static struct chromInfo *loadChromInfo(struct sqlConnection *conn)
{
struct chromInfo *ret = NULL;
char **row;
char query[256];
int chromCount = 0;
cInfoHash = newHash(0);
if (workChr)
sqlSafef(query, ArraySize(query), "SELECT * FROM chromInfo WHERE "
"chrom='%s' ORDER BY chrom DESC", workChr);
else
sqlSafef(query, ArraySize(query),
"SELECT * FROM chromInfo ORDER BY chrom DESC");
struct sqlResult *sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct chromInfo *el;
struct chromInfo *ci;
AllocVar(ci);
el = chromInfoLoad(row);
ci->chrom = cloneString(el->chrom);
ci->size = el->size;
slAddHead(&ret, ci);
hashAddInt(cInfoHash, el->chrom, el->size);
++chromCount;
}
sqlFreeResult(&sr);
verbose(2,"#\tchrom count: %d\n", chromCount);
return (ret);
}
static struct hash *chromInfoHash(struct sqlConnection *conn)
/* Build up hash of chromInfo keyed by name */
{
struct sqlResult *sr;
char **row;
struct hash *hash = hashNew(0);
sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
while ((row = sqlNextRow(sr)) != NULL)
{
struct chromInfo *ci = chromInfoLoad(row);
hashAdd(hash, ci->chrom, ci);
}
sqlFreeResult(&sr);
return hash;
}
struct chromInfo *chromInfoLoadAllByChar(char *fileName, char chopper)
/* Load all chromInfo from a chopper separated file.
* Dispose of this with chromInfoFreeList(). */
{
struct chromInfo *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[3];
while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
{
el = chromInfoLoad(row);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct chromInfo *chromInfoLoadAll(char *fileName)
/* Load all chromInfo from a whitespace-separated file.
* Dispose of this with chromInfoFreeList(). */
{
struct chromInfo *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[3];
while (lineFileRow(lf, row))
{
el = chromInfoLoad(row);
slAddHead(&list, el);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct chromInfo *createChromInfoList(char *name, char *database)
/* Load up chromosome information for chrom 'name'.
* If name is NULL or "all" then load all chroms.
* Similar to featureBits.c - could be moved to library */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row;
int loaded=0;
struct chromInfo *ret = NULL;
unsigned totalSize = 0;
/* do the query */
if (!name || sameWord(name, "all"))
sr = sqlGetResult(conn, "NOSQLINJ select * from chromInfo");
else
{
char select[256];
sqlSafef(select, ArraySize(select), "select * from chromInfo where chrom='%s'", name);
sr = sqlGetResult(conn, select);
}
/* read the rows and build the chromInfo list */
while ((row = sqlNextRow(sr)) != NULL)
{
struct chromInfo *el;
struct chromInfo *ci;
AllocVar(ci);
el = chromInfoLoad(row);
ci->chrom = cloneString(el->chrom);
ci->size = el->size;
totalSize += el->size;
slAddHead(&ret, ci);
++loaded;
}
if (loaded < 1)
errAbort("ERROR: can not find chrom name: '%s'\n", name ? name : "NULL");
slReverse(&ret);
if (!name || sameWord(name, "all"))
verbose(2, "#\tloaded size info for %d chroms, total size: %u\n",
loaded, totalSize);
sqlFreeResult(&sr);
hFreeConn(&conn);
return ret;
}
static struct chromInfo *fbCreateChromInfoList(char *name, char *database)
/* Load up all chromosome infos. */
{
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr = NULL;
char **row;
int loaded=0;
struct chromInfo *ret = NULL;
unsigned totalSize = 0;
if (sameWord(name, "all"))
sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
else
{
char select[256];
sqlSafef(select, ArraySize(select), "select * from chromInfo where chrom='%s'",
name);
sr = sqlGetResult(conn, select);
}
while ((row = sqlNextRow(sr)) != NULL)
{
struct chromInfo *el;
struct chromInfo *ci;
AllocVar(ci);
el = chromInfoLoad(row);
ci->chrom = cloneString(el->chrom);
ci->size = el->size;
totalSize += el->size;
slAddHead(&ret, ci);
++loaded;
}
if (loaded < 1)
errAbort("ERROR: can not find chrom name: '%s'\n", name);
slReverse(&ret);
if (sameWord(name, "all"))
verbose(2, "#\tloaded size info for %d chroms, total size: %u\n",
loaded, totalSize);
sqlFreeResult(&sr);
sqlDisconnect(&conn);
return ret;
}
struct chromInfo *getAllChromInfo(char *database)
/* Return list of info for all chromosomes. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
struct chromInfo *ci, *ciList = NULL;
sr = sqlGetResult(conn, "NOSQLINJ select * from chromInfo");
while ((row = sqlNextRow(sr)) != NULL)
{
ci = chromInfoLoad(row);
slAddHead(&ciList, ci);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
slReverse(&ciList);
return ciList;
}
struct chromInfo *readChroms(struct hash *chromHash, struct sqlConnection *conn)
/* Return chromosomes in list/hash. */
{
struct chromInfo *chrom, *chromList = NULL;
char query[512];
char **row;
struct sqlResult *sr;
sqlSafef(query, sizeof query, "select * from chromInfo");
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
chrom = chromInfoLoad(row);
hashAddUnique(chromHash, chrom->chrom, chrom);
slAddHead(&chromList, chrom);
}
sqlFreeResult(&sr);
slReverse(&chromList);
return chromList;
}
struct chromInfo *loadAllChromInfo(char *database)
/* Load up all chromosome infos. */
{
struct chromInfo *list = NULL, *el;
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr = NULL;
char **row;
sr = sqlGetResult(conn, "NOSQLINJ select * from chromInfo");
while ((row = sqlNextRow(sr)) != NULL)
{
el = chromInfoLoad(row);
slAddHead(&list, el);
}
sqlFreeResult(&sr);
slReverse(&list);
sqlDisconnect(&conn);
printf("Loaded %d chromosomes\n", slCount(list));
return list;
}
/* Copied from hgLoadWiggle. */
static struct hash *loadAllChromInfo()
/* Load up all chromosome infos. */
{
struct chromInfo *el;
struct sqlConnection *conn = sqlConnect(database);
struct sqlResult *sr = NULL;
struct hash *ret;
char **row;
ret = newHash(0);
sr = sqlGetResult(conn, "NOSQLINJ select * from chromInfo");
while ((row = sqlNextRow(sr)) != NULL)
{
el = chromInfoLoad(row);
verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size);
hashAdd(ret, el->chrom, (void *)(& el->size));
}
sqlFreeResult(&sr);
sqlDisconnect(&conn);
return ret;
}
