struct ffAli *cutAtBigIntrons(struct ffAli *ffList, int maxIntron,
int *pScore, enum ffStringency stringency,
boolean isProt, bioSeq *tSeq, struct trans3 *t3List,
struct ffAli **returnLeftovers)
/* Return ffList up to the first intron that's too big.
* Put the rest of the blocks back onto the leftovers list. */
{
struct ffAli *prevFf, *ff, *cutFf = NULL;
prevFf = ffList;
for (ff = prevFf->right; ff != NULL; ff = ff->right)
{
int nhStart = trans3GenoPos( ff->hStart, tSeq, t3List, FALSE);
int ohEnd = trans3GenoPos(prevFf->hEnd , tSeq, t3List, TRUE);
int dt = nhStart - ohEnd;
if (dt > maxIntron)
{
cutFf = prevFf;
break;
}
prevFf = ff;
}
if (cutFf != NULL)
{
ff = cutFf->right;
cutFf->right = NULL;
ff->left = NULL;
ffCat(returnLeftovers, &ff);
if (isProt)
*pScore = ffScoreProtein(ffList, stringency);
else
*pScore = ffScore(ffList, stringency);
}
return ffList;
}
void showBundle(struct ssBundle *bun, boolean isRc)
/* Display a bundle for user. */
{
struct ssFfItem *ffi;
for (ffi = bun->ffList; ffi != NULL; ffi = ffi->next)
{
struct ffAli *left, *right;
int score;
DNA *needle = bun->qSeq->dna;
DNA *hay = bun->genoSeq->dna;
left = ffi->ff;
right = ffRightmost(left);
score = ffScore(left, ffTight);
printf("%s:%d-%d of %d %s:%d-%d of %d strand %c score %d\n",
bun->genoSeq->name, left->hStart - hay, right->hEnd - hay, bun->genoSeq->size,
bun->qSeq->name, left->nStart - needle, right->nEnd - needle, bun->qSeq->size,
(isRc ? '-' : '+'), score);
}
}
int ffScoreCdna(struct ffAli *ali)
/* Figure out overall score of this alignment.
* Perfect match is number of bases in needle. */
{
return ffScore(ali, ffCdna);
}