idare.imagenode.internal

Class IDAREImageNodeApp

java.lang.Object

idare.imagenode.internal.IDAREImageNodeApp

All Implemented Interfaces:

org.cytoscape.event.CyListener, org.cytoscape.session.events.SessionAboutToBeSavedListener

public class IDAREImageNodeApp
extends Object
implements org.cytoscape.session.events.SessionAboutToBeSavedListener

The core class of the app, generates necessary objects for the class and provides them to external requests.

Author:

Thomas Pfau

Constructor Summary

Constructors

Constructor and Description
IDAREImageNodeApp(org.cytoscape.service.util.CyServiceRegistrar reg, IDARESettingsManager ism) Basic constructor that gets the IDareSettingsManager along with a CyServiceRegistrar to obtain all necessary services.

Method Summary

Modifier and Type	Method and Description
void	deRegisterDataSetProperties(Class<? extends DataSet> dataSetClass, DataSetLayoutProperties props) Deregister DataSetProperties from a DataSet of the given Type.
void	deRegisterDataSetReader(IDAREDatasetReader reader) Deregister an IDAREDatasetReader from being available in the app.
void	deregisterDataSetType(DataSet ds) Deregister a the an available DataSet class based on an instance of the class.
void	deRegisterPlugin(IDAREPlugin plugin) UnRegister a plugin.
Vector<org.cytoscape.application.swing.AbstractCyAction>	getActions() Get the actions used in this app
ActiveNodeManager	getActiveNodeManager() Get the ActiveNodeManager created by this App
DataSetManager	getDatasetManager() Get the DataSetManager created by this App
DataSetControlPanel	getDataSetPanel() Obtain the DataSetControlPanel generated by this instance of IDARE.
HashMap<org.cytoscape.work.AbstractTaskFactory,Vector<Properties>>	getFactories() Get the Task Factories used in the App.
ImageStorage	getImageStorage() Get the ImageStorage created by this App
LayoutIOManager	getLayoutIOManager() Get The LayoutIOManager
IDARELegend	getLegend() Get the IDARELegend generated by this instance of IDARE.
NodeManager	getNodeManager() Get the NodeManager created by this App
IDARESettingsManager	getSettingsManager() Get the IDARESettingsManager created by this App
StyleManager	getStyleManager() Obtain the StyleManager generated by this instance of IDARE.
IDAREVisualStyle	getVisualStyle() Get the IDAREVisualStyle created by this App
void	handleEvent(org.cytoscape.session.events.SessionAboutToBeSavedEvent arg0)
void	handleSessionLoadedEvent(org.cytoscape.session.events.SessionLoadedEvent arg0) Handle a session load event.
Collection<DataSetLayoutProperties>	registerDataSetProperties(Class<? extends DataSet> dataSetClass, Collection<DataSetLayoutProperties> props) Register DataSetProperties for a DataSet of the given Type.
boolean	registerDataSetProperties(Class<? extends DataSet> dataSetClass, DataSetLayoutProperties props) Register DataSetProperties for a DataSet of the given Type.
void	registerDataSetReader(IDAREDatasetReader reader) Register an IDAREDatasetReader to be available in the app.
void	registerDataSetType(DataSet ds) Register a the type of a dataset provided to the set of avilable DataSet classes
void	registerPlugin(IDAREPlugin plugin) Register a plugin.
void	unregisterAll() Unregister all Types of DataSet, that were before registered.
protected void	updateServices(IDAREPlugin plugin, Vector<IDAREService> services, boolean registered, org.cytoscape.work.TaskMonitor monitor)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IDAREImageNodeApp

public IDAREImageNodeApp(org.cytoscape.service.util.CyServiceRegistrar reg,
                         IDARESettingsManager ism)

Basic constructor that gets the IDareSettingsManager along with a CyServiceRegistrar to obtain all necessary services.

Parameters:

reg - The CyServiceRegistrar for the current bundle

ism - The IDARESettingsManager used in this app

Method Detail

getStyleManager

public StyleManager getStyleManager()

Obtain the StyleManager generated by this instance of IDARE.

Returns:

The StyleManager used by this instance

getDataSetPanel

public DataSetControlPanel getDataSetPanel()

Obtain the DataSetControlPanel generated by this instance of IDARE.

Returns:

The DataSetControlPanel used by this instance

getLegend

public IDARELegend getLegend()

Get the IDARELegend generated by this instance of IDARE.

Returns:

The IDARELegend used by this instance

getVisualStyle

public IDAREVisualStyle getVisualStyle()

Get the IDAREVisualStyle created by this App

Returns:

The IDAREVisualStyle used by this instance

getImageStorage

public ImageStorage getImageStorage()

Get the ImageStorage created by this App

Returns:

The ImageStorage used by this instance

getNodeManager

public NodeManager getNodeManager()

Get the NodeManager created by this App

Returns:

The NodeManager used by this instance

getDatasetManager

public DataSetManager getDatasetManager()

Get the DataSetManager created by this App

Returns:

The DataSetManager used by this instance

getActiveNodeManager

public ActiveNodeManager getActiveNodeManager()

Get the ActiveNodeManager created by this App

Returns:

The ActiveNodeManager used by this instance

registerDataSetType

public void registerDataSetType(DataSet ds)
                         throws DuplicateIDException

Register a the type of a dataset provided to the set of avilable DataSet classes

Parameters:

ds - An instance of a DataSet which is of the class to register.

Throws:

DuplicateIDException - if there are two datasets with the same type name

deregisterDataSetType

public void deregisterDataSetType(DataSet ds)

Deregister a the an available DataSet class based on an instance of the class.

Parameters:

ds - An instance of a DataSet object that belongs t the class that is supposed to be registered

registerDataSetProperties

public boolean registerDataSetProperties(Class<? extends DataSet> dataSetClass,
                                         DataSetLayoutProperties props)

Register DataSetProperties for a DataSet of the given Type.

Parameters:

dataSetClass - the classname of the DataSet, for which to add the properties

props - The DataSetproperties to make available.

Returns:

whether the dataset type could be added

registerDataSetProperties

public Collection<DataSetLayoutProperties> registerDataSetProperties(Class<? extends DataSet> dataSetClass,
                                                                     Collection<DataSetLayoutProperties> props)

Register DataSetProperties for a DataSet of the given Type.

Parameters:

dataSetClass - the classname of the DataSet, for which to add the properties

props - The collection of DataSetproperties to make available to this type of dataset.

Returns:

A set of Properties that could not be registered

deRegisterDataSetProperties

public void deRegisterDataSetProperties(Class<? extends DataSet> dataSetClass,
                                        DataSetLayoutProperties props)

Deregister DataSetProperties from a DataSet of the given Type.

Parameters:

dataSetClass - the classname of the DataSet to deregister the properties from

props - The properties to deregister.

deRegisterDataSetReader

public void deRegisterDataSetReader(IDAREDatasetReader reader)

Deregister an IDAREDatasetReader from being available in the app.

Parameters:

reader - the IDAREDatasetReader to deregister.

registerDataSetReader

public void registerDataSetReader(IDAREDatasetReader reader)

Register an IDAREDatasetReader to be available in the app.

Parameters:

reader - the IDAREDatasetReader to register.

unregisterAll

public void unregisterAll()

Unregister all Types of DataSet, that were before registered. This will reset the NodeManager, as all Sets have been disabled and will also reset the ImageStorage.

getSettingsManager

public IDARESettingsManager getSettingsManager()

Get the IDARESettingsManager created by this App

Returns:

The IDARESettingsManager used by this instance

handleSessionLoadedEvent

public void handleSessionLoadedEvent(org.cytoscape.session.events.SessionLoadedEvent arg0)

Handle a session load event. This class does not implement the SessionLoadedListener itself, as the order of loading is relevant.

Parameters:

arg0 - The SessionLoadedEvent that provides information on the state of the app in the loaded session.

handleEvent

public void handleEvent(org.cytoscape.session.events.SessionAboutToBeSavedEvent arg0)

Specified by:

handleEvent in interface org.cytoscape.session.events.SessionAboutToBeSavedListener

getFactories

public HashMap<org.cytoscape.work.AbstractTaskFactory,Vector<Properties>> getFactories()

Get the Task Factories used in the App.

Returns:

the TaskFactories produced by the IDARE App matched to all properties for which they should eb registered

getLayoutIOManager

public LayoutIOManager getLayoutIOManager()

Get The LayoutIOManager

Returns:

The Layoutmanager of this app

getActions

public Vector<org.cytoscape.application.swing.AbstractCyAction> getActions()

Get the actions used in this app

Returns:

The Vector of AbstractCyActions generated by this App.

registerPlugin

public void registerPlugin(IDAREPlugin plugin)

Register a plugin.

Parameters:

plugin - the plugin to register

deRegisterPlugin

public void deRegisterPlugin(IDAREPlugin plugin)

UnRegister a plugin.

Parameters:

plugin - the plugin to unregister.

updateServices

protected void updateServices(IDAREPlugin plugin,
                              Vector<IDAREService> services,
                              boolean registered,
                              org.cytoscape.work.TaskMonitor monitor)
                       throws IllegalAccessException,
                              InstantiationException

Throws:

IllegalAccessException

InstantiationException