org.cytoscape.cyni
Interface CyCyniAlgorithm

All Known Implementing Classes:

AbstractCyniAlgorithm

public interface CyCyniAlgorithm

An interface specific to Cyni algorithms.

Method Summary

Object	createCyniContext(org.cytoscape.model.CyTable table, CyCyniMetricsManager metricsManager, org.cytoscape.work.TunableSetter tunableSetter, Map<String,Object> mparams) Returns a new cyni context object.
org.cytoscape.work.TaskIterator	createTaskIterator(Object context, org.cytoscape.model.CyNetworkFactory networkFactory, org.cytoscape.view.model.CyNetworkViewFactory networkViewFactory, org.cytoscape.model.CyNetworkManager networkManager, org.cytoscape.model.CyNetworkTableManager netTableMgr, org.cytoscape.model.subnetwork.CyRootNetworkManager rootNetMgr, org.cytoscape.view.vizmap.VisualMappingManager vmMgr, org.cytoscape.view.model.CyNetworkViewManager networkViewManager, org.cytoscape.view.layout.CyLayoutAlgorithmManager layoutManager, CyCyniMetricsManager metricsManager) Creates a task iterator containing the cyni tasks.
CyniCategory	getCategory() A method to get the category of the algorithm
String	getName() Returns the computer-readable name of the Cyni Algorithm.
boolean	isReady(Object Context) Returns true if the task factory is ready to produce a task iterator.
boolean	supportsSelectedOnly() Tests to see if this Cyni supports doing a Cyni Algorithm on a subset of the nodes.

Method Detail

createTaskIterator

org.cytoscape.work.TaskIterator createTaskIterator(Object context,
                                                   org.cytoscape.model.CyNetworkFactory networkFactory,
                                                   org.cytoscape.view.model.CyNetworkViewFactory networkViewFactory,
                                                   org.cytoscape.model.CyNetworkManager networkManager,
                                                   org.cytoscape.model.CyNetworkTableManager netTableMgr,
                                                   org.cytoscape.model.subnetwork.CyRootNetworkManager rootNetMgr,
                                                   org.cytoscape.view.vizmap.VisualMappingManager vmMgr,
                                                   org.cytoscape.view.model.CyNetworkViewManager networkViewManager,
                                                   org.cytoscape.view.layout.CyLayoutAlgorithmManager layoutManager,
                                                   CyCyniMetricsManager metricsManager)

Creates a task iterator containing the cyni tasks.

Parameters:

context - The cyni context for this cyni algorithm.

networkFactory - The network factory to create a new network

networkViewFactory - The network view factory to create a new network view

networkManager - The network manager

netTableMgr - The network table manager

rootNetMgr - The root network manager

networkViewManager - The network view manager

layoutManager - The layout manager to apply a layout if a new network is created

tunableSetter - the setter if cyni is not called through the GUI

metricsManager - The metrics manager to access to all available metrics

mparams - The map to the input paramters to be used if cyni is not called through the GUI

Returns:

taskIterator contains cyni tasks.

isReady

boolean isReady(Object Context)

Returns true if the task factory is ready to produce a task iterator.

Parameters:

Context - The layout context for this cyni algorithm.

Returns:

true if the task factory is ready to produce a task iterator.

createCyniContext

Object createCyniContext(org.cytoscape.model.CyTable table,
                         CyCyniMetricsManager metricsManager,
                         org.cytoscape.work.TunableSetter tunableSetter,
                         Map<String,Object> mparams)

Returns a new cyni context object. This method can be used to create custom configurations for cyni algorithms.

Parameters:

table - The table where to get the data.

metricsManager - The cyni metrics manager.

tunableSetter - The tunable setter to set the parameters if not GUI is used.

mparams - The map of each one of the parameters with the value of the parameter.

Returns:

a new cyni context object.

supportsSelectedOnly

boolean supportsSelectedOnly()

Tests to see if this Cyni supports doing a Cyni Algorithm on a subset of the nodes.

Returns:

true if cyni algorithm supports only applying the algorithm on a subset of the nodes

getName

String getName()

Returns the computer-readable name of the Cyni Algorithm. To get a human readable name, use toString().

Returns:

The computer-readable name of the Cyni Algorithm.

getCategory

CyniCategory getCategory()

A method to get the category of the algorithm

Returns:

the Cyni category for the algorithm