org.cytoscape.application

Interface CyApplicationManager

public interface CyApplicationManager

Basic access to current and/or currently selected networks, views and rendering engines in an instance of Cytoscape.

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

Module: application-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>application-api</artifactId>
</dependency>

Method Summary

Modifier and Type	Method and Description
File	getCurrentDirectory() Get the current working directory.
CyNetwork	getCurrentNetwork() Provides access to the current network.
CyNetworkView	getCurrentNetworkView() Returns the current network view.
NetworkViewRenderer	getCurrentNetworkViewRenderer() Returns the NetworkViewRenderer associated with the current RenderingEngine.
RenderingEngine<CyNetwork>	getCurrentRenderingEngine() Returns the rendering engine associated with the current network view.
CyTable	getCurrentTable() Returns the currently active table.
NetworkViewRenderer	getDefaultNetworkViewRenderer() Returns the NetworkViewRenderer that should be used to create CyNetworkViews.
NetworkViewRenderer	getNetworkViewRenderer(String rendererId) Returns the NetworkViewRenderer that has the passed id or null if it doesn't exist.
Set<NetworkViewRenderer>	getNetworkViewRendererSet() Returns a set with all the NetworkViewRenderer objects that have been registered.
List<CyNetwork>	getSelectedNetworks() Returns the list of selected networks.
List<CyNetworkView>	getSelectedNetworkViews() Returns the list of selected network views.
void	reset() Releases all currently held references and resources.
boolean	setCurrentDirectory(File dir) Set the current working directory.
void	setCurrentNetwork(CyNetwork net) Sets the current network to the specified network.
void	setCurrentNetworkView(CyNetworkView netView) Sets the current network view to the specified network view.
void	setCurrentRenderingEngine(RenderingEngine<CyNetwork> engine) Sets the current rendering engine.
void	setCurrentTable(CyTable table) Sets the currently active table.
void	setDefaultNetworkViewRenderer(NetworkViewRenderer renderer) Sets the NetworkViewRenderer that should be used to create CyNetworkViews.
void	setSelectedNetworks(List<CyNetwork> nets) Sets the networks specified as selected.
void	setSelectedNetworkViews(List<CyNetworkView> views) Sets the specified network views as selected.

Method Detail

getCurrentNetwork

CyNetwork getCurrentNetwork()

Provides access to the current network.

Returns:

the current network or null if there is no current network

setCurrentNetwork

void setCurrentNetwork(CyNetwork net)

Sets the current network to the specified network. If the passed network is different from the current one, a SetCurrentNetworkEvent is fired. If the passed network is not yet selected, any selected networks are unselected before the passed one is selected. That means that the SetSelectedNetworksEvent can also be fired.

Parameters:

net - The network that will become the current network.

getCurrentNetworkView

CyNetworkView getCurrentNetworkView()

Returns the current network view.

Returns:

the current network view or null if no network is currently being visualized

setCurrentNetworkView

void setCurrentNetworkView(CyNetworkView netView)

Sets the current network view to the specified network view.

Parameters:

netView - The network view to become the current network view.

getSelectedNetworks

List<CyNetwork> getSelectedNetworks()

Returns the list of selected networks.

Returns:

The list of selected networks.

getSelectedNetworkViews

List<CyNetworkView> getSelectedNetworkViews()

Returns the list of selected network views.

Returns:

The list of selected network views.

setSelectedNetworkViews

void setSelectedNetworkViews(List<CyNetworkView> views)

Sets the specified network views as selected.

Parameters:

views - The list of network views to be selected.

setSelectedNetworks

void setSelectedNetworks(List<CyNetwork> nets)

Sets the networks specified as selected.

Parameters:

nets - The networks to be selected.

getCurrentRenderingEngine

RenderingEngine<CyNetwork> getCurrentRenderingEngine()

Returns the rendering engine associated with the current network view.

Returns:

The rendering engine associated with the current network view.

setCurrentRenderingEngine

void setCurrentRenderingEngine(RenderingEngine<CyNetwork> engine)

Sets the current rendering engine.

Parameters:

engine - The rendering engine that should be made current.

getCurrentTable

CyTable getCurrentTable()

Returns the currently active table.

Returns:

the currently active CyTable.

setCurrentTable

void setCurrentTable(CyTable table)

Sets the currently active table.

Parameters:

table - The table that should be made current.

reset

void reset()

Releases all currently held references and resources.

getCurrentNetworkViewRenderer

NetworkViewRenderer getCurrentNetworkViewRenderer()

Returns the NetworkViewRenderer associated with the current RenderingEngine.

Returns:

the NetworkViewRenderer associated with the current RenderingEngine

getDefaultNetworkViewRenderer

NetworkViewRenderer getDefaultNetworkViewRenderer()

Returns the NetworkViewRenderer that should be used to create CyNetworkViews.

Returns:

the NetworkViewRenderer that should be used to create CyNetworkViews.

setDefaultNetworkViewRenderer

void setDefaultNetworkViewRenderer(NetworkViewRenderer renderer)

Sets the NetworkViewRenderer that should be used to create CyNetworkViews.

Parameters:

renderer - the NetworkViewRenderer that should be used by default.

getNetworkViewRenderer

NetworkViewRenderer getNetworkViewRenderer(String rendererId)

Returns the NetworkViewRenderer that has the passed id or null if it doesn't exist.

Parameters:

rendererId -

Returns:

the NetworkViewRenderer that should be used to create CyNetworkViews

getNetworkViewRendererSet

Set<NetworkViewRenderer> getNetworkViewRendererSet()

Returns a set with all the NetworkViewRenderer objects that have been registered.

Returns:

the complete set of all the currently known renderers

getCurrentDirectory

File getCurrentDirectory()

Get the current working directory.

Returns:

a File pointing to the current working directory as set in Properties, or user.dir if a value is not set (or if the set value is not a valid directory)

setCurrentDirectory

boolean setCurrentDirectory(File dir)

Set the current working directory.

Parameters:

dir - a File object pointing to an existing directory

Returns:

true if successful, false if the specified File is not a directory or does not exist