/*
* depth: the current depth of how much is sorted.
* bound: how far to sort.
*/
void MediankeyBoundedQuicksort(unsigned char text[], UInt index[], UInt length,
UInt low, UInt high, int depth, int bound, UInt maxChar, UInt *freq) {
if (high - low <= 1)
return;
if (depth > bound)
return;
bool deleteFreq = false;
if (freq == NULL) {
UInt ci;
maxChar = 0;
for (ci = low; ci < high; ci++) {
UInt c = text[index[ci]+depth];
if ( c > maxChar) {
maxChar = c;
}
}
freq = ProtectedNew<UInt>(maxChar+1);
deleteFreq = true;
}
Nucleotide medianChar = ComputeMedianValue(text, index, length, low, high, depth, maxChar, freq );
UInt medianCharPos = FindFirstOf(text, index, low, high, depth, medianChar);
UInt medLeft, lastLeft;
UInt medRight, lastRight;
//
// Pack the median characters into the sides of the array.
//
SwapIndices(index[low], index[medianCharPos]);
medLeft = lastLeft = low+1;
medRight = lastRight = high-1;
for(;;) {
Nucleotide nuc;
while(lastLeft <= lastRight and (nuc = text[index[lastLeft]+depth]) <= medianChar) {
if (nuc == medianChar) {
SwapIndices(index[medLeft], index[lastLeft]);
medLeft++;
}
lastLeft++;
}
while(lastLeft <= lastRight and (nuc = text[index[lastRight]+depth]) >= medianChar) {
if (nuc == medianChar) {
SwapIndices(index[medRight], index[lastRight]);
medRight--;
}
lastRight--;
}
if (lastLeft > lastRight) {
// done with median sort.
break;
}
//
// Otherwise, this ends with an index at the left out of order
// from the right
assert(text[index[lastLeft]+depth] > text[index[lastRight]+depth]);
SwapIndices(index[lastLeft], index[lastRight]);
}
//
// Now join the indices of the median charactes in the middle of the
// array.
//
// move left outside to middle
UInt swapLeftLength = std::min(medLeft - low, lastLeft - medLeft);
VecSwap(low, lastLeft - swapLeftLength, swapLeftLength, index);
// move right outside to middle
UInt swapRightLength = std::min(high - medRight - 1, medRight - lastRight);
VecSwap(lastRight+1, high-swapRightLength, swapRightLength, index);
UInt medianStartIndex = low + lastLeft - medLeft;
UInt medianEndIndex = lastRight + (high - medRight);
// Sort the suffices with keys lower than the median.
// Since these may contain multiple keys that are less than the
// median, the same depth is used.
MediankeyBoundedQuicksort(text, index, length,
low,
medianStartIndex,
depth, bound, maxChar,freq);
if (medianEndIndex - medianStartIndex > 1) {
MediankeyBoundedQuicksort(text, index, length,
medianStartIndex, medianEndIndex, depth+1, bound, maxChar, freq);
}
MediankeyBoundedQuicksort(text, index, length,
medianEndIndex,
high,
depth, bound, maxChar, freq);
if (deleteFreq) {delete [] freq; freq = NULL;}
}
int AString<B>::FindFirstOf(const tchar *s, int from) const
{
return FindFirstOf(strlen__(s), s, from);
}
