int basePositionToXAxis( int base, int seqStart, int seqEnd, int
width, int xOff )
{
double scale = scaleForPixels(width);
double x1 = round((double)((int)base-seqStart)*scale) + xOff;
return(x1);
}
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 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);
}
}
static void contigDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw contig items. */
{
struct ctgPos *ctg;
int y = yOff;
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
int x1,x2,w;
boolean isFull = (vis == tvFull);
int ix = 0;
char *s;
double scale = scaleForPixels(width);
for (ctg = tg->items; ctg != NULL; ctg = ctg->next)
{
x1 = round((double)((int)ctg->chromStart-winStart)*scale) + xOff;
x2 = round((double)((int)ctg->chromEnd-winStart)*scale) + xOff;
/* Clip here so that text will tend to be more visible... */
if (x1 < xOff)
x1 = xOff;
if (x2 > xOff + width)
x2 = xOff + width;
w = x2-x1;
if (w < 1)
w = 1;
hvGfxBox(hvg, x1, y, w, heightPer, color);
s = abbreviateContig(ctg->contig, tl.font, w);
if (s != NULL)
hvGfxTextCentered(hvg, x1, y, w, heightPer, MG_WHITE, tl.font, s);
if (isFull)
y += lineHeight;
else
{
mapBoxHc(hvg, ctg->chromStart, ctg->chromEnd, x1,y,w,heightPer, tg->track,
tg->mapItemName(tg, ctg),
tg->itemName(tg, ctg));
}
++ix;
}
}
struct preDrawContainer *bedGraphLoadPreDraw(struct track *tg, int seqStart, int seqEnd, int width)
/* Do bits that load the predraw buffer tg->preDrawContainer. */
{
/* Just need to do this once... */
if (tg->preDrawContainer)
return tg->preDrawContainer;
struct bedGraphItem *wi;
double pixelsPerBase = scaleForPixels(width);
double basesPerPixel = 1.0;
int i; /* an integer loop counter */
if (pixelsPerBase > 0.0)
basesPerPixel = 1.0 / pixelsPerBase;
/* Allocate predraw and save it and related info in the track. */
struct preDrawContainer *pre = tg->preDrawContainer = initPreDrawContainer(width);
struct preDrawElement *preDraw = pre->preDraw; /* to accumulate everything in prep for draw */
int preDrawZero = pre->preDrawZero; /* location in preDraw where screen starts */
int preDrawSize = pre->preDrawSize; /* size of preDraw array */
/* walk through all the data fill in the preDraw array */
for (wi = tg->items; wi != NULL; wi = wi->next)
{
double dataValue = wi->dataValue; /* the data value to graph */
/* Ready to draw, what do we know:
* the feature being processed:
* chrom coords: [wi->start : wi->end)
* its data value: dataValue = wi->dataValue
*
* The drawing window, in pixels:
* xOff = left margin, yOff = top margin, h = height of drawing window
* drawing window in chrom coords: seqStart, seqEnd
* 'basesPerPixel' is known, 'pixelsPerBase' is known
*/
/* let's check end point screen coordinates. If they are
* the same, then this entire data block lands on one pixel,
* It is OK if these end up + or -, we do want to
* keep track of pixels before and after the screen for
* later smoothing operations
*/
int x1 = (wi->start - seqStart) * pixelsPerBase;
int x2 = (wi->end - seqStart) * pixelsPerBase;
if (x2 > x1)
{
for (i = x1; i <= x2; ++i)
{
int xCoord = preDrawZero + i;
if ((xCoord >= 0) && (xCoord < preDrawSize))
{
++preDraw[xCoord].count;
if (dataValue > preDraw[xCoord].max)
preDraw[xCoord].max = dataValue;
if (dataValue < preDraw[xCoord].min)
preDraw[xCoord].min = dataValue;
preDraw[xCoord].sumData += dataValue;
preDraw[xCoord].sumSquares += dataValue * dataValue;
}
}
}
else
{ /* only one pixel for this block of data */
int xCoord = preDrawZero + x1;
/* if the point falls within our array, record it.
* the (wi->validCount > 0) is a safety check. It
* should always be true unless the data was
* prepared incorrectly.
*/
if ((xCoord >= 0) && (xCoord < preDrawSize))
{
++preDraw[xCoord].count;
if (dataValue > preDraw[xCoord].max)
preDraw[xCoord].max = dataValue;
if (dataValue < preDraw[xCoord].min)
preDraw[xCoord].min = dataValue;
preDraw[xCoord].sumData += dataValue;
preDraw[xCoord].sumSquares += dataValue * dataValue;
}
}
} /* for (wi = tg->items; wi != NULL; wi = wi->next) */
return pre;
}
static void cgDrawEither(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis,
char *binFileName)
/* Draw chromosome graph - either built in or not. */
{
struct chromGraphSettings *cgs = tg->customPt;
int x,y,lastX=0,lastY=0, llastX = 0, llastY = 0;
int height = tg->height;
int maxGapToFill = cgs->maxGapToFill;
int lastPos = -maxGapToFill-1;
double minVal = cgs->minVal;
double yScale = (height-1)/(cgs->maxVal - minVal);
double xScale = scaleForPixels(width);
Color myColor = cgColorLikeHgGenome(tg, hvg);
/* Draw background lines in full mode. */
if (vis == tvFull && cgs->linesAtCount != 0)
{
int i;
Color lightBlue = hvGfxFindRgb(hvg, &guidelineColor);
for (i=0; i<cgs->linesAtCount; ++i)
{
y = height - 1 - (cgs->linesAt[i] - minVal)*yScale + yOff;
hvGfxBox(hvg, xOff, y, width, 1, lightBlue);
}
}
if (binFileName)
{
struct chromGraphBin *cgb = chromGraphBinOpen(binFileName);
if (chromGraphBinSeekToChrom(cgb, chromName))
{
int seqStartMinus = seqStart - cgs->maxGapToFill;
while (chromGraphBinNextVal(cgb))
{
int pos = cgb->chromStart;
if (pos >= seqStartMinus)
{
double val = cgb->val;
x = (pos - seqStart)*xScale + xOff;
y = height - 1 - (val - minVal)*yScale + yOff;
if (x >= xOff)
{
if (pos - lastPos <= maxGapToFill)
{
if (llastX != lastX || llastY != lastY || lastX != x || lastY != y)
hvGfxLine(hvg, lastX, lastY, x, y, myColor);
}
else
hvGfxDot(hvg, x, y, myColor);
}
llastX = lastX;
llastY = lastY;
lastX = x;
lastY = y;
lastPos = pos;
if (pos >= seqEnd)
break;
}
}
}
}
else
{
struct sqlConnection *conn = hAllocConn(database);
char query[512];
struct sqlResult *sr;
char **row;
/* Construct query. Set up a little more than window so that
* we can draw connecting lines. */
sqlSafef(query, sizeof(query),
"select chromStart,val from %s "
"where chrom='%s' and chromStart>=%d and chromStart<%d",
tg->table, chromName,
seqStart - cgs->maxGapToFill, seqEnd + cgs->maxGapToFill);
sr = sqlGetResult(conn, query);
/* Loop through drawing lines from one point to another unless
* the points are too far apart. */
while ((row = sqlNextRow(sr)) != NULL)
{
int pos = sqlUnsigned(row[0]);
double val = atof(row[1]);
x = (pos - seqStart)*xScale + xOff;
y = height - 1 - (val - minVal)*yScale + yOff;
if (x >= xOff)
{
if (pos - lastPos <= maxGapToFill)
{
if (llastX != lastX || llastY != lastY || lastX != x || lastY != y)
hvGfxLine(hvg, lastX, lastY, x, y, myColor);
}
else
hvGfxDot(hvg, x, y, myColor);
}
llastX = lastX;
llastY = lastY;
lastX = x;
lastY = y;
lastPos = pos;
if (pos >= seqEnd)
break;
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
/* Do map box */
xOff = hvGfxAdjXW(hvg, xOff, width);
char *encodedTrack = cgiEncode(tg->track);
if (theImgBox && curImgTrack)
{
char link[512]; // FIXME: winStart/winEnd are not right when using a portal
safef(link,sizeof(link),"%s&c=%s&o=%d&t=%d&g=%s", hgcNameAndSettings(),
chromName, winStart, winEnd, encodedTrack);
#ifdef IMAGEv2_SHORT_MAPITEMS
if (xOff < insideX && xOff+width > insideX)
warn("cgDrawEither(%s) map item spanning slices. LX:%d TY:%d RX:%d BY:%d link:[%s]",
encodedTrack,xOff, yOff, xOff+width, yOff+height, link);
#endif//def IMAGEv2_SHORT_MAPITEMS
imgTrackAddMapItem(curImgTrack,link,NULL,xOff,yOff,xOff+width,yOff+height,tg->track);
}
else
{
hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", xOff, yOff, xOff+width,
yOff+height);
hPrintf("HREF=\"%s&o=%d&t=%d&g=%s&c=%s&l=%d&r=%d&db=%s&pix=%d\">\n",
hgcNameAndSettings(), winStart, winEnd, encodedTrack, chromName, winStart, winEnd,
database, tl.picWidth);
}
}
static void wiggleLinkedFeaturesDraw(struct track *tg,
int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Currently this routine is adapted from Terry's
* linkedFeatureSeriesDraw() routine.
* It is called for 'sample' tracks as specified in the trackDb.ra.
* and it looks at the cart to decide whether to interpolate, fill blocks,
* and use anti-aliasing.*/
{
int i;
struct linkedFeatures *lf;
struct simpleFeature *sf;
int y = yOff;
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
int x1,x2;
boolean isFull = (vis == tvFull);
Color bColor = tg->ixAltColor;
double scale = scaleForPixels(width);
int prevX = -1;
int gapPrevX = -1;
double prevY = -1;
double y1 = -1, y2;
int ybase;
int sampleX, sampleY; /* A sample in sample coordinates.
* Sample X coordinate is chromosome coordinate.
* Sample Y coordinate is usually 0-1000 */
int binCount = 1.0/tg->scaleRange; /* Maximum sample Y coordinate. */
int bin; /* Sample Y coordinates are first converted to
* bin coordinates, and then to pixels. I'm not
* totally sure why. */
int currentX, currentXEnd, currentWidth;
int leftSide, rightSide;
int noZoom = 1;
enum wiggleOptEnum wiggleType;
char *interpolate = NULL;
char *aa = NULL;
boolean antiAlias = FALSE;
int fill;
int lineGapSize;
double min0, max0;
char o1[128]; /* Option 1 - linear interp */
char o2[128]; /* Option 2 - anti alias */
char o3[128]; /* Option 3 - fill */
char o4[128]; /* Option 4 - minimum vertical range cutoff of plot */
char o5[128]; /* Option 5 - maximum vertical range cutoff of plot */
char o6[128]; /* Option 6 - max gap where interpolation is still done */
char cartStr[64];
char *fillStr;
double hFactor;
double minRange, maxRange;
double minRangeCutoff, maxRangeCutoff;
Color gridColor = hvGfxFindRgb(hvg, &guidelineColor); /* for horizontal lines*/
lf=tg->items;
if(lf==NULL) return;
//take care of cart options
safef( o1, 128,"%s.linear.interp", tg->track);
safef( o2, 128, "%s.anti.alias", tg->track);
safef( o3, 128,"%s.fill", tg->track);
safef( o4, 128,"%s.min.cutoff", tg->track);
safef( o5, 128,"%s.max.cutoff", tg->track);
safef( o6, 128,"%s.interp.gap", tg->track);
interpolate = cartUsualString(cart, o1, "Linear Interpolation");
wiggleType = wiggleStringToEnum(interpolate);
aa = cartUsualString(cart, o2, "on");
antiAlias = sameString(aa, "on");
//don't fill gcPercent track by default (but fill others)
if(sameString( tg->table, "pGC") && sameString(database,"zooHuman3"))
{
fillStr = cartUsualString(cart, o3, "0");
}
else
{
fillStr = cartUsualString(cart, o3, "1");
}
fill = atoi(fillStr);
cartSetString(cart, o3, fillStr );
//the 0.1 is so the label doesn't get truncated with integer valued user input min
//display range.
minRangeCutoff = max( atof(cartUsualString(cart,o4,"0.0"))-0.1, tg->minRange );
maxRangeCutoff = min( atof(cartUsualString(cart,o5,"1000.0"))+0.1, tg->maxRange);
lineGapSize = atoi(cartUsualString(cart, o6, "200"));
//update cart settings to reflect truncated range cutoff values
cartSetString( cart, "win", "F" );
safef( cartStr, 64, "%g", minRangeCutoff );
cartSetString( cart, o4, cartStr );
safef( cartStr, 64, "%g", maxRangeCutoff );
cartSetString( cart, o5, cartStr );
heightPer = tg->heightPer+1;
hFactor = (double)heightPer*tg->scaleRange;
//errAbort( "min=%g, max=%g\n", minRangeCutoff, maxRangeCutoff );
if( sameString( tg->table, "zoo" ) || sameString( tg->table, "zooNew" ) )
binCount = binCount - 100; //save some space at top, between each zoo species
minRange = whichSampleBin( minRangeCutoff, tg->minRange, tg->maxRange, binCount );
maxRange = whichSampleBin( maxRangeCutoff, tg->minRange, tg->maxRange, binCount );
//errAbort( "(%g,%g) cutoff=(%g,%g)\n", tg->minRange, tg->maxRange, minRangeCutoff, maxRangeCutoff );
if( sameString( tg->table, "zoo" ) || sameString( tg->table, "zooNew" ) )
{
/*Always interpolate zoo track (since gaps are explicitly defined*/
lineGapSize = -1;
}
else if( tg->minRange == 0 && tg->maxRange == 8 ) //range for all L-score tracks
{
if( isFull )
{
min0 = whichSampleNum( minRange, tg->minRange, tg->maxRange, binCount );
max0 = whichSampleNum( maxRange, tg->minRange, tg->maxRange, binCount );
for( i=1; i<=6; i++ )
drawWiggleHorizontalLine(hvg, (double)i, min0, max0,
binCount, y, hFactor, heightPer, gridColor );
}
}
for(lf = tg->items; lf != NULL; lf = lf->next)
{
gapPrevX = -1;
prevX = -1;
ybase = (int)((double)y+hFactor+(double)heightPer);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
sampleX = sf->start;
sampleY = sf->end - sampleX; // Stange encoding but so it is.
// It is to deal with the fact that
// for a BED: sf->end = sf->start + length
// but in our case length = height (or y-value)
// so to recover height we take
// height = sf->end - sf->start.
// Otherwise another sf variable would
// be needed.
/*mapping or sequencing gap*/
if (sampleY == 0)
{
bin = -whichSampleBin( (int)((maxRange - minRange)/5.0+minRange),
minRange, maxRange, binCount );
y1 = (int)((double)y+((double)bin)* hFactor+(double)heightPer);
if( gapPrevX >= 0 )
drawScaledBox(hvg, sampleX, gapPrevX, scale,
xOff, (int)y1, (int)(.10*heightPer), shadesOfGray[2]);
gapPrevX = sampleX;
prevX = -1; /*connect next point with gray bar too*/
continue;
}
if (sampleY > maxRange)
sampleY = maxRange;
if (sampleY < minRange)
sampleY = minRange;
bin = -whichSampleBin( sampleY, minRange, maxRange, binCount );
x1 = round((double)(sampleX-winStart)*scale) + xOff;
y1 = (int)((double)y+((double)bin)* hFactor+(double)heightPer);
if (prevX > 0)
{
y2 = prevY;
x2 = round((double)(prevX-winStart)*scale) + xOff;
if( wiggleType == wiggleLinearInterpolation )
/*connect samples*/
{
if( lineGapSize < 0 || prevX - sampleX <= lineGapSize )
/*don't interpolate over large gaps*/
{
if (fill)
hvGfxFillUnder(hvg, x1,y1, x2,y2, ybase, bColor);
else
hvGfxLine(hvg, x1,y1, x2,y2, color);
}
}
}
//if( x1 < 0 || x1 > tl.picWidth )
//printf("x1 = %d, sampleX=%d, winStart = %d\n<br>", x1, sampleX, winStart );
if( x1 >= 0 && x1 <= tl.picWidth )
{
/* Draw the points themselves*/
drawScaledBox(hvg, sampleX, sampleX+1, scale, xOff, (int)y1-1, 3, color);
if( fill )
drawScaledBox(hvg, sampleX, sampleX+1, scale, xOff, (int)y1+2,
ybase-y1-2, bColor);
}
prevX = gapPrevX = sampleX;
prevY = y1;
}
leftSide = max( tg->itemStart(tg,lf), winStart );
rightSide = min( tg->itemEnd(tg,lf), winEnd );
currentX = round((double)((int)leftSide-winStart)*scale) + xOff;
currentXEnd = round((double)((int)rightSide-winStart)*scale) + xOff;
currentWidth = currentXEnd - currentX;
if( noZoom && isFull )
{
fprintf(stderr, "mapBoxHc(id: %s;) in wiggleLinkedFeatures\n",
tg->track);
mapBoxHc(hvg, lf->start, lf->end, currentX ,y, currentWidth,
heightPer, tg->track, tg->mapItemName(tg, lf), tg->itemName(tg, lf));
if( lf->next != NULL )
y += sampleUpdateY( lf->name, lf->next->name, lineHeight );
else
y += lineHeight;
}
}
}
static void goldDrawDense(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw golden path items. */
{
int baseWidth = seqEnd - seqStart;
struct agpFrag *frag;
struct agpGap *gap;
int y = yOff;
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
int x1,x2,w;
int midLineOff = heightPer/2;
boolean isFull = (vis == tvFull);
Color brown = color;
Color gold = tg->ixAltColor;
Color pink = 0;
Color pink1 = hvGfxFindColorIx(hvg, 240, 140, 140);
Color pink2 = hvGfxFindColorIx(hvg, 240, 100, 100);
int ix = 0;
double scale = scaleForPixels(width);
/* Draw gaps if any. */
if (!isFull)
{
int midY = y + midLineOff;
for (gap = tg->customPt; gap != NULL; gap = gap->next)
{
if (!sameWord(gap->bridge, "no"))
{
drawScaledBox(hvg, gap->chromStart, gap->chromEnd, scale, xOff, midY, 1, brown);
}
}
}
for (frag = tg->items; frag != NULL; frag = frag->next)
{
x1 = round((double)((int)frag->chromStart-winStart)*scale) + xOff;
x2 = round((double)((int)frag->chromEnd-winStart)*scale) + xOff;
w = x2-x1;
color = ((ix&1) ? gold : brown);
pink = ((ix&1) ? pink1 : pink2);
if (w < 1)
w = 1;
if (sameString(frag->type, "A")) color = pink;
hvGfxBox(hvg, x1, y, w, heightPer, color);
if (isFull)
y += lineHeight;
else if (baseWidth < 10000000)
{
char status[256];
sprintf(status, "%s:%d-%d %s %s:%d-%d",
frag->frag, frag->fragStart, frag->fragEnd,
frag->strand,
frag->chrom, frag->chromStart, frag->chromEnd);
mapBoxHc(hvg, frag->chromStart, frag->chromEnd, x1,y,w,heightPer, tg->track,
frag->frag, status);
}
++ix;
}
}
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]));
}
