my ($self, $db) = @_;
  if($db){
    if(!($db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))){
      throw("Must pass SupportingEvidenceInfo:db a DBAdaptor not a $db");
    }
    $self->{'db'} = $db;
  }
  return $self->{'db'};

  my ($self, $stable_id, $id_type, $db) = @_;
  $db = $self->db if(!$db);
  $id_type = $self->id_type if(!$id_type);
  my $sql = "select ".$id_type."_id ".
    "from ".$id_type."_stable_id ".
      "where stable_id = ?";
  print "SQL: $sql\n " if($self->verbose);
  my $sth = $db->dbc->prepare($sql);
  $sth->execute($stable_id);
  my ($dbID) = $sth->fetchrow;
  return $dbID;

  my ($self, $feature_id, $evidence_type, $id_type) = @_;
  my $sql = ("select distinct(hit_name) ".
             "from $evidence_type, supporting_feature, ".
             "exon_transcript, exon, transcript ".
             "where ".$evidence_type."_id = feature_id ".
             "and feature_type = '$evidence_type'". 
             "and supporting_feature.exon_id = exon_transcript.exon_id ". 
             "and exon_transcript.transcript_id = ".
             "transcript.transcript_id ".
             "and transcript.".$id_type."_id = $feature_id");
  return $sql;

  my ($self, $transcript_id, $id_type, $evidence_type, $primary, $db) = @_;
  if(!$db){
    $db = $self->db;
  }
  if(!$evidence_type){
    $evidence_type = $self->evidence_type;
  }
  if(!$id_type){
    $id_type = $self->id_type;
  }
  if(!$primary){
    $primary = $self->primary_evidence;
  }
  my @protein_ids;
  my $sql;
  if($primary){
    $sql = $self->primary_evidence_from_feature_id_sql($transcript_id,
                                                       $evidence_type,
                                                       $id_type);
  }else{
    $sql = $self->evidence_from_feature_id_sql($transcript_id,
                                               $evidence_type,
                                               $id_type);
  }
  print "SQL: ".$sql."\n" if($self->verbose);
  my $sth = $db->dbc->prepare($sql);
  $sth->execute();
  while(my ($protein_id) = $sth->fetchrow){
    print"Have protein id ".$protein_id."\n" if($self->verbose);
    push(@protein_ids, $protein_id);
  }
  $self->fetch_descriptions(\@protein_ids);

   my ($self, $value) = @_;
  if($value){
    $self->{'evidence_type'} = $value;
  }
  return $self->{'evidence_type'} || 'protein_align_feature';

  my ($self, $evidence_id, $evidence_type, $id_type, $gene_type) = @_;
  my $sql = ("SELECT distinct(transcript.".$id_type."_id) ".
             "FROM transcript, exon_transcript, supporting_feature, ".
             "$evidence_type, gene ".
             "WHERE hit_name = '$evidence_id' ".
             "AND ".$evidence_type."_id = feature_id ".
             "AND feature_type = '$evidence_type' ".
             "AND supporting_feature.exon_id = exon_transcript.exon_id ".
             "AND exon_transcript.transcript_id = ".
             "transcript.transcript_id ".
             "AND transcript.gene_id = gene.gene_id");
  $sql .= " AND biotype = '".$gene_type."'" if($gene_type);
  return $sql;
}


1;

  my ($self, $evidence_id, $evidence_type, $id_type, $gene_type) = @_;
  my $sql = ("SELECT distinct(transcript.".$id_type."_id) ".
             "FROM transcript, transcript_supporting_feature, ".
             "gene, $evidence_type ".
             "WHERE transcript.gene_id = gene.gene_id ".
             "and transcript.transcript_id = ".
             "transcript_supporting_feature.transcript_id ".
             "and feature_type  = '$evidence_type' ".
             "and feature_id = ".$evidence_type."_id ".
             "and hit_name = '$evidence_id' ");
  $sql .= "and biotype = '".$gene_type."' " if($gene_type);
  return $sql;

  my ($self, $evidence_id, $gene_type, $evidence_type, $id_type, 
      $primary, $db) = @_;
  if(!$db){
    $db = $self->db;
  }
  if(!$evidence_type){
    $evidence_type = $self->evidence_type;
  }
  if(!$id_type){
    $id_type = $self->id_type;
  }
  if(!$primary){
    $primary = $self->primary_evidence;
  }
  my $sql;
  if($primary){
    $sql = $self->feature_id_from_primary_evidence_sql($evidence_id,
                                                       $evidence_type,
                                                       $id_type,
                                                       $gene_type);
  }else{
    $sql = $self->feature_id_from_evidence_sql($evidence_id,
                                               $evidence_type,
                                               $id_type,
                                               $gene_type);
  }
  print "SQL:".$sql."\n" if($self->verbose);
  my $sth = $db->dbc->prepare($sql);
  $sth->execute();
  while(my ($feature_id) = $sth->fetchrow){
    if($self->info){
      print $evidence_id." ";
      my $adaptor = $self->get_adaptor($id_type, $db);
      my $feature = $adaptor->fetch_by_dbID($feature_id);
      $self->print_feature_info($feature);
    }else{
      print $evidence_id ." ".$feature_id."\n";
    }
  }

  my ($self, $protein_ids) = @_;
  
 ID:foreach my $id(@$protein_ids){
    if($id =~ /(S+)-\1/){
      $id = 1;
    }
    if($self->have_pfetch){
      my $command = "pfetch -D ".$id."\n";
      print $command."\n" if($self->verbose);
      open(FH, $command." | ") or throw("failed to open ".$command);
    LINE:while(<FH>){
        if(/no\s+match/){
          print $id." has no match\n";
          next LINE;
        }
        print;
      }
      close(FH) or throw("Failed to close $command");
    }else{
      print $id."\n";
    }
  }

  my ($self, $id_type, $db) = @_;
  $db = $self->db if(!$db);
  $id_type = $id_type if(!$id_type);
  if($id_type eq 'gene'){
    return $db->get_GeneAdaptor;
  }elsif($id_type eq 'transcript'){
    return $db->get_TranscriptAdaptor;
  }
  throw("Failed to get adaptor for feature type ".$id_type);

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

   my ($self, $value) = @_;
  if($value){
    $self->{'id_type'} = $value;
  }
  return $self->{'id_type'} || 'gene';

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

  my ($class, @args) = @_;
  my $self = bless {},$class;
  return $self;

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

  my ($self, $feature_id, $evidence_type, $id_type) = @_;
  my $sql = ("SELECT distinct(hit_name) ".
             "FROM transcript, ".
             "transcript_supporting_feature, ".
             "$evidence_type ".
             "WHERE transcript.".$id_type."_id = ".$feature_id." ".
             "and transcript.transcript_id = ".
             "transcript_supporting_feature.transcript_id ".
             "and feature_type = '".$evidence_type."' ".
             "and feature_id = ".$evidence_type."_id ");
  return $sql;

  my ($self, $feature) = @_;
  throw("Must pass print_feature_info a feature") if(!$feature);
  my $info_string = $feature->dbID." ";
  $info_string .= $feature->stable_id if($feature->stable_id);
  $info_string .= $feature->slice->seq_region_name." ".
    $feature->slice->coord_system_name." ".$feature->start." ".
      $feature->end." ".$feature->strand."\n";
  print $info_string."\n";

  my ($self, $file) = @_;
  open(FH, $file) or throw("Failed to open ".$file);
  my @ids;
  while(<FH>){
    chomp;
    my ($id) = split;
    push(@ids, $id);
  }
  close(FH) or throw("Failed to close ".$file);
  return\@ ids;
}


#Methods to return the SQL

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

  Arg [1]   : SupportingEvidenceInfo
  Arg [2]   : value of variable
  Function  : container for specified variable. This pod refers to the
  seven methods below, db, verbose, info, evidence_type, id_type 
  have_pfetch and primary_evidence. These are simple containers which do no
  more than hold and return an given value
  Returntype: value of variable
  Exceptions: some throw if type is incorrect
  Example   : my $db = SupportingEvidenceInfo->db;

  Arg [1]   : SupportingEvidenceInfo
  Function  : These methods all take arguments to be used to produce
  an sql string to be used in order to fetch either evidence or feature
  ids. What is different is if they fetch on the basis of primary evidence
  associated with whole transcripts or all the evidence associated with each
  exon
  Returntype: string
  Exceptions: none
  Example   :