protected void write(Organism organism) throws ApplicationException {
// write out nodeDegree objects
NodeDegrees nodeDegrees = new NodeDegrees(Data.CORE, organism.getId());
nodeDegrees.setDegrees(degreesInOrganism);
cache.putNodeDegrees(nodeDegrees);
// update datasetInfo
DatasetInfo datasetInfo = cache.getDatasetInfo(organism.getId());
datasetInfo.setNumInteractingGenes(numConnectedGenes);
cache.putDatasetInfo(datasetInfo);
}
public void processOrganism(Organism organism) throws Exception {
logger.info(
String.format(
"computing degrees for organism %d (%s)", organism.getId(), organism.getName()));
allocDataStructures(organism);
computeDegrees(organism);
countNodesWithPositiveDegree();
write(organism);
log();
}
private Organism getHumanOrganism(DataSet data) throws DataStoreException {
String human = "H. Sapiens";
human = human.toLowerCase();
List<Organism> organisms = data.getMediatorProvider().getOrganismMediator().getAllOrganisms();
for (Organism organism : organisms) {
String organismName = organism.getName();
String organismAlias = organism.getAlias();
if (organismName.toLowerCase().equals(human) || organismAlias.toLowerCase().equals(human)) {
return organism;
}
}
return null;
}
protected void allocDataStructures(Organism organism) throws ApplicationException {
// annotation matrix
NodeIds nodeIds = cache.getNodeIds(organism.getId());
numGenes = nodeIds.getNodeIds().length;
degreesInOrganism = new DenseVector(numGenes);
}
private EnrichmentEngineRequestDto createEnrichmentRequest(
RelatedGenesEngineResponseDto response) {
if (human.getOntology() == null) {
return null;
}
EnrichmentEngineRequestDto request = new EnrichmentEngineRequestDto();
request.setProgressReporter(NullProgressReporter.instance());
request.setMinCategories(MIN_CATEGORIES);
request.setqValueThreshold(Q_VALUE_THRESHOLD);
request.setOrganismId(human.getId());
request.setOntologyId(human.getOntology().getId());
Set<Long> nodes = new HashSet<Long>();
for (NetworkDto network : response.getNetworks()) {
for (InteractionDto interaction : network.getInteractions()) {
nodes.add(interaction.getNodeVO1().getId());
nodes.add(interaction.getNodeVO2().getId());
}
}
request.setNodes(nodes);
return request;
}
private RelatedGenesEngineRequestDto createRequest() throws ApplicationException {
RelatedGenesEngineRequestDto request = new RelatedGenesEngineRequestDto();
request.setNamespace(GeneMania.DEFAULT_NAMESPACE);
request.setOrganismId(human.getId());
request.setInteractionNetworks(collapseNetworks(networks));
Set<Long> nodes = new HashSet<Long>();
for (String geneName : genes) {
nodes.add(data.getCompletionProvider(human).getNodeId(geneName));
}
request.setPositiveNodes(nodes);
request.setLimitResults(geneLimit);
request.setCombiningMethod(combiningMethod);
request.setScoringMethod(org.genemania.type.ScoringMethod.DISCRIMINANT);
return request;
}
protected void computeDegrees(Organism organism) throws ApplicationException {
Collection<Collection<Long>> groupedNetworks = getAllNetworks(organism);
degreesInOrganism.zero();
DenseVector degreesInNetwork = new DenseVector(numGenes);
for (Collection<Long> networks : groupedNetworks) {
for (long networkId : networks) {
degreesInNetwork.zero();
Network network = cache.getNetwork(Data.CORE, organism.getId(), networkId);
SymMatrix networkData = network.getData();
networkData.columnSums(degreesInNetwork.getData());
degreesInOrganism.add(degreesInNetwork);
}
}
}
public void setNetworks(Set<String> n) {
Map<InteractionNetworkGroup, Collection<InteractionNetwork>> groupMembers =
new HashMap<InteractionNetworkGroup, Collection<InteractionNetwork>>();
Collection<InteractionNetworkGroup> groups = human.getInteractionNetworkGroups();
Set<String> notHandled = n;
for (InteractionNetworkGroup group : groups) {
if (n.contains(group.getName())) {
notHandled.remove(group.getName());
List<InteractionNetwork> networkMembers = new ArrayList<InteractionNetwork>();
Collection<InteractionNetwork> networks = group.getInteractionNetworks();
for (InteractionNetwork network : networks) {
networkMembers.add(network);
}
if (networkMembers.size() > 0) {
groupMembers.put(group, networkMembers);
}
}
}
networks = groupMembers;
}