private void addLinks(LinkTriple[] links) {
CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
// CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
Map<CyNode, Boolean> updateList = new HashMap<CyNode, Boolean>();
CyNetwork net = Cytoscape.getCurrentNetwork();
for (LinkTriple link : links) {
CyNode src = Cytoscape.getCyNode(link.subj.toString());
CyNode dst = Cytoscape.getCyNode(link.obj.toString());
if (src == null) {
src = net.addNode(Cytoscape.getCyNode(link.subj.toString(), true));
if (link.subj.getType() != null)
nodeAttr.setAttribute(src.getIdentifier(), "NodeType", link.subj.getType());
}
if (dst == null) {
dst = net.addNode(Cytoscape.getCyNode(link.obj.toString(), true));
if (link.obj.getType() != null)
nodeAttr.setAttribute(dst.getIdentifier(), "NodeType", link.obj.getType());
}
CyEdge edge =
Cytoscape.getCyEdge(
link.subj.toString(), "link", link.obj.toString(), link.pred.toString());
// if ( link.pred != null )
// edgeAttr.setAttribute(edge.getIdentifier(), "EdgeType", link.pred.toString() );
net.addEdge(edge);
updateList.put(src, true);
updateList.put(dst, true);
}
Cytoscape.getCurrentNetworkView()
.applyLayout(new GridNodeLayout(), updateList.keySet().toArray(new CyNode[0]), null);
Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
}
private SortedSet<String> getPathwaySetFromReactionNodes(CyNetwork network) {
SortedSet<String> pathwaySet = new TreeSet<String>();
for (Object node : network.nodesList()) {
CyNode cyNode = (CyNode) node;
String pathway =
Attributes.node.getStringAttribute(
cyNode.getIdentifier(), ReactionAttribute.PATHWAY.toAttributeName());
if (pathway != null) {
pathwaySet.add(pathway);
}
}
return pathwaySet;
}
@Override
public Collection<CyNode> getNeighbours(CyNode node) {
Collection<CyNode> neighbours = new HashSet<CyNode>();
CyNetwork network = getProxied();
int nodeIndex = node.getRootGraphIndex();
for (int index : network.getAdjacentEdgeIndicesArray(nodeIndex, true, true, true)) {
CyEdge edge = (CyEdge) network.getEdge(index);
CyNode other = (CyNode) edge.getSource();
if (other.getRootGraphIndex() == nodeIndex) {
other = (CyNode) edge.getTarget();
if (other.getRootGraphIndex() == nodeIndex) {
continue;
}
}
neighbours.add((CyNode) other);
}
return neighbours;
}
private void applySelectionToCRNetwork(CyNetwork network, Set<String> selection) {
Set<CyNode> nodesSet = new HashSet<CyNode>();
for (Object node : network.nodesList()) {
CyNode cyNode = (CyNode) node;
String pathway =
Attributes.node.getStringAttribute(
cyNode.getIdentifier(), ReactionAttribute.PATHWAY.toAttributeName());
if (pathway != null && selection.contains(pathway)) {
nodesSet.add(cyNode);
for (Object neighbor : network.neighborsList(cyNode)) {
CyNode neighborNode = (CyNode) neighbor;
nodesSet.add(neighborNode);
}
}
}
network.setSelectedNodeState(nodesSet, true);
network.setSelectedEdgeState(network.getConnectingEdges(new ArrayList<CyNode>(nodesSet)), true);
}
@SuppressWarnings("unchecked")
@Override
public void actionPerformed(ActionEvent ae) {
String action = ae.getActionCommand();
LinkTriple[] addNodes = null;
if (action.equals("Fetch")) {
addNodes = iSparql.ExploreURI(urlText.getText());
addLinks(addNodes);
// Cytoscape.getCurrentNetwork().addNode( Cytoscape.getCyNode( urlText.getText(), true ) );
}
if (action.equals("Fetch Selected")) {
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<LinkTriple> nodeList = new LinkedList<LinkTriple>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
for (LinkTriple newNode : iSparql.ExploreURI(node.getIdentifier())) {
nodeList.add(newNode);
}
}
if (filterCheckbox.getState())
addLinks(iSparql.NodeFilter(null, nodeList.toArray(new LinkTriple[0])));
else addLinks(nodeList.toArray(new LinkTriple[0]));
}
if (action.equals("Find Nodes")) {
CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<Map<String, Object>> nodeList = new LinkedList<Map<String, Object>>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
Map<String, Object> map = new HashMap<String, Object>();
String id = node.getIdentifier();
map.put("ID", id);
for (String attr : nodeAttr.getAttributeNames()) {
if (nodeAttr.hasAttribute(id, attr)) {
System.out.println(id + " " + attr + " " + nodeAttr.getType(attr));
if (nodeAttr.getType(attr) == CyAttributes.TYPE_STRING) {
Object iAttr = nodeAttr.getAttribute(id, attr);
map.put(attr, iAttr);
}
}
}
nodeList.add(map);
}
LinkTriple[] links = iSparql.NodeSearch(null, nodeList, "ID");
addLinks(links);
}
if (action.equals("Edit Namespaces")) {
Map<String, String> nameMap = prefs.getNameSpaces();
Map<String, String> newMap = NameSpaceEditor.EditDialog(nameMap);
for (String key : nameMap.keySet()) {
prefs.removeNameSpace(key);
}
for (String key : newMap.keySet()) {
prefs.addNameSpace(key, newMap.get(key));
}
}
}
public gpClique[] creategpClique() {
gpClique[] gps = new gpClique[2];
gps[0] = new gpClique();
gps[1] = new gpClique();
Iterator<Edge> edgeIt = nw.edgesIterator();
CyAttributes edgeAtt = Cytoscape.getEdgeAttributes();
ArrayList largeALNodes = new ArrayList();
ArrayList targetALNodes = new ArrayList();
ArrayList matchALNodes = new ArrayList();
while (edgeIt.hasNext()) {
Edge edge = edgeIt.next();
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p2")) {
largeALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
largeALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
continue; // go directly next step
}
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p1")) {
targetALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
targetALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
continue;
}
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("pd")) {
matchALNodes.add(
new Integer(
nw.getEdgeSourceIndex(
edge
.getRootGraphIndex()))); // the matched node(containing "-") of target
// network
matchALNodes.add(
new Integer(
nw.getEdgeTargetIndex(
edge
.getRootGraphIndex()))); // the matched node(containing "-") of large
// network
continue;
}
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "File Format error!");
return null;
}
Iterator matchALNIt = matchALNodes.iterator();
CyNode node;
Integer it;
while (matchALNIt.hasNext()) {
it = (Integer) matchALNIt.next();
node =
Cytoscape.getCyNode(
nw.getNode(it.intValue()).getIdentifier().substring(1),
true); // get node according to its identifier
matchNodes.add(node);
if (!targetALNodes.contains(
node.getRootGraphIndex())) // matched node,but not a node of network
{
nw.addNode(node);
targetALNodes.add(node.getRootGraphIndex()); // add to network
}
it = (Integer) matchALNIt.next();
node =
Cytoscape.getCyNode(
nw.getNode(it.intValue()).getIdentifier().substring(1),
true); // get node according to its identifier
matchNodes.add(node);
if (!largeALNodes.contains(node.getRootGraphIndex())) {
nw.addNode(node);
largeALNodes.add(node.getRootGraphIndex());
}
}
gps[0].setgpNodes(largeALNodes);
gps[1].setgpNodes(targetALNodes);
return gps;
}