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#undef SEARCH_FUNCTION_NAME
#if ALIGN_WITH_BACKPOINTER
#define SEARCH_FUNCTION_NAME search
#else // ALIGN_WITH_BACKPOINTER is false
#define SEARCH_FUNCTION_NAME search_without_backpointer
#endif // ALIGN_WITH_BACKPOINTER
/*
Input:
Global: radious, similarity, sortedStrings.
Output:
Global: searchResults.
*/
void SEARCH_FUNCTION_NAME(const PositionType l, const PositionType r, PositionType pos, const Index intervalIndex, const uint16_t tableIndex, const int globalOffset)
{
DpTable *table = tables[tableIndex];
std::vector<CharType> *localWord = &word[tableIndex];
std::vector<PositionType> *localWordMinLength = &wordMinLength[tableIndex];
std::vector<PositionType> *localLeft = &left[tableIndex];
std::vector<PositionType> *localRight = &right[tableIndex];
std::vector<PositionType> *localMinCost = &minCost[tableIndex];
CostType maxLengthRadious = std::min(static_cast<CostType>(floor((1 - similarity) * sortedStringsLengthsMaxTree[tableIndex][intervalIndex])), radious);
if (mismatches >= 0)
maxLengthRadious = static_cast<CostType>(radious);
PositionType minSortedStringsLength = sortedStringsLengthsMinTree[tableIndex][intervalIndex];
PositionType maxRight = querySequenceLength - minSortedStringsLength + radious;
do {
if (sortedStrings[globalOffset + l][pos] != sortedStrings[globalOffset + r][pos]) {
PositionType mid = (l + r) / 2;
Index leftIntervalIndex = intervalIndex + 1;
Index rightIntervalIndex = 2 * (mid - l + 1) + intervalIndex;
if (sortedStringsLengthsMinTree[tableIndex][leftIntervalIndex] < sortedStringsLengthsMinTree[tableIndex][rightIntervalIndex]) {
SEARCH_FUNCTION_NAME(l, mid, pos, leftIntervalIndex, tableIndex, globalOffset);
SEARCH_FUNCTION_NAME(mid + 1, r, pos, rightIntervalIndex, tableIndex, globalOffset);
} else {
SEARCH_FUNCTION_NAME(mid + 1, r, pos, rightIntervalIndex, tableIndex, globalOffset);
SEARCH_FUNCTION_NAME(l, mid, pos, leftIntervalIndex, tableIndex, globalOffset);
}
return;
}
if (endOfStringChar == sortedStrings[globalOffset + l][pos]) {
SearchResult result;
PositionType minPos = std::max(0, (*localLeft)[pos] + pos);
for(PositionType i = minPos + 1; i <= (*localRight)[pos] + pos; ++i)
if ((*table)(pos, i) < (*table)(pos, minPos))
minPos = i;
// Check the number of differences is less than or equal to similarity times the length of the shorter sequence.
float acceptable_differences = pos * (1 - similarity);
if (mismatches >= 0)
acceptable_differences = mismatches;
if ((*table)(pos, minPos) <= acceptable_differences) {
if (outputMultipleAlignment) {
boost::tie(result.cost, result.func) = findAlignmentFunction(pos, querySequenceLength, minPos);
}
// Try to lower the amount of time we try to claim the lock.
//if (l <= r){
//pthread_mutex_lock(&running_mutex);
for (PositionType i = l; i <= r; ++i) {
result.number = i + globalOffset;
threadSearchResults[tableIndex].push_back(result);
//++resultsCounter[tableIndex];
} // for (PositionType i = l;; i <= r; ++i)
} // if (table(pos, minPos) <= pos * (1 - similarity))
return;
}
if ((*localWord)[pos + 1] != sortedStrings[globalOffset + l][pos]
|| (*localWordMinLength)[pos + 1] > minSortedStringsLength
) {
// Row table(pos + 1, *) must be updated.
// Thus minCost[pos + 1] must be updated.
(*localWord)[pos + 1] = sortedStrings[globalOffset + l][pos];
(*localWord)[pos + 2] = invalidChar;
(*localWordMinLength)[pos + 1] = minSortedStringsLength;
{ // Update the row table(pos + 1, *)
const PositionType minColumn = std::max(0, (*localLeft)[pos] + (pos + 1));
const PositionType maxColumn = std::min(querySequenceLength, (*localRight)[pos] + (pos + 1));
CostType currentMinCost = MAX_COST;
CostType currentCost;
#if ALIGN_WITH_BACKPOINTER
BackPointer currentPointer;
#endif // ALIGN_WITH_BACKPOINTER
const PositionType i = pos + 1;
const CharType c1 = (*localWord)[i];
CharType c2; // = querySequencePointer[j - 1]
CostType matchCost, gapCost2, gapCost1;
CostType leftCost, downLeftCost, downCost;
leftCost = MAX_COST;
if (minColumn > 0) {
downLeftCost = (*table)(i - 1, minColumn - 1);
} else {
downLeftCost = MAX_COST;
}
for (PositionType j = minColumn; j <= maxColumn; ++j) {
{ // Update table(i, j) = table(pos + 1, j)
#if ALIGN_WITH_BACKPOINTER
currentPointer = ROOT;
#endif // ALIGN_WITH_BACKPOINTER
currentCost = MAX_COST;
// c1 == word[i]
c2 = querySequencePointer[j - 1];
matchCost = downLeftCost + cost(c1, c2);
if (matchCost < currentCost) {
currentCost = matchCost;
#if ALIGN_WITH_BACKPOINTER
currentPointer = DOWN_LEFT;
#endif // ALIGN_WITH_BACKPOINTER
}
gapCost2 = leftCost + cost(gapChar, c2);
if (gapCost2 < currentCost) {
currentCost = gapCost2;
#if ALIGN_WITH_BACKPOINTER
currentPointer = LEFT;
#endif // ALIGN_WITH_BACKPOINTER
}
downCost = (*table)(i - 1, j);
gapCost1 = downCost + cost(c1, gapChar);
if (gapCost1 < currentCost) {
currentCost = gapCost1;
#if ALIGN_WITH_BACKPOINTER
currentPointer = DOWN;
#endif // ALIGN_WITH_BACKPOINTER
}
(*table)(i, j) = currentCost;
#if ALIGN_WITH_BACKPOINTER
backTable(i, j) = currentPointer;
#endif // ALIGN_WITH_BACKPOINTER
leftCost = currentCost;
downLeftCost = downCost;
} // Update table(i, j) = table(pos + 1, j)
if (currentCost < currentMinCost)
currentMinCost = currentCost;
} // for (PositionType j...
(*localMinCost)[pos + 1] = currentMinCost;
}
if ((*localRight)[pos] + (pos + 1) < querySequenceLength)
(*table)(pos + 1, (*localRight)[pos] + (pos + 1) + 1) = MAX_COST;
{ // Find left[pos + 1].
PositionType j = std::max(-(pos + 1), (*localLeft)[pos]);
PositionType maxIndex = std::min(querySequenceLength - (pos + 1), (*localRight)[pos]);
while ((j <= maxIndex) && ((*table)(pos + 1, j + (pos + 1)) > radious))
++j;
if (j == -(pos + 1))
(*localLeft)[pos + 1] = j - 1;
else
(*localLeft)[pos + 1] = j;
}
{ // Find right[pos + 1].
PositionType j = std::min(querySequenceLength - (pos + 1), (*localRight)[pos]);
PositionType minIndex = std::max(-(pos + 1), (*localLeft)[pos]);
while ((j >= minIndex) && ((*table)(pos + 1, j + (pos + 1)) > radious))
--j;
(*localRight)[pos + 1] = std::min(j, maxRight);
} // Find right[pos + 1]
} // if (word[pos + 1] != sortedStrings[l][pos])
} while ((*localMinCost)[++pos] <= maxLengthRadious);
}
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