/**
* Compute the Information contents of the vertices specified in the given stack.
*
* @param allDescendantsInc a map containing the set of inclusive descendants for all the vertices
* contained in the graph. The information content will be computed for each vertices
* composing the stack considering the number of vertices in the graph equaling the number of
* vertices in the stack. Note that the number of descendant is considered to be inclusive
* i.e. the count of descendants of a concepts x must also count x.
* @return a result stack storing the information for each concepts specified in the result stack
* specified in parameter.
* @throws SLIB_Ex_Critic
*/
public Map<URI, Double> compute(Map<URI, Set<URI>> allDescendantsInc) throws SLIB_Ex_Critic {
Map<URI, Double> results = new HashMap<URI, Double>();
double x, cur_ic, nbDesc;
double setSize = allDescendantsInc.size(); // i.e. number of concepts in the processed graph
for (URI v : allDescendantsInc.keySet()) {
nbDesc = allDescendantsInc.get(v).size();
try {
cur_ic = computeIC(nbDesc, setSize);
} catch (SLIB_Ex_Critic e) {
throw new SLIB_Ex_Critic("Error computing IC of concept " + v + "\n" + e.getMessage());
}
results.put(v, cur_ic);
}
return results;
}
@Override
public void populate(GDataConf conf, G g) throws SLIB_Exception {
this.graph = g;
default_namespace = (String) conf.getParameter(ARG_PREFIX);
if (default_namespace == null) {
default_namespace = graph.getURI().getNamespace();
}
try {
logger.info("-------------------------------------");
logger.info("Loading Mesh XML");
logger.info("-------------------------------------");
idToConcepts = new HashMap<String, MeshConcept>();
SAXParserFactory parserfactory = SAXParserFactory.newInstance();
SAXParser saxParser;
saxParser = parserfactory.newSAXParser();
saxParser.parse(conf.getLoc(), new MeshXMLHandler(this));
logger.info(
"Number of descriptor loaded " + concepts.size() + " (ignored " + conceptIgnored + ")");
logger.info("Loading relationships ");
// Create universal root if required
URI universalRoot = OWL.THING;
if (!graph.containsVertex(universalRoot)) {
graph.addV(universalRoot);
}
// create relationships and roots of each tree
for (Entry<String, MeshConcept> e : idToConcepts.entrySet()) {
MeshConcept c = e.getValue();
URI vConcept = getOrCreateVertex(c.descriptorUI);
for (String treeNumber : c.treeNumberList) {
String parentId = getParentId(treeNumber);
if (parentId != null) {
MeshConcept parent = idToConcepts.get(parentId);
if (parent == null) {
throw new SLIB_Ex_Critic(
"Cannot locate parent identified by TreeNumber "
+ treeNumber
+ "\nError occured processing\n"
+ c);
} else {
// System.out.println("\t" + parentId + "\t" + parent.descriptorUI);
URI vParent = getOrCreateVertex(parent.descriptorUI);
E edge = new Edge(vConcept, RDFS.SUBCLASSOF, vParent);
g.addE(edge);
}
} else {
/* Those vertices are the inner roots of each trees,
* i.e. Psychiatry and Psychology [F] tree has for inner roots:
* - Behavior and Behavior Mechanisms [F01]
* - Psychological Phenomena and Processes [F02]
* - Mental Disorders [F03]
* - Behavioral Disciplines and Activities [F04]
* A vertex has already been created for each inner root (e.g. F01, F02, F03, F04)
* , we therefore create a vertex for the tree root (e.g. F).
* Finally all the tree roots are rooted by a global root which do not
* correspond to a concept specified into the mesh.
*
* More information about MeSH trees at http://www.nlm.nih.gov/mesh/trees.html
*/
// we link the tree inner root to the root tree
char localNameTreeRoot = treeNumber.charAt(0); // id of the tree root
URI rootTree = getOrCreateVertex(localNameTreeRoot + ""); // e.g. F
E treeInnerRootToTreeRoot = new Edge(vConcept, RDFS.SUBCLASSOF, rootTree);
g.addE(treeInnerRootToTreeRoot);
// logger.debug("Creating Edge : " + treeInnerRootToTreeRoot);
// we link the tree root to the universal root
E treeRootToUniversalRoot = new Edge(rootTree, RDFS.SUBCLASSOF, universalRoot);
g.addE(treeRootToUniversalRoot);
// logger.debug("Creating Edge : " + treeRootToUniversalRoot);
}
}
}
} catch (IOException ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
} catch (ParserConfigurationException ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
} catch (SAXException ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
} catch (SLIB_Ex_Critic ex) {
throw new SLIB_Ex_Critic(ex.getMessage());
}
logger.info("MESH loader - process performed");
logger.info("-------------------------------------");
}
