Uses of Package
cytoscape

Packages that use cytoscape

cytoscape	Core Cytoscape Classes.
cytoscape.actions	UI classes that are attached to menu items in the menu or tool bar of the window.
cytoscape.data	Basic data classes used by Cytoscape.
cytoscape.data.ontology
cytoscape.data.ontology.readers
cytoscape.data.readers	Reader classes for the basic data types in cytoscape.data.
cytoscape.data.writers
cytoscape.dialogs	UI classes for performing some action, generally more complicated than those contained in the cytoscape.actions package.
cytoscape.ding
cytoscape.giny
cytoscape.groups
cytoscape.layout	Classes providing some kind of graph layout functionality.
cytoscape.plugin	Classes related to Cytoscape plugins.
cytoscape.util	This package contains utility classes which are deemed generally useful, but which do not clearly belong to any other package.
cytoscape.util.swing
cytoscape.view	Classes that provide a window to display a graph and UI components connected to that window, such as the menus.
cytoscape.visual	Framework for generalized mappings from graph attributes to visual attributes.
cytoscape.visual.calculators	Objects that calculate from the data attributes the value for one visual attribute, such as color, shape, or size.
cytoscape.visual.mappings	The Mappings are used by Calculators to map graph attributes to visual attribute values.

Classes in cytoscape used by cytoscape

CyEdge

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

CyNetworkEvent
Events of this class are fired from a CyNetwork object when something happens to the network.

CyNetworkListener
Interface for listeners that respond to CyNetwork events.

CyNode

Classes in cytoscape used by cytoscape.actions

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.data

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

CyNode

Classes in cytoscape used by cytoscape.data.ontology

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.data.ontology.readers

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.data.readers

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.data.writers

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.dialogs

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.ding

CyEdge

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

CyNode

Classes in cytoscape used by cytoscape.giny

CyEdge

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

CyNetworkListener
Interface for listeners that respond to CyNetwork events.

CyNode

Classes in cytoscape used by cytoscape.groups

CyEdge

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

CyNode

Classes in cytoscape used by cytoscape.layout

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.plugin

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.util

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.util.swing

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.view

CyEdge

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

CyNode

Classes in cytoscape used by cytoscape.visual

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.visual.calculators

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

Classes in cytoscape used by cytoscape.visual.mappings

CyNetwork
CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.