void loadGappedBed(struct track *tg)
/* Convert bed info in window to linked feature. */
{
struct sqlResult *sr;
char **row;
int rowOffset;
struct bed *bed;
struct linkedFeatures *lfList = NULL, *lf;
struct trackDb *tdb = tg->tdb;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
boolean useItemRgb = FALSE;
useItemRgb = bedItemRgb(tdb);
if (tg->isBigBed)
{ // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks
bigBedAddLinkedFeaturesFrom(tg, chromName, winStart, winEnd,
scoreMin, scoreMax, useItemRgb, 12, &lfList);
}
else
{
/* Use tg->tdb->track because subtracks inherit composite track's tdb
* by default, and the variable is named after the composite track. */
struct sqlConnection *conn = hAllocConn(database);
char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL);
if (scoreFilterClause != NULL)
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd,scoreFilterClause, &rowOffset);
freeMem(scoreFilterClause);
}
else
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
}
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoad12(row+rowOffset);
adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax);
lf = lfFromBedExtra(bed, scoreMin, scoreMax);
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
slAddHead(&lfList, lf);
bedFree(&bed);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
slReverse(&lfList);
if(tg->extraUiData)
filterBed(tg, &lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
struct linkedFeatures *bedMungToLinkedFeatures(struct bed **pBed, struct trackDb *tdb,
int fieldCount, int scoreMin, int scoreMax, boolean useItemRgb)
/* Convert bed to a linkedFeature, destroying bed in the process. */
{
struct bed *bed = *pBed;
if (fieldCount < 12)
bed8To12(bed);
adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax);
struct linkedFeatures *lf = lfFromBedExtra(bed, scoreMin, scoreMax);
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
bedFree(pBed);
return lf;
}
static struct linkedFeatures *lfFromEncodePeak(struct slList *item, struct trackDb *tdb,
int scoreMin, int scoreMax)
/* Translate an {encode,narrow,broad,gapped}Peak item into a linkedFeatures. */
{
struct encodePeak *peak = (struct encodePeak *)item;
struct linkedFeatures *lf;
struct simpleFeature *sfList = NULL;
if (!peak)
return NULL;
AllocVar(lf);
lf->start = peak->chromStart;
lf->end = peak->chromEnd;
if (peak->peak > -1)
{
lf->tallStart = peak->chromStart + peak->peak;
lf->tallEnd = lf->tallStart + 1;
}
lf->filterColor = -1;
lf->orientation = orientFromChar(peak->strand[0]);
adjustBedScoreGrayLevel(tdb, (struct bed *)peak, scoreMin, scoreMax);
lf->grayIx = grayInRange((int)peak->score, scoreMin, scoreMax);
lf->name = cloneString(peak->name);
if (peak->blockCount > 0)
{
int i;
for (i = 0; i < peak->blockCount; i++)
{
struct simpleFeature *sf;
AllocVar(sf);
sf->start = lf->start + peak->blockStarts[i];
sf->end = lf->start + peak->blockStarts[i] + peak->blockSizes[i];
sf->grayIx = lf->grayIx;
slAddHead(&sfList, sf);
}
slReverse(&sfList);
}
else
{
AllocVar(sfList);
sfList->start = lf->start;
sfList->end = lf->end;
sfList->grayIx = lf->grayIx;
}
lf->components = sfList;
return lf;
}
void bedDrawSimpleAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y,
double scale, MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single simple bed item at position. */
{
struct bed *bed = item;
int heightPer = tg->heightPer;
int s = max(bed->chromStart, winStart), e = min(bed->chromEnd, winEnd);
if (s > e)
return;
int x1 = round((s-winStart)*scale) + xOff;
int x2 = round((e-winStart)*scale) + xOff;
int w = x2 - x1;
if (w < 1)
w = 1;
struct trackDb *tdb = tg->tdb;
int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));
int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000"));
char *directUrl = trackDbSetting(tdb, "directUrl");
boolean withHgsid = (trackDbSetting(tdb, "hgsid") != NULL);
boolean thickDrawItem = (trackDbSetting(tdb, "thickDrawItem") != NULL);
if (tg->itemColor != NULL)
{
color = tg->itemColor(tg, bed, hvg);
}
else if (tg->colorShades)
{
adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax);
color = tg->colorShades[grayInRange(bed->score, scoreMin, scoreMax)];
}
/* Keep the item at least 4 pixels wide at all viewpoints */
if (thickDrawItem && (w < 4))
{
x1 -= ((5-w) >> 1);
w = 4;
x2 = x1 + w;
}