use Bio::Tools::Prints;
  my $prints_parser = new Bio::Tools::Prints(-fh =>$filehandle );
  while( my $prints_feat = $prints_parser->next_result ) {
        push @prints_feat, $prints_feat;
  }

 PRINTScan II is a PRINTS fingerprint identification algorithm.
 Copyright (C) 1998,1999  Phil Scordis

      my($class,@args) = @_;

      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);

      return $self;

      my ($self) = @_;
     my %printsac;
     my @features;
     my $line;
     my $sequenceId;
     
     while ($_=$self->_readline()) {
      
      
           $line = $_;
           chomp $line;

           if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following:

              ($sequenceId) = $line =~ /^\s*(\w+)/;
              $self->seqname($sequenceId);
              next;
           }
         
              
           if ($line =~ s/^1TBH//) {
               my  ($id) = $line =~ /^\s*(\w+)/;
               my ($ac) = $line =~ /(PR\w+)\s*$/;
               $printsac{$id} = $ac;
               $self->print_sac(\%printsac);
               next;
           }
             
             
           if ($line =~ s/^3TB//) {
              
                  
              
              
              if ($line =~ s/^[HN]//) {
                   my($num)="";
                   $line =~ s/^\s+//;

                   my @elements = split /\s+/, $line;

                   my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements;
    
                   my $start = $matchPosition;
                   my $end = $matchPosition + $motifLength - 1;
                   my $print_sac = $self->print_sac;
                   
                   my %printsac =  %{$print_sac};
                   my $print =  $printsac{$fingerprintName};
                   my $seqname=$self->seqname;
                   my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue";
                   my $new_feat =  $self->create_feature($feat,$seqname);
                   return $new_feat;
               }
               if ($line =~ s/^F//) {
                   return;  
               }
                   next;                                                                                                                               }
            next;         
 
      }

       my ($self, $feat,$sequenceId) = @_;

       my @f = split (/,/,$feat);
       # create feature object
        my $feature= Bio::SeqFeature::Generic->new(-seq_id    =>$sequenceId,
                                                   -start=>$f[1],
                                                   -end  => $f[2],
                                                   -score      => $f[4],
                                                   -source     => "PRINTS",
                                                   -primary    =>$f[0],
                                                   -logic_name => "PRINTS",
                                                   );
        $feature->add_tag_value('evalue',$f[5]);
        $feature->add_tag_value('percent_id',$f[3]);
        

     
    return  $feature;

    my($self,$printsac)=@_;
 
   if(defined($printsac))
   {
       $self->{'print_sac'}=$printsac;
   }
    return $self->{'print_sac'};

    my($self,$seqname)=@_;

    if(defined($seqname))
    {
        $self->{'seqname'}=$seqname;
    }

    return $self->{'seqname'};

 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to
 the Bioperl mailing list.  Your participation is much appreciated.

 bioperl-l@bioperl.org              - General discussion
 http://bioperl.org/MailList.shtml  - About the mailing lists

 Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via
 email or the web:

 bioperl-bugs@bioperl.org
 http://bugzilla.bioperl.org/

 Email: fugui@worf.fugu-sg.org

 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _