CytoscapeEditorFramework - Cytoscape Wiki

Extensible Framework for Cytoscape Editor

Note: This framework will be superceded by the CytoscapeEditor3.0 framework. Please refer to that page for details.

Cytoscape has a set of editors that enable the user to build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window. The palette contains a set of shapes (for nodes) and arrows (for edges). The shapes on the palette are defined by the current Visual Style, with Node Shape and Node Color mapping into the shape and color of a node, and Edge Target Arrow mapping into the target arrow of an edge.

The set of classes for the CytoscapeEditor is are extensible by both developers and end users. End users can extend the editor by defining a new visual style in which Node Shape, Node Color, and Edge Target Arrow are associated with a controlling attribute, defaulting to NODE_TYPE and EDGE_TYPE, respectively. Developers can extend the editor framework by plugging in semantic callback methods that are invoked when editor operations, such as adding and deleting Nodes and Edges, are performed. Such semantic methods might include

restricting the kinds of Nodes that can be connected to a particular type of Edge, or
prompting the user, when a Node has been dropped onto the canvas, to select and entity from a database.

Developers may also provide new editors, palette shapes, and event handlers by extending the classes in the editor framework.

The packages, interfaces and classes that exist in the CytoscapeEditor in Cytoscape version 2.3. are:

Package	Class or Interface	Description
cytoscape.editor		top-level classes and interfaces
	CytoscapeEditor	interface for common methods that all editors must implement, such as adding/deleting nodes and edges, handling palette controls
	CytoscapeEditorFactory	Interface used for building new instances of editors. Before an editor can be built, it first needs to be registered with the CytoscapeEditorManager
	CytoscapeEditorManager	Static routines for managing editors, views, event handlers, global variables
	CytoscapeEditorPlugin	encapsulating plugin class that builds the initial set of editors
	GraphicalEntity	Interface for defining draggable/droppable visual components. Graphical entities are associated with semantic objects, i.e. Nodes and Edges, that are created when the graphical entities are dropped onto the canvas.
	InvalidEditorException	Creates a new exception when there is no registered editor corresponding to the editor type suppied to the CytoscapeEditorFactory.getEditor() method
cytoscape.editor.editors		classes for editors provided with Cytoscape
	BasicCytoscapeEditor	provides base-level functionality present in all editors, such as adding and deleting nodes and edges, building palettes
	DefaultCytoscapeEditor	An example editor that extends the Basic'CytoscapeEditor and contains one default Node and one default Edge on its palette. This editor defines the Node and Edge shapes on its palette using the current Visual Style
	SimpleBioMoleculeEditor	an example editor that defines the nodes and shapes on its palette using the SimpleBioMolecule Visual Style, which contains a simple set of colored shapes that represent biological entities
	MapBioMoleculeToVisualStyle	Creates the SimpleBioMolecule Visual Style
	SimpleBioPAX_Editor	a example editor that defines the nodes and shapes on its palette using a Visual Style that maps node shapes and colors according to the value of the "BIOPAX_NODE_TYPE" attribute and maps edge target arrows according to the value of the "BIOPAX_EDGE_TYPE" attribute. (Note that this is not yet a fully functional BioPAX editor)
cytoscape.editor.event		event handlers used by the different editors
	NetworkEditEventAdapter	contains stub methods for handling mouse actions, drag/drop actions, attribute value change events
	BasicCytoShapeTranfserHandler	A transfer handler for shapes that are dragged from the palette onto the canvas.
	NetworkEditEventAdapter	contains stub methods for handling mouse actions, drag/drop actions, attribute value change events
	BasicNetworkEditEventHandler	extends NetworkEditEventAdapter, implementing methods for handling mouse actions, drag/drop actions, attribute value change events, as well as three core methods for creating Nodes and beginning and finishing Edges
	PaletteNetworkEditEventHandler	extends the BasicNetworkEditEventHandler with the capability to drag and drop shapes from a palette onto the canvas
	BioPAXNetworkEditEventHandler	extends the PaletteNetworkEditEventHandler with methods for setting BioPAX-related attributes on Nodes and Edges
cytoscape.editor.impl		implementation and utility classes
	BasicCytoShapeEntity	base class for draggable/droppable shapes on the palette
	CytoShapeIcon	Specialized Icon for Cytoscape editor palette entry. Renders icon based upon input shape, size, color, as defined by the Visual Style that is used by the current editor.
	ShapePalette	methods for building, displaying the palette, adding shapes to the palette, rendering shapes, and handling drag/drop events. (Should this be an Interface with extending classes?)
	CytoscapeEditorFactoryImpl	implementation of CytoscapeEditorFactory Interface, builds new instances of editors and network edit event adapters
	CytoscapeEditorManagerSupport	provides non-static methods needed by the CytoscapeEditorManager, such as listeners for Swing property changes, graph perspective changes, and visual style changes
	StringTransferHandler	base class for the TransferHandler used by the ShapePalette for drag operations
cytoscape.editor.actions		actions associated with buttons and other UI components
	NewNetworkAction	creates a new network and associates an editor with it
	DeleteAction	context menu item for deleting selected Nodes and Edges (not used in Cytoscape version 2.2)
	UndoAction	action for undoing an edit
	RedoAction	action for redoing an edit

Add a comment about these ideas: /Editor Framework Comment

Open Issues

How much can be made user-extensible? It would be straightforward -- but not interactive -- to enable the user to define a new palette by building a visual style for it. Could event handling and semantics be made user-extensible as well? Should it be?
Where best to put hooks for semantic processing? Should they be at the point of adding a node and starting and finishing an edge? Should it be more fine-grained, e.g. place a hook in all events that are responded to, such as mousePressed()?
How best to make decisions based upon results of semantic processing? Should the semantic processing callback method return a boolean result, a result of false resulting in aborting the node or edge addition? Alternatively, should it return an object that contains attributes and other information for the Node or Edge to be added? Would that be required in order to do things like add from databases?
How to make accelerators and other functionality more accessible/apparent to the end user? Can't expect that the user will read the Help docs; it should be a walk up and use functionality.
For Cytoscape 2.3, the undo facility is implemented as a single stack of undoable edits, all of which are deleted when the user switches views. This is much simpler and less ambiguous than earlier strategies which attempted to keep one edit stack for each view.
Does there need to be a BioPAX exporter to go with a BioPAX editor?
Are there still remnants of Piccolo code that need to be removed?

The attachment CytoscapeEditor.zip contains a snapshot of Java source and javadoc folders as of Sunday, 25th June 2006.

Add a comment about these issues: /Editor Framework Issues Comment