private Collection getNeighbors(CyNode node) {
Set result = new HashSet();
Collection edges = network.getAdjacentEdgeList(node, org.cytoscape.model.CyEdge.Type.ANY);
if (edges == null || edges.size() == 0) return result;
Long targetID = node.getSUID();
for (Iterator iterator = edges.iterator(); iterator.hasNext(); ) {
CyEdge curEdge = (CyEdge) iterator.next();
if (curEdge.getSource().getSUID() != targetID) result.add(curEdge.getSource());
else if (curEdge.getTarget().getSUID() != targetID) result.add(curEdge.getTarget());
}
return result;
}
/** {@inheritDoc} */
@Override
public Evidence[] mapEdgeToEvidence(Graph graph, Edge edge) {
if (graph == null) throw new NullPointerException("graph cannot be null");
if (edge == null) throw new NullPointerException("edge cannot be null");
if (edge.metadata == null) return new Evidence[0];
Object evidences = edge.metadata.get("evidences");
if (evidences == null || !(evidences instanceof List)) return new Evidence[0];
List<Map> evidenceMap = typedList(((List) evidences), Map.class);
List<Evidence> evidenceList = new ArrayList<Evidence>();
for (Map item : evidenceMap) {
@SuppressWarnings("unchecked")
Map<String, Object> evMap = (Map<String, Object>) item;
Evidence ev = new Evidence();
ev.belStatement = getOrEmptyString("bel_statement", evMap).replace("\\\"", "\"");
ev.summaryText = getOrEmptyString("summary_text", evMap);
Citation citation = new Citation();
@SuppressWarnings("unchecked")
Map<String, Object> citationMap = (Map<String, Object>) evMap.get("citation");
if (citationMap != null) {
citation.id = getOrEmptyString("id", citationMap);
citation.type = getOrEmptyString("type", citationMap);
citation.name = getOrEmptyString("name", citationMap);
}
ev.citation = citation;
BiologicalContext context = new BiologicalContext();
@SuppressWarnings("unchecked")
Map<String, Object> contextMap = (Map<String, Object>) evMap.get("biological_context");
if (contextMap != null) {
context.speciesCommonName = getOrEmptyString("species_common_name", contextMap);
context.ncbiTaxId = getOrZero("ncbi_tax_id", contextMap);
Set<String> varying = new HashSet<String>(contextMap.keySet());
varying.removeAll(asList("species_common_name", "ncbi_tax_id"));
for (String key : varying) {
context.variedAnnotations.put(key, contextMap.get(key));
}
ev.biologicalContext = context;
}
evidenceList.add(ev);
}
return evidenceList.toArray(new Evidence[evidenceList.size()]);
}
/** {@inheritDoc} */
@Override
public Evidence[] mapFromTable(CyEdge edge, CyTable table) {
if (edge == null) throw new NullPointerException("edge cannot be null");
if (table == null) throw new NullPointerException("table cannot be null");
Set<String> nonAnnotationColumns =
new HashSet<String>(
asList(
CyNetwork.SUID,
NETWORK_SUID,
NETWORK_NAME,
EDGE_SUID,
BEL_STATEMENT,
SUMMARY_TEXT,
CITATION_ID,
CITATION_NAME,
CITATION_TYPE,
SPECIES));
Collection<CyRow> evidenceRows = table.getMatchingRows(EDGE_SUID, edge.getSUID());
List<Evidence> evidences = new ArrayList<Evidence>(evidenceRows.size());
if (!evidenceRows.isEmpty()) {
for (CyRow evRow : evidenceRows) {
Evidence e = new Evidence();
e.belStatement = evRow.get(BEL_STATEMENT, String.class);
e.summaryText = evRow.get(SUMMARY_TEXT, String.class);
e.citation = new Citation();
e.citation.id = evRow.get(CITATION_ID, String.class);
e.citation.name = evRow.get(CITATION_NAME, String.class);
e.citation.type = evRow.get(CITATION_TYPE, String.class);
e.biologicalContext = new BiologicalContext();
e.biologicalContext.speciesCommonName = evRow.get(SPECIES, String.class);
e.biologicalContext.variedAnnotations = new HashMap<String, Object>();
for (Entry<String, Object> columnValue : evRow.getAllValues().entrySet()) {
if (nonAnnotationColumns.contains(columnValue.getKey())) continue;
e.biologicalContext.variedAnnotations.put(columnValue.getKey(), columnValue.getValue());
}
evidences.add(e);
}
}
return evidences.toArray(new Evidence[evidences.size()]);
}