytoscape.model used by org.cytoscape.view.layout

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.
CyRow	This interface represents one row in a CyTable.

Classes in org.cytoscape.model used by org.cytoscape.view.model

Class	Description
CyDisposable	An interface for objects that require an explicit clean up at the end of their lifecycle.
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.view.model.events

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.view.presentation

Class	Description
CyDisposable	An interface for objects that require an explicit clean up at the end of their lifecycle.

Classes in org.cytoscape.model used by org.cytoscape.view.presentation.annotations

Class	Description
CyNode	An object that represents a node (vertex) within a network of nodes and edges.

Classes in org.cytoscape.model used by org.cytoscape.view.presentation.customgraphics

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.

Classes in org.cytoscape.model used by org.cytoscape.view.presentation.property

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.

Classes in org.cytoscape.model used by org.cytoscape.view.presentation.property.values

Class	Description
CyEdge	An object that represents an edge within a network of nodes (vertices) and edges.

Classes in org.cytoscape.model used by org.cytoscape.view.vizmap

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyRow	This interface represents one row in a CyTable.

Classes in org.cytoscape.model used by org.cytoscape.view.vizmap.gui

Class	Description
CyNetwork	CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.

Classes in org.cytoscape.model used by org.cytoscape.view.vizmap.gui.editor

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.

Classes in org.cytoscape.model used by org.cytoscape.view.vizmap.mappings

Class	Description
CyIdentifiable	CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
CyRow	This interface represents one row in a CyTable.