void KMLNetOutput::createKML(const std::string& fileWithNodes, const std::string& kmlFileName){
std::cout << "KML will be written to: " << kmlFileName << std::endl;
int nbNodes = net_->getNbNodes();
std::vector<FPType> xCoord(nbNodes, 0);
std::vector<FPType> yCoord(nbNodes, 0);
std::vector<int> nodeID(nbNodes, 0);
readCoord(fileWithNodes, xCoord, yCoord, nodeID);
FileWriter writeKml(kmlFileName);
writeKml.writeLine(createKmlHeader());
for (StarLink* link = net_->beginOnlyLink(); link != NULL; link = net_->getNextOnlyLink()) {
if (shouldCreatePlacemark(link)) {
int tail = link->getNodeFromIndex();
int head = link->getNodeToIndex();
FPType x1 = xCoord[tail];
FPType y1 = yCoord[tail];
FPType x2 = xCoord[head];
FPType y2 = yCoord[head];
if (x1 == 0 && y1 == 0) std::cout << "Missing node coordinate: " << link->getNodeFrom() <<
" link: " << link->toString() << std::endl;
if (x2 == 0 && y2 == 0) std::cout << "Missing node coordinate: " << link->getNodeTo() <<
" link: " << link->toString() << std::endl;
if (x1 != 0 && y1 != 0 && x2 != 0 && y2 != 0)
writeKml.writeLine(createPlacemark(x1, y1, x2, y2, link));
}
}
writeKml.writeLine(createKmlFooter());
};
// Get the substring of the full path string starting from position fromX
// to position toY on the first and last vertices, respectively.
// dirX is the direction along contig X towards vertex Y, vis-versa for dirY
std::string SGWalk::getFragmentString(const Vertex* pX, const Vertex* pY,
int fromX, int toY,
EdgeDir dirX, EdgeDir dirY) const
{
std::string out;
// Calculate the portion of X that we should include in the string
// If dirX is SENSE, we take the everything after position fromX
// otherwise we take everything up to and including fromX
SeqCoord xCoord(0,0,pX->getSeqLen());
if(dirX == ED_SENSE)
{
xCoord.interval.start = fromX;
xCoord.interval.end = pX->getSeqLen() - 1;
}
else
{
xCoord.interval.start = 0;
xCoord.interval.end = fromX;
}
// Handle the trivial case where pX == pY and the walk is found immediately
if(m_edges.empty() && pX == pY)
{
if(dirY == ED_SENSE)
{
xCoord.interval.start = toY;
}
else
{
xCoord.interval.end = toY;
}
}
if(!xCoord.isValid())
return "";
//
out.append(m_pStartVertex->getSeq().substr(xCoord.interval.start, xCoord.length()));
// Determine if the string should go to the end of the last vertex
// in the path
size_t stop = m_edges.size();
// The first edge is always in correct frame of reference
// so the comp is EC_SAME. This variable tracks where the
// string that is being added is different from the starting sequence
// and needs to be flipped
EdgeComp currComp = EC_SAME;
// If the walk direction is antisense, we reverse every component and then
// reverse the entire string to generate the final string
bool reverseAll = !m_edges.empty() && m_edges[0]->getDir() == ED_ANTISENSE;
if(reverseAll)
out = reverse(out);
for(size_t i = 0; i < stop; ++i)
{
Edge* pYZ = m_edges[i];
bool isLast = i == (stop - 1);
if(!isLast)
{
// Append the extension string without modification
std::string edge_str = pYZ->getLabel();
assert(edge_str.size() != 0);
if(currComp == EC_REVERSE)
edge_str = reverseComplement(edge_str);
if(reverseAll)
edge_str = reverse(edge_str);
out.append(edge_str);
}
else
{
//
const Edge* pZY = pYZ->getTwin();
// get the unmatched coordinates on pY
SeqCoord unmatched = pZY->getMatchCoord().complement();
// Now, we have to shrink the unmatched interval on Y to
// only incude up to toY
if(dirY == ED_SENSE)
unmatched.interval.start = toY;
else
unmatched.interval.end = toY;
if(!unmatched.isValid())
return "";
std::string seq = unmatched.getSubstring(pY->getStr());
if(pYZ->getComp() != currComp)
seq = reverseComplement(seq);
if(reverseAll)
seq = reverse(seq);
out.append(seq);
}
// Calculate the next comp, between X and Z
EdgeComp ecYZ = pYZ->getComp();
EdgeComp ecXZ;
if(ecYZ == EC_SAME)
ecXZ = currComp;
else
ecXZ = !currComp;
currComp = ecXZ;
}
if(reverseAll)
out = reverse(out);
return out;
}
