private SortedSet<String> getPathwaySetFromEnzymeReactionEdges(CyNetwork network) {
SortedSet<String> pathwaySet = new TreeSet<String>();
for (Object edge : network.edgesList()) {
CyEdge cyEdge = (CyEdge) edge;
List<?> pathways =
Attributes.edge.getListAttribute(
cyEdge.getIdentifier(), EnzymeReactionAttribute.PATHWAYS.toAttributeName());
if (pathways != null) {
for (Object pathway : pathways) pathwaySet.add(pathway.toString());
}
}
return pathwaySet;
}
private SortedSet<String> getPathwaySetFromReactionEdges(CyNetwork network) {
SortedSet<String> pathwaySet = new TreeSet<String>();
for (Object edge : network.edgesList()) {
CyEdge cyEdge = (CyEdge) edge;
String pathway =
Attributes.edge.getStringAttribute(
cyEdge.getIdentifier(), ReactionAttribute.PATHWAY.toAttributeName());
if (pathway != null) {
pathwaySet.add(pathway);
}
}
return pathwaySet;
}
private void applySelectionToCompoundNetwork(CyNetwork network, Set<String> selection) {
Set<CyNode> nodesSet = new HashSet<CyNode>();
Set<CyEdge> edgesSet = new HashSet<CyEdge>();
for (Object edge : network.edgesList()) {
CyEdge cyEdge = (CyEdge) edge;
String pathway =
Attributes.edge.getStringAttribute(
cyEdge.getIdentifier(), ReactionAttribute.PATHWAY.toAttributeName());
if (pathway != null && selection.contains(pathway)) {
nodesSet.add((CyNode) cyEdge.getSource());
nodesSet.add((CyNode) cyEdge.getTarget());
edgesSet.add(cyEdge);
}
}
network.setSelectedNodeState(nodesSet, true);
network.setSelectedEdgeState(edgesSet, true);
}
@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 applySelectionToCGNetwork(CyNetwork network, Set<String> selection) {
Set<CyNode> nodesSet = new HashSet<CyNode>();
Set<CyEdge> edgesSet = new HashSet<CyEdge>();
for (Object edge : network.edgesList()) {
CyEdge cyEdge = (CyEdge) edge;
List<?> pathways =
Attributes.edge.getListAttribute(
cyEdge.getIdentifier(), EnzymeReactionAttribute.PATHWAYS.toAttributeName());
for (Object pathway : pathways) {
if (selection.contains(pathway)) {
nodesSet.add((CyNode) cyEdge.getSource());
nodesSet.add((CyNode) cyEdge.getTarget());
edgesSet.add(cyEdge);
break;
}
}
}
network.setSelectedNodeState(nodesSet, true);
network.setSelectedEdgeState(edgesSet, true);
}