/* -*-Java-*-
********************************************************************************
*
* File: CytoscapeEditorPlugin.java
* RCS: $Header: $
* Description:
* Author: Allan Kuchinsky
* Created: Mon Aug 01 08:42:41 2005
* Modified: Mon Aug 18 07:41:47 2008 (Michael L. Creech) creech@w235krbza760
* Language: Java
* Package:
/*
Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
any later version.
This library is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
documentation provided hereunder is on an "as is" basis, and the
Institute for Systems Biology and the Whitehead Institute
have no obligations to provide maintenance, support,
updates, enhancements or modifications. In no event shall the
Institute for Systems Biology and the Whitehead Institute
be liable to any party for direct, indirect, special,
incidental or consequential damages, including lost profits, arising
out of the use of this software and its documentation, even if the
Institute for Systems Biology and the Whitehead Institute
have been advised of the possibility of such damage. See
the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*
* Revisions:
*
* Wed Jul 09 10:21:03 2008 (Michael L. Creech) creech@w235krbza760
* Updated to version 2.60.
* Tue Oct 30 11:22:23 2007 (Michael L. Creech) creech@w235krbza760
* Updated to version 2.53.
* Thu Oct 25 13:30:25 2007 (Michael L. Creech) creech@w235krbza760
* Updated to version 2.52.
* Thu Jul 19 13:29:22 2007 (Michael L. Creech) creech@w235krbza760
* Removed use of _initialized and simplified to assume CytoscapeEditor
* is always loaded before any other editor. Removed
* unneeded definitions of getPluginInfoObject() and describe().
* Fri May 11 16:37:23 2007 (Michael L. Creech) creech@w235krbza760
* Updated VERSION to 2.50 and added getPluginInfoObject() for Cytoscape 2.5.
* Fri Dec 15 10:08:07 2006 (Michael L. Creech) creech@w235krbza760
* Hacked a fix for not reinitializing the plugin if it is loaded
* first by another plugin.
* Sat Aug 05 08:14:51 2006 (Michael L. Creech) creech@w235krbza760
* Removed deprecated call to CytoscapeInit.getDefaultVisualStyle() in
* initializeCytoscapeEditor().
* Mon Jul 24 08:43:51 2006 (Michael L. Creech) creech@w235krbza760
* Removed some misleading code--println that editor is loaded and
* initialization code as though editor is initialized via a menu item, when
* it is not.
********************************************************************************
*/
package cytoscape.editor;
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
import cytoscape.editor.neo4j.neoPlugin;
import cytoscape.plugin.CytoscapePlugin;
/**
* core plugin for CytoscapeEditor.
*
* @author Allan Kuchinsky, Agilent Technologies
* @version 1.0
*
*/
public class CytoscapeEditorPlugin extends CytoscapePlugin {
// MLC 07/20/07:
// private static boolean _initialized = false;
// MLC 07/20/07:
private static final double VERSION = 2.60;
/**
* Creates a new CytoscapeEditorPlugin object.
*/
public CytoscapeEditorPlugin() {
// MLC 07/24/06 BEGIN:
// CytoscapeEditorManager.log("CytoscapeEditor loaded ");
// MainPluginAction mpa = new MainPluginAction();
// CytoscapeEditorManager.setRunningEditorFramework(true);
// CytoscapeEditorManager.log("Setting up CytoscapeEditor");
// mpa.initializeCytoscapeEditor();
// MLC 07/23/07:
//CytoscapeEditorManager.setLoggingEnabled(true);
initializeCytoscapeEditor();
//Trying to create a Plugin that reads from a Neo4j database
//neoPlugin neo4j=new neoPlugin();
// MLC 07/24/06 END.
}
// MLC 07/20/07 BEGIN:
// // overrides CytoscapePlugin.getPluginInfoObject():
// public PluginInfo getPluginInfoObject() {
// PluginInfo info = new PluginInfo();
// info.setName("CytoscapeEditor");
// info.setDescription("Add nodes and edges to a Cytoscape Network.");
//// info.setCategory(PluginInfo.Category.CORE);
//// info.setPluginVersion("2.5.01");
// info.setCytoscapeVersion("2.5");
// // info.setProjectUrl("http://www.cytoscape.org/download_agilent_literature_search_v2.5.php?file=litsearch_v2.4");
// info.addAuthor("Allan Kuchinsky", "Agilent Labs");
// info.addAuthor("Michael Creech", "Blue Oak Software");
// return info;
// }
// MLC 07/20/07 END.
// MLC 07/20/07 BEGIN:
// /**
// * Overrides CytoscapePlugin.describe():
// */
// public String describe() {
// return "Add nodes and edges to a Cytoscape Network. ";
// }
/**
* sets various flags and registers various editors with the CytoscapeEditorManager
*
*/
private void initializeCytoscapeEditor() {
// public static void initializeCytoscapeEditor() {
//if (_initialized) {
// return;
// }
// CytoscapeEditorManager.setRunningEditorFramework(true);
// CytoscapeEditorManager.setEditingEnabled(true);
// MLC 07/20/07 END.
CytoscapeEditorManager.initialize();
// add default palette-based editor
CytoscapeEditorManager.register(CytoscapeEditorManager.DEFAULT_EDITOR_TYPE,
"cytoscape.editor.event.PaletteNetworkEditEventHandler",
// AJK: 02/03/06 have Default editor use current visual
// style
CytoscapeEditorManager.NODE_TYPE, CytoscapeEditorManager.EDGE_TYPE, CytoscapeEditorManager.NETWORK_TYPE, CytoscapeEditorManager.ANNOTATION_TEXT_TYPE, CytoscapeEditorManager.ANNOTATION_SHAPE_TYPE, CytoscapeEditorManager.ANNOTATION_BOUNDED_TYPE, CytoscapeEditorManager.ANNOTATION_IMAGE_TYPE,
CytoscapeEditorManager.ANY_VISUAL_STYLE);
// AJK: 12/09/06 SimpleBioMoleculeEditor deleted
/*
CytoscapeEditorManager.register("SimpleBioMoleculeEditor",
"cytoscape.editor.event.PaletteNetworkEditEventHandler",
CytoscapeEditorManager.NODE_TYPE, CytoscapeEditorManager.EDGE_TYPE,
MapBioMoleculeEditorToVisualStyle.BIOMOLECULE_VISUAL_STYLE);
*/
// AJK: 12/09/06 BEGIN
// register an editor to handle BioPAX visual style
// TODO: this is a short-term contingency, to be overhauled
// when vizmapper is overhauled for Cytoscape 2.5
// CytoscapeEditorManager.register("cytoscape.editor.editors.SimpleBioPAXEditor",
// "cytoscape.editor.event.PaletteNetworkEditEventHandler",
// "biopax.entity_type", // controlling node attribute
// "BIOPAX_EDGE_TYPE", // controlling edge type
// "BioPAX v 0_5");
//
// AJK: 12/09/06 END
String editorName = CytoscapeEditorManager.DEFAULT_EDITOR_TYPE;
try {
CytoscapeEditor cyEditor = CytoscapeEditorFactory.INSTANCE.getEditor(editorName);
CytoscapeEditorManager.setCurrentEditor(cyEditor);
// MLC 08/06/06:
// CytoscapeEditorManager.setDefaultEditor(cyEditor);
} catch (InvalidEditorException ex) {
CytoscapeEditorManager.log("Error: cannot set up Cytoscape Editor: " + editorName);
}
Cytoscape.getDesktop().setVisualStyle(Cytoscape.getVisualMappingManager()
.getCalculatorCatalog()
.getVisualStyle( // MLC 08/06/06:
// CytoscapeInit.getDefaultVisualStyle()));
// MLC 08/06/06:
CytoscapeInit.getProperties().getProperty("defaultVisualStyle")));
// MLC 07/20/07:
// _initialized = true;
}
// MLC 07/24/06 BEGIN:
// public class MainPluginAction extends AbstractAction {
// public MainPluginAction() {
// super("Cytoscape Editor");
// }
//
// /**
// * Gives a description of this plugin.
// */
// public String describe() {
// StringBuffer sb = new StringBuffer();
// sb.append("Add nodes and edges to a Cytoscape Network. ");
// return sb.toString();
// }
//
// /**
// * This method is called when the user selects the menu item.
// */
// public void actionPerformed(ActionEvent ae) {
// initializeCytoscapeEditor();
// }
//
// /**
// * sets various flags and registers various editors with the CytoscapeEditorManager
// *
// */
// public void initializeCytoscapeEditor() {
//
//
// CytoscapeEditorManager.setEditingEnabled(false);
//
// CytoscapeEditorManager.initialize();
//
// // add default palette-based editor
// CytoscapeEditorManager.register(
// CytoscapeEditorManager.DEFAULT_EDITOR_TYPE,
// "cytoscape.editor.event.PaletteNetworkEditEventHandler",
// // AJK: 02/03/06 have Default editor use current visual
// // style
// CytoscapeEditorManager.NODE_TYPE,
// CytoscapeEditorManager.EDGE_TYPE,
// CytoscapeEditorManager.ANY_VISUAL_STYLE);
//
// CytoscapeEditorManager.register("SimpleBioMoleculeEditor",
// "cytoscape.editor.event.PaletteNetworkEditEventHandler",
// CytoscapeEditorManager.NODE_TYPE,
// CytoscapeEditorManager.EDGE_TYPE,
// MapBioMoleculeEditorToVisualStyle.BIOMOLECULE_VISUAL_STYLE);
//
// String editorName = CytoscapeEditorManager.DEFAULT_EDITOR_TYPE;
// try {
// CytoscapeEditor cyEditor = CytoscapeEditorFactory.INSTANCE
// .getEditor(editorName);
// CytoscapeEditorManager.setCurrentEditor(cyEditor);
// CytoscapeEditorManager.setDefaultEditor(cyEditor);
// } catch (InvalidEditorException ex) {
// CytoscapeEditorManager.log("Error: cannot set up Cytoscape Editor: "
// + editorName);
// }
//
// Cytoscape.getDesktop().setVisualStyle(
// Cytoscape.getVisualMappingManager()
// .getCalculatorCatalog().getVisualStyle(
// CytoscapeInit.getDefaultVisualStyle()));
// }
//
// }
// MLC 07/24/06 END.
}