[Gmod-gbrowse-cmts] Generic-Genome-Browser/lib/Bio/DB/Das Chado.pm,1.62.2.1,1.62.2.2

[Allen D. <all...@us...>]

Update of /cvsroot/gmod/Generic-Genome-Browser/lib/Bio/DB/Das
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23312/lib/Bio/DB/Das

Modified Files:
      Tag: gbrowse-template-branch
	Chado.pm 
Log Message:
changes to implement Bio::Das::FeatureTypeI for chado.


Index: Chado.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/lib/Bio/DB/Das/Chado.pm,v
retrieving revision 1.62.2.1
retrieving revision 1.62.2.2
diff -C2 -d -r1.62.2.1 -r1.62.2.2
*** Chado.pm	18 Sep 2004 05:41:15 -0000	1.62.2.1
--- Chado.pm	6 Oct 2004 05:46:32 -0000	1.62.2.2
***************
*** 402,407 ****
  feature appears in the database.
  
! NOTE: This currently raises a "not-implemented" exception, as the
! BioSQL API does not appear to provide this functionality.
  
  =cut
--- 402,407 ----
  feature appears in the database.
  
! NONO NOTE: This currently raises a "not-implemented" exception, as the
! NONO BioSQL API does not appear to provide this functionality.
  
  =cut
***************
*** 417,420 ****
--- 417,457 ----
  
  
+   #FIXME this code is almost identical to that in map2type.  we need a refactor here
+   if(!$self->{'types'}){
+     my $dbh = $self->dbh();
+ 
+     my $cvterm_query = qq(
+     SELECT c.*, dbxref.accession
+       FROM
+         (SELECT cv.name AS cv, cvterm.name AS term, cvterm.definition AS definition, cvterm.dbxref_id
+           FROM
+             cv, cvterm
+           WHERE
+             cvterm.cv_id = cv.cv_id
+               AND
+             cv.name IN ('Sequence Ontology','Relationship Ontology')
+         ) AS c
+       LEFT JOIN
+         dbxref
+       ON
+         (c.dbxref_id = dbxref.dbxref_id)
+       ORDER BY cv,term
+     );
+ 
+     my $sth = $dbh->prepare($cvterm_query) or warn "unable to prepare select cvterms";
+     $sth->execute or $self->throw("unable to select cvterms");
+ 
+     while (my $row = $sth->fetchrow_hashref) {
+       my $type = Bio::DB::Das::Chado::Type->new();
+       $type->name( $row->{'term'} );
+       $type->definition( $row->{'definition'} );
+       $type->accession( $row->{'accession'} );
+       $type->ontology( $row->{'cv'} );
+ 
+       push @{ $self->{'types'} }, $type;
+     }
+   }
+ 
+   return @{ $self->{'types'} };
  }