Uses of Package
org.cytoscape.model
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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 applicationsorg.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 configuringCyGroup
s.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 CytoscapeCyNetworkView
.org.cytoscape.view.presentation.customgraphics This package provides an API for augmenting aRenderingEngine
s 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 NodeShapeorg.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 creatingCyTable
objects.CyTableManager A singleton object for managing registeredCyTable
s. -
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 inCyNetwork
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 registeredCyTable
s. -
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.