private TreeMap<Integer, Domain> collapseRepeats(TreeMap<Integer, Domain> doms) {
TreeMap<Integer, Domain> collpasedDomains = new TreeMap<Integer, Domain>();
ArrayList<Domain> domainHolding = new ArrayList<Domain>();
Domain lastDom = null;
for (Domain cDom : doms.values()) {
if (lastDom == null) {
domainHolding.add(cDom);
lastDom = cDom;
continue;
}
if (lastDom.ID.equals(cDom.ID)) domainHolding.add(cDom);
else {
if (domainHolding.size() >= repNo) {
Domain firstRepDom = domainHolding.get(0);
Domain d = new Domain(lastDom.ID, firstRepDom.aliFrom, lastDom.aliTo, -1, -1, -1);
d.setComment("collapsed " + domainHolding.size() + " instances");
collpasedDomains.put(d.aliFrom, d);
} else {
for (Domain d : domainHolding) collpasedDomains.put(d.aliFrom, d);
}
domainHolding.clear();
domainHolding.add(cDom);
}
lastDom = cDom;
}
if (domainHolding.size() >= repNo) {
Domain firstRepDom = domainHolding.get(0);
Domain d = new Domain(lastDom.ID, firstRepDom.aliFrom, lastDom.aliTo, -1, -1, -1);
d.setComment("collapsed " + domainHolding.size() + " instances");
collpasedDomains.put(d.aliFrom, d);
} else {
for (Domain d : domainHolding) collpasedDomains.put(d.aliFrom, d);
}
return collpasedDomains;
}
private TreeMap<Integer, Domain> mergeHits(TreeMap<Integer, Domain> doms) {
Domain lastDom = null, mergedDom = null;
int lastStart = 0;
int numOfMerged = 1; // n merge operations means n+1 merged domains
TreeMap<Integer, Domain> modifedDoms = new TreeMap<Integer, Domain>();
for (int startPos : doms.keySet()) {
Domain curDom = doms.get(startPos);
if (lastDom != null) {
// if the same domain type...
if (lastDom.getID().equals(curDom.getID())) {
// ... check if split hits present
if ((lastDom.getHmmTo() < curDom.getHmmFrom())
&& (lastDom.getAliTo() < curDom.getAliFrom())) {
numOfMerged += 1;
// if we alread started a merged domain, extend
if (mergedDom != null) {
mergedDom.setAliTo(curDom.getAliTo());
mergedDom.setComment(numOfMerged + " merged hits");
}
// else start new merged Domain
else {
mergedDom =
new Domain(
curDom.getID(),
lastDom.getAliFrom(), // from beginning of last domain
curDom.getAliTo(), // to end of current domain
lastDom.getHmmFrom(),
curDom.getHmmTo(),
-1); // evalue?
mergedDom.setComment(numOfMerged + " merged hits");
}
}
// last domain ID is the same, but hits are not split
else {
modifedDoms.put(lastStart, lastDom);
}
}
// last domain ID is different from current domain ID
else {
// first add merged domain, if present
if (mergedDom != null) {
modifedDoms.put(mergedDom.aliFrom, mergedDom);
}
// all is well - we will keep the last domain
else {
modifedDoms.put(lastStart, lastDom);
}
mergedDom = null;
numOfMerged = 1;
}
}
lastStart = startPos;
lastDom = curDom;
}
if (mergedDom != null) {
mergedDom.setComment(numOfMerged + " merged hits");
modifedDoms.put(mergedDom.aliFrom, mergedDom);
}
// all is well - we will keep the last domain
else modifedDoms.put(lastStart, lastDom);
return modifedDoms;
}