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 void wikiTrackLoadItems(struct track *tg)
/* Load the items from the wikiTrack table */
{
struct bed *bed;
struct sqlConnection *wikiConn = wikiConnect();
struct sqlResult *sr;
char **row;
int rowOffset;
char where[256];
struct linkedFeatures *lfList = NULL, *lf;
int scoreMin = 0;
int scoreMax = 99999;
safef(where, ArraySize(where), "db='%s'", database);
sr = hRangeQuery(wikiConn, tg->table, chromName, winStart, winEnd, where, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
struct wikiTrack *item = wikiTrackLoad(row);
AllocVar(bed);
bed->chrom = cloneString(item->chrom);
bed->chromStart = item->chromStart;
bed->chromEnd = item->chromEnd;
bed->name = cloneString(item->name);
bed->score = item->score;
safecpy(bed->strand, sizeof(bed->strand), item->strand);
bed->thickStart = item->chromStart;
bed->thickEnd = item->chromEnd;
bed->itemRgb = hexToDecimal(item->color);
bed8To12(bed);
lf = lfFromBedExtra(bed, scoreMin, scoreMax);
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
/* overload itemAttr fields to be able to pass id to hgc click box */
struct itemAttr *id;
AllocVar(id);
id->chromStart = item->id;
lf->itemAttr = id;
slAddHead(&lfList, lf);
wikiTrackFree(&item);
}
sqlFreeResult(&sr);
wikiDisconnect(&wikiConn);
slSort(&lfList, linkedFeaturesCmp);
/* read-only option 2012-06-25 */
if ((! wikiTrackReadOnly()) && wikiTrackEnabled(database, NULL))
{
// add special item to allow creation of new entries
AllocVar(bed);
bed->chrom = chromName;
bed->chromStart = winStart;
bed->chromEnd = winEnd;
bed->name = cloneString("Make new entry");
bed->score = 100;
bed->strand[0] = ' '; /* no barbs when strand is unknown */
bed->thickStart = winStart;
bed->thickEnd = winEnd;
bed->itemRgb = 0xcc0000;
bed8To12(bed);
lf = lfFromBedExtra(bed, scoreMin, scoreMax);
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
slAddHead(&lfList, lf);
}
tg->items = lfList;
} /* static void wikiTrackLoadItems(struct track *tg) */
