void aligmentStr(char** query_str, char** target_str, Alignment* alignment, const char gap_item) {
/* code take from SW# (its a private function)*/
Chain* query = alignmentGetQuery(alignment);
int query_start = alignmentGetQueryStart(alignment);
Chain* target = alignmentGetTarget(alignment);
int target_start = alignmentGetTargetStart(alignment);
int path_len = alignmentGetPathLen(alignment);
int query_idx = query_start;
int target_idx = target_start;
*query_str = new char[path_len];
*target_str = new char[path_len];
int i;
for (i = 0; i < path_len; ++i) {
char query_chr;
char target_chr;
switch (alignmentGetMove(alignment, i)) {
case MOVE_LEFT:
query_chr = gap_item;
target_chr = chainGetChar(target, target_idx);
target_idx++;
break;
case MOVE_UP:
query_chr = chainGetChar(query, query_idx);
target_chr = gap_item;
query_idx++;
break;
case MOVE_DIAG:
query_chr = chainGetChar(query, query_idx);
target_chr = chainGetChar(target, target_idx);
query_idx++;
target_idx++;
break;
default:
// error
return;
}
(*query_str)[i] = query_chr;
(*target_str)[i] = target_chr;
}
}
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;
}