static void cytoBandDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw cytoBand items. */
{
struct cytoBand *band = item;
int heightPer = tg->heightPer;
int x1,x2,w;
x1 = round((double)((int)tg->itemStart(tg,band) - winStart)*scale) + xOff;
x2 = round((double)((int)tg->itemEnd(tg,band) - winStart)*scale) + xOff;
/* Clip here so that text will tend to be more visible... */
if (x1 < xOff)
x1 = xOff;
if (x2 > insideX + insideWidth)
x2 = insideX + insideWidth;
w = x2-x1;
if (w < 1)
w = 1;
hCytoBandDrawAt(band, hvg, x1, y, w, heightPer, hCytoBandDbIsDmel(database), font,
mgFontPixelHeight(font), tg->ixColor, tg->ixAltColor,
shadesOfGray, maxShade);
if(tg->mapsSelf)
tg->mapItem(tg, hvg, band, band->name, band->name, band->chromStart, band->chromEnd,
x1, y, w, heightPer);
else
mapBoxHc(hvg, band->chromStart, band->chromEnd, x1,y,w,heightPer, tg->track,
band->name, band->name);
}
static void doMapBoxPerRow(struct track *tg,
int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
{
int fontHeight = mgFontLineHeight(font);
int numRows = tg->height / fontHeight;
struct customTrack *ct = tg->customPt;
char itemBuffer[1024];
if (ct)
// this should have the trash file name instead of spacer
// but the click handler doesn't use it anyway
safef(itemBuffer, sizeof itemBuffer, "%s %s","spacer","zoom in");
else
safef(itemBuffer, sizeof itemBuffer, "zoom in");
while(numRows--)
{
char buffer[1024];
safef(buffer, sizeof buffer,
"Too many items in display. Zoom in to click on items. (%d)",numRows);
mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width, fontHeight,
tg->track, itemBuffer,
buffer);
yOff += fontHeight;
}
// just do this once
tg->customInt = 0;
}
void altGraphXMap(char *tableName, struct altGraphX *ag, struct hvGfx *hvg, int start, int end,
int x, int y, int width, int height)
/* Create a link to hgc for altGraphX track without using a track
* structure. */
{
char buff[32];
snprintf(buff, sizeof(buff), "%d", ag->id);
mapBoxHc(hvg, start, end, x, y, width, height, tableName, buff, "altGraphX Details");
}
void altGraphXMapItem(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 link to hgc for altGraphX track */
{
struct altGraphX *ag = item;
char buff[32];
snprintf(buff, sizeof(buff), "%d", ag->id);
mapBoxHc(hvg, start, end, x, y, width, height, tg->track, buff, "altGraphX Details");
}
static void pubsMapItem(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 mouse over with title for pubs blat features. */
{
if (!theImgBox || tg->limitedVis != tvDense || !tdbIsCompositeChild(tg->tdb))
{
struct linkedFeatures *lf = item;
pubsAddExtra(tg, lf);
struct pubsExtra* extra = lf->extra;
char *mouseOver = NULL;
if (extra != NULL)
mouseOver = extra->mouseOver;
else
mouseOver = itemName;
mapBoxHc(hvg, start, end, x, y, width, height, tg->track, mapItemName, mouseOver);
}
}
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;
}
}
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;
}
}