void drawPlus(struct memGfx *mg, int x, int y, Color color)
/* Draw a little tiny plus symbol centered at x/y. */
{
int plusSize = 5;
int plusOff = 2;
mgDrawBox(mg, x-plusOff, y, plusSize, 1, color);
mgDrawBox(mg, x, y-plusOff, 1, plusSize, color);
}
static struct memGfx *altColorLabels(char **labels, int labelCount, int width)
/* Return a memory image with alternating colors. */
{
struct memGfx *mg = NULL;
Color c1,c2;
MgFont *font = mgMediumFont();
int lineHeight = mgFontLineHeight(font)-1;
int height = lineHeight * labelCount, i;
int y = 0;
/* Allocate picture and set up colors. */
mg = mgNew(width, height);
c1 = mgFindColor(mg, 0xE0, 0xE0, 0xFF);
c2 = mgFindColor(mg, 0xFF, 0xC8, 0xC8);
/* Draw text. */
for (i=labelCount-1; i >= 0; --i)
{
Color c = ((i&1) ? c2 : c1);
mgDrawBox(mg, 0, y, width, lineHeight, c);
mgTextRight(mg, 0+1, y+1, width-1, lineHeight, MG_BLACK, font, labels[i]);
y += lineHeight;
}
return mg;
}
void plot(struct memGfx *mg, int x, int y, char *name, Color color)
/* Plot a point. */
{
// y = mg->height - 1 - y;
if (plotName)
{
mgTextCentered(mg, x-1, y-1, 3, 3, color, font, name);
}
else
mgDrawBox(mg, x-1, y-1, 3, 3, color);
}
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);
}
