static void RefSeq_RefSeq_close(RefSeq *const super)
{
TableReaderRefSeq const *const reader = super->u.refSeq.reader;
super->u.refSeq.reader = NULL;
TableReaderRefSeq_Whack(reader);
}
LIB_EXPORT rc_t CC TableReaderRefSeq_MakeTable(const TableReaderRefSeq** cself, const VDBManager* vmgr,
const VTable* table, uint32_t options, size_t cache)
{
rc_t rc = 0;
TableReaderRefSeq* self = NULL;
if( cself == NULL || table == NULL ) {
rc = RC(rcAlign, rcType, rcConstructing, rcParam, rcNull);
} else if( (self = calloc(1, sizeof(*self))) == NULL ) {
rc = RC(rcAlign, rcType, rcConstructing, rcMemory, rcExhausted);
} else {
const TableReader* tmp;
TableReaderColumn static_cols[] = {
/* order important, see code below! */
{0, "MAX_SEQ_LEN", {NULL}, 0, 0},
{0, "SEQ_ID", {NULL}, 0, 0},
{0, "TOTAL_SEQ_LEN", {NULL}, 0, 0},
{0, "CIRCULAR", {NULL}, 0, 0},
{0, "MD5", {NULL}, 0, ercol_Optional},
{0, NULL, {NULL}, 0, 0}
};
if( (rc = TableReader_Make(&tmp, table, static_cols, 0)) == 0 ) {
if( (rc = TableReader_ReadRow(tmp, 1)) == 0 ) {
self->max_seq_len = static_cols[0].base.u32[0];
self->total_seq_len = static_cols[2].base.u64[0];
if( self->total_seq_len != static_cols[2].base.u64[0] ) {
rc = RC(rcAlign, rcType, rcConstructing, rcData, rcOutofrange);
}
if( static_cols[1].base.var != NULL ) {
if ( static_cols[ 1 ].len > sizeof( self->seq_id ) - 1 )
{
rc = RC( rcAlign, rcType, rcConstructing, rcBuffer, rcInsufficient );
}
else
{
string_copy( self->seq_id, ( sizeof self->seq_id ) - 1, static_cols[1].base.str, static_cols[1].len );
self->seq_id[ static_cols[ 1 ].len ] = '\0';
}
}
self->circular = static_cols[3].base.buul[0];
if( static_cols[4].base.var != NULL ) {
memcpy(self->md5, static_cols[4].base.var, sizeof(self->md5));
self->has_md5 = true;
}
}
TableReader_Whack(tmp);
}
memcpy(self->cols, TableReaderRefSeq_cols, sizeof(TableReaderRefSeq_cols));
if( options & errefseq_4NA) {
self->cols[0].flags |= ercol_Skip;
self->cols[1].flags &= ~ercol_Skip;
self->read = &self->cols[1];
} else {
self->read = &self->cols[0];
}
self->seq_len = &self->cols[3];
rc = TableReader_Make(&self->base, table, self->cols, cache);
}
if( rc == 0 ) {
*cself = self;
/* ALIGN_DBG("table 0x%p opened 0x%p", table, self); */
} else {
TableReaderRefSeq_Whack(self);
ALIGN_DBGERRP("table for 0x%p", rc, table);
}
return rc;
}
