static void setEopMB(struct mimeBuf *b)
/* do a search for boundary, set eop End Of Part if found */
{
if (b->blen > 0)
b->eop = memMatch(b->boundary, b->blen, b->i, b->eoi - b->i);
else
b->eop = NULL;
}
static void getChunkMB(struct mimeBuf *b, char **address, int *size, boolean *hasZeros)
/* Pass back address and size of chunk, and whether it contains embedded zeros.
The chunk is the largest piece of data left in the buffer up to the eod or eop. */
{
char *eoc = b->eop ? b->eop : b->eod; /* end of chunk */
//debug
//fprintf(stderr,"pre-getChunkMB dumpMB: ");
//dumpMB(b); //debug
*address=b->i;
*size=eoc - b->i;
*hasZeros = (memMatch("", 1,*address, *size) != NULL);
b->i = eoc;
}
static int countOccurrences(char *needle, int nLen, char *haystack, int hLen)
/* count # of occurrences of needle in haystack */
{
int count = 0;
char *match=NULL;
while((match=memMatch(needle, nLen, haystack, hLen)) != NULL)
{
++count;
hLen -= (match - haystack) + nLen;
if (hLen < 1)
break;
haystack=match+nLen;
}
return count;
}
static boolean jiggleSmallExons(struct ffAli *ali, struct dnaSeq *nSeq, struct dnaSeq *hSeq)
/* See if can jiggle small exons to match splice sites a little
* better. */
{
struct ffAli *left, *mid, *right;
int orient;
boolean creeped = FALSE;
if (ffAliCount(ali) < 3)
return FALSE;
orient = ffIntronOrientation(ali);
left = ali;
mid = left->right;
right = mid->right;
while (right != NULL)
{
int midSizeN = mid->nEnd - mid->nStart;
if (midSizeN < 10 && mid->hStart - left->hEnd > 1 && right->hStart - mid->hEnd > 1)
{
DNA *spLeft, *spRight; /* Splice sites on either side of exon. */
DNA exonX[10+2+2]; /* Storage for exon with splice sites. */
DNA *match;
static int creeps[4][2] = { {2, 2}, {2, 1}, {1, 2}, {1, 1},};
int creepIx, creepL, creepR;
DNA *hs = mid->hStart, *he = mid->hEnd;
DNA *hMin = left->hEnd, *hMax = right->hStart;
if (orient >= 0)
{
spLeft = "ag";
spRight = "gt";
}
else
{
spLeft = "ac";
spRight = "ct";
}
for (creepIx=0; creepIx<4; ++creepIx)
{
creepL = creeps[creepIx][0];
creepR = creeps[creepIx][1];
/* Check to see if we already match consensus, and if so just bail. */
if (hs[-1] == spLeft[1] && he[0] == spRight[0])
{
if ((creepL == 1 || hs[-2] == spLeft[0])
&& (creepR == 1 || he[1] == spRight[1]))
{
break;
}
}
memcpy(exonX, spLeft + 2 - creepL, creepL);
memcpy(exonX + creepL, mid->nStart, midSizeN);
memcpy(exonX + creepL + midSizeN, spRight, creepR);
match = memMatch(exonX, midSizeN + creepR + creepL, hMin, hMax - hMin);
if (match != NULL)
{
mid->hStart = match + creepL;
mid->hEnd = mid->hStart + (he - hs);
creeped = TRUE;
break;
}
}
}
left = mid;
mid = right;
right = right->right;
}
if (creeped)
ffSlideIntrons(ali);
return creeped;
}