/**
* Query all nodes of worm regulatory network.
*
* @param model the Model
* @param executor to run the query
* @return interactionNodeSet
*/
private static void queryWormRegulatoryNodes(Model model, PathQueryExecutor executor) {
interactionNodeSetWorm = new LinkedHashSet<CytoscapeNetworkNodeData>();
PathQuery query = new PathQuery(model);
query.addViews(
"NetworkProperty.node.primaryIdentifier",
"NetworkProperty.node.symbol",
"NetworkProperty.node.id",
"NetworkProperty.type",
"NetworkProperty.value");
query.addConstraint(Constraints.eq("NetworkProperty.node.organism.shortName", "C. elegans"));
ExportResultsIterator result;
try {
result = executor.execute(query);
} catch (ObjectStoreException e) {
throw new RuntimeException("Error retrieving results.", e);
}
while (result.hasNext()) {
List<ResultElement> row = result.next();
String featurePId = (String) row.get(0).getField();
String featureSymbol = (String) row.get(1).getField();
Integer id = (Integer) row.get(2).getField();
String key = (String) row.get(3).getField();
String value = (String) row.get(4).getField();
CytoscapeNetworkNodeData aNode = new CytoscapeNetworkNodeData();
aNode.setInterMineId(id);
aNode.setSourceId(String.valueOf(id)); // Use IM Id instead of PId
if (featureSymbol == null || featureSymbol.length() < 1) {
aNode.setSourceLabel(featurePId);
} else {
aNode.setSourceLabel(featureSymbol);
}
if (interactionNodeSetWorm.contains(aNode)) {
for (CytoscapeNetworkNodeData n : interactionNodeSetWorm) {
if (n.getInterMineId() == id) {
n.getExtraInfo().put(key, value);
}
}
} else {
Map<String, String> extraInfo = new HashMap<String, String>();
extraInfo.put(key, value);
aNode.setExtraInfo(extraInfo);
}
interactionNodeSetWorm.add(aNode);
}
}
/**
* Query all nodes of fly regulatory network.
*
* @param model the Model
* @param executor to run the query
* @return interactionNodeSet
*/
private static void queryFlyRegulatoryNodes(Model model, PathQueryExecutor executor) {
interactionNodeSetFly = new LinkedHashSet<CytoscapeNetworkNodeData>();
PathQuery query = new PathQuery(model);
query.addViews(
"NetworkProperty.node.primaryIdentifier",
"NetworkProperty.node.symbol",
"NetworkProperty.node.id",
"NetworkProperty.value");
query.addConstraint(Constraints.eq("NetworkProperty.node.primaryIdentifier", "FBgn*"));
ExportResultsIterator result;
try {
result = executor.execute(query);
} catch (ObjectStoreException e) {
throw new RuntimeException("Error retrieving results.", e);
}
while (result.hasNext()) {
List<ResultElement> row = result.next();
String featurePId = (String) row.get(0).getField();
String featureSymbol = (String) row.get(1).getField();
Integer featureIMId = (Integer) row.get(2).getField();
String position = (String) row.get(3).getField();
CytoscapeNetworkNodeData aNode = new CytoscapeNetworkNodeData();
aNode.setInterMineId(featureIMId);
aNode.setSourceId(featurePId);
if (featureSymbol == null || featureSymbol.length() < 1) {
aNode.setSourceLabel(featurePId);
} else {
aNode.setSourceLabel(featureSymbol);
}
aNode.setPosition(position);
interactionNodeSetFly.add(aNode);
}
}