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 );
}
}
void bamDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single bam linkedFeatures item. Borrows a lot from linkedFeaturesDrawAt,
* but cuts a lot of unneeded features (like coding region) and adds a couple
* additional sources of color. */
{
struct linkedFeatures *lf = item;
struct simpleFeature *sf;
int heightPer = tg->heightPer;
int x1 = round((double)((int)lf->start-winStart)*scale) + xOff;
int x2 = round((double)((int)lf->end-winStart)*scale) + xOff;
int w = x2-x1;
int midY = y + (heightPer>>1);
char *exonArrowsDense = trackDbSettingClosestToHome(tg->tdb, "exonArrowsDense");
boolean exonArrowsEvenWhenDense = (exonArrowsDense != NULL && SETTING_IS_ON(exonArrowsDense));
boolean exonArrows = (tg->exonArrows &&
(vis != tvDense || exonArrowsEvenWhenDense));
struct dnaSeq *mrnaSeq = NULL;
enum baseColorDrawOpt drawOpt = baseColorDrawOff;
boolean indelShowDoubleInsert, indelShowQueryInsert, indelShowPolyA;
struct psl *psl = (struct psl *)(lf->original);
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
bool baseQualMode = (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_BASE_QUAL));
char *qSeq = lf->extra;
if (vis != tvDense && isNotEmpty(qSeq) && !sameString(qSeq, "*"))
{
drawOpt = baseColorDrawSetup(hvg, tg, lf, &mrnaSeq, &psl);
if (drawOpt > baseColorDrawOff)
exonArrows = FALSE;
}
static Color darkBlueColor = 0;
static Color darkRedColor = 0;
if (darkRedColor == 0)
{
darkRedColor = hvGfxFindColorIx(hvg, 100,0,0);
darkBlueColor = hvGfxFindColorIx(hvg, 0,0,100);
}
if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
color = (lf->orientation < 0) ? darkRedColor : darkBlueColor;
else if (lf->filterColor != 0)
{
// In bamTrack, lf->filterColor is an RGBA value
color = lf->filterColor;
}
else if (tg->colorShades)
color = tg->colorShades[lf->grayIx];
else
color = tg->ixColor;
indelEnabled(cart, tg->tdb, basesPerPixel, &indelShowDoubleInsert, &indelShowQueryInsert,
&indelShowPolyA);
if (!indelShowDoubleInsert)
innerLine(hvg, x1, midY, w, color);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
int s = sf->start, e = sf->end;
if (e <= s || e < winStart || s > winEnd)
continue;
if (baseQualMode)
color = tg->colorShades[sf->grayIx];
baseColorDrawItem(tg, lf, sf->grayIx, hvg, xOff, y, scale, font, s, e, heightPer,
zoomedToCodonLevel, mrnaSeq, sf, psl, drawOpt, MAXPIXELS, winStart, color);
if (tg->exonArrowsAlways ||
(exonArrows &&
(sf->start <= winStart || sf->start == lf->start) &&
(sf->end >= winEnd || sf->end == lf->end)))
{
Color barbColor = hvGfxContrastingColor(hvg, color);
x1 = round((double)((int)s-winStart)*scale) + xOff;
x2 = round((double)((int)e-winStart)*scale) + xOff;
w = x2-x1;
clippedBarbs(hvg, x1+1, midY, x2-x1-2, tl.barbHeight, tl.barbSpacing, lf->orientation,
barbColor, TRUE);
}
}
if (indelShowDoubleInsert && psl)
{
int intronGap = 0;
if (vis != tvDense)
intronGap = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "intronGap", "0"));
lfDrawSpecialGaps(lf, intronGap, TRUE, 0, tg, hvg, xOff, y, scale, color, color, vis);
}
if (vis != tvDense)
{
/* If highlighting differences between aligned sequence and genome when
* zoomed way out, this must be done in a separate pass after exons are
* drawn so that exons sharing the pixel don't overdraw differences. */
if ((indelShowQueryInsert || indelShowPolyA) && psl)
baseColorOverdrawQInsert(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart,
drawOpt, indelShowQueryInsert, indelShowPolyA);
baseColorOverdrawDiff(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart, drawOpt);
baseColorDrawCleanup(lf, &mrnaSeq, &psl);
}
}