static void loadCytoBandsIdeo(struct track *tg)
/* Load up cytoBandIdeo from database table to track items. */
{
if (tg->isBigBed)
{
struct lm *lm = lmInit(0);
int start = 0;
int end = hChromSize(database, chromName);
struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, start, end, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
for (bb = bbList; bb != NULL; bb = bb->next)
{
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
struct cytoBand *bed = cytoBandLoad(bedRow);
slAddHead(&tg->items, bed);
}
slReverse(&tg->items);
lmCleanup(&lm);
return;
}
char query[256];
sqlSafef(query, sizeof(query),
"select * from cytoBandIdeo where chrom like '%s'", chromName);
if(hTableExists(database, "cytoBandIdeo"))
bedLoadItemByQuery(tg, "cytoBandIdeo", query, (ItemLoader)cytoBandLoad);
if(slCount(tg->items) == 0)
{
tg->limitedVisSet = TRUE;
tg->limitedVis = tvHide;
}
}
void bigBedAddLinkedFeaturesFrom(struct track *track,
char *chrom, int start, int end, int scoreMin, int scoreMax, boolean useItemRgb,
int fieldCount, struct linkedFeatures **pLfList)
/* Read in items in chrom:start-end from bigBed file named in track->bbiFileName, convert
* them to linkedFeatures, and add to head of list. */
{
struct lm *lm = lmInit(0);
struct trackDb *tdb = track->tdb;
struct bigBedInterval *bb, *bbList = bigBedSelectRange(track, chrom, start, end, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
char *scoreFilter = cartOrTdbString(cart, track->tdb, "scoreFilter", NULL);
char *mouseOverField = cartOrTdbString(cart, track->tdb, "mouseOverField", NULL);
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
int mouseOverIdx = bbExtraFieldIndex(tdb, mouseOverField);
for (bb = bbList; bb != NULL; bb = bb->next)
{
char* mouseOver = restField(bb, mouseOverIdx);
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
struct bed *bed = bedLoadN(bedRow, fieldCount);
struct linkedFeatures *lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount,
scoreMin, scoreMax, useItemRgb);
if (scoreFilter == NULL || lf->score >= minScore)
slAddHead(pLfList, lf);
lf->mouseOver = mouseOver; // leaks some memory, cloneString handles NULL ifself
if (sameString(track->tdb->type, "bigGenePred"))
lf->original = genePredFromBigGenePred(chromName, bb);
}
lmCleanup(&lm);
}
static void lrgLoadItems(struct track *tg)
/* Load LRGs in range, translate to linkedFeatures and store as tg->items. */
{
struct lm *lm = lmInit(0);
struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, winStart, winEnd, lm);
for (bb = bbList; bb != NULL; bb = bb->next)
{
char *lrgRow[LRG_NUM_COLS];
char startBuf[16], endBuf[16];
int bbFieldCount = bigBedIntervalToRow(bb, chromName, startBuf, endBuf, lrgRow,
ArraySize(lrgRow));
if (bbFieldCount != LRG_NUM_COLS)
errAbort("lrgLoadItems: expected %d columns for row has %d", LRG_NUM_COLS, bbFieldCount);
struct lrg *lrg = lrgLoad(lrgRow);
slAddHead(&(tg->items), lrgToLf(lrg));
}
slReverse(&(tg->items));
lmCleanup(&lm);
}
void loadSimpleBed(struct track *tg)
/* Load the items in one track - just move beds in
* window... */
{
struct bed *(*loader)(char **row);
struct bed *bed, *list = NULL;
char **row;
int rowOffset;
char *words[3];
int wordCt;
char query[128];
char *setting = NULL;
bool doScoreCtFilter = FALSE;
int scoreFilterCt = 0;
char *topTable = NULL;
if (tg->bedSize <= 3)
loader = bedLoad3;
else if (tg->bedSize == 4)
loader = bedLoad;
else if (tg->bedSize == 5)
loader = bedLoad5;
else
loader = bedLoad6;
// pairedTagAlign loader is required for base coloring using sequence from seq1 & seq2
// after removing optional bin column, this loader assumes seq1 and seq2 are in
// row[6] and row[7] respectively of the sql result.
if ((setting = trackDbSetting(tg->tdb, BASE_COLOR_USE_SEQUENCE))
&& sameString(setting, "seq1Seq2"))
loader = bedLoadPairedTagAlign;
/* limit to a specified count of top scoring items.
* If this is selected, it overrides selecting item by specified score */
if ((setting = trackDbSettingClosestToHome(tg->tdb, "filterTopScorers")) != NULL)
{
wordCt = chopLine(cloneString(setting), words);
if (wordCt >= 3)
{
doScoreCtFilter = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE,
"filterTopScorersOn",sameString(words[0], "on"));
scoreFilterCt = cartUsualIntClosestToHome(cart, tg->tdb, FALSE,
"filterTopScorersCt", atoi(words[1]));
topTable = words[2];
/* if there are not too many rows in the table then can define */
/* top table as the track or subtrack table */
if (sameWord(topTable, "self"))
topTable = cloneString(tg->table);
}
}
/* Get list of items */
if (tg->isBigBed)
{ // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks
char *scoreFilter = cartOrTdbString(cart, tg->tdb, "scoreFilter", NULL);
struct lm *lm = lmInit(0);
struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, winStart, winEnd, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
for (bb = bbList; bb != NULL; bb = bb->next)
{
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
bed = loader(bedRow);
if (scoreFilter == NULL || bed->score >= minScore)
slAddHead(&list, bed);
}
lmCleanup(&lm);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
struct sqlResult *sr = NULL;
/* limit to items above a specified score */
char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL);
if (doScoreCtFilter && (topTable != NULL) && hTableExists(database, topTable))
{
sqlSafef(query, sizeof(query),"select * from %s order by score desc limit %d",
topTable, scoreFilterCt);
sr = sqlGetResult(conn, query);
rowOffset = hOffsetPastBin(database, hDefaultChrom(database), topTable);
}
else if(scoreFilterClause != NULL && tg->bedSize >= 5)
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, scoreFilterClause, &rowOffset);
}
else
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
}
freeMem(scoreFilterClause);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = loader(row+rowOffset);
slAddHead(&list, bed);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
if (doScoreCtFilter)
{
/* filter out items not in this window */
struct bed *newList = bedFilterListInRange(list, NULL, chromName, winStart, winEnd);
list = newList;
}
slReverse(&list);
tg->items = list;
}
