struct vGfx *vgOpenPng(int width, int height, char *fileName, boolean useTransparency)
/* Open up something that will write out a PNG file upon vgClose.
* If useTransparency, then the first color in memgfx's colormap/palette is
* assumed to be the image background color, and pixels of that color
* are made transparent. */
{
struct memPng *png;
struct memGfx *mg;
struct vGfx *vg;
/* Set up virtual graphics with memory methods. */
vg = vgHalfInit(width, height);
vgMgMethods(vg);
vg->close = (vg_close)memPngClose;
/* Get our mg + fileName structure. We're forcing
* inheritence from mg essentially. */
AllocVar(png);
png->fileName = cloneString(fileName);
png->useTransparency = useTransparency;
/* Fill in the mg part of this structure with normal memGfx. */
mg = mgNew(width, height);
if (png->useTransparency)
mgClearPixelsTrans(mg);
else
mgClearPixels(mg);
png->mg = *mg;
freez(&mg); /* We don't need this copy any more. */
vg->data = png;
return vg;
}
struct vGfx *vgOpenGif(int width, int height, char *fileName, boolean useTransparency)
/* Open up something that will someday be a PostScript file. */
{
struct memGif *gif;
struct memGfx *mg;
struct vGfx *vg;
/* Set up virtual graphics with memory methods. */
vg = vgHalfInit(width, height);
vgMgMethods(vg);
vg->close = (vg_close)memGifClose;
/* Get our mg + fileName structure. We're forcing
* inheritence from mg essentially. */
AllocVar(gif);
gif->fileName = cloneString(fileName);
gif->useTransparency = useTransparency;
/* Fill in the mg part of this structure with normal memGfx. */
mg = mgNew(width, height);
mgClearPixels(mg);
gif->mg = *mg;
freez(&mg); /* We don't need this copy any more. */
vg->data = gif;
return vg;
}
struct memGfx *getScaledMg(int bases, int height)
/* Allocate a memGfx big enough for bases. */
{
int width = baseToDot(bases);
struct memGfx *mg;
uglyf("Allocatting memory graphic of %d x %d (for %d bases)\n", width, height, bases);
mg = mgNew(width, height);
mgClearPixels(mg);
return mg;
}
void chkGlue(char *bacAcc, char *finBac, char *unfinBac, char *gluedBac, int trim, char *repeatMask)
/* Display glued and unglued form of BAC. */
{
int trackCount = 1;
int pixWidth, pixHeight;
int x, y;
struct memGfx *mg;
struct tempName gifTn, mapTn;
FILE *mapFile;
printf("See picture at bottom for overview of where contigs align.\n\n");
/* Figure out basic dimensions and allocate picture. */
font = mgSmallFont();
trackWidth = 700;
trackHeight = mgFontPixelHeight(font) + 4;
pixWidth = trackWidth + 2*border;
pixHeight = trackCount * (trackHeight+border) + border;
x = y = border;
mg = mgNew(pixWidth, pixHeight);
mgClearPixels(mg);
makeBlockColors(mg);
/* Create map file. */
makeTempName(&mapTn, "glu", ".map");
mapFile = mustOpen(mapTn.forCgi, "wb");
mapWriteHead(mapFile, pixWidth, pixHeight, bacAcc, trim, repeatMask);
/* Write out tracks onto picture. */
aliTrack(bacAcc, finBac, unfinBac, mg, x, y, mapFile, trim, repeatMask);
/* Save pic and tell html file about it. */
makeTempName(&gifTn, "glu", ".gif");
mgSaveGif(mg, gifTn.forCgi);
printf("<INPUT TYPE=HIDDEN NAME=map VALUE=\"%s\">\n", mapTn.forCgi);
printf(
"<P><INPUT TYPE=IMAGE SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d NAME = \"clickMe\" ALIGN=BOTTOM><BR>\n",
gifTn.forHtml, pixWidth, pixHeight);
printf("Click on contig for detailed alignment\n");
/* Write end of map */
mapWriteBox(mapFile, mtNone, 0, 0, pixWidth, pixHeight, NULL, 0, 0, 0, 0, 0);
mapWriteBox(mapFile, mtEnd, 0, 0, pixWidth, pixHeight, NULL, 0, 0, 0, 0, 0);
/* Clean up. */
fclose(mapFile);
mgFree(&mg);
}
void agpVsMap(char *agpName, char *infoName, char *gifName)
/* agpVsMap - Plot clones in agp vs. map coordinates. */
{
struct mapPos *mapList, *mp;
struct agpFrag *agpList, *bp;
struct hash *cloneHash = newHash(14);
struct hashEl *hel;
struct cloneInfo *cloneList = NULL, *clone;
struct memGfx *mg = NULL;
int pixWidth = 600;
int pixHeight = 600;
int rulerHeight = 20;
int maxMapPos = 0, maxAgpPos = 0;
double scaleMap, scaleAgp;
Color orange, green;
mapList = readInfoFile(infoName);
agpList = readAgpFile(agpName);
for (mp = mapList; mp != NULL; mp = mp->next)
{
if (mp->phase > 0)
{
AllocVar(clone);
hel = hashAddUnique(cloneHash, mp->cloneName, clone);
clone->name = hel->name;
clone->mp = mp;
slAddHead(&cloneList, clone);
if (mp->pos > maxMapPos) maxMapPos = mp->pos;
}
}
slReverse(&cloneList);
for (bp = agpList; bp != NULL; bp = bp->next)
{
if (bp->chromStart > maxAgpPos) maxAgpPos = bp->chromStart;
}
/* Draw scatterplot on bitmap. */
mg = mgNew(pixWidth, pixHeight);
mgClearPixels(mg);
orange = mgFindColor(mg, 210, 150, 0);
green = mgFindColor(mg, 0, 200, 0);
mgDrawRuler(mg, 0, pixHeight-rulerHeight, rulerHeight, pixWidth, MG_BLACK,
mgSmallFont(), 0, maxMapPos+1);
scaleMap = (double)pixWidth/(double)(maxMapPos+1.0);
scaleAgp = (double)(pixHeight)/(double)(maxAgpPos+1.0);
for (bp = agpList; bp != NULL; bp = bp->next)
{
char cloneName[128];
fragToCloneName(bp->frag, cloneName);
clone = hashFindVal(cloneHash, cloneName);
if (clone == NULL)
warn("%s is in %s but not %s", cloneName,
agpName, infoName);
else
{
int x = round(scaleMap*clone->mp->pos);
int y = pixHeight - round(scaleAgp*bp->chromStart);
int phase = clone->mp->phase;
int back;
if (phase <= 1) back = green;
else if (phase == 2) back = orange;
else back = MG_RED;
drawPlus(mg, x, y, back);
}
}
mgSaveGif(mg, gifName);
}
void makePlot(struct clonePos *xList, struct clonePos *yList, struct hash *yHash)
/* Write out graphics for plot. */
{
struct memGfx *mg = NULL;
struct tempName gifTn;
char *mapName = "map";
struct clonePos *xp, *yp;
int i, j, x, y, nextX, nextY;
int divisions = 10;
double invZoom = 1.0/zoom;
double magnify = 2.0;
double newZoom = zoom*magnify;
double invNewZoom = 1.0/newZoom;
int xCount = slCount(xList);
plotName = (xCount/zoom < 50);
if (xList == NULL || yList == NULL)
return;
font = mgSmallFont();
posSpan(xList, &xStart, &xEnd);
posSpan(yList, &yStart, &yEnd);
if (pix < 50 || pix > 5000)
errAbort("Pixels out of range - must be between 50 an 5000");
mg = mgNew(pix, pix);
mgClearPixels(mg);
/* Plot dots. */
for (xp = xList; xp != NULL; xp = xp->next)
{
if ((yp = hashFindVal(yHash, xp->name)) != NULL)
{
zoomScale(xp->pos, yp->pos, &x, &y);
plot(mg, x, y, xp->name, MG_BLACK);
}
}
/* Make zooming image map. */
printf("<MAP Name=%s>\n", mapName);
for (i=0; i<divisions; ++i)
{
double cenX = xOff + (i + 0.5) * (invZoom / divisions);
double sx = cenX - invNewZoom/2;
x = i*pix/divisions;
nextX = (i+1)*pix/divisions;
for (j=0; j<divisions; ++j)
{
double cenY = yOff + (j + 0.5) * (invZoom / divisions);
double sy = cenY - invNewZoom/2;
y = j*pix/divisions;
nextY = (j+1)*pix/divisions;
mapZoomIn(x, y, nextX - x, nextY - y, sx, sy, zoom*magnify);
}
}
printf("</MAP>\n");
/* Save image in temp dir. */
makeTempName(&gifTn, "wikPic", ".gif");
mgSaveGif(mg, gifTn.forCgi, FALSE);
printf(
"<P><IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>\n",
gifTn.forHtml, pix, pix, mapName);
mgFree(&mg);
/* Print some extra info. */
printf("X has %d elements ranging from %d to %d<BR>\n", slCount(xList), xStart, xEnd);
printf("Y has %d elements ranging from %d to %d<BR>\n", slCount(yList), yStart, yEnd);
}
