/**
* Uses the given PathAccessor to access fields of the seed and return only new elements that is
* not in the given element set (all).
*
* @param pa accessor to the filed
* @param seed entities to get their fields
* @param all already found values
* @return new values
*/
protected Set access(PathAccessor pa, Set<BioPAXElement> seed, Set<BioPAXElement> all) {
Set set = pa.getValueFromBeans(seed);
set.removeAll(all);
// remove blacklisted
if (blacklist == null) return set;
else return blacklist.getNonUbiqueObjects(set);
}
/**
* Checks the gained and and lost features to predict the activity change is the desired change.
* If exact matching (terms with locations) is not conclusive, then terms without locations are
* checked. If still not conclusive, then approximate matching is used.
*
* @param match current pattern match
* @param ind mapped indices
* @return true if the modification gain or loss is mapped to the desired change
*/
@Override
public boolean satisfies(Match match, int... ind) {
BioPAXElement ele1 = match.get(ind[0]);
BioPAXElement ele2 = match.get(ind[1]);
EntityReference er = ((SimplePhysicalEntity) ele1).getEntityReference();
Set set1 = pa.getValueFromBean(ele1);
Set set2 = pa.getValueFromBean(ele2);
Set gain = new HashSet(set2);
gain.removeAll(set1);
Set loss = new HashSet(set1);
loss.removeAll(set2);
int activatingCnt = 0;
int inhibitingCnt = 0;
for (Object o : gain) {
if (activityFeat.get(er).contains(o)) activatingCnt++;
if (inactivityFeat.get(er).contains(o)) inhibitingCnt++;
}
for (Object o : loss) {
if (inactivityFeat.get(er).contains(o)) activatingCnt++;
if (activityFeat.get(er).contains(o)) inhibitingCnt++;
}
// Match without considering the locations
Set<String> gainTypes = null;
Set<String> lossTypes = null;
if (activatingCnt + inhibitingCnt == 0) {
gainTypes = extractModifNames(gain);
lossTypes = extractModifNames(loss);
for (String s : gainTypes) {
if (activityStr.get(er).contains(s)) activatingCnt++;
if (inactivityStr.get(er).contains(s)) inhibitingCnt++;
}
for (String s : lossTypes) {
if (inactivityStr.get(er).contains(s)) activatingCnt++;
if (activityStr.get(er).contains(s)) inhibitingCnt++;
}
}
// Try to match modifications with approximate name matching
if (activatingCnt + inhibitingCnt == 0) {
for (String genName : general) {
boolean foundInActivating = setContainsGeneralTerm(activityStr.get(er), genName);
boolean foundInInhibiting = setContainsGeneralTerm(inactivityStr.get(er), genName);
if (foundInActivating == foundInInhibiting) continue;
boolean foundInGain = setContainsGeneralTerm(gainTypes, genName);
boolean foundInLose = setContainsGeneralTerm(lossTypes, genName);
if (foundInGain == foundInLose) continue;
if (foundInActivating && foundInGain) activatingCnt++;
else if (foundInInhibiting && foundInLose) activatingCnt++;
else if (foundInActivating && foundInLose) inhibitingCnt++;
else /*if (foundInInhibiting && foundInGain)*/ inhibitingCnt++;
}
}
if (activatingCnt > 0 && inhibitingCnt > 0) return false;
return activating ? activatingCnt > 0 : inhibitingCnt > 0;
}