void alignmentsExtract(std::vector<Chain*>& dst, Chain* query, DbAlignment** alignments,
int alignments_length) {
int query_len = chainGetLength(query);
char* alignment_str = new char[query_len];
int query_start, length;
Chain* target = nullptr;
char* query_str = nullptr;
char* target_str = nullptr;
Alignment* alignment = nullptr;
const char gap_item = '-';
for (int i = 0; i < alignments_length; ++i) {
target = dbAlignmentGetTarget(alignments[i]);
query_start = dbAlignmentGetQueryStart(alignments[i]);
length = dbAlignmentGetPathLen(alignments[i]);
alignment = dbAlignmentToAlignment(alignments[i]);
aligmentStr(&query_str, &target_str, alignment, gap_item);
alignmentDelete(alignment);
int j = 0;
for (; j < query_start; ++j) {
alignment_str[j] = 'X';
}
for (int k = 0; k < length; ++k) {
if (query_str[k] != gap_item) {
if (target_str[k] != gap_item) {
alignment_str[j++] = target_str[k];
} else {
alignment_str[j++] = 'X';
}
}
}
for (; j < query_len; ++j) {
alignment_str[j] = 'X';
}
dst.push_back(chainCreate((char*) chainGetName(target), strlen(chainGetName(target)),
alignment_str, query_len));
delete[] query_str;
delete[] target_str;
}
delete[] alignment_str;
}
static void* alignThread(void* param) {
AlignContext* context = (AlignContext*) param;
DbAlignment** dbAlignment = context->dbAlignment;
int type = context->type;
Chain* query = context->query;
int queryIdx = context->queryIdx;
Chain* target = context->target;
int targetIdx = context->targetIdx;
double value = context->value;
int score = context->score;
Scorer* scorer = context->scorer;
int* cards = context->cards;
int cardsLen = context->cardsLen;
// align
Alignment* alignment;
alignScoredPair(&alignment, type, query, target, scorer, score, cards, cardsLen, NULL);
// check scores
int s1 = alignmentGetScore(alignment);
int s2 = score;
ASSERT(s1 == s2, "Scores don't match %d %d, (%s %s)", s1, s2,
chainGetName(query), chainGetName(target));
// extract info
int queryStart = alignmentGetQueryStart(alignment);
int queryEnd = alignmentGetQueryEnd(alignment);
int targetStart = alignmentGetTargetStart(alignment);
int targetEnd = alignmentGetTargetEnd(alignment);
int pathLen = alignmentGetPathLen(alignment);
char* path = (char*) malloc(pathLen);
alignmentCopyPath(alignment, path);
alignmentDelete(alignment);
// create db alignment
*dbAlignment = dbAlignmentCreate(query, queryStart, queryEnd, queryIdx,
target, targetStart, targetEnd, targetIdx, value, score, scorer, path,
pathLen);
return NULL;
}
