Uses of Package
org.cytoscape.model
Package
Description
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.
This package provides Cytoscape version number, application-wide setting,
basic access to current network, selected networks, views and rendering engines.
This package provides application events/listeners, including
Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/
setSelectedNetwork.
This package defines the various interfaces, abstract classes, and enums
that represent the Cytoscape Swing Application API.
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.
Tunable classes useful for command applications
Various types and utility methods relating to attribute equations.
This package provides an API for creating and managing
groups in Cytoscape.
An api for configuring
CyGroup
s.This package contains the various events and listeners
related to group management, creation, and destruction.
Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
This package provides factory interfaces to be used by anyone wishing to provide
export or writing capabilities to the rest of Cytoscape.
This package provides a mechanism for executing remote jobs from within Cytoscape.
This package has the core interfaces of network and
table data structures that are foundational to Cytoscape.
This package contains the event interfaces necessary for communicating
with the classes in org.cytoscape.model.
This package contains rootnetwork and subnetwork extensions to the
CyNetwork interface that provide a more complex meta-network
data model.
This package contains the interfaces and classes necessary to capturing,
storing, and retrieving the state of a Cytoscape session.
This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
This package provides a variety of task factory interfaces for creating
new instances of network and other objects.
This package include a set of task factory interfaces that allow
the modification or editing of various objects within Cytoscape.
This package includes a set of task factory interfaces showing and hiding
nodes and edges within network views.
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.
This package contains a set of task factory interfaces used for
exporting or writing a variety of Cytoscape objects to files.
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.
Module for View Models and Visual Properties.
Definitions for View-Model related events and their listeners.
API set for rendering engines (visualizers).
This package provides support for graphical annotations associated with a Cytoscape
CyNetworkView
.This package provides an API for augmenting a
RenderingEngine
s
node rendering with custom graphics.Implementations of basic VisualProperty objects and VisualLexicons.
Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShape
Visual Mapping basic API module.
This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.
Provides editors for Visual Properties and editor managers for VizMap GUI.
APIs for different mapping functions -- continuous mapping, discrete mapping and pass through mapping.
-
-
-
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionThis class describes a column in a CyTable.An object that represents an edge within a network of nodes (vertices) and edges.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.
-
-
ClassDescriptionThis class describes a column in a CyTable.An object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.
-
-
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.
-
ClassDescriptionCyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.A singleton factory object used for instantiating CyNetwork objects.Basic access to networks and view in an instance of Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.A simple representation of a table object consisting of rows and columns.
-
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.Basic access to networks and view in an instance of Cytoscape.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionThis class describes a column in a CyTable.An interface for objects that require an explicit clean up at the end of their lifecycle.An object that represents an edge within a network of nodes (vertices) and edges.The Type enum is used by methods in
CyNetwork
to restrict the edges that match a query.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.Mutability of the table specifies whether or not it is able to be deleted..A description of the initial size of the table.The SavePolicy of an object specifies whether or not it will be saved.Information object for columns that stores extra Virtual Column information if applicable. -
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.Basic access to networks and view in an instance of Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.A singleton object for managing registered
CyTable
s. -
ClassDescriptionAn interface for objects that require an explicit clean up at the end of their lifecycle.An object that represents an edge within a network of nodes (vertices) and edges.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.A simple representation of a table object consisting of rows and columns.The SavePolicy of an object specifies whether or not it will be saved.
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.A snapshot of information about a relationship shared between a CyTable instance and an associated CyNetworks.
-
ClassDescriptionThis class describes a column in a CyTable.An object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionCyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
-
ClassDescriptionThis class describes a column in a CyTable.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionAn object that represents a node (vertex) within a network of nodes and edges.
-
ClassDescriptionCyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
-
-
ClassDescriptionThis class describes a column in a CyTable.An object that represents an edge within a network of nodes (vertices) and edges.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.
-
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.This interface represents one row in a CyTable.
-
ClassDescriptionAn interface for objects that require an explicit clean up at the end of their lifecycle.An object that represents an edge within a network of nodes (vertices) and edges.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.CyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.An object that represents a node (vertex) within a network of nodes and edges.
-
-
-
ClassDescriptionThis class describes a column in a CyTable.An interface for objects that require an explicit clean up at the end of their lifecycle.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.This interface represents one row in a CyTable.A simple representation of a table object consisting of rows and columns.A snapshot of information about a relationship shared between a CyTable instance and an associated CyNetworks.
-
ClassDescriptionAn interface for objects that require an explicit clean up at the end of their lifecycle.
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.An object that represents a node (vertex) within a network of nodes and edges.
-
ClassDescriptionThis class describes a column in a CyTable.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.This interface represents one row in a CyTable.
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
-
ClassDescriptionAn object that represents an edge within a network of nodes (vertices) and edges.
-
ClassDescriptionThis class describes a column in a CyTable.CyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.This interface represents one row in a CyTable.
-
-
ClassDescriptionCyNetwork is the primary interface for representing a network (graph) data structure in Cytoscape.
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.
-
ClassDescriptionCyIdentifiable is an interface that indicates that the implementing object can be considered a key into a table.This interface represents one row in a CyTable.