static
rc_t RefNameMake ( RefName **objp, const VTable *tbl, const VCursor *native_curs )
{
rc_t rc;
/* create the object */
RefName *obj = malloc ( sizeof * obj );
if ( obj == NULL ) {
rc = RC ( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
} else {
obj->curs=NULL;
/* open the reference cursor */
rc = AlignRefTableCursor(tbl, native_curs, &obj->curs, NULL);
if(rc == 0){
/* add columns to cursor */
rc = VCursorAddColumn(obj->curs, &obj->name_idx, "(utf8)REF_NAME");
if( GetRCObject(rc) == rcColumn && GetRCState(rc) == rcNotFound ) {
rc = VCursorAddColumn(obj->curs, &obj->name_idx, "(utf8)NAME");
}
if(GetRCState(rc) == rcExists){
rc = 0;
}
if( rc == 0 ) {
*objp = obj;
return 0;
}
VCursorRelease ( obj -> curs );
}
free ( obj );
}
return rc;
}
static
rc_t RefPosMake ( RefPos **objp, const VTable *tbl, const VCursor *native_curs )
{
rc_t rc;
/* create the object */
RefPos *obj = malloc ( sizeof * obj );
if ( obj == NULL ) {
rc = RC ( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
} else {
obj->curs=NULL;
BSTreeInit(&obj->tr_range);
/* open the reference table cursor*/
if( (rc = AlignRefTableCursor(tbl, native_curs, &obj->curs, NULL)) == 0 ) {
uint32_t itmp;
if( (rc = VCursorAddColumn(obj->curs, &itmp, "(U32)MAX_SEQ_LEN")) == 0 || GetRCState(rc) == rcExists) {
const void *base;
uint32_t row_len;
rc = VCursorCellDataDirect(obj->curs, 1, itmp, NULL, &base, NULL, &row_len);
if(rc == 0) {
assert(row_len == 1);
memcpy(&obj->max_seq_len, base, 4);
}
}
if( GetRCObject(rc) == rcColumn && GetRCState(rc) == rcNotFound ) {
/*** no MAX_SEQ_LEN means that REF_POS==REF_START **/
VCursorRelease(obj->curs);
obj->curs = NULL;
obj->max_seq_len = 0;
obj->name_range_idx = 0;
obj->name_idx = 0;
rc = 0;
} else if( rc == 0 ) {
/* add columns to cursor */
rc = VCursorAddColumn(obj->curs, &obj->name_idx, "(utf8)NAME");
if(rc == 0 || GetRCState(rc) == rcExists)
rc = VCursorAddColumn(obj->curs, &obj->name_range_idx, "NAME_RANGE");
if(GetRCState(rc) == rcExists)
rc = 0;
}
}
if( rc == 0 ) {
*objp = obj;
} else {
VCursorRelease(obj->curs);
free(obj);
}
}
return rc;
}
static
rc_t LocalRefIDMake ( LocalRefID **objp, const VTable *tbl, const VCursor *native_curs)
{
rc_t rc;
/* create the object */
LocalRefID *obj = malloc ( sizeof * obj );
if ( obj == NULL )
{
rc = RC( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
const VCursor *curs=NULL;
/* open the reference table cursor*/
rc = AlignRefTableCursor( tbl, native_curs, &curs, NULL );
if ( rc == 0 )
{
uint32_t itmp;
rc = VCursorAddColumn( curs, &itmp, "(U32)MAX_SEQ_LEN" );
if ( rc == 0 || GetRCState( rc ) == rcExists )
{
const void *base;
uint32_t row_len;
rc = VCursorCellDataDirect( curs, 1, itmp, NULL, &base, NULL, &row_len );
if ( rc == 0 )
{
assert( row_len == 1 );
memmove( &obj->max_seq_len, base, 4 );
}
}
if ( ( GetRCObject( rc ) == ( enum RCObject )rcColumn ) && ( GetRCState( rc ) == rcNotFound ) )
{
obj->max_seq_len = 0;
rc = 0;
}
VCursorRelease( curs );
if ( rc == 0 )
{
*objp = obj;
return 0;
}
}
free ( obj );
}
return rc;
}
static
rc_t RefSeqIDMake ( RefSeqID **objp, const VTable *tbl, const VCursor *native_curs )
{
rc_t rc;
/* create the object */
RefSeqID *obj = malloc ( sizeof * obj );
if ( obj == NULL )
{
rc = RC( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
obj->curs=NULL;
SUB_DEBUG( ( "SUB.Make in 'align_ref_seq_id.c'\n" ) );
/* open the reference cursor */
rc = AlignRefTableCursor( tbl, native_curs, &obj->curs, NULL );
if ( rc == 0 )
{
/* add columns to cursor */
rc = VCursorAddColumn( obj->curs, &obj->seqID_idx, "SEQ_ID" );
if ( GetRCObject( rc ) == ( enum RCObject ) rcColumn && GetRCState( rc ) == rcNotFound )
{
rc = VCursorAddColumn( obj->curs, &obj->seqID_idx, "REF_SEQ_ID" );
}
if ( GetRCState( rc ) == rcExists )
{
rc = 0;
}
if ( rc == 0 )
{
*objp = obj;
return 0;
}
VCursorRelease ( obj -> curs );
}
free ( obj );
}
return rc;
}