void bamPairedDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
/* Draw a bam linked features series item at position. (like linkedFeaturesSeriesDrawAt,
* but calls bamDrawAt instead of linkedFeaturesDrawAt) */
{
struct linkedFeaturesSeries *lfs = item;
struct linkedFeatures *lf;
int midY = y + (tg->heightPer>>1);
int prevEnd = lfs->start;
if ((lf = lfs->features) == NULL)
return;
for (lf = lfs->features; lf != NULL; lf = lf->next)
{
int x1 = round((double)((int)prevEnd-winStart)*scale) + xOff;
int x2 = round((double)((int)lf->start-winStart)*scale) + xOff;
int w = x2-x1;
if (w > 0)
hvGfxLine(hvg, x1, midY, x2, midY, color);
bamDrawAt(tg, lf, hvg, xOff, y, scale, font, color, vis);
prevEnd = lf->end;
}
}
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;
}
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 altGraphXDrawAt(struct track *tg, void *item, struct hvGfx *hvg,
int xOff, int yOff, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw an altGraphX at the specified location. */
{
int i = 0;
int s =0, e=0;
int heightPer = tg->heightPer;
int start = 0, end = 0;
struct altGraphX *ag = item;
int width = 0;
int x1, x2;
/* Create a link to hgc. */
if(tg->mapsSelf && tg->mapItem)
{
char name[256];
int nameWidth = 0;
int textX = 0;
start = max(winStart, ag->tStart);
end = min(winEnd, ag->tEnd);
width = (end - start) * scale;
x1 = round((double)((int) start - winStart)*scale) + xOff;
textX = x1;
if(width == 0)
width = 1;
/* If there isn't enough room on before the left edge snap the
label to the left edge. */
if(withLeftLabels && tg->limitedVis == tvPack)
{
safef(name, sizeof(name), "%s", tg->itemName(tg, ag));
nameWidth = mgFontStringWidth(font, name);
textX = textX - (nameWidth + tl.nWidth/2);
if(textX < insideX)
textX = insideX - nameWidth;
width = width + (x1 - textX);
}
tg->mapItem(tg, hvg, ag, "notUsed", "notUsed", ag->tStart, ag->tEnd, textX, yOff, width, heightPer);
}
/* Draw the edges (exons and introns). */
for(i= 0; i < ag->edgeCount; i++)
{
Color color2;
s = ag->vPositions[ag->edgeStarts[i]];
e = ag->vPositions[ag->edgeEnds[i]];
color2 = MG_BLACK;
/* If you want to shade by number of transcripts uncomment next line. */
/* color2 = altGraphXColorForEdge(hvg, ag, i); */
if(isExon(ag, i))
{
if(vis == tvPack)
drawScaledBox(hvg, s, e, scale, xOff, yOff+heightPer/2, heightPer/2, color2);
else
drawScaledBox(hvg, s, e, scale, xOff, yOff, heightPer, color2);
}
else
{
int midX;
s = ag->vPositions[ag->edgeStarts[i]];
e = ag->vPositions[ag->edgeEnds[i]];
x1 = round((double)((int) s - winStart)*scale) + xOff;
x2 = round((double)((int) e - winStart)*scale) + xOff;
if(vis == tvPack)
{
midX = (x1+x2)/2;
hvGfxLine(hvg, x1, yOff+heightPer/2, midX, yOff, color2);
hvGfxLine(hvg, midX, yOff, x2, yOff+heightPer/2, color2);
}
else
hvGfxLine(hvg, x1, yOff+heightPer/2, x2, yOff+heightPer/2, color2);
}
}
}
static int rDrawTreeInLabelArea(struct hacTree *ht, struct hvGfx *hvg, enum yRetType yType, int x,
yFromNodeFunc *yFromNode, void *yh, struct titleHelper *th,
boolean drawRectangle)
/* Recursively draw the haplotype clustering tree in the left label area.
* Returns pixel height for use at non-leaf levels of tree. */
{
const int branchW = 4;
int labelEnd = leftLabelX + leftLabelWidth;
if (yType == yrtStart || yType == yrtEnd)
{
// We're just getting vertical span of a leaf cluster, not drawing any lines.
int yLeft, yRight;
if (ht->left)
yLeft = rDrawTreeInLabelArea(ht->left, hvg, yType, x, yFromNode, yh, th, drawRectangle);
else
yLeft = yFromNode(ht->itemOrCluster, yh, yType);
if (ht->right)
yRight = rDrawTreeInLabelArea(ht->right, hvg, yType, x, yFromNode, yh, th, drawRectangle);
else
yRight = yFromNode(ht->itemOrCluster, yh, yType);
if (yType == yrtStart)
return min(yLeft, yRight);
else
return max(yLeft, yRight);
}
// Otherwise yType is yrtMidPoint. If we have 2 children, we'll be drawing some lines:
if (ht->left != NULL && ht->right != NULL)
{
int midY;
if (ht->childDistance == 0 || x+(2*branchW) > labelEnd)
{
// Treat this as a leaf cluster.
// Recursing twice is wasteful. Could be avoided if this, and yFromNode,
// returned both yStart and yEnd. However, the time to draw a tree of
// 2188 hap's (1kG phase1 interim) is in the noise, so I consider it
// not worth the effort of refactoring to save a sub-millisecond here.
int yStartLeft = rDrawTreeInLabelArea(ht->left, hvg, yrtStart, x+branchW,
yFromNode, yh, th, drawRectangle);
int yEndLeft = rDrawTreeInLabelArea(ht->left, hvg, yrtEnd, x+branchW,
yFromNode, yh, th, drawRectangle);
int yStartRight = rDrawTreeInLabelArea(ht->right, hvg, yrtStart, x+branchW,
yFromNode, yh, th, drawRectangle);
int yEndRight = rDrawTreeInLabelArea(ht->right, hvg, yrtEnd, x+branchW,
yFromNode, yh, th, drawRectangle);
int yStart = min(yStartLeft, yStartRight);
int yEnd = max(yEndLeft, yEndRight);
midY = (yStart + yEnd) / 2;
Color col = (ht->childDistance == 0) ? purple : MG_BLACK;
if (drawRectangle || ht->childDistance != 0)
{
hvGfxLine(hvg, x+branchW, yStart, x+branchW, yEnd-1, col);
hvGfxLine(hvg, x+branchW, yStart, labelEnd, yStart, col);
hvGfxLine(hvg, x+branchW, yEnd-1, labelEnd, yEnd-1, col);
}
else
{
hvGfxLine(hvg, x, midY, x+1, midY, col);
hvGfxLine(hvg, x+1, midY, labelEnd-1, yStart, col);
hvGfxLine(hvg, x+1, midY, labelEnd-1, yEnd-1, col);
}
addClusterMapItem(ht, x, yStart, labelEnd, yEnd-1, th);
}
else
{
int leftMid = rDrawTreeInLabelArea(ht->left, hvg, yrtMidPoint, x+branchW,
yFromNode, yh, th, drawRectangle);
int rightMid = rDrawTreeInLabelArea(ht->right, hvg, yrtMidPoint, x+branchW,
yFromNode, yh, th, drawRectangle);
midY = (leftMid + rightMid) / 2;
hvGfxLine(hvg, x+branchW, leftMid, x+branchW, rightMid, MG_BLACK);
addClusterMapItem(ht, x, min(leftMid, rightMid), x+branchW-1, max(leftMid, rightMid), th);
}
if (drawRectangle || ht->childDistance != 0)
hvGfxLine(hvg, x, midY, x+branchW, midY, MG_BLACK);
return midY;
}
else if (ht->left != NULL)
return rDrawTreeInLabelArea(ht->left, hvg, yType, x, yFromNode, yh, th, drawRectangle);
else if (ht->right != NULL)
return rDrawTreeInLabelArea(ht->right, hvg, yType, x, yFromNode, yh, th, drawRectangle);
// Leaf node -- return pixel height. Draw a line if yType is midpoint.
int y = yFromNode(ht->itemOrCluster, yh, yType);
if (yType == yrtMidPoint && x < labelEnd)
{
hvGfxLine(hvg, x, y, labelEnd, y, purple);
addClusterMapItem(ht, x, y, labelEnd, y+1, th);
}
return y;
}
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 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);
}
}
}
}