static struct ffAli *smoothSmallGaps(struct dnaSeq *qSeq, struct dnaSeq *tSeq,
struct ffAli *ffList)
/* Fill in small double sided gaps where possible. */
{
struct ffAli *left = ffList, *right;
boolean smoothed = FALSE;
if (ffList == NULL) return NULL;
for (;;)
{
if ((right = left->right) == NULL)
break;
if (smoothOneGap(left, right, ffList))
smoothed = TRUE;
left = right;
}
if (smoothed)
{
ffList = ffMergeNeedleAlis(ffList, TRUE);
}
return ffList;
}
void ssStitch(struct ssBundle *bundle, enum ffStringency stringency,
int minScore, int maxToReturn)
/* Glue together mrnas in bundle as much as possible. Returns number of
* alignments after stitching. Updates bundle->ffList with stitched
* together version. */
{
struct dnaSeq *qSeq = bundle->qSeq;
struct dnaSeq *genoSeq = bundle->genoSeq;
struct ffAli *ffList = NULL;
struct ssFfItem *ffl;
struct ffAli *bestPath;
int score;
boolean firstTime = TRUE;
if (bundle->ffList == NULL)
return;
/* The score may improve when we stitch together more alignments,
* so don't let minScore be too harsh at this stage. */
if (minScore > 20)
minScore = 20;
/* Create ffAlis for all in bundle and move to one big list. */
for (ffl = bundle->ffList; ffl != NULL; ffl = ffl->next)
{
ffCat(&ffList, &ffl->ff);
}
slFreeList(&bundle->ffList);
ffAliSort(&ffList, ffCmpHitsNeedleFirst);
ffList = ffMergeClose(ffList, qSeq->dna, genoSeq->dna);
while (ffList != NULL)
{
ssFindBest(ffList, qSeq, genoSeq, stringency,
bundle->isProt, bundle->t3List,
&bestPath, &score, &ffList);
bestPath = ffMergeNeedleAlis(bestPath, TRUE);
bestPath = ffRemoveEmptyAlis(bestPath, TRUE);
if (!bestPath)
{
ffFreeAli(&ffList);
break;
}
bestPath = ffMergeHayOverlaps(bestPath);
bestPath = ffRemoveEmptyAlis(bestPath, TRUE);
bestPath = forceMonotonic(bestPath, qSeq, genoSeq, stringency,
bundle->isProt, bundle->t3List);
if (firstTime && stringency == ffCdna && bundle->avoidFuzzyFindKludge == FALSE)
{
/* Only look for middle exons the first time. Next times
* this might regenerate most of the first alignment... */
bestPath = smallMiddleExons(bestPath, bundle, stringency);
}
bestPath = ffMergeNeedleAlis(bestPath, TRUE);
if (ffIntronMax != ffIntronMaxDefault)
{
bestPath = cutAtBigIntrons(bestPath, ffIntronMax, &score, stringency,
bundle->isProt, genoSeq, bundle->t3List,
&ffList);
}
if (!bundle->isProt)
ffSlideIntrons(bestPath);
bestPath = ffRemoveEmptyAlis(bestPath, TRUE);
if (score >= minScore)
{
AllocVar(ffl);
ffl->ff = bestPath;
slAddHead(&bundle->ffList, ffl);
}
else
{
ffFreeAli(&bestPath);
ffFreeAli(&ffList);
break;
}
firstTime = FALSE;
if (--maxToReturn <= 0)
{
ffFreeAli(&ffList);
break;
}
}
slReverse(&bundle->ffList);
return;
}
