static boolean checkSeqSimilar(struct dnaSeq *a, struct dnaSeq *b, int minScore)
/* Check that two sequences are similar. Assumes sequences are same size. */
{
int size = a->size;
int size1 = size-1;
return dnaScoreMatch(a->dna, b->dna, size) >= minScore
|| dnaScoreMatch(a->dna+1, b->dna, size1) >= minScore
|| dnaScoreMatch(a->dna, b->dna+1, size1) >= minScore;
}
int rangeScore(struct gfRange *range, struct dnaSeq *qSeq)
/* Return score associated with range. */
{
struct gfRange *comp;
struct dnaSeq *tSeq;
int score = 0;
for (comp = range->components; comp != NULL; comp = comp->next)
{
tSeq = comp->tSeq;
score += dnaScoreMatch(tSeq->dna + range->tStart, qSeq->dna + range->qStart,
range->tEnd - range->tStart);
if (comp->next != NULL)
score -= 4;
}
return score;
}
int ffScoreSomeAlis(struct ffAli *ali, int count, enum ffStringency stringency)
/* Figure out score of count alis. */
{
int score = 0;
int oneScore;
while (--count >= 0)
{
int len = ali->hEnd - ali->hStart;
struct ffAli *right = ali->right;
oneScore = dnaScoreMatch(ali->hStart, ali->nStart, len);
score += oneScore;
if (count > 0) /* Calculate gap penalty */
score -= ffGapPenalty(ali, right,stringency);
ali = right;
}
return score;
}
static int findCrossover(struct ffAli *left, struct ffAli *right, int overlap, boolean isProt)
/* Find ideal crossover point of overlapping blocks. That is
* the point where we should start using the right block rather
* than the left block. This point is an offset from the start
* of the overlapping region (which is the same as the start of the
* right block). */
{
int bestPos = 0;
char *nStart = right->nStart;
char *lhStart = left->hEnd - overlap;
char *rhStart = right->hStart;
int i;
int (*scoreMatch)(char a, char b);
int score, bestScore;
if (isProt)
{
scoreMatch = aaScore2;
score = bestScore = aaScoreMatch(nStart, rhStart, overlap);
}
else
{
scoreMatch = dnaScore2;
score = bestScore = dnaScoreMatch(nStart, rhStart, overlap);
}
for (i=0; i<overlap; ++i)
{
char n = nStart[i];
score += scoreMatch(lhStart[i], n);
score -= scoreMatch(rhStart[i], n);
if (score > bestScore)
{
bestScore = score;
bestPos = i+1;
}
}
return bestPos;
}