my $self = shift if (defined(caller(1)));

  my $source_id = shift;
  my $species_id = shift;
  my $files       = shift;
  my $release_file   = shift;
  my $verbose       = shift;

  my $file = @{$files}[0];
  my $file_desc = @{$files}[1];

  #
  # Get the descriptions from the desc file.
  #
  my $go_io = $self->get_filehandle($file_desc);
    
  if ( !defined $go_io ) {
    print STDERR "ERROR: Could not open $file_desc\n";
    return 1;    # 1 error
  }
  
  my %go_to_desc;
  print "description file for GO\n" if($verbose);
  my $term = undef;
  my $desc = undef;
  while ( $_ = $go_io->getline() ) {
    if(/\<id\>(GO:\d+)\<\/id\>/){
      $term = $1;
    }
    elsif(/\<name\>(.*)\<\/name\>/){
      if(defined($term)){
        $go_to_desc{$term} = $1;
      } 
      $term = undef;
    }
  }
  $go_io->close();


  my %wrongtype;

  #get the "main" GO source id.
  $source_id = $self->get_source_id_for_source_name("GO","main");


  #get the mapping that are already there so that we don't get lots of duplicates.
  # stored in the global hash xref_dependent_mapped.
  $self->get_dependent_mappings($source_id);

  if(!defined($species_id)){
    $species_id = $self->get_species_id_for_filename($file);
  }

  my $swiss_miss=0;
  my (%swiss) = %{$self->get_valid_codes("uniprot",$species_id)};

  my $refseq_miss=0;
  my (%refseq) = %{$self->get_valid_codes("refseq",$species_id)};

  # complication with GO xrefs from JAX - linked to MGI symbols, which are themselves
  # dependent, so we need to get the MGI->Uniprot mapping and store the *Uniprot*
  # as the master xref
  my %mgi_to_uniprot = %{
    $self->get_existing_mappings( "MGI", "Uniprot/Swissprot",
                                  $species_id ) };

  my %worm;
  my %worm_label;
  my $wormset;
  my %fish;
  my $fishset;

  my $count  = 0;



  my %sp2tax     =  $self->species_id2taxonomy();  #some species have multiple
                                                                    #tax_id i.e. strains
  
  my @tax_ids = @{$sp2tax{$species_id}};
  foreach my $tax_id ( @tax_ids){

    my $go_io = $self->get_filehandle($file);
    
    if ( !defined $go_io ) {
      print STDERR "ERROR: Could not open $file\n";
      return 1;    # 1 error
    }
    
    print "processing for taxon: $tax_id\n" if($verbose);
    my $taxon_line = "taxon:".$tax_id;
    my $miss =0;
    while ( $_ = $go_io->getline() ) {
      if(/$taxon_line/){
	chomp;
	my @array = split (/\t/,$_);
	
	# Skip "NOT" terms entirely
	next if ($array[3] eq "NOT");
	
	$array[9] =~ s/\'/\\\'/g;
	my $master=0;
	if($array[0] =~ /ENSEMBL/){
	  #these might be good for a check
	  # match GO to Uniprot
	  # match Uniprot to ENSEMBL
	  # check ENSEMBL's are the same.
	}
	elsif($array[0] =~ /RefSeq/){
	  if($refseq{$array[1]}) {
	    $self->add_to_xrefs($refseq{$array[1]},$array[4],'',$array[4],$go_to_desc{$array[4]} || '',$array[6],$source_id,$species_id);
	    $count++;
	    #print join (" ", "RefSeq" ,$refseq{$array[1]}, $array[4], "\n");
	  }
	  else{
	    $refseq_miss++;
	  }	
	}
	elsif($array[0] =~ /UniProt/){
	  if($swiss{$array[1]}){
	    $self->add_to_xrefs($swiss{$array[1]},$array[4],'',$array[4],$go_to_desc{$array[4]} || '',$array[6],$source_id,$species_id);
	    $count++;
	    #print join (" ", "UniProt" ,$swiss{$array[1]}, $array[4], "\n");
	  }
	  else{
	    $swiss_miss++;
	  }
	}
	elsif($array[0] =~ /^WB/){
	  #WB      CE20707 ZYG-9           GO:0008017      WB:WBPaper00003099|PMID:9606208 ISS             F                       protein  taxon:6239      20030829        WB
	  if(!defined($wormset)){
	    $wormset = 1;
	    %worm = %{$self->get_valid_xrefs_for_direct_xrefs('worm')};
	  }
	  my $worm_acc=$array[1];
	  if(!defined($worm{$worm_acc})){ 
	    if(defined($worm{$array[10]})){
	      $worm_acc = $array[10];
	    }
	    elsif(defined($worm{$array[2]})){
	      $worm_acc = $array[2];
	    }
	  }
	  
	  if(defined($worm{$worm_acc})){ 	
	    my ($xref_id, $stable_id, $type, $link) = split(/::/,$worm{$worm_acc});
	    
	    my $new_xref_id=$self->get_xref($array[4],$source_id, $species_id);
	    
	    if(!defined($new_xref_id)){
	      $new_xref_id = $self->add_xref($array[4],undef,$array[4],"", $source_id, $species_id, "DIRECT");
	      $count++;
	    }
	    if(!defined($self->get_direct_xref($stable_id,$type, $array[6]))){
	      $self->add_direct_xref($new_xref_id, $stable_id, $type, $array[6]);
	    }
	  }
	  else{
	    $miss++;
	  }
	}
	elsif($array[0] =~ /^ZFIN/){
	  #ZFIN    ZDB-GENE-030131-5418    rfng            GO:0030902      ZFIN:ZDB-PUB-050125-4|PMID:15659486     IMP     ZFIN:ZDB-MRPHLNO-050308-5     radical fringe homolog (Drosophila)              gene    taxon:7955      20050310        ZFIN
	  if(!defined($fishset)){
	    $fishset = 1;
	    %fish = %{$self->get_valid_xrefs_for_dependencies
			('ZFIN_ID','Uniprot/SPTREMBL','RefSeq_peptide',
			 'Uniprot/SWISSPROT')};
	  }
	  if(defined($fish{$array[1]})){
	    $self->add_to_xrefs($fish{$array[1]},$array[4],'',$array[4],'',$array[6],$source_id,$species_id);
	    $count++;
	  }
	}
	
	elsif($array[0] =~ /MGI/){
	  # MGI	MGI:1923501	0610007P08Rik		GO:0004386	MGI:MGI:1354194	IEA		F	RIKEN cDNA 0610007P08 gene		gene	taxon:10090	20060213	UniProt
	  #  0         1                2         3             4                  5        6             7         8
	  if($mgi_to_uniprot{$array[1]}){
	    $self->add_to_xrefs($mgi_to_uniprot{$array[1]}, $array[4], '', $array[4], $go_to_desc{$array[4]} || '', $array[6], $source_id, $species_id);
	    $count++;
	    #print join (" ", "MGI" ,$mgi_to_uniprot{$array[1]}, $array[4], "\n");
	  }
	}
	
	elsif(!defined($wrongtype{$array[0]})){
	  print STDERR "WARNING: unknown type ".$array[0]."\n" if($verbose);
	  $wrongtype{$array[0]} = 1;
	}
      }
    }
    
    $go_io->close();

    print "\t$count GO dependent xrefs added $refseq_miss refseq not found and $swiss_miss Swissprot not found\n " if($verbose); 
  }
  if ( defined $release_file ) {
    # Parse and set release information from $release_file.
    my $release_io = $self->get_filehandle($release_file);
    
    # Slurp mode.
    local $/;
    my $release = <$release_io>;
    $release_io->close();
    
    $release =~ tr /\n/ /;
    $release =~
          s#.*The following table describes.*?of (GOA.*?)<ul>.*#$1#;
	    $release =~ s#<[^>]+>##g;
	      
	      print "GO release: '$release'\n" if($verbose);
    $self->set_release( $source_id, $release );
  }
  
  return 0;
}

1;