/**
* Query all edges of worm regulatory network.
*
* @param model the Model
* @param executor to run the query
* @return interactionEdgeSet
*/
private static void queryWormRegulatoryEdges(Model model, PathQueryExecutor executor) {
interactionEdgeSetWorm = new LinkedHashSet<CytoscapeNetworkEdgeData>();
PathQuery query = new PathQuery(model);
query.addViews(
"Regulation.type", // interaction type, e.g. TF-TF
"Regulation.source.primaryIdentifier",
"Regulation.source.symbol",
"Regulation.source.id",
"Regulation.target.primaryIdentifier",
"Regulation.target.symbol",
"Regulation.target.id");
query.addConstraint(Constraints.eq("Regulation.source.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 interactionType = (String) row.get(0).getField();
String sourcePId = (String) row.get(1).getField();
String sourceSymbol = (String) row.get(2).getField();
Integer sourceId = (Integer) row.get(3).getField();
String targetPId = (String) row.get(4).getField();
String targetSymbol = (String) row.get(5).getField();
Integer targetId = (Integer) row.get(6).getField();
// TODO Hack for a database issue
// if ("blmp-1".equals(targetSymbol)) {
// targetId = 1644007904;
// }
//
// if ("unc-130".equals(targetSymbol)) {
// targetId = 1644015202;
// }
//
// if ("mab-5".equals(targetSymbol)) {
// targetId = 1644006300;
// }
//
// if ("mdl-1".equals(targetSymbol)) {
// targetId = 1644006399;
// }
//
// if ("elt-3".equals(targetSymbol)) {
// targetId = 1644003204;
// }
//
// if ("lin-11".equals(targetSymbol)) {
// targetId = 1644006039;
// }
//
// if ("skn-1".equals(targetSymbol)) {
// targetId = 1644009973;
// }
//
// if ("egl-27".equals(targetSymbol)) {
// targetId = 1644003074;
// }
CytoscapeNetworkEdgeData aEdge = new RegulatoryNetworkEdgeData();
aEdge.setSourceId(String.valueOf(sourceId));
if (sourceSymbol == null || sourceSymbol.length() < 1) {
aEdge.setSourceLabel(sourcePId);
} else {
aEdge.setSourceLabel(sourceSymbol);
}
aEdge.setTargetId(String.valueOf(targetId));
if (targetSymbol == null || targetSymbol.length() < 1) {
aEdge.setTargetLabel(targetPId);
} else {
aEdge.setTargetLabel(targetSymbol);
}
aEdge.setInteractionType(interactionType);
interactionEdgeSetWorm.add(aEdge);
}
}
/**
* Query all edges of fly regulatory network.
*
* @param model the Model
* @param executor to run the query
* @return interactionEdgeSet
*/
private static void queryFlyRegulatoryEdges(Model model, PathQueryExecutor executor) {
interactionEdgeSetFly = new LinkedHashSet<CytoscapeNetworkEdgeData>();
// TODO fly doesn't use IM Object id
PathQuery query = new PathQuery(model);
query.addViews(
"Regulation.type", // interaction type, e.g. TF-TF
"Regulation.source.primaryIdentifier",
"Regulation.source.symbol",
"Regulation.target.primaryIdentifier",
"Regulation.target.symbol");
query.addConstraint(Constraints.eq("Regulation.source.primaryIdentifier", "FBgn*"), "A");
query.addConstraint(Constraints.eq("Regulation.target.primaryIdentifier", "FBgn*"), "B");
query.setConstraintLogic("A and B");
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 interactionType = (String) row.get(0).getField();
String sourceNodePId = (String) row.get(1).getField();
String sourceNodeSymbol = (String) row.get(2).getField();
String targetNodePId = (String) row.get(3).getField();
String targetNodeSymbol = (String) row.get(4).getField();
CytoscapeNetworkEdgeData aEdge = new CytoscapeNetworkEdgeData();
// Handle bidirectional edges
if (interactionEdgeSetFly.isEmpty()) {
aEdge.setSourceId(sourceNodePId);
if (sourceNodeSymbol == null || sourceNodeSymbol.length() < 1) {
aEdge.setSourceLabel(sourceNodePId);
} else {
aEdge.setSourceLabel(sourceNodeSymbol);
}
aEdge.setTargetId(targetNodePId);
if (targetNodeSymbol == null || targetNodeSymbol.length() < 1) {
aEdge.setTargetLabel(targetNodePId);
} else {
aEdge.setTargetLabel(targetNodeSymbol);
}
aEdge.setInteractionType(interactionType);
aEdge.setDirection("one");
interactionEdgeSetFly.add(aEdge);
} else {
aEdge.setSourceId(sourceNodePId);
if (sourceNodeSymbol == null || sourceNodeSymbol.length() < 1) {
aEdge.setSourceLabel(sourceNodePId);
} else {
aEdge.setSourceLabel(sourceNodeSymbol);
}
aEdge.setTargetId(targetNodePId);
if (targetNodeSymbol == null || targetNodeSymbol.length() < 1) {
aEdge.setTargetLabel(targetNodePId);
} else {
aEdge.setTargetLabel(targetNodeSymbol);
}
// miRNA-TF and TF-miRNA are the same interaction type
if ("TF-miRNA".equals(interactionType) || "miRNA-TF".equals(interactionType)) {
String uniType = "miRNA-TF";
aEdge.setInteractionType(uniType);
} else {
aEdge.setInteractionType(interactionType);
}
String interactingString = aEdge.generateInteractionString();
String interactingStringRev = aEdge.generateReverseInteractionString();
// Get a list of interactionString from interactionSet
LinkedHashSet<String> intcStrSet = new LinkedHashSet<String>();
for (CytoscapeNetworkEdgeData edgedata : interactionEdgeSetFly) {
intcStrSet.add(edgedata.generateInteractionString());
}
// A none dulipcated edge
if (!(intcStrSet.contains(interactingString)
|| intcStrSet.contains(interactingStringRev))) {
aEdge.setDirection("one");
interactionEdgeSetFly.add(aEdge);
} else { // duplicated edge
// Pull out the CytoscapeNetworkEdgeData which contains the current
// interactionString
for (CytoscapeNetworkEdgeData edgedata : interactionEdgeSetFly) {
if (edgedata.generateInteractionString().equals(interactingString)
|| edgedata.generateInteractionString().equals(interactingStringRev)) {
edgedata.setDirection("both");
aEdge.setInteractionType(interactionType);
}
}
}
}
}
}
