private boolean isDiseaseObject(Renderable r, Set<Long> diseaseIds) {
if (r instanceof FlowLine) {
FlowLine fl = (FlowLine) r;
return isFlowLineRelatedToSet(fl, diseaseIds);
}
// Assume normal objects only: this is a very strong assumption
if (r.getReactomeId() == null) return false;
// A PE may be represented multiple times in a pathway diagram. Some of them
// are linked to normal reactions, and some linked to disease reactions.
// Have to check these cases.
if (r instanceof HyperEdge) return diseaseIds.contains(r.getReactomeId());
if (r instanceof Node) {
Node node = (Node) r;
List<HyperEdge> edges = node.getConnectedReactions();
boolean isDisease = false;
for (HyperEdge edge : edges) {
if (edge instanceof FlowLine) {
isDisease = isFlowLineRelatedToSet((FlowLine) edge, diseaseIds);
} else if (edge.getReactomeId() != null && diseaseIds.contains(edge.getReactomeId())) {
isDisease = true;
}
if (isDisease) return true;
}
}
return false;
}
public void randomlyMapDiseaseNodesToNormalNodes(
Map<Node, GKInstance> normalToDiseaseEntity,
Collection<GKInstance> mapped,
List<GKInstance> diseaseInputs,
List<Node> normalNodes) {
if (diseaseInputs != null && diseaseInputs.size() > 0) {
normalNodes.removeAll(normalToDiseaseEntity.keySet());
if (normalNodes.size() > 0) {
for (GKInstance input : diseaseInputs) {
// if (mapped.contains(input))
if (contains(input, mapped)) continue; // it has been mapped already
// Check if it has been used based on DB_ID
Node matched = null;
for (Node node : normalNodes) {
if (node.getReactomeId().equals(input.getDBID())) {
matched = node;
break;
}
}
if (matched == null)
// Just pick up the first node
matched = normalNodes.get(0);
normalToDiseaseEntity.put(matched, input);
normalNodes.remove(matched);
if (normalNodes.size() == 0) break;
}
}
}
}
private boolean isNormalObject(Renderable r, Set<Long> normalIds) {
if (r instanceof HyperEdge) {
if (r instanceof FlowLine) return isFlowLineRelatedToSet((FlowLine) r, normalIds);
// Most likely the following statements should not be reached. But place
// here just in case.
if (r.getReactomeId() == null) return true;
if (normalIds.contains(r.getReactomeId())) return true;
} else if (r instanceof Node) {
if (r instanceof ProcessNode) return true; // Should be used only for normal pathway.
if (r.getReactomeId() == null) return true;
// Check if it is linked to another disease entities
Node node = (Node) r;
List<HyperEdge> edges = node.getConnectedReactions();
boolean isNormal = false;
for (HyperEdge edge : edges) {
if (edge instanceof FlowLine) isNormal = isFlowLineRelatedToSet((FlowLine) edge, normalIds);
if (isNormal) return true;
if (edge.getReactomeId() != null && normalIds.contains(edge.getReactomeId())) return true;
// Some special cases that use links
if (!(edge instanceof EntitySetAndEntitySetLink)
&& !(edge instanceof EntitySetAndMemberLink)
&& edge.getReactomeId() == null) return true;
}
}
return false;
}
/**
* Overlay a single disease reaction onto a normal reaction.
*
* @param normalReaction
* @param diseaseReaction
* @param overlaidObjects
*/
private void overlayDiseaseReaction(HyperEdge normalReaction, GKInstance diseaseReaction)
throws Exception {
// Make a copy of the HyperEdge for future process that is related to Vertex and JSON generation
HyperEdge reactionCopy = normalReaction.shallowCopy();
reactionCopy.setReactomeId(diseaseReaction.getDBID());
reactionCopy.setDisplayName(diseaseReaction.getDisplayName());
reactionCopy.setLineColor(DefaultRenderConstants.DEFAULT_DISEASE_BACKGROUND);
displayedObject.addComponent(reactionCopy);
overlaidObjects.add(reactionCopy);
// Want to handle inputs, outputs and catalysts since regulators can
// be ignored
List<Node> nodes = new ArrayList<Node>();
nodes.addAll(normalReaction.getInputNodes());
nodes.addAll(normalReaction.getOutputNodes());
nodes.addAll(normalReaction.getHelperNodes());
// List objects not listed in the disease reaction as crossed objects
Set<GKInstance> participants = InstanceUtilities.getReactionParticipants(diseaseReaction);
Set<Long> diseaseIds = new HashSet<Long>();
for (GKInstance participant : participants) {
diseaseIds.add(participant.getDBID());
if (participant.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasMember)) {
List<GKInstance> list = participant.getAttributeValuesList(ReactomeJavaConstants.hasMember);
if (list != null && list.size() > 0) {
for (GKInstance inst : list) diseaseIds.add(inst.getDBID());
}
}
if (participant.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasCandidate)) {
List<GKInstance> list =
participant.getAttributeValuesList(ReactomeJavaConstants.hasCandidate);
if (list != null && list.size() > 0) {
for (GKInstance inst : list) diseaseIds.add(inst.getDBID());
}
}
}
Set<GKInstance> lofInstances = new HashSet<GKInstance>();
Map<Node, GKInstance> normalToDiseaseEntity =
mapMutatedToNormalNodes(diseaseReaction, normalReaction, nodes, lofInstances);
for (Node node : nodes) {
if (!diseaseIds.contains(node.getReactomeId())) {
// Check if it should be mapped to a normal entity
GKInstance diseaseEntity = normalToDiseaseEntity.get(node);
if (diseaseEntity == null) crossedObjects.add(node); // Just crossed out
else {
Node diseaseNode =
replaceNormalNode(node, diseaseEntity, contains(diseaseEntity, lofInstances));
if (diseaseNode == null) continue; // Just in case
// Re-link to diseaseNode
ConnectInfo connectInfo = reactionCopy.getConnectInfo();
List<?> widgets = connectInfo.getConnectWidgets();
for (Object obj : widgets) {
ConnectWidget widget = (ConnectWidget) obj;
if (widget.getConnectedNode() == node) widget.replaceConnectedNode(diseaseNode);
}
}
} else overlaidObjects.add(node);
}
}
/**
* Map mutated nodes in a disease reaction to displayed nodes in a normal reaction. The mapping is
* based on sharing of referenceEntity. This may not be reliable!
*
* @param diseaseReaction
* @param nodes
* @throws InvalidAttributeException
* @throws Exception @TODO: add a new attribute normalEntity in the PhysicalEntity class.
*/
private Map<Node, GKInstance> mapMutatedToNormalNodes(
GKInstance diseaseReaction,
HyperEdge normalReaction,
List<Node> nodes,
Set<GKInstance> lofInstances)
throws InvalidAttributeException, Exception {
List<GKInstance> efs =
diseaseReaction.getAttributeValuesList(ReactomeJavaConstants.entityFunctionalStatus);
// Map mutated entities to normal entities via ReferenceGeneProduct
Map<Node, GKInstance> normalToDiseaseEntity = new HashMap<Node, GKInstance>();
if (efs == null) return normalToDiseaseEntity;
for (GKInstance ef : efs) {
GKInstance pe = (GKInstance) ef.getAttributeValue(ReactomeJavaConstants.physicalEntity);
if (pe != null) {
Set<GKInstance> refEntities = getReferenceEntity(pe);
// want to find the matched node
for (Node node : nodes) {
if (node.getReactomeId() == null) continue;
GKInstance nodeInst = adaptor.fetchInstance(node.getReactomeId());
Set<GKInstance> nodeRefEntities = getReferenceEntity(nodeInst);
nodeRefEntities.retainAll(refEntities);
if (nodeRefEntities.size() > 0) {
normalToDiseaseEntity.put(node, pe);
if (isLOFEntity(ef)) {
lofInstances.add(pe);
}
break;
}
}
}
}
// TODO: May have to consider stoichiometries too!!!
// In gain of functions, some inputs or outputs may not be used by normal reactions.
// This method will do its best to map these reaction participants
Collection<GKInstance> mapped = normalToDiseaseEntity.values();
// First check inputs
List<GKInstance> diseaseInputs =
diseaseReaction.getAttributeValuesList(ReactomeJavaConstants.input);
List<Node> normalNodes = normalReaction.getInputNodes();
randomlyMapDiseaseNodesToNormalNodes(normalToDiseaseEntity, mapped, diseaseInputs, normalNodes);
// Check outputs
List<GKInstance> diseaseOutputs =
diseaseReaction.getAttributeValuesList(ReactomeJavaConstants.output);
normalNodes = normalReaction.getOutputNodes();
randomlyMapDiseaseNodesToNormalNodes(
normalToDiseaseEntity, mapped, diseaseOutputs, normalNodes);
// Check helpers
GKInstance ca =
(GKInstance) diseaseReaction.getAttributeValue(ReactomeJavaConstants.catalystActivity);
if (ca != null) {
List<GKInstance> catalysts = ca.getAttributeValuesList(ReactomeJavaConstants.physicalEntity);
normalNodes = normalReaction.getHelperNodes();
randomlyMapDiseaseNodesToNormalNodes(normalToDiseaseEntity, mapped, catalysts, normalNodes);
}
return normalToDiseaseEntity;
}
/**
* If a FlowLine connects two normal object, it should be a normal object. Otherwise, it should be
* a disease object.
*
* @param flowLine
* @param ids
* @return
*/
private boolean isFlowLineRelatedToSet(FlowLine flowLine, Set<Long> ids) {
Node input = flowLine.getInputNode(0);
Node output = flowLine.getOutputNode(0);
if (input != null
&& (ids.contains(input.getReactomeId()) || input instanceof ProcessNode)
&& // ProcessNode should be used in normal pathway only
output != null
&& (ids.contains(output.getReactomeId()) || output instanceof ProcessNode)) return true;
// if (output != null && normalIds.contains(output.getReactomeId()))
// return true;
return false;
}
private void drawCrosses(Graphics g, List<Node> nodes, Rectangle clip) {
Graphics2D g2 = (Graphics2D) g;
Stroke oldStroke = g2.getStroke();
Stroke stroke = new BasicStroke(DefaultRenderConstants.DEFAULT_RED_CROSS_WIDTH);
g2.setStroke(stroke);
Paint oldPaint = g2.getPaint();
g2.setColor(Color.RED);
for (Node node : nodes) {
Rectangle r = node.getBounds();
if (!clip.intersects(r)) continue;
g2.drawLine(r.x, r.y, r.x + r.width, r.y + r.height);
g2.drawLine(r.x, r.y + r.height, r.x + r.width, r.y);
}
g2.setStroke(oldStroke);
g2.setPaint(oldPaint);
}
private Node replaceNormalNode(
Node normalNode, GKInstance diseaseEntity, Boolean needDashedBorder) {
Node diseaseNode = normalToDiseaseNode.get(normalNode);
if (diseaseNode != null) return diseaseNode;
try {
// If a node exists already, it should use
for (Renderable r : diseaseComps) {
if (diseaseEntity.getDBID().equals(r.getReactomeId()) && r instanceof Node) {
// This is rather arbitrary: if two nodes are very close,
// use the existing one.
int dx = Math.abs(r.getPosition().x - normalNode.getPosition().x);
int dy = Math.abs(r.getPosition().y - normalNode.getPosition().y);
if (dx < 10 && dy < 10) {
// We don't need to create a new Node if it exists already
normalToDiseaseNode.put(normalNode, (Node) r);
overlaidObjects.add(r); // Add it to overlaid object to cover edges
return (Node) r;
}
}
}
diseaseNode = normalNode.getClass().newInstance();
RenderUtility.copyRenderInfo(normalNode, diseaseNode);
// The following should NOT be called since NodeAttachment is
// related to disease entity only.
// TODO: Need to support this. Currently it is not supported!!! See example
// in PI3/AKT cancer pathway.
// diseaseNode.setNodeAttachmentsLocally(node.getNodeAttachments());
diseaseNode.setDisplayName(diseaseEntity.getDisplayName());
diseaseNode.setReactomeId(diseaseEntity.getDBID());
diseaseNode.invalidateBounds();
diseaseNode.setRenderer(normalNode.getRenderer());
diseaseNode.setLineColor(DefaultRenderConstants.DEFAULT_DISEASE_BACKGROUND);
diseaseNode.setNeedDashedBorder(needDashedBorder);
RenderUtility.hideCompartmentInNodeName(diseaseNode);
overlaidObjects.add(diseaseNode);
displayedObject.addComponent(diseaseNode);
normalToDiseaseNode.put(normalNode, diseaseNode);
return diseaseNode;
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
private void checkLossOfFunctionNodes() {
try {
lofNodes = new ArrayList<Node>();
List<Renderable> components = displayedObject.getComponents();
if (components == null || components.size() == 0) return;
for (Renderable r : components) {
if (r instanceof Node || r.getReactomeId() == null) continue;
if (!diseaseIds.contains(r.getReactomeId())) continue;
GKInstance inst = adaptor.fetchInstance(r.getReactomeId());
if (!inst.getSchemClass().isa(ReactomeJavaConstants.ReactionlikeEvent)
|| !inst.getSchemClass().isValidAttribute(ReactomeJavaConstants.entityFunctionalStatus))
continue;
List<GKInstance> efs =
inst.getAttributeValuesList(ReactomeJavaConstants.entityFunctionalStatus);
Set<GKInstance> lofPEs = new HashSet<GKInstance>();
for (GKInstance ef : efs) {
GKInstance pe = (GKInstance) ef.getAttributeValue(ReactomeJavaConstants.physicalEntity);
if (isLOFEntity(ef)) lofPEs.add(pe);
}
List<Node> nodes = ((HyperEdge) r).getConnectedNodes();
for (Node node : nodes) {
if (node.getReactomeId() == null) continue;
GKInstance nodeInst = adaptor.fetchInstance(node.getReactomeId());
Set<GKInstance> nodeRefEntities = getReferenceEntity(nodeInst);
for (GKInstance lofPE : lofPEs) {
Set<GKInstance> lofRefEntities = getReferenceEntity(lofPE);
lofRefEntities.retainAll(nodeRefEntities);
if (lofRefEntities.size() > 0) {
// A LOF node
lofNodes.add(node);
break;
}
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
private void drawComponents(
Graphics g, List<Renderable> comps, Rectangle clip, boolean drawEdgeFirst) {
List<HyperEdge> edges = new ArrayList<HyperEdge>();
for (Renderable obj : comps) {
if (obj instanceof HyperEdge) edges.add((HyperEdge) obj);
}
if (drawEdgeFirst) {
// Draw HyperEdges
for (HyperEdge reaction : edges) {
// Have to validate connect nodes first in case empty bounds
List<Node> nodes = reaction.getConnectedNodes();
for (Node node : nodes) node.validateBounds(g);
reaction.validateConnectInfo();
if (clip.intersects(reaction.getBounds())) reaction.render(g);
}
}
// Draw complexes now
drawComplexes(comps, clip, g);
for (Renderable obj : comps) {
if (obj instanceof RenderableCompartment
|| obj instanceof RenderableComplex
|| obj instanceof RenderablePathway) continue; // Escape it. It should be drawn earlier.
if (obj instanceof Node) {
Node node = (Node) obj;
if (getHidePrivateNote() && (node instanceof Note) && ((Note) node).isPrivate()) continue;
node.validateBounds(g);
if (clip.intersects(node.getBounds())) node.render(g);
}
}
if (!drawEdgeFirst) {
// Draw HyperEdges
for (HyperEdge reaction : edges) {
reaction.validateConnectInfo();
if (clip.intersects(reaction.getBounds())) reaction.render(g);
}
}
}
@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);
}