static void multiWigDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw items in multiWig container. */
{
struct track *subtrack;
char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
boolean overlay = isOverlayTypeAggregate(aggregate);
int y = yOff;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
int height = subtrack->totalHeight(subtrack, vis);
hvGfxSetClip(hvg, xOff, y, width, height);
if (sameString(WIG_AGGREGATE_TRANSPARENT, aggregate))
hvGfxSetWriteMode(hvg, MG_WRITE_MODE_MULTIPLY);
if (overlay)
subtrack->lineHeight = tg->lineHeight;
subtrack->drawItems(subtrack, seqStart, seqEnd, hvg, xOff, y, width, font, color, vis);
if (!overlay)
y += height + 1;
hvGfxSetWriteMode(hvg, MG_WRITE_MODE_NORMAL);
hvGfxUnclip(hvg);
}
}
char *url = trackUrl(tg->track, chromName);
//fprintf(stderr, "mapBoxHgcOrHgGene(id: %s;) in multiWigDraw\n",
// tg->track);
mapBoxHgcOrHgGene(hvg, seqStart, seqEnd, xOff, y, width, tg->height, tg->track, tg->track, NULL,
url, TRUE, NULL);
}
static void drawTreeInLabelArea(struct hacTree *ht, struct hvGfx *hvg, int yOff, int clipHeight,
struct yFromNodeHelper *yHelper, struct titleHelper *titleHelper,
boolean drawRectangle)
/* Draw the haplotype clustering in the left label area (as much as fits there). */
{
// Figure out which hvg to use, save current clipping, and clip to left label coords:
struct hvGfx *hvgLL = (hvgSide != NULL) ? hvgSide : hvg;
int clipXBak, clipYBak, clipWidthBak, clipHeightBak;
hvGfxGetClip(hvgLL, &clipXBak, &clipYBak, &clipWidthBak, &clipHeightBak);
hvGfxUnclip(hvgLL);
hvGfxSetClip(hvgLL, leftLabelX, yOff, leftLabelWidth, clipHeight);
// Draw the tree:
int x = leftLabelX;
(void)rDrawTreeInLabelArea(ht, hvgLL, yrtMidPoint, x, yFromHapNode, yHelper, titleHelper,
drawRectangle);
// Restore the prior clipping:
hvGfxUnclip(hvgLL);
hvGfxSetClip(hvgLL, clipXBak, clipYBak, clipWidthBak, clipHeightBak);
}
static void altGraphXDrawPackTrack(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draws the blocks for an alt-spliced gene and the connections */
{
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
double scale = scaleForPixels(width);
if(vis == tvFull)
{
hvGfxSetClip(hvg, insideX, yOff, insideWidth, tg->height);
altGraphXDrawPack(tg->items, tg->ss, hvg, xOff, yOff, width, heightPer, lineHeight,
winStart, winEnd, scale, font, color, shadesOfGray,
tg->track, altGraphXMap);
hvGfxUnclip(hvg);
}
}
struct hvGfx *oneTrackMakeTrackHvg(char *trackName, char *gifName)
/* Set up a single track, load it, draw it and return the graphics object: */
{
char *visStr = cloneString(
cartUsualString(cart, trackName, hTrackOpenVis(trackName)) );
cartSetString(cart, trackName, visStr);
struct trackDb *tdb = hTrackDbForTrack(trackName);
tdbSortPrioritiesFromCart(cart, &tdb);
if(tdb->subtracks)
tdbSortPrioritiesFromCart(cart, &(tdb->subtracks));
struct track *tg = trackFromTrackDb(tdb);
tg->visibility = hTvFromString(visStr);
trackList = tg;
tg->loadItems(tg);
limitVisibility(tg);
int height = tg->totalHeight(tg, tg->limitedVis);
struct hvGfx *hvg = hvGfxOpenGif(insideWidth, height, gifName, TRUE);
initColors(hvg);
findTrackColors(hvg, tg);
/* This is the only image we'll draw, so offset=(0,0). */
int xOff = 0, yOff = 0;
MgFont *font = tl.font;
hvGfxSetClip(hvg, xOff, yOff, insideWidth, tg->height);
tg->drawItems(tg, winStart, winEnd, hvg, xOff, yOff, insideWidth, font,
hvGfxFindRgb(hvg, &tg->color), tg->limitedVis);
/* MEMORY LEAK -- Freeing items slows hgTracks down unacceptably so we
* don't do it, and it has become vestigial. For example, wigFreeItems
* is a no-op because the author noted that it is never invoked. */
#ifdef SLOW
tg->freeItems(tg);
#endif /* SLOW */
return hvg;
}
char *altGraphXMakeImage(struct altGraphX *ag)
/* create a drawing of splicing pattern */
{
MgFont *font = mgSmallFont();
int fontHeight = mgFontLineHeight(font);
struct spaceSaver *ssList = NULL;
struct hash *heightHash = NULL;
int rowCount = 0;
struct tempName gifTn;
int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
int pixHeight = 0;
struct hvGfx *hvg;
int lineHeight = 0;
double scale = 0;
Color shadesOfGray[9];
int maxShade = ArraySize(shadesOfGray)-1;
scale = (double)pixWidth/(ag->tEnd - ag->tStart);
lineHeight = 2 * fontHeight +1;
altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount);
hashFree(&heightHash);
pixHeight = rowCount * lineHeight;
makeTempName(&gifTn, "hgc", ".png");
hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
makeGrayShades(hvg, maxShade, shadesOfGray);
hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight);
altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1,
ag->tStart, ag->tEnd, scale,
font, MG_BLACK, shadesOfGray, "Dummy", NULL);
hvGfxUnclip(hvg);
hvGfxClose(&hvg);
printf(
"<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
gifTn.forHtml, pixWidth, pixHeight);
return cloneString(gifTn.forHtml);
}
void cytoBandIdeoDraw(struct track *tg,
int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw the entire chromosome with a little red box around our
current position. */
{
double scale = 0;
int xBorder = 4;
int x1, x2;
int yBorder = 0;
int chromSize = hChromSize(database, chromName);
struct cytoBand *cbList = NULL, *cb = NULL;
scale = (double) (width - (2 * xBorder)) / chromSize;
/* Subtrack 10 for the 5 pixels buffer on either side. */
tg->heightPer -= 11;
tg->lineHeight -= 11;
/* Time to draw the bands. */
hvGfxSetClip(hvg, xOff, yOff, width, tg->height);
genericDrawItems(tg, 0, chromSize, hvg, xOff+xBorder, yOff+5, width-(2*xBorder), font, color, tvDense);
x1 = round((winStart)*scale) + xOff + xBorder -1;
x2 = round((winEnd)*scale) + xOff + xBorder -1;
if(x1 >= x2)
x2 = x1+1;
yBorder = tg->heightPer + 7 + 1;
/* Draw an outline around chromosome for visualization purposes. Helps
to make the chromosome look better. */
hvGfxLine(hvg, xOff+xBorder, yOff+4, xOff+width-xBorder, yOff+4, MG_BLACK);
hvGfxLine(hvg, xOff+xBorder, yOff+yBorder-3, xOff+width-xBorder, yOff+yBorder-3, MG_BLACK);
hvGfxLine(hvg, xOff+xBorder, yOff+4, xOff+xBorder, yOff+yBorder-3, MG_BLACK);
hvGfxLine(hvg, xOff+width-xBorder, yOff+4, xOff+width-xBorder, yOff+yBorder-3, MG_BLACK);
/* Find and draw the centromere which is defined as the
two bands with gieStain "acen" */
cbList = tg->items;
for(cb = cbList; cb != NULL; cb = cb->next)
{
/* If centromere do some drawing. */
if(sameString(cb->gieStain, "acen"))
{
int cenLeft, cenRight, cenTop, cenBottom;
/* Get the coordinates of the edges of the centromere. */
cenLeft = round((cb->chromStart)*scale) + xOff + xBorder;
cenRight = round((cb->next->chromEnd)*scale) + xOff + xBorder;
cenTop = yOff+4;
cenBottom = yOff + yBorder - 3;
/* Draw centromere itself. */
hCytoBandDrawCentromere(hvg, cenLeft, cenTop, cenRight - cenLeft,
cenBottom-cenTop+1, MG_WHITE, hCytoBandCentromereColor(hvg));
break;
}
}
/* Draw a red box around all positions in windows for this chromName.
* Double thick so two pixels thick each. */
struct window *window;
for (window=windows; window; window=window->next)
{
if (!sameString(chromName, window->chromName))
continue;
x1 = round((window->winStart)*scale) + xOff + xBorder -1;
x2 = round((window->winEnd)*scale) + xOff + xBorder -1;
hvGfxBox(hvg, x1, yOff+1, x2-x1, 2, MG_RED);
hvGfxBox(hvg, x1, yOff + yBorder - 1, x2-x1, 2, MG_RED);
hvGfxBox(hvg, x1, yOff+1, 2, yBorder, MG_RED);
hvGfxBox(hvg, x2, yOff+1, 2, yBorder, MG_RED);
}
hvGfxUnclip(hvg);
/* Put back the lineHeight for the track
now that we are done spoofing tgDrawItems(). */
tg->heightPer += 11;
tg->lineHeight += 11;
}
void bigDrawWarning(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg,
int xOff, int yOff, int width, MgFont *font, Color color,
enum trackVisibility vis)
/* Draw the network error message, for the first window only.
* Use the entire screen space across all windows. */
{
if (currentWindow != windows)
return;
int clipXBak, clipYBak, clipWidthBak, clipHeightBak;
hvGfxGetClip(hvg, &clipXBak, &clipYBak, &clipWidthBak, &clipHeightBak);
hvGfxUnclip(hvg);
hvGfxSetClip(hvg, fullInsideX, yOff, fullInsideWidth, tg->height);
xOff = fullInsideX;
width = fullInsideWidth;
char message[1024];
Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
char *errMsg = bigWarnReformat(tg->networkErrMsg);
char *nl = errMsg;
int sl = strlen(errMsg);
// in some cases, cannot use tg-> values, so recalc local equivalents.
int heightPer = tl.fontHeight; /* Height per item line minus border. */
int lineHeight = heightPer+4; /* Height per item line including border. */
if (lineHeight > tg->height)
lineHeight = tg->height;
int n = bigWarnNumLines(errMsg); /* Lines of warning text */
int m = tg->height / lineHeight; /* Lines of text space available */
if (m < 1)
m = 1;
// make yellow background to draw user's attention to the err msg
if (!sameOk(parentContainerType(tg), "multiWig")) // multiWig knows full parent height
hvGfxBox(hvg, xOff, yOff, width, tg->height, yellow);
// leading blank lines if any
int bl = (m-n)/2;
int i;
for(i=0;i<bl;++i)
yOff += lineHeight;
int l = 0;
while (TRUE)
{
char *msg = nl;
nl = strchr(nl,'\n');
if (nl)
nl[0] = 0;
if (nl || ((sl > 0) && (errMsg[sl-1]!='\n')))
{
safef(message, sizeof(message), "%s", msg);
hvGfxTextCentered(hvg, xOff, yOff, width, lineHeight, MG_BLACK, font, message);
yOff += lineHeight;
++l;
if (l > n)
break;
if (l > m)
break;
}
if (!nl)
break;
++nl;
}
freeMem(errMsg);
hvGfxUnclip(hvg);
hvGfxSetClip(hvg, clipXBak, clipYBak, clipWidthBak, clipHeightBak);
}
static void multiWigDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw items in multiWig container. */
{
struct track *subtrack;
boolean errMsgShown = FALSE;
int y = yOff;
boolean errMsgFound = FALSE;
int numTracks = 0;
// determine if any subtracks had errors and count them up
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack) )
{
numTracks++;
if (subtrack->networkErrMsg)
errMsgFound = TRUE;
}
}
if (errMsgFound)
{
Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
hvGfxBox(hvg, xOff, yOff, width, tg->height, yellow);
}
struct wigCartOptions *wigCart = tg->wigCartData;
struct wigGraphOutput *wgo = setUpWgo(xOff, yOff, width, tg->height, numTracks, wigCart, hvg);
// we want to the order to be the same in all the modes
if (wigCart->aggregateFunction == wiggleAggregateStacked)
slReverse(&tg->subtracks);
/* Cope with autoScale and stacked bars - we do it here rather than in the child tracks, so that
* all children can be on same scale. */
double minVal, maxVal;
/* Force load of all predraw arrays so can do calcs. Build up list, and then
* figure out max/min. No worries about multiple loading, the loaders protect
* themselves. */
struct slRef *refList = NULL;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
struct preDrawContainer *pre = subtrack->loadPreDraw(subtrack, seqStart, seqEnd, width);
if (pre != NULL) // pre maybe null if the load fails
{
preDrawWindowFunction(pre->preDraw, pre->preDrawSize, wigCart->windowingFunction,
wigCart->transformFunc, wigCart->doNegative);
preDrawSmoothing(pre->preDraw, pre->preDrawSize, wigCart->smoothingWindow);
pre->smoothingDone = TRUE;
refAdd(&refList, pre);
}
}
}
slReverse(&refList);
minMaxVals(refList, &minVal, &maxVal, wigCart->windowingFunction, wigCart->alwaysZero, wgo->yOffsets);
slFreeList(&refList);
if (!wigCart->autoScale)
{
minVal = wigCart->minY;
maxVal = wigCart->maxY;
}
/* Loop through again setting up the wigCarts of the children to have minY/maxY for
* our limits and autoScale off. */
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (!isSubtrackVisible(subtrack))
continue;
struct wigCartOptions *wigCart = subtrack->wigCartData;
wigCart->minY = minVal;
wigCart->maxY = maxVal;
wigCart->autoScale = wiggleScaleManual;
struct preDrawContainer *pre = subtrack->preDrawContainer;
if (pre != NULL) // pre maybe null if the load fails
{
pre->graphUpperLimit = maxVal;
pre->graphLowerLimit = minVal;
}
}
int numTrack = 0;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
if (!subtrack->networkErrMsg || !errMsgShown)
{
if (subtrack->networkErrMsg)
errMsgShown = TRUE;
wgo->numTrack = numTrack++;
subtrack->wigGraphOutput = wgo;
int height = subtrack->totalHeight(subtrack, vis);
hvGfxSetClip(hvg, xOff, y, width, height);
if (wigCart->aggregateFunction != wiggleAggregateNone)
subtrack->lineHeight = tg->lineHeight;
subtrack->drawItems(subtrack, seqStart, seqEnd, hvg, xOff, y, width, font, color, vis);
if (wigCart->aggregateFunction == wiggleAggregateNone)
{
y += height + 1;
wgo->yOff = y;
}
hvGfxUnclip(hvg);
}
}
}
if (wigCart->aggregateFunction == wiggleAggregateTransparent)
{
floatPicIntoHvg(wgo->image, xOff, yOff, hvg);
floatPicFree((struct floatPic **)&wgo->image);
}
char *url = trackUrl(tg->track, chromName);
mapBoxHgcOrHgGene(hvg, seqStart, seqEnd, xOff, yOff, width, tg->height, tg->track, tg->track, NULL,
url, TRUE, NULL);
}
