Both run() and set_release() are now proper methods.

Give all files to the parser, not just the first one.  The parser will
have to know what order the files are in (e.g. the Interpro parser knows
that the second file is a HTML file that contains release information).

NB: This means that the ordering of the list of URLs in the source_url
meta data table is important!

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -40,6 +40,8 @@ my (
 
 sub run
 {
+    my $self = shift;
+
     (
         $host,           $port,             $dbname,
         $user,           $pass,             my $speciesr,
@@ -330,9 +332,16 @@ sub run
 
     if ( $parse and @new_file and defined $file_cs ) {
       print "Parsing '" . join( "', '", @new_file ) . "' with $parser\n";
+
       eval "require XrefParser::$parser";
       my $new = "XrefParser::$parser"->new();
-      if ( $new->run( $source_id, $species_id, $dir . '/' . $new_file[0] ) )
+
+      if (
+          $new->run(
+              $source_id, $species_id,
+              map( $dir . '/' . $_, @new_file )
+          )
+        )
       {
           $summary{$parser}++;
       }
@@ -341,9 +350,11 @@ sub run
       update_source( $dbi, $source_url_id, $file_cs,
           $dir . '/' . $new_file[0] );
       
-      # set release if specified
-      set_release($release, $source_id) if ($release);
-      
+      # Set release if specified
+      if ( defined $release ) {
+          $self->set_release( $release, $source_id );
+      }
+
       unlink("$dir/$new_file[0]") if ($cleanup);
       
     }
@@ -943,7 +954,8 @@ sub update_source
       . "upload_date=NOW() "
       . "WHERE source_url_id=$source_url_id";
 
-    # TODO release?
+    # The release is set by the individual parser by calling the
+    # inherited set_release() method.
 
     $dbi->prepare($sql)->execute() || croak( $dbi->errstr() );
 }
@@ -1467,6 +1479,7 @@ sub get_sub_list{
 
 sub set_release
 {
+    my $self = shift;
     my ( $release, $source_id ) = @_;
 
     my $dbi = dbi();