void AssemblyJobSsDeBruijn::findBestLinks(DeBruijnGraph* graph){
char nucs[] = {'A','T','C','G'};
for (DeBruijnGraph::Iterator nodeIt = graph->begin(); nodeIt != graph->end(); ++nodeIt){
DeBruijnNode* currentNode = *nodeIt;
DeBruijnNode* best5pLink = 0;
float best5pLinkScore = 0;
DeBruijnNode* best3pLink = 0;
float best3pLinkScore = 0;
for (int n = 0; n < 4; ++n){
DeBruijnNode* cand5pLink = currentNode->get5pLink(nucs[n]);
if (cand5pLink != 0){
// take the worse of the two linkage scores
float next5pLinkScore;
if (currentNode->get5pLinkScore(nucs[n]) > cand5pLink->get3pLinkScore(currentNode->get3pNuc()) ){
next5pLinkScore = cand5pLink->get3pLinkScore(currentNode->get3pNuc());
} else { next5pLinkScore = currentNode->get5pLinkScore(nucs[n]); }
if (next5pLinkScore > best5pLinkScore){
best5pLinkScore = next5pLinkScore;
best5pLink = cand5pLink;
}
}
DeBruijnNode* cand3pLink = currentNode->get3pLink(nucs[n]);
if (cand3pLink != 0){
// take the worse of the two linkage scores
float next3pLinkScore;
if (currentNode->get3pLinkScore(nucs[n]) > cand3pLink->get5pLinkScore(currentNode->get5pNuc()) ){
next3pLinkScore = cand3pLink->get5pLinkScore(currentNode->get5pNuc());
} else { next3pLinkScore = currentNode->get3pLinkScore(nucs[n]); }
if (next3pLinkScore > best3pLinkScore){
best3pLinkScore = next3pLinkScore;
best3pLink = cand3pLink;
}
}
}
currentNode->setBest5pLink(best5pLink);
currentNode->setBest3pLink(best3pLink);
}
// FOURTH resolve best-edge conflicts
for (DeBruijnGraph::Iterator nodeIt = graph->begin(); nodeIt != graph->end(); ++nodeIt){
DeBruijnNode* currentNode = *nodeIt;
DeBruijnNode* best5pLink = currentNode->best5pLink();
if (best5pLink != 0 and best5pLink->best3pLink() != currentNode){
DeBruijnNode* bestRecip = best5pLink->best3pLink();
if (bestRecip == 0){ best5pLink->setBest3pLink(currentNode); }
else { currentNode->setBest5pLink( 0 ); }
}
DeBruijnNode* best3pLink = currentNode->best3pLink();
if (best3pLink != 0 and best3pLink->best5pLink() != currentNode){
DeBruijnNode* bestRecip = best3pLink->best5pLink();
if (bestRecip == 0){ best3pLink->setBest5pLink(currentNode); }
else { currentNode->setBest3pLink( 0 ); }
}
}
}
ScoredSeq* AssemblyJobSsDeBruijn::makeSeqFromPath(DeBruijnNode* node5p, DeBruijnNode* node3p, long numNodes){
long seqLen = _kmerSize + numNodes - 1;
char* cSeq = new char[seqLen + 1];
cSeq[seqLen] = '\0';
float* scores = new float[seqLen];
float* links = new float[seqLen-1];
// do the initial kmer and any overlapping positions
node5p->getKmer(cSeq,0);
float firstScore = node5p->getKmerScore();
for (int n = 0; n < _kmerSize; ++n){
scores[n] = firstScore;
if (n < _kmerSize - 1){ links[n] = firstScore; }
}
// fill in the rest
DeBruijnNode* currentNode = node5p;
DeBruijnNode* priorNode = 0;
long pos5p = 0;
long pos3p = _kmerSize - 1;
while (currentNode != node3p){
// increment
pos5p++;
pos3p++;
priorNode = currentNode;
currentNode = currentNode->best3pLink();
// fill in values
cSeq[pos3p] = currentNode->get3pNuc();
scores[pos3p] = currentNode->getKmerScore();
links[pos3p-1] = priorNode->get3pLinkScore( currentNode->get3pNuc() );
if (links[pos5p-1] < currentNode->get5pLinkScore( cSeq[pos5p-1] )){
links[pos5p-1] = currentNode->get5pLinkScore( cSeq[pos5p-1] );
}
for (long pos = pos5p; pos < pos3p; ++pos){
if (scores[pos] < currentNode->getKmerScore()){ scores[pos] = currentNode->getKmerScore(); }
}
}
ScoredSeq* novelSeq = new ScoredSeqShallow(true, cSeq, scores, links, seqLen);
//ScoredSeq* novelSeq = ScoredSeq::getScoredSeq(cSeq, scores, links, seqLen);
/*
delete [] cSeq;
delete [] scores;
delete [] links;
*/
return novelSeq;
}
