static void encodePeakDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw the peak from the linkedFeature. Currently this doesn't draw any */
/* sorta shading based on the signalValue/pValue. */
{
struct linkedFeatures *lf = item;
int heightPer = tg->heightPer;
int shortOff = heightPer/4;
int shortHeight = heightPer - 2*shortOff;
Color rangeColor = shadesOfGray[lf->grayIx];
Color peakColor = (tg->ixColor != blackIndex()) ? tg->ixColor : getOrangeColor();;
if (lf->components)
{
struct simpleFeature *sf;
drawScaledBox(hvg, lf->start, lf->end, scale, xOff, y+(heightPer/2), 1, rangeColor);
for (sf = lf->components; sf != NULL; sf = sf->next)
drawScaledBox(hvg, sf->start, sf->end, scale, xOff, y+shortOff,
shortHeight, rangeColor);
}
else
drawScaledBox(hvg, lf->start, lf->end, scale, xOff, y+shortOff,
shortHeight, rangeColor);
if ((lf->tallEnd > 0) && (lf->tallStart < lf->end))
drawScaledBox(hvg, lf->tallStart, lf->tallEnd, scale, xOff, y,
heightPer, peakColor);
}
void tigrOperonDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw the operon at position. */
{
struct linkedFeatures *lf = item;
struct simpleFeature *sf;
int heightPer = tg->heightPer;
int x1,x2;
int s, e;
Color *shades = tg->colorShades;
int midY = y + (heightPer>>1);
int w;
color = tg->ixColor;
x1 = round((double)((int)lf->start-winStart)*scale) + xOff;
x2 = round((double)((int)lf->end-winStart)*scale) + xOff;
w = x2-x1;
innerLine(hvg, x1, midY, w, color);
if (vis == tvFull || vis == tvPack)
clippedBarbs(hvg, x1, midY, w, 2, 5, lf->orientation, color, FALSE);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
s = sf->start; e = sf->end;
/* shade ORF (exon) based on the grayIx value of the sf */
color = shades[sf->grayIx];
drawScaledBox(hvg, s, e, scale, xOff, y, heightPer, color );
}
}
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 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);
}
}
}