cytoscape.editor.editors
Class SimpleBioMoleculeEditor

java.lang.Object
  extended bycytoscape.editor.editors.BasicCytoscapeEditor
      extended bycytoscape.editor.editors.SimpleBioMoleculeEditor
All Implemented Interfaces:
CytoscapeEditor, ding.view.EdgeContextMenuListener, java.util.EventListener, cytoscape.data.FlagEventListener, ding.view.NodeContextMenuListener

public class SimpleBioMoleculeEditor
extends BasicCytoscapeEditor

An example editor that extends the basic Cytoscape editor and is based upon a drag-and-drop and palette framework into which developers plug in semantics. The framework consists of

The dropping of shapes onto the canvas results in the addition of nodes and edges to the current Cytoscape network, as defined by the behavior of the event handler that responds to the drop events. In the simple "BioMolecule" editor, there are node types for proteins, catalysis, small molecules, and biochemical reactions, as well as a directed edge types for activation, inhibition, and catalysis.

Version:
1.0
Author:
Allan Kuchinsky
See Also:
PaletteNetworkEditEventHandler

Field Summary
static java.lang.String ACTIVATION
           
static java.lang.String BIOMOLECULE_VISUAL_STYLE
           
static java.lang.String CATALYSIS
           
static java.lang.String EDGE_TYPE
           
static java.lang.String INHIBITION
           
static MapBioMoleculeEditorToVisualStyle mpbv
          class used to construct visual style used by the SimpleBioMoleculeEditor
static java.lang.String NODE_TYPE
           
 
Fields inherited from class cytoscape.editor.editors.BasicCytoscapeEditor
BIOPAX_NAME_ATTRIBUTE
 
Constructor Summary
SimpleBioMoleculeEditor()
           
 
Method Summary
 void buildVisualStyle()
          build the visualStyle for this editor this code should be overidden by more specialized editors that programmatically create a visual style
 void disableControls(java.util.List args)
          sets controls invisible when editor type is switched
 void enableControls(java.util.List args)
          sets controls visible when editor type is switched back to this editor
 void initializeControls(java.util.List args)
          specialized initialization code for editor, called by CytoscapeEditorManager when a new editor is built.
 
Methods inherited from class cytoscape.editor.editors.BasicCytoscapeEditor
addEdge, addEdge, addEdge, addEdge, addEdgeContextMenuItems, addNode, addNode, addNode, addNode, addNodeContextMenuItems, deleteEdge, deleteNode, getControllingEdgeAttribute, getControllingNodeAttribute, getEditorName, getNetworkEditEventAdapter, menuItemExists, onFlagEvent, setControllingEdgeAttribute, setControllingNodeAttribute, setEditorName, setNetworkEditEventAdapter
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

NODE_TYPE

public static final java.lang.String NODE_TYPE
See Also:
Constant Field Values

EDGE_TYPE

public static final java.lang.String EDGE_TYPE
See Also:
Constant Field Values

ACTIVATION

public static final java.lang.String ACTIVATION
See Also:
Constant Field Values

INHIBITION

public static final java.lang.String INHIBITION
See Also:
Constant Field Values

CATALYSIS

public static final java.lang.String CATALYSIS
See Also:
Constant Field Values

BIOMOLECULE_VISUAL_STYLE

public static final java.lang.String BIOMOLECULE_VISUAL_STYLE
See Also:
Constant Field Values

mpbv

public static MapBioMoleculeEditorToVisualStyle mpbv
class used to construct visual style used by the SimpleBioMoleculeEditor

Constructor Detail

SimpleBioMoleculeEditor

public SimpleBioMoleculeEditor()
Method Detail

buildVisualStyle

public void buildVisualStyle()
Description copied from class: BasicCytoscapeEditor
build the visualStyle for this editor this code should be overidden by more specialized editors that programmatically create a visual style

Specified by:
buildVisualStyle in interface CytoscapeEditor
Overrides:
buildVisualStyle in class BasicCytoscapeEditor

initializeControls

public void initializeControls(java.util.List args)
specialized initialization code for editor, called by CytoscapeEditorManager when a new editor is built. gets the mappings from the visual style and uses them to construct shapes for the palette

Specified by:
initializeControls in interface CytoscapeEditor
Overrides:
initializeControls in class BasicCytoscapeEditor
Parameters:
args - an arbitrary list of arguments passed to initialization routine. Not used in this editor

disableControls

public void disableControls(java.util.List args)
sets controls invisible when editor type is switched

Specified by:
disableControls in interface CytoscapeEditor
Overrides:
disableControls in class BasicCytoscapeEditor
Parameters:
args - args an arbitrary list of arguments (not used in this editor)

enableControls

public void enableControls(java.util.List args)
sets controls visible when editor type is switched back to this editor

Specified by:
enableControls in interface CytoscapeEditor
Overrides:
enableControls in class BasicCytoscapeEditor
Parameters:
args - args an arbitrary list of arguments (not used in this editor) *