| 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.
|
| Class and 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. |
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and Description |
|---|
| CyTable
A simple representation of a table object consisting of rows
and columns.
|
| Class and 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.
|
| Class and Description |
|---|
| CyColumn
This class describes a column in a CyTable.
|
| CyTable
A simple representation of a table object consisting of rows
and columns.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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. |
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and Description |
|---|
| CyNetwork
CyNetwork is the primary interface for representing a network (graph)
data structure in Cytoscape.
|
| Class and 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.
|
| Class and 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.
|
| Class and Description |
|---|
| CyNetwork
CyNetwork is the primary interface for representing a network (graph)
data structure in Cytoscape.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and 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.
|
| Class and Description |
|---|
| CyDisposable
An interface for objects that require an explicit clean up at the end of
their lifecycle.
|
| Class and Description |
|---|
| CyNode
An object that represents a node (vertex) within a network
of nodes and edges.
|
| Class and Description |
|---|
| CyIdentifiable
CyIdentifiable is an interface that indicates that the implementing
object can be considered a key into a table.
|
| Class and Description |
|---|
| CyIdentifiable
CyIdentifiable is an interface that indicates that the implementing
object can be considered a key into a table.
|
| Class and Description |
|---|
| CyEdge
An object that represents an edge within a network of nodes (vertices)
and edges.
|
| Class and 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.
|
| Class and Description |
|---|
| CyNetwork
CyNetwork is the primary interface for representing a network (graph)
data structure in Cytoscape.
|
| Class and Description |
|---|
| CyIdentifiable
CyIdentifiable is an interface that indicates that the implementing
object can be considered a key into a table.
|
| Class and 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.
|
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