package org.gvt.action;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level2.pathway;
import org.biopax.paxtools.model.level2.conversion;
import org.biopax.paxtools.model.level2.pathwayComponent;
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.eclipse.swt.graphics.Color;
import org.gvt.ChisioMain;
import org.gvt.GraphAnimation;
import org.gvt.editpart.ChsScalableRootEditPart;
import org.gvt.figure.HighlightLayer;
import org.gvt.model.biopaxl2.BioPAXEdge;
import org.gvt.model.biopaxl2.BioPAXGraph;
import org.gvt.model.biopaxl2.IBioPAXNode;
import org.gvt.model.biopaxl2.Conversion;
import org.gvt.util.BioPAXReader;
import org.patika.mada.graph.GraphObject;
import java.util.*;
/**
* @author Ozgun Babur
*
* Copyright: Bilkent Center for Bioinformatics, 2007 - present
*/
public class UpdatePathwayAction extends Action
{
private ChisioMain main;
/**
* If true, then all open views will be updated. Otherwise only the current view will be
* updated.
*/
private boolean allOpenPathways;
/**
* Parameter for recreating root graph.
*/
private boolean withRoot;
/**
* This collection is used when user wants to update contents of the pathway.
*/
private Collection<GraphObject> withContent;
public UpdatePathwayAction(ChisioMain main, boolean allOpenPathways)
{
super(allOpenPathways ? "Update All Open Pathways" : "Update Pathway");
if (allOpenPathways)
{
setImageDescriptor(ImageDescriptor.createFromFile(ChisioMain.class, "icon/pathway-update-all.png"));
}
this.setToolTipText(this.getText());
this.main = main;
this.allOpenPathways = allOpenPathways;
withRoot = allOpenPathways;
}
public UpdatePathwayAction(ChisioMain main, Collection<GraphObject> withContent)
{
this(main, false);
this.withContent = withContent;
}
// Replace graph
private void updateViewerContent(ScrollingGraphicalViewer viewer)
{
BioPAXGraph graph = (BioPAXGraph) viewer.getContents().getModel();
// Updating is supported only for mechanistic views
if (!graph.isMechanistic()) return;
// Remember highlighted object's original nodes (members of chisio root graph)
Map<Integer, Color> highlightMap = new HashMap<Integer, Color>();
for (Object o : graph.getNodes())
{
IBioPAXNode node = (IBioPAXNode) o;
if (node.isHighlighted())
{
highlightMap.put(node.getIDHash(), node.getHighlightColor());
}
}
for (Object o : graph.getEdges())
{
BioPAXEdge edge = (BioPAXEdge) o;
if (edge.isHighlighted())
{
highlightMap.put(edge.getIDHash(), edge.getHighlightColor());
}
}
// Reset highlight
HighlightLayer hLayer = (HighlightLayer)
((ChsScalableRootEditPart) viewer.getRootEditPart()).getLayer(
HighlightLayer.HIGHLIGHT_LAYER);
hLayer.removeAll();
hLayer.highlighted.clear();
viewer.deselectAll();
// Record layout
graph.recordLayout();
// Create updated graph
pathway p = graph.getPathway();
// Update pathway components if update needed
if (withContent != null)
{
for (pathwayComponent pc : new HashSet<pathwayComponent>(p.getPATHWAY_COMPONENTS()))
{
p.removePATHWAY_COMPONENTS(pc);
}
Set<conversion> convSet = new HashSet<conversion>();
for (GraphObject go : withContent)
{
if (go instanceof Conversion)
{
Conversion conv = (Conversion) go;
conversion cnv = conv.getConversion();
convSet.add(cnv);
}
}
Set<pathwayComponent> components = p.getPATHWAY_COMPONENTS();
for (conversion cnv : convSet)
{
if (!components.contains(cnv))
{
p.addPATHWAY_COMPONENTS(cnv);
}
}
}
// Excise pathway
BioPAXGraph newGraph = main.getRootGraph().excise(p);
newGraph.setName(p.getNAME());
newGraph.setAsRoot();
// Replace the graph
viewer.setContents(newGraph);
// Use same layout
boolean layedout = newGraph.fetchLayout();
if (!layedout)
{
new CoSELayoutAction(main).run();
}
viewer.deselectAll();
GraphAnimation.run(viewer);
// Recover highlights
for (Object o : newGraph.getNodes())
{
IBioPAXNode node = (IBioPAXNode) o;
if (highlightMap.containsKey(node.getIDHash()))
{
node.setHighlightColor(highlightMap.get(node.getIDHash()));
node.setHighlight(true);
}
}
for (Object o : newGraph.getEdges())
{
BioPAXEdge edge = (BioPAXEdge) o;
if (highlightMap.containsKey(edge.getIDHash()))
{
edge.setHighlightColor(highlightMap.get(edge.getIDHash()));
edge.setHighlight(true);
}
}
}
private void updateRoot()
{
BioPAXGraph root = (BioPAXGraph) new BioPAXReader(main.getOwlModel()).readXMLFile(null);
main.setRootGraph(root);
}
public void run()
{
Model model = main.getOwlModel();
if (model == null)
{
MessageDialog.openError(main.getShell(), "Error!",
"Load or query a BioPAX model first!");
return;
}
if (withRoot)
{
updateRoot();
}
if (allOpenPathways)
{
for (ScrollingGraphicalViewer viewer : main.getTabToViewerMap().values())
{
updateViewerContent(viewer);
}
}
else
{
updateViewerContent(main.getViewer());
}
}
}