Added add_direct_xref() - will be needed for future parsers that create...

Added add_direct_xref() - will be needed for future parsers that create direct_xrefs (e.g. CCDSParser).

Made add_xref return xref_id of last-inserted xref so that it can be passed to add_direct_xref.

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -12,6 +12,7 @@ use Getopt::Long;
 my $base_dir = ".";
 
 my $add_xref_sth = undef;
+my $add_direct_xref_sth = undef;
 my $add_dependent_xref_sth = undef;
 my $get_xref_sth = undef;
 
@@ -732,15 +733,18 @@ sub get_xref{
   return undef;
 }
 
-sub add_xref{
- my ($self,$acc,$version,$label,$description,$source_id,$species_id) = @_;
+sub add_xref {
+
+  my ($self,$acc,$version,$label,$description,$source_id,$species_id) = @_;
 
   if(!defined($add_xref_sth)){
     $add_xref_sth = dbi->prepare("INSERT INTO xref (accession,version,label,description,source_id,species_id) VALUES(?,?,?,?,?,?)");
   }
  $add_xref_sth->execute($acc,$version,$label,$description,$source_id,$species_id) 
    || die "$acc\t$label\t\t$source_id\t$species_id\n";
- 
+
+  return $add_xref_sth->{'mysql_insertid'};
+
 }
 
 
@@ -762,6 +766,20 @@ sub add_to_xrefs{
 
 }
 
+# --------------------------------------------------------------------------------
+# Add a single record to the direct_xref table.
+# Note that an xref must already have been added to the xref table (xref_id passed as 1st arg)
+
+sub add_direct_xref {
+
+  my ($self, $general_xref_id, $ensembl_stable_id, $ensembl_type, $linkage_xref) = @_;
+
+  $add_direct_xref_sth = dbi->prepare("INSERT INTO direct_xref VALUES(?,?,?,?)") if (!defined($add_direct_xref_sth));
+
+  $add_direct_xref_sth->execute($general_xref_id, $ensembl_stable_id, $ensembl_type, $linkage_xref);
+
+}
+
 # --------------------------------------------------------------------------------
 
 # Remove potentially problematic characters from string used for file/dir names