long AssemblyJobSsDeBruijn::combineTreesMidHelp(SeqNode* topNodeA, int kmerSize,
SeqNode* branchA, SeqNode* branchB, int remainingKmer){
char nucs[] = {'A','T','C','G'};
long newNodeSum = 0;
if (remainingKmer == 1){
for (int n = 0; n < 4; ++n){
DeBruijnNode* newNodeB = dynamic_cast<DeBruijnNode*>(branchB->getBranch(nucs[n]));
if (newNodeB != 0){
DeBruijnNode* newNodeA = dynamic_cast<DeBruijnNode*>(branchA->getBranch(nucs[n]));
if (newNodeA == 0){
newNodeA = new DeBruijnNode(branchA,nucs[n]);
branchA->addBranch( newNodeA );
newNodeSum += 1;
}
newNodeA->addKmerScore( newNodeB->getKmerScore() );
newNodeSum += combineTreesBottomHelp(topNodeA, kmerSize, newNodeA, newNodeB);
}
}
} else {
for (int n = 0; n < 4; ++n){
SeqNode* newNodeB = branchB->getBranch(nucs[n]);
if (newNodeB != 0){
SeqNode* newNodeA = branchA->getBranch(nucs[n]);
if (newNodeA == 0){
newNodeA = new NucNode(branchA,nucs[n]);
branchA->addBranch( newNodeA );
}
newNodeSum += combineTreesMidHelp(topNodeA, kmerSize, newNodeA, newNodeB, remainingKmer-1);
}
}
}
return newNodeSum;
}
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;
}
void AssemblyJobSsDeBruijn::testTreeConstructionHelper(set<ScoredSeq*>* foundKmers, SeqNode* node, int stepsToBottom){
if (stepsToBottom == 0){
DeBruijnNode* dbNode = dynamic_cast<DeBruijnNode*>(node);
foundKmers->insert( new ScoredSeqMonoScore(dbNode->getKmer(), dbNode->getKmerScore()) );
//foundKmers->insert( ScoredSeq::getScoredSeq(dbNode->getKmer(), dbNode->getKmerScore()) );
} else {
char nucList[] = {'A','T','C','G'};
for (int n = 0; n < 4; ++n){
SeqNode* nextNode = node->getBranch( nucList[n] );
if (nextNode != 0){ testTreeConstructionHelper( foundKmers, nextNode, stepsToBottom-1 ); }
}
}
}
