/**
* Calculate scores for each entry in the EntrySet. The scores are added to the EntrySet directly
* and the scoring report will be returned.
*
* @param entrySet the entry set where the scores will be added to
* @return scoring report
* @throws PsiscoreException
*/
public List<String> calculateScores(EntrySet entrySet) throws PsiscoreException {
if (entrySet.getEntries() == null) {
throw new PsiscoreException("EntrySet does not contain any entries", new PsiscoreFault());
}
List<String> report = new ArrayList<String>();
int scored = 0;
int unscored = 0;
int totalConfidences = 0;
// go over all entries
Iterator<Entry> it = entrySet.getEntries().iterator();
scoringParameters.setScoresAdded(false);
while (it.hasNext()) {
Entry entry = it.next();
// and go over all interactions in that entry
Collection<Interaction> interactions = entry.getInteractions();
for (Iterator<Interaction> interactionIt = interactions.iterator();
interactionIt.hasNext(); ) {
Interaction interaction = interactionIt.next();
Collection<Confidence> confidences = null;
// and request the scores for that interaction
try {
confidences = getInteractionScores(interaction);
} catch (ScoringException e) {
report.add(e.getMessage());
}
// confidences = null;
if (confidences == null || confidences.size() == 0) {
unscored++;
} else if (confidences.size() > 0) {
scoringParameters.setScoresAdded(true);
scored++;
totalConfidences += confidences.size();
interaction.getConfidences().addAll(confidences);
}
}
}
report.add(
totalConfidences
+ " confidences scores added for "
+ scored
+ " interactions, nothing added for "
+ unscored
+ " interactions");
return report;
}
/** Perform Mapping. */
public void doMapping() {
// Create Entry Set and Entry
entrySet = new EntrySet();
entrySet.setLevel(2);
entrySet.setVersion(5);
EntrySet.Entry entry = new EntrySet.Entry();
// Get Interactor List
EntrySet.Entry.InteractorList interactorList = getInteractorList();
// Get Interaction List
EntrySet.Entry.InteractionList interactionList = getInteractionList();
// Add to Entry node
entry.setInteractorList(interactorList);
entry.setInteractionList(interactionList);
entrySet.getEntry().add(entry);
}
