BasicMapper.pm

  # If same source, need to do more work
  if ($pos_a == $pos_b) {

   if ($src_a eq "Uniprot/SWISSPROT" || $src_a =~ /RefSeq/) {

     # Compare on query identities, then target identities if queries are the same
     my $key_a = $xref_to_object->{$a}; # e.g. "Translation|1234"
     my $key_b = $xref_to_object->{$b};
     my ($type_a, $object_a) = split(/\|/, $key_a);
     my ($type_b, $object_b) = split(/\|/, $key_b);

     return 0 if ($type_a != $type_b); # only compare like with like

     my $query_identity_a = $object_xref_identities{$object_a}->{$a}->{"query_identity"};
     my $query_identity_b = $object_xref_identities{$object_b}->{$b}->{"query_identity"};

     return ($query_identity_a <=> $query_identity_b) if ($query_identity_a != $query_identity_b);

     my $target_identity_a = $object_xref_identities{$object_a}->{$a}->{"target_identity"};
     my $target_identity_b = $object_xref_identities{$object_b}->{$b}->{"target_identity"};

     return ($target_identity_a <=> $target_identity_b);

   } elsif ($src_a eq "Uniprot/SPTREMBL") {

     # Compare on words
     my $wrd_idx_a = find_match($xref_descriptions{$a}, @words);
     my $wrd_idx_b = find_match($xref_descriptions{$b}, @words);
     return $wrd_idx_a <=> $wrd_idx_b;

   } else {

     return 0;

   }
    return 0;

  } else {

    return $pos_a <=> $pos_b;

  }
}

# load external_db (if it's empty) from ../external_db/external_dbs.txt

sub upload_external_db {

  my $row = @{$core_dbi->selectall_arrayref("SELECT COUNT(*) FROM external_db")}[0];
  my $count = @{$row}[0];

  if ($count == 0) {
    my $edb = cwd() . "/../external_db/external_dbs.txt";
    print "external_db table is empty, uploading from $edb\n";
    my $edb_sth = $core_dbi->prepare("LOAD DATA INFILE \'$edb\' INTO TABLE external_db");
    $edb_sth->execute();
  } else {
    print "external_db table already has $count rows, will not change it\n";
   }

}

1;