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#include "pp_fastBlockSearcher.hh"
#include <sstream>
int PP::FsHitType::maxIntronLen = 100000;
double PP::FsHitType::intronMalus = 1e-5;
int PP::FsSeedCollection::expSeedCount = 10000;
double PP::FsSeedCollection::maxCoverage = 0.8;
void PP::FsHitCollection::newHit(FsHitType* ht) {
allHits.push_back(ht);
vector<HitQueue>& allQueues = pendingHits[ht->reverse];
int b = ht->reverse ? ht->blockNo+1 : ht->blockNo-1;
if (b>=0 && b<size)
ht->linkTo(allQueues[b]);
if (ht->reverse)
for (b=ht->blockNo; b>0; b--)
ht->pushOn(allQueues[b]);
else
for (b=ht->blockNo; b<size-1; b++)
ht->pushOn(allQueues[b]);
// Put this entry in to the final result container
if (finalResult.empty()) {
finalResult.push_back(ht);
return;
}
int i = finalResult.size()-1;
while (i>=0 && finalResult[i]->start() > ht->start())
i--;
if (i>=0 && finalResult[i]->head == ht->head) {
if (finalResult[i]->pathScore < ht->pathScore)
finalResult[i] = ht;
} else if (i == finalResult.size()-1) {
finalResult.push_back(ht);
} else {
int j = finalResult.size()-1;
finalResult.push_back(finalResult.back());
while (--j>i)
finalResult[j+1] = finalResult[j];
finalResult[i+1] = ht;
}
}
void PP::FsHitCollection::storeBestResults(multimap<double, FsHitType>& result, int mincount, double threshold) {
int maxcount = finalResult.size();
result.clear();
if (mincount > maxcount)
mincount = maxcount;
int i;
for (i=0; i<mincount; i++) {
FsHitType* ht = finalResult[i];
result.insert(make_pair(ht->pathScore, *ht));
}
if (mincount) for(; i<maxcount; i++) {
FsHitType* ht = finalResult[i];
double sc = ht->pathScore;
double listSc = result.begin()->second.pathScore;
if (listSc > threshold)
break;
if (listSc > sc)
continue;
result.erase(result.begin());
result.insert(make_pair(sc, *ht));
}
for (; i<maxcount; i++) {
FsHitType* ht = finalResult[i];
if (ht->pathScore > threshold)
result.insert(make_pair(ht->pathScore, *ht));
}
}
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