static void wikiTrackMapItem(struct track *tg, struct hvGfx *hvg, void *item,
char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height)
/* create a special map box item with different i=hgcClickName and
* pop-up statusLine with the item name
*/
{
char *userName;
/* already been determined to be enabled by getting here, need to verify
* userName vs editors and vs owner
*/
(void) wikiTrackEnabled(database, &userName);
char *hgcClickName = tg->mapItemName(tg, item);
char *statusLine = tg->itemName(tg, item);
boolean editor = isWikiEditor(userName);
struct wikiTrack *wikiItem = NULL;
boolean enableHgcClick = FALSE;
/* allow hgc click (i.e. delete privs) if the following are true
1. this is the item 0 "add new item"
2. logged into the wiki
3. user is an editor or user is the owner
*/
if (differentWord("0", hgcClickName))
wikiItem = findWikiItemId(hgcClickName);
else
enableHgcClick = TRUE; /* item 0 "add new item" must go to hgc */
if (wikiItem)
{
if (isNotEmpty(userName) && sameWord(userName, wikiItem->owner))
enableHgcClick = TRUE; /* owner has delete privls */
if (editor)
enableHgcClick = TRUE; /* editors have delete privls */
}
if (enableHgcClick)
{
mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track,
hgcClickName, statusLine, NULL, FALSE, NULL );
}
else
{ /* go directly to the wiki description */
char *directUrl = wikiUrl(wikiItem);
mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track,
hgcClickName, statusLine, directUrl, FALSE, NULL);
freeMem(directUrl);
}
}
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);
}
void mapBoxForCenterVariant(struct vcfRecord *rec, struct hvGfx *hvg, struct track *tg,
int xOff, int yOff, int width)
/* Special mouseover for center variant */
{
struct dyString *dy = dyStringNew(0);
unsigned int chromStartMap = vcfRecordTrimIndelLeftBase(rec);
unsigned int chromEndMap = vcfRecordTrimAllelesRight(rec);
gtSummaryString(rec, dy);
dyStringAppend(dy, " Haplotypes sorted on ");
char *centerChrom = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "centerVariantChrom");
if (centerChrom == NULL || !sameString(chromName, centerChrom))
dyStringAppend(dy, "middle variant by default. ");
else
dyStringAppend(dy, "this variant. ");
dyStringAppend(dy, "To anchor sorting to a different variant, click on that variant and "
"then click on the 'Use this variant' button below the variant name.");
const double scale = scaleForPixels(width);
int x1 = round((double)(rec->chromStart-winStart)*scale) + xOff;
int x2 = round((double)(rec->chromEnd-winStart)*scale) + xOff;
int w = x2-x1;
if (w <= 1)
{
x1--;
w = 3;
}
mapBoxHgcOrHgGene(hvg, chromStartMap, chromEndMap, x1, yOff, w, tg->height, tg->track,
rec->name, dy->string, NULL, TRUE, NULL);
}
static void cgapSageMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end,
int x, int y, int width, int height)
{
struct linkedFeatures *lf = item;
mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height,
tg->track, itemName, NULL, NULL, TRUE,
(char *)lf->extra);
}
static void drawOneRec(struct vcfRecord *rec, unsigned short *gtHapOrder, unsigned short gtHapCount,
struct track *tg, struct hvGfx *hvg, int xOff, int yOff, int width,
boolean isClustered, boolean isCenter, enum hapColorMode colorMode)
/* Draw a stack of genotype bars for this record */
{
unsigned int chromStartMap = vcfRecordTrimIndelLeftBase(rec);
unsigned int chromEndMap = vcfRecordTrimAllelesRight(rec);
const double scale = scaleForPixels(width);
int x1 = round((double)(rec->chromStart-winStart)*scale) + xOff;
int x2 = round((double)(rec->chromEnd-winStart)*scale) + xOff;
int w = x2-x1;
if (w <= 1)
{
x1--;
w = 3;
}
// When coloring mode is altOnly, we draw one extra pixel row at the top & one at bottom
// to show the locations of variants, since the reference alleles are invisible:
int extraPixel = 0;
int hapHeight = tg->height - CLIP_PAD;
if (colorMode == altOnlyMode)
{
hvGfxLine(hvg, x1, yOff, x2, yOff, (isClustered ? purple : shadesOfGray[5]));
extraPixel = 1;
hapHeight -= extraPixel*2;
}
double hapsPerPix = (double)gtHapCount / hapHeight;
int pixIx;
for (pixIx = 0; pixIx < hapHeight; pixIx++)
{
int gtHapOrderIxStart = (int)(hapsPerPix * pixIx);
int gtHapOrderIxEnd = round(hapsPerPix * (pixIx + 1));
if (gtHapOrderIxEnd == gtHapOrderIxStart)
gtHapOrderIxEnd++;
int unks = 0, refs = 0, alts = 0;
int gtHapOrderIx;
for (gtHapOrderIx = gtHapOrderIxStart; gtHapOrderIx < gtHapOrderIxEnd; gtHapOrderIx++)
{
int gtHapIx = gtHapOrder[gtHapOrderIx];
int hapIx = gtHapIx & 1;
int gtIx = gtHapIx >>1;
struct vcfGenotype *gt = &(rec->genotypes[gtIx]);
if (gt->isPhased || gt->isHaploid || (gt->hapIxA == gt->hapIxB))
{
int alIx = hapIx ? gt->hapIxB : gt->hapIxA;
if (alIx < 0)
unks++;
else if (alIx > 0)
alts++;
else
refs++;
}
else
unks++;
}
int y = yOff + extraPixel + pixIx;
Color col;
if (colorMode == baseMode)
col = colorByBase(refs, alts, unks, rec->alleles[0], rec->alleles[1]);
else if (colorMode == refAltMode)
col = colorByRefAlt(refs, alts, unks);
else
col = colorByAltOnly(refs, alts, unks);
if (col != MG_WHITE)
hvGfxLine(hvg, x1, y, x2, y, col);
}
int yBot = yOff + tg->height - CLIP_PAD - 1;
if (isCenter)
{
if (colorMode == altOnlyMode)
{
// Colorful outline to distinguish this variant:
hvGfxLine(hvg, x1-1, yOff, x1-1, yBot, purple);
hvGfxLine(hvg, x2+1, yOff, x2+1, yBot, purple);
hvGfxLine(hvg, x1-1, yOff, x2+1, yOff, purple);
hvGfxLine(hvg, x1-1, yBot, x2+1, yBot, purple);
}
else
{
// Thick black lines to distinguish this variant:
hvGfxBox(hvg, x1-3, yOff, 3, tg->height, MG_BLACK);
hvGfxBox(hvg, x2, yOff, 3, tg->height, MG_BLACK);
hvGfxLine(hvg, x1-2, yOff, x2+2, yOff, MG_BLACK);
hvGfxLine(hvg, x1-2, yBot, x2+2, yBot, MG_BLACK);
}
// Mouseover was handled already by mapBoxForCenterVariant
}
else
{
struct dyString *dy = dyStringNew(0);
gtSummaryString(rec, dy);
mapBoxHgcOrHgGene(hvg, chromStartMap, chromEndMap, x1, yOff, w, tg->height, tg->track,
rec->name, dy->string, NULL, TRUE, NULL);
}
if (colorMode == altOnlyMode)
hvGfxLine(hvg, x1, yBot, x2, yBot, (isClustered ? purple : shadesOfGray[5]));
}
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);
}
static void longRangeDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw a list of longTabix structures. */
{
double scale = scaleForWindow(width, seqStart, seqEnd);
struct bed *beds = tg->items;
unsigned int maxWidth;
struct longRange *longRange;
char buffer[1024];
char itemBuf[2048];
char statusBuf[2048];
safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, LONG_MINSCORE);
double minScore = sqlDouble(cartUsualString(cart, buffer, LONG_DEFMINSCORE));
struct longRange *longRangeList = parseLongTabix(beds, &maxWidth, minScore);
for(longRange=longRangeList; longRange; longRange=longRange->next)
{
safef(itemBuf, sizeof itemBuf, "%d", longRange->id);
safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
boolean sOnScreen = (longRange->s >= seqStart) && (longRange->s < seqEnd);
unsigned sx = 0, ex = 0;
if (sOnScreen)
sx = (longRange->s - seqStart) * scale + xOff;
if (differentString(longRange->sChrom, longRange->eChrom))
{
if (!sOnScreen)
continue;
// draw the foot
int footWidth = scale * (longRange->sw / 2);
hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, MG_BLUE);
int height = tg->height/2;
if (tg->visibility == tvDense)
height = tg->height;
unsigned yPos = yOff + height;
hvGfxLine(hvg, sx, yOff, sx, yPos, MG_BLUE);
if (tg->visibility == tvFull)
{
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - 2, yOff, 4, tg->height/2,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
safef(buffer, sizeof buffer, "%s:%d", longRange->eChrom, longRange->e);
hvGfxTextCentered(hvg, sx, yPos + 2, 4, 4, MG_BLUE, font, buffer);
int width = vgGetFontStringWidth(hvg->vg, font, buffer);
int height = vgGetFontPixelHeight(hvg->vg, font);
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - width/2, yPos, width, height,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
}
}
else
{
boolean eOnScreen = (longRange->e >= seqStart) && (longRange->e < seqEnd);
if (!(sOnScreen || eOnScreen))
continue;
if (eOnScreen)
ex = (longRange->e - seqStart) * scale + xOff;
double longRangeWidth = longRange->e - longRange->s;
int peak = (tg->height - 15) * ((double)longRangeWidth / maxWidth) + yOff + 10;
if (tg->visibility == tvDense)
peak = yOff + tg->height;
if (sOnScreen)
{
int footWidth = scale * (longRange->sw / 2);
hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, color);
hvGfxLine(hvg, sx, yOff, sx, peak, color);
}
if (eOnScreen)
{
int footWidth = scale * (longRange->ew / 2);
hvGfxLine(hvg, ex - footWidth, yOff, ex + footWidth, yOff, color);
hvGfxLine(hvg, ex, yOff, ex, peak, color);
}
if (tg->visibility == tvFull)
{
unsigned sPeak = sOnScreen ? sx : xOff;
unsigned ePeak = eOnScreen ? ex : xOff + width;
hvGfxLine(hvg, sPeak, peak, ePeak, peak, color);
safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
if (sOnScreen)
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sx - 2, yOff, 4, peak - yOff,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
if (eOnScreen)
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, ex - 2, yOff, 4, peak - yOff,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sPeak, peak-2, ePeak - sPeak, 4,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
}
}
}
}
