void gdfRcGene(struct gdfGene *gene, int size)
/* Flip gene to other strand. Assumes dataPoints are already
* moved into range from 0-size */
{
struct gdfDataPoint *s = gene->dataPoints, *e, temp;
int count = gene->dataCount;
int i;
int halfCount = count/2;
for (i=0; i<count; ++i)
{
s->start = reverseOffset(s->start, size) + 1;
++s;
}
s = gene->dataPoints;
e = s + gene->dataCount-1;
for (i=0; i<halfCount; i += 1)
{
memcpy(&temp, s, sizeof(temp));
memcpy(s, e, sizeof(temp));
memcpy(e, &temp, sizeof(temp));
s += 1;
e -= 1;
}
}
static void fixDirectionAndOffsets(struct gffGene *gene, char *dna, long dnaSize, int newStart)
/* Reverse complement DNA if gene is on negative strand.
* Update offsets of exons and introns in gene to
* make them point into dna, rather than into gff->dna.
*/
{
long oldStart;
long offset;
GffIntron *intron;
GffExon *exon;
long temp;
oldStart = gene->start;
offset = oldStart - newStart;
gene->start -= offset;
gene->end -= offset;
for (intron = gene->introns; intron != NULL; intron = intron->next)
{
intron->start -= offset;
intron->end -= offset;
}
for (exon = gene->exons; exon != NULL; exon = exon->next)
{
exon->start -= offset;
exon->end -= offset;
}
if (gene->strand == '-')
{
reverseComplement(dna, dnaSize);
temp = reverseOffset(gene->start, dnaSize);
gene->start = reverseOffset(gene->end, dnaSize);
gene->end = temp;
for (intron = gene->introns; intron != NULL; intron = intron->next)
{
temp = reverseOffset(intron->start, dnaSize);
intron->start = reverseOffset(intron->end, dnaSize);
intron->end = temp;
}
for (exon = gene->exons; exon != NULL; exon = exon->next)
{
temp = reverseOffset(exon->start, dnaSize);
exon->start = reverseOffset(exon->end, dnaSize);
exon->end = temp;
}
slReverse(&gene->introns);
slReverse(&gene->exons);
gene->strand = '+';
}
}
void aliTrack(char *bacAcc, char *wholeName, char *partsName,
struct memGfx *mg, int x, int y, FILE *mapFile, int trim, char *repeatMask)
/* Write out one alignment track. */
{
struct dnaSeq *whole, *partList, *part;
bits16 contig;
int maxBlockSize = 5000;
int wholeSize;
struct patSpace *ps;
DNA *wholeDna;
whole = faReadAllDna(wholeName);
if (slCount(whole) > 1)
warn("%d sequences in %s, only using first", slCount(whole), wholeName);
wholeDna = whole->dna;
wholeSize = whole->size;
ps = makePatSpace(&whole, 1, oocFile, 5, 500);
partList = faReadAllDna(partsName);
printf("%d contigs in %s\n\n", slCount(partList), partsName);
for (part = partList, contig = 0; part != NULL; part = part->next, ++contig)
{
DNA *dna = part->dna;
int dnaSize = part->size;
int start, size;
int subIx = 0;
char numText[12];
Color color = blockColors[contig%ArraySize(blockColors)];
sprintf(numText, "%d", contig+1);
for (start = trim; start < dnaSize-trim; start += size)
{
struct ffAli *left, *right;
boolean rc;
int score;
size = dnaSize - start-trim;
if (size > maxBlockSize)
size = maxBlockSize;
if (!fastFind(dna+start, size, ps, &left, &rc, &score) )
{
printf("Contig %d.%d:%d-%d of %d UNALIGNED\n",
contig+1, subIx, start, start+size, dnaSize);
}
else
{
int x1, x2;
int xo, w;
double quality;
int qStart, qSize, tStart,tSize;
char qualityString[40];
right = left;
while (right->right != NULL)
right = right->right;
qStart = left->nStart - dna;
qSize = right->nEnd - left->nStart;
if (rc)
{
int rcEnd = right->nEnd - (dna+start) - 1;
qStart = reverseOffset(rcEnd, size) + start;
}
tStart = left->hStart - wholeDna;
tSize = right->hEnd - left->hStart;
quality = 100.0 * score / qSize;
if (quality >= 25.0)
sprintf(qualityString, "%4.1f%%", quality);
else
sprintf(qualityString, "<50%%");
printf("<A HREF=\"../cgi-bin/chkGlue.exe?bacAcc=%s&contig=%d&qStart=%d&qSize=%d&tStart=%d&tSize=%d&repeatMask=%s\">",
bacAcc, contig, qStart, qSize, tStart, tSize, repeatMask);
printf("Contig %d.%d:%d-%d %c of %d aligned %d-%d of %d aliSize %d quality %s</A>\n",
contig+1, subIx, qStart, qStart+qSize,
(rc ? '-' : '+'), dnaSize,
tStart, tStart + tSize,
wholeSize,
qSize, qualityString);
x1 = roundingScale(trackWidth, left->hStart - wholeDna, wholeSize);
x2 = roundingScale(trackWidth, right->hEnd - wholeDna, wholeSize);
xo = x1+x;
w = x2-x1;
mapWriteBox(mapFile, mtBlock, xo, y, w, trackHeight,
bacAcc, contig, qStart, qSize, tStart, tSize);
mgDrawBox(mg, xo, y, w, trackHeight, color);
mgTextCentered(mg, xo, y, w, trackHeight, MG_WHITE, font, numText);
ffFreeAli(&left);
}
++subIx;
}
}
freePatSpace(&ps);
freeAllSeq(&whole);
freeAllSeq(&partList);
}
