my $proto = shift;
    my $self  = $proto->SUPER::new(@_);

    return $self;
}

1;

  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 $source_name = $self->get_source_name_for_source_id ($source_id) ;  
  # the source name defines how to parse the header 

  # different formats for different sources (all have entries in external_db.txt and populate_metadata.sql )
  # 
  #
  # SOURCES  :  cint_jgi_v1  AND cint_aniseed_jgi_v1 
  # -------------------------------------------------
  #
  #  filename :  ciona.prot.fasta 
  #  >ci0100130001
  #  MLPIVDFKQCRPSVEASDKEINETAKLLVDALSTVGFAYLKNCGIKKNCRRSQKHRG*MGGVRYLYYPPI
  #  RVNIPDDEVKRNSIRRSIGYFVFPDDDVVINQPLQFKGDADVPDPVKDPITALKYIQQKLSHTCQNT*
  # 
  #
  #
  # SOURCES :  cint_jgi_v2  && cint_aniseed_jgi_v2  
  # ------------------------------------------------
  #
  # filename : FM1.aa.fasta
  #   >jgi|Cioin2|201001|fgenesh3_pm.C_chr_01p000019
  #  MQQQQQDDLVVKLVLVGDGGVGKTTFVKRHLTGEFEKKYVATLGVEVHPIVFQTQRGRIRFNVWDTAGQE
  #  DEDDDL*
  #



  my @xrefs;

  local $/ = "\n>";

  my $file_io = $self->get_filehandle($file);

  if ( !defined $file_io ) {
    print STDERR "ERROR: Could not open $file\n";
    return 1;    # 1 is an error
  }

  while ( $_ = $file_io->getline() ) {

    next if (/^File:/);   # skip header

    my $xref;

    my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n"); 

      my @attr = split/\|/, $header ; 
      my $acession = $header ;
    
    # split header in different ways according to source name : 
    my ( $version,$label  ) ;      
    if ($source_name=~m/cint_jgi_v1/) { 
      # header format is  >ci0100146277
      # we want  146277
      ($acession = $header)  =~s/\w{6}//;  
      $version = "JGI 1.0" ;  
    
    } elsif ($source_name=~m/cint_aniseed_jgi_v1/) { 
      # header format is  >ci0100146277, we want this 
      $version = "JGI 1.0" ;  


    } elsif ($source_name=~m/cint_jgi_v2/) { 
      $acession = $attr[2]  ; 
      $version = "JGI 2.0" ;  
      $label = $attr[3] ; 
    } elsif ($source_name=~m/cint_aniseed_jgi_v2/) { 
      my $aniseed_prefix = "ci0200" ; 
      $acession = $aniseed_prefix . $attr[2]  ; 
      $version = "JGI 2.0" ;  

    }else { 
      print STDERR "WARNING : The source-name specified in the populate_metatable.sql file is\n" .
        "WARNING : not matching the differnt cases specified in JGI_Parser.pm - plese\n" .  
          "WARNING : edit the parser\n " ; 
      return 1;    
    } 
    #print "ACCESSION $acession\n" ;  

    # make sequence into one long string
    $sequence =~ s/\n//g;

    # build the xref object and store it
    $xref->{ACCESSION}     = $acession;
    $xref->{LABEL}         = $acession;
    $xref->{SEQUENCE}      = $sequence;
    $xref->{SOURCE_ID}     = $source_id;
    $xref->{SPECIES_ID}    = $species_id;
    $xref->{SEQUENCE_TYPE} = $self->get_sequence_type();
    $xref->{STATUS}        = 'experimental';

    # pull cg_name from peptide files as well and create dependent xrefs
#    if ($self->get_sequence_type() =~ /peptide/) {
#      my ($cg_name) = $cg =~ /cg_name=(.*)/;
#      my %dep;
#      $dep{SOURCE_NAME} = 'JGI__Gene';
#      $dep{LINKAGE_SOURCE_ID} = $xref->{SOURCE_ID};
#      $dep{SOURCE_ID} = $celera_gene_source_id;
#      $dep{ACCESSION} = $cg_name;
#      push @{$xref->{DEPENDENT_XREFS}}, \%dep; # array of hashrefs
#    }
#
    push @xrefs, $xref;

  }

  $file_io->close();

  print scalar(@xrefs) . " JGI_ xrefs succesfully parsed\n" if($verbose);

  XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);

  return 0; # successful