@Before
public void setup() {
nw = new Network();
nw.setName("test network");
dp = new DensityMap();
nw.setNodes(new ArrayList<edu.berkeley.path.model_elements_base.Node>());
nw.setLinks(new ArrayList<edu.berkeley.path.model_elements_base.Link>());
Node nd1;
Node nd2;
Link ln;
nd1 = new Node();
nd1.setId(1L);
nd1.setName("one");
nd1.setType("Highway");
nw.getNodes().add(nd1);
nd2 = new Node();
nd2.setId(2L);
nd2.setName("two");
nd2.setType("Highway");
nw.getNodes().add(nd2);
ln = new Link();
ln.setId(3L);
ln.setName("three");
ln.setType("Highway");
ln.setLaneCount(4.0);
ln.setLength(1000.0);
ln.setBegin(nd1);
ln.setEnd(nd2);
nw.getLinks().add(ln);
}
/**
* a network is a collection of (possibly degenerate) interactions. the R client should pass 3
* arrays of strings, having the following structure
*
* <p>edges consist of strings like "VNG0723G::VNG1233G::PhylogeneticProfile" node attributes:
* "VNG1233G::commonName::pepq2" edge attributes:
* "VNG0723G::VNG1233G::PhylogeneticProfile::confidence::0.533"
*/
public void createAndBroadcastNetwork(
String[] interactionStrings,
String[] nodeAttributeStrings,
String[] edgeAttributeStrings,
String name) {
Network network = new Network();
addMetaDataToNetwork(network);
network.setName(name);
network.setSpecies(defaultSpecies);
for (String interactionString : interactionStrings) {
String[] tokens = interactionString.split("::");
int tokenCount = tokens.length;
// for (int t=0; t < tokens.length; t++)
// System.out.println (" edge token " + t + ": " + tokens [t]);
if (tokenCount == 1 && tokens[0].trim().length() > 0) {
// System.out.println ("adding one orphan node to network: " + tokens [0]);
network.add(tokens[0]);
} else if (tokenCount == 3) {
String sourceNode = tokens[0];
String targetNode = tokens[1];
String interactionType = tokens[2];
network.add(new Interaction(sourceNode, targetNode, interactionType));
} // else: good interaction
} // for i
// System.out.println ("nodeAttributeStrings count: " + nodeAttributeStrings.length);
for (String nodeAttributeString : nodeAttributeStrings) {
// System.out.println (" " + nodeAttributeStrings [i]);
String[] tokens = nodeAttributeString.split("::");
if (tokens.length == 3) {
String nodeName = tokens[0].trim();
String attributeName = tokens[1].trim();
String rawValue = tokens[2].trim();
Object value = StringToObjectConverter.convert(rawValue);
network.addNodeAttribute(nodeName, attributeName, value);
} // if 3 tokens
} // for i
// System.out.println ("edgeAttributeStrings count: " + edgeAttributeStrings.length);
for (String edgeAttributeString : edgeAttributeStrings) {
// System.out.println (" " + edgeAttributeStrings [i]);
String[] tokens = edgeAttributeString.split("::");
if (tokens.length == 5) {
String sourceNode = tokens[0].trim();
String targetNode = tokens[1].trim();
String edgeType = tokens[2].trim();
String attributeName = tokens[3].trim();
String rawValue = tokens[4].trim();
Object value = StringToObjectConverter.convert(rawValue);
String edgeName = sourceNode + " (" + edgeType + ") " + targetNode;
network.addEdgeAttribute(edgeName, attributeName, value);
} // if 5 tokens
} // for i
// System.out.println ("RShellGoose, about to broadcast network");
// System.out.println (" node count: " + network.getNodes().length);
// System.out.println (" connected: " + network.getConnectedNodes ().size ());
// System.out.println (" orphan: " + network.getOrphanNodes().length);
try {
gaggleBoss.broadcastNetwork(myGaggleName, targetGoose, network);
} catch (RemoteException rex) {
System.err.println("error broadcasting network from RShellGoose " + myGaggleName);
rex.printStackTrace();
}
} // createAndBroadcastNetwork