void hgSeqOptions(struct cart *cart, char *db, char *table)
/* Print out HTML FORM entries for gene region and sequence display options. */
{
struct hTableInfo *hti;
char chrom[32];
char rootName[256];
if ((table == NULL) || (table[0] == 0))
{
hti = NULL;
}
else
{
hParseTableName(db, table, rootName, chrom);
hti = hFindTableInfo(db, chrom, rootName);
if (hti == NULL)
webAbort("Error", "Could not find table info for table %s (%s)",
rootName, table);
}
hgSeqOptionsHtiCart(hti, cart);
}
int hgSeqItemsInRange(char *db, char *table, char *chrom, int chromStart,
int chromEnd, char *sqlConstraints)
/* Print out dna sequence of all items (that match sqlConstraints, if nonNULL)
in the given range in table. Return number of items. */
{
struct hTableInfo *hti;
struct bed *bedList;
char rootName[256];
char parsedChrom[32];
int itemCount;
hParseTableName(db, table, rootName, parsedChrom);
hti = hFindTableInfo(db, chrom, rootName);
if (hti == NULL)
webAbort("Error", "Could not find table info for table %s (%s)",
rootName, table);
bedList = hGetBedRange(db, table, chrom, chromStart, chromEnd,
sqlConstraints);
itemCount = hgSeqBed(db, hti, bedList);
bedFreeList(&bedList);
return itemCount;
}
int checkTableCoords(char *db)
/* Check several invariants (see comments in check*() above),
* summarize errors, return nonzero if there are errors. */
{
struct sqlConnection *conn = hAllocConn(db);
struct slName *tableList = NULL, *curTable = NULL;
struct slName *allChroms = NULL;
boolean gotError = FALSE;
allChroms = hAllChromNames(db);
if (theTable == NULL)
tableList = getTableNames(conn);
else if (sqlTableExists(conn, theTable))
tableList = newSlName(theTable);
else
errAbort("Error: specified table \"%s\" does not exist in database %s.",
theTable, db);
for (curTable = tableList; curTable != NULL; curTable = curTable->next)
{
struct hTableInfo *hti = NULL;
struct slName *chromList = NULL, *chromPtr = NULL;
char *table = curTable->name;
char tableChrom[32], trackName[128], tableChromPrefix[33];
hParseTableName(db, table, trackName, tableChrom);
hti = hFindTableInfo(db, tableChrom, trackName);
if (hti != NULL && hti->isPos)
{
/* watch out for presence of both split and non-split tables;
* hti for non-split will be replaced with hti of split. */
if (splitAndNonSplitExist(conn, table, tableChrom))
continue;
safef(tableChromPrefix, sizeof(tableChromPrefix), "%s_", tableChrom);
if (hti->isSplit)
chromList = newSlName(tableChrom);
else
chromList = allChroms;
/* invariant: chrom must be described in chromInfo. */
/* items with bad chrom will be invisible to hGetBedRange(), so
* catch them here by SQL query. */
/* The SQL query is too huge for scaffold-based db's, check count: */
if (hChromCount(db) <= MAX_SEQS_SUPPORTED)
{
if (isNotEmpty(hti->chromField))
{
struct dyString *bigQuery = newDyString(1024);
dyStringClear(bigQuery);
sqlDyStringPrintf(bigQuery, "select count(*) from %s where ",
table);
for (chromPtr=chromList; chromPtr != NULL;
chromPtr=chromPtr->next)
{
sqlDyStringPrintf(bigQuery, "%s != '%s' ",
hti->chromField, chromPtr->name);
if (chromPtr->next != NULL)
dyStringAppend(bigQuery, "AND ");
}
gotError |= reportErrors(BAD_CHROM, table,
sqlQuickNum(conn, bigQuery->string));
dyStringFree(&bigQuery);
}
for (chromPtr=chromList; chromPtr != NULL; chromPtr=chromPtr->next)
{
char *chrom = chromPtr->name;
struct bed *bedList = hGetBedRange(db, table, chrom, 0, 0, NULL);
if (hti->isSplit && isNotEmpty(hti->chromField))
gotError |= checkSplitTableOnlyChrom(bedList, table, hti,
tableChrom);
gotError |= checkStartEnd(bedList, table, hti,
testChromSize(chrom));
if (hti->hasCDS)
gotError |= checkCDSStartEnd(bedList, table, hti);
if (hti->hasBlocks && !ignoreBlocks)
gotError |= checkBlocks(bedList, table, hti);
bedFreeList(&bedList);
}
}
}
}
return gotError;
}
