void gifLabelVerticalText(char *fileName, char **labels, int labelCount,
int height)
/* Make a gif file with given labels. This will check to see if fileName
* exists already, and if so do nothing. */
{
struct memGfx *straight = altColorLabels(labels, labelCount, height);
struct memGfx *rotated = mgRotate90(straight);
char tempName[512];
safef(tempName, sizeof(tempName), "%s_trash", fileName);
mgSaveGif(rotated, tempName); /* note we cannot delete this later because of permissions */
/* the savings here is in the user's own browser cache - not updated if no change */
if (!sameFileContents(tempName,fileName))
mgSaveGif(rotated, fileName);
mgFree(&straight);
mgFree(&rotated);
}
void gifLabelVerticalText(char *fileName, char **labels, int labelCount,
int height)
/* Make a gif file with given labels. This will check to see if fileName
* exists already and has not changed, and if so do nothing. */
{
struct memGfx *straight = altColorLabels(labels, labelCount, height);
struct memGfx *rotated = mgRotate90(straight);
struct memGfx *existing = NULL;
#ifdef USE_PNG
struct tempName tn;
makeTempName(&tn, "gifLabelVertTemp", ".png");
mgSavePng(rotated, tn.forCgi, FALSE);
rename(tn.forCgi, fileName);
#else
if (fileExists(fileName))
existing = mgLoadGif(fileName);
/* the savings here is in the user's own browser cache - not updated if no change */
if (!sameGifContents(rotated, existing))
{
struct tempName tn;
makeTempName(&tn, "gifLabelVertTemp", ".gif");
mgSaveGif(rotated, tn.forCgi, FALSE);
rename(tn.forCgi, fileName);
}
#endif
mgFree(&straight);
mgFree(&rotated);
if (existing)
mgFree(&existing);
}
void memGifClose(struct memGif **pG)
/* Write out and close and free. */
{
struct memGif *g = *pG;
if (g != NULL)
{
struct memGfx *mg = (struct memGfx *)g;
mgSaveGif(mg, g->fileName, g->useTransparency);
freez(&g->fileName);
mgFree(&mg);
*pG = NULL;
}
}
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 gcSquiggle(char *chromName, char *destDir, char *type, bool thick, bool line)
/* Make gcSquiggle pic for chromosome. */
{
char gifName[512];
int chromSize = hChromSize(chromName);
struct memGfx *mg = getScaledMg(chromSize, squiggleHeight);
int dotWidth = mg->width;
char nibName[512];
FILE *nibFile;
int nibChromSize;
struct dnaSeq *seq = NULL;
double lastGcPercent = (gcPercentMin+gcPercentMax)/2;
double gcPercent;
int startBase = 0, endBase = 0, baseWidth;
int lastDot = -1, dot;
int realBaseCount;
int gcBaseCount;
bool lastMissing = TRUE;
int squigHeight = squiggleHeight-thick;
int y1,y2;
sprintf(gifName, "%s/%sgc%s.gif", destDir, chromName, type);
sprintf(nibName, "%s/%s.nib", nibDir, chromName);
nibOpenVerify(nibName, &nibFile, &nibChromSize);
if (nibChromSize != chromSize)
errAbort("Disagreement on size of %s between database and %s\n",
chromName, nibName);
for (dot = 0; dot <dotWidth; ++dot)
{
startBase = endBase;
endBase = dotToBase(dot+1);
if (endBase > nibChromSize)
endBase = nibChromSize;
baseWidth = endBase-startBase;
seq = nibLdPart(nibName, nibFile, nibChromSize, startBase, baseWidth);
realBaseCount = realDnaCount(seq->dna, seq->size);
gcBaseCount = gcDnaCount(seq->dna, seq->size);
if (realBaseCount < 20)
{
/* Add psuedocounts from last time if sample is small. */
lastMissing = TRUE;
}
else
{
gcPercent = (double)gcBaseCount/(double)realBaseCount;
y2 = gcScaleRange(gcPercent, squigHeight);
if (line && !lastMissing)
{
y1 = gcScaleRange(lastGcPercent, squigHeight);
mgDrawLine(mg, dot-1, y1, dot, y2, MG_BLACK);
if (thick)
{
mgDrawLine(mg, dot-1, y1+1, dot, y2+1, MG_BLACK);
}
}
else
{
mgPutDot(mg, dot, y2, MG_BLACK);
if (thick)
mgPutDot(mg, dot, y2+1, MG_BLACK);
}
lastGcPercent = gcPercent;
lastMissing = FALSE;
}
freeDnaSeq(&seq);
}
fclose(nibFile);
mgSaveGif(mg, gifName);
mgFree(&mg);
}
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);
}
