static void showTableFieldsCt(char *db, char *table, boolean withGetButton)
/* Put up html table with a check box for each field of custom
* track. */
{
struct customTrack *ct = ctLookupName(table);
char *type = ct->dbTrackType;
if (type == NULL)
type = ct->tdb->type;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct asObject *asObj = asForTdb(conn, ct->tdb);
if (asObj)
{
struct slName *fieldList = NULL;
if (ct->dbTableName != NULL)
{
if (isVcfTable(table, NULL))
fieldList = vcfGetFields();
else
fieldList = sqlListFields(conn, ct->dbTableName);
}
if (fieldList == NULL)
fieldList = asColNames(asObj);
showTableFieldsOnList(db, table, asObj, fieldList, FALSE, withGetButton);
asObjectFree(&asObj);
slNameFreeList(&fieldList);
}
else
showBedTableFields(db, table, ct->fieldCount, withGetButton);
hFreeConn(&conn);
}
struct bptFile *bigBedOpenExtraIndex(struct bbiFile *bbi, char *fieldName, int *retFieldIx)
/* Return index associated with fieldName. Aborts if no such index. Optionally return
* index in a row of this field. */
{
struct udcFile *udc = bbi->udc;
boolean isSwapped = bbi->isSwapped;
struct asObject *as = bigBedAsOrDefault(bbi);
struct asColumn *col = asColumnFind(as, fieldName);
if (col == NULL)
errAbort("No field %s in %s", fieldName, bbi->fileName);
int colIx = slIxFromElement(as->columnList, col);
if (retFieldIx != NULL)
*retFieldIx = colIx;
asObjectFree(&as);
/* See if we have any extra indexes, and if so seek to there. */
bits64 offset = bbi->extraIndexListOffset;
if (offset == 0)
errAbort("%s has no indexes", bbi->fileName);
udcSeek(udc, offset);
/* Go through each extra index and see if it's a match */
int i;
for (i=0; i<bbi->extraIndexCount; ++i)
{
bits16 type = udcReadBits16(udc, isSwapped);
bits16 fieldCount = udcReadBits16(udc, isSwapped);
bits64 fileOffset = udcReadBits64(udc, isSwapped);
udcSeekCur(udc, 4); // skip over reserved bits
if (type != 0)
{
warn("Don't understand type %d", type);
internalErr();
}
if (fieldCount == 1)
{
bits16 fieldId = udcReadBits16(udc, isSwapped);
udcSeekCur(udc, 2); // skip over reserved bits
if (fieldId == colIx)
{
udcSeek(udc, fileOffset);
struct bptFile *bpt = bptFileAttach(bbi->fileName, udc);
return bpt;
}
}
else
{
warn("Not yet understanding indexes on multiple fields at once.");
internalErr();
}
}
errAbort("%s is not indexed in %s", fieldName, bbi->fileName);
return NULL;
}
struct slName *bigBedListExtraIndexes(struct bbiFile *bbi)
/* Return list of names of extra indexes beyond primary chrom:start-end one" */
{
struct udcFile *udc = bbi->udc;
boolean isSwapped = bbi->isSwapped;
/* See if we have any extra indexes, and if so seek to there. */
bits64 offset = bbi->extraIndexListOffset;
if (offset == 0)
return NULL;
udcSeek(udc, offset);
/* Construct list of field that are being indexed. List is list of
* field numbers within asObj. */
int i;
struct slInt *intList = NULL, *intEl;
for (i=0; i<bbi->extraIndexCount; ++i)
{
bits16 type,fieldCount;
type = udcReadBits16(udc, isSwapped);
fieldCount = udcReadBits16(udc, isSwapped);
udcSeekCur(udc, sizeof(bits64)); // skip over fileOffset
udcSeekCur(udc, 4); // skip over reserved bits
if (fieldCount == 1)
{
bits16 fieldId = udcReadBits16(udc, isSwapped);
udcSeekCur(udc, 2); // skip over reserved bits
intEl = slIntNew(fieldId);
slAddHead(&intList, intEl);
}
else
{
warn("Not yet understanding indexes on multiple fields at once.");
internalErr();
}
}
/* Now have to make an asObject to find out name that corresponds to this field. */
struct asObject *as = bigBedAsOrDefault(bbi);
/* Make list of field names out of list of field numbers */
struct slName *nameList = NULL;
for (intEl = intList; intEl != NULL; intEl = intEl->next)
{
struct asColumn *col = slElementFromIx(as->columnList, intEl->val);
if (col == NULL)
{
warn("Inconsistent bigBed file %s", bbi->fileName);
internalErr();
}
slNameAddHead(&nameList, col->name);
}
asObjectFree(&as);
return nameList;
}
void asObjectFreeList(struct asObject **pList)
/* free a list of asObject */
{
struct asObject *el, *next;
for (el = *pList; el != NULL; el = next)
{
next = el->next;
asObjectFree(&el);
}
*pList = NULL;
}
