void Grid::simplify()
{
extendLeft();
extendRight();
extendUp();
extendDown();
merge();
}
void BWTTraverse::extractSG(const BWT* pBWT, const BWT* pRevBWT, const unsigned int len)
{
WARN_ONCE("Skipping bwt[0]");
// Keep a bool vector marking which entries in pBWT have been visited
size_t n_elems = pBWT->getBWLen();
bool_vec visited(n_elems, false);
size_t count = 0;
size_t currIdx = 1;
while(currIdx < n_elems)
{
// Invariant: currIdx is the index into pBWT that is the lowest index that has not been visited
// Left-extend the entry at currIdx into a string of length len
std::string str;
str.reserve(len);
// Get the first character of the suffix starting at this position
char first = pBWT->getF(currIdx);
str += first;
BWTInterval range(currIdx, currIdx);
while(str.length() < len)
{
char b = pBWT->getChar(range.lower);
if(b == '$')
break;
str += b;
BWTAlgorithms::updateInterval(range, b, pBWT);
}
// The string was built backwards, reverse it
str = reverse(str);
if(str.length() < len)
{
visited[currIdx] = true;
}
else if(!visited[range.lower])
{
markVisited(str, visited, pBWT);
//std::cout << currIdx << " interval: " << range << " string: " << str << "\n";
extendLeft(len, str, visited, pBWT, pRevBWT);
extendRight(len, str, visited, pBWT, pRevBWT, false);
printf(">%zu %zu 0\n%s\n", count++, str.length(), str.c_str());
}
currIdx++;
}
}
