package org.gvt.action;
import org.eclipse.gef.ui.parts.ScrollingGraphicalViewer;
import org.eclipse.jface.action.Action;
import org.eclipse.jface.dialogs.MessageDialog;
import org.eclipse.jface.resource.ImageDescriptor;
import org.gvt.ChisioMain;
import org.gvt.model.BioPAXGraph;
import org.gvt.util.PathwayHolder;
/**
* Action for closing the currently open tab.
*
* @author Ozgun Babur
*
* Copyright: Bilkent Center for Bioinformatics, 2007 - present
*/
public class DuplicatePathwayAction extends Action
{
private ChisioMain main;
/**
* Constructor
*/
public DuplicatePathwayAction(ChisioMain main)
{
super("Duplicate Pathway");
setImageDescriptor(ImageDescriptor.createFromFile(ChisioMain.class, "icon/pathway-create-duplicate.png"));
setToolTipText(getText());
this.main = main;
}
public void run()
{
ScrollingGraphicalViewer viewer = main.getViewer();
BioPAXGraph pathwayGraph = main.getPathwayGraph();
if (pathwayGraph == null)
{
MessageDialog.openError(main.getShell(), "Error!", "No BioPAX pathway.");
return;
}
if (viewer != null)
{
BioPAXGraph original = (BioPAXGraph) viewer.getContents().getModel();
if (!original.isMechanistic())
{
MessageDialog.openError(main.getShell(), "Not Supported!",
"Duplication is supported only in mechanistic views.");
return;
}
original.recordLayout();
PathwayHolder p = original.getPathway();
BioPAXGraph graph = main.getRootGraph().excise(p);
graph.setPathway(null);
String name = p.getName();
// If the name contains a copy number at the end (like "pathway name (2)"), remove it
if (name.indexOf(" ") > 0)
{
String last = name.substring(name.lastIndexOf(" ") + 1);
if (last.indexOf("(") == 0 && last.indexOf(")") == last.length() - 1)
{
boolean isdigit = true;
for (int i = 1; isdigit && i < last.length() - 1; i++)
{
isdigit = Character.isDigit(last.charAt(i));
}
if (isdigit) name = name.substring(0, name.lastIndexOf(" "));
}
}
graph.setName(name);
main.createNewTab(graph);
graph.fetchLayout(original.getPathwayRDFID());
}
}
}