/** Split objects into normal and disease components */
private void splitObjects() {
normalIds = new HashSet<Long>();
diseaseIds = new HashSet<Long>();
RenderablePathway diagram = (RenderablePathway) getRenderable();
if (pathway == null || diagram.getReactomeDiagramId() == null) return;
try {
GKInstance pdInst = adaptor.fetchInstance(diagram.getReactomeDiagramId());
// Get the disease pathway instance
List<GKInstance> pathways =
pdInst.getAttributeValuesList(ReactomeJavaConstants.representedPathway);
GKInstance diseasePathway = null;
GKInstance normalPathway = null;
GKInstance disease = (GKInstance) pathway.getAttributeValue(ReactomeJavaConstants.disease);
if (disease == null && contains(pathway, pathways)) {
normalPathway = pathway;
} else {
diseasePathway = pathway;
// There should be a normal pathway contained by a disease pathway
List<?> subPathways = diseasePathway.getAttributeValuesList(ReactomeJavaConstants.hasEvent);
for (Object obj : subPathways) {
GKInstance subPathway = (GKInstance) obj;
disease = (GKInstance) subPathway.getAttributeValue(ReactomeJavaConstants.disease);
if (disease == null && contains(subPathway, pathways)) {
normalPathway = subPathway;
break;
}
}
}
if (normalPathway != null) {
// Get all disease related objects
Set<GKInstance> normalEvents = InstanceUtilities.grepPathwayEventComponents(normalPathway);
for (GKInstance inst : normalEvents) normalIds.add(inst.getDBID());
Set<GKInstance> normalEntities = InstanceUtilities.grepPathwayParticipants(normalPathway);
for (GKInstance inst : normalEntities) normalIds.add(inst.getDBID());
if (diseasePathway != null) {
Set<GKInstance> allEvents = InstanceUtilities.grepPathwayEventComponents(diseasePathway);
allEvents.removeAll(normalEvents);
for (GKInstance inst : allEvents) {
diseaseIds.add(inst.getDBID());
// Want to make sure disease pathways are connected to objects
if (inst.getSchemClass().isa(ReactomeJavaConstants.ReactionlikeEvent)) {
Set<GKInstance> rxtEntities = InstanceUtilities.getReactionParticipants(inst);
for (GKInstance rxtEntity : rxtEntities) {
diseaseIds.add(rxtEntity.getDBID());
}
}
}
// Set<GKInstance> allEntities =
// InstanceUtilities.grepPathwayParticipants(diseasePathway);
// allEntities.removeAll(normalEntities);
// for (GKInstance inst : allEntities)
// diseaseIds.add(inst.getDBID());
}
}
splitComponents();
} catch (Exception e) {
e.printStackTrace();
}
}
@Override
public void paint(Graphics g) {
// Clear the editor
Graphics2D g2 = (Graphics2D) g;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
// In case g is provided by other graphics context (e.g during exporting)
g2.setFont(getFont());
g2.setBackground(background);
Dimension size = getPreferredSize();
g2.clearRect(0, 0, size.width, size.height);
// TODO: Delete the follow two statements. For test only
// g2.setPaint(Color.yellow);
// g2.fillRect(0, 0, size.width, size.height);
// Enable zooming
g2.scale(scaleX, scaleY);
List comps = displayedObject.getComponents();
// Draw nodes first
if (comps == null || comps.size() == 0) return;
java.util.List edges = new ArrayList();
Rectangle clip = g.getClipBounds();
// Draw Compartments first
List<RenderableCompartment> compartments = drawCompartments(g, comps, null, clip);
drawComponents(g, normalComps, clip);
if (isForNormal) {
// Replace the original components with new set of Renderable objects for further processing
RenderablePathway pathway = (RenderablePathway) displayedObject;
List<Renderable> components = pathway.getComponents();
components.clear();
components.addAll(normalComps);
components.addAll(compartments); // Don't forget them
return;
}
// Draw a transparent background: light grey
Color color = new Color(204, 204, 204, 175);
g2.setPaint(color);
// Dimension size = getPreferredSize();
// Preferred size has been scaled. Need to scale it back
g2.fillRect(0, 0, (int) (size.width / scaleX + 1.0d), (int) (size.height / scaleY + 1.0d));
// Draw disease related objects
for (Renderable r : diseaseComps) {
if (lofNodes.contains(r)) ((Node) r).setNeedDashedBorder(true);
}
drawComponents(g, diseaseComps, clip);
if (overlaidObjects.size() > 0)
drawComponents(
g,
overlaidObjects,
clip,
true); // Want to draw edge first so that no validation is needed.
if (crossedObjects.size() > 0) drawCrosses(g, crossedObjects, clip);
RenderablePathway pathway = (RenderablePathway) displayedObject;
pathway.setBgComponents(new ArrayList<Renderable>(normalComps));
List<Renderable> fgComps = new ArrayList<Renderable>();
fgComps.addAll(diseaseComps);
fgComps.addAll(overlaidObjects);
// Don't want to place compartments and pathway
for (Iterator<Renderable> it = fgComps.iterator(); it.hasNext(); ) {
Renderable r = it.next();
if (r instanceof RenderableCompartment || r instanceof RenderablePathway) it.remove();
}
pathway.setFgComponents(fgComps);
}