Bio-DB-SeqFeature

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lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm  view on Meta::CPAN

}

sub _update_attribute_index {
  my $self = shift;
  my ($obj,$id) = @_;
  my $attribute = $self->_attribute_table;
  $self->_delete_index($attribute,$id);

  my $sth = $self->_prepare("INSERT INTO $attribute (id,attribute_id,attribute_value) VALUES (?,?,?)");
  for my $tag ($obj->get_all_tags) {
    my $tagid = $self->_attributeid($tag);
    for my $value ($obj->get_tag_values($tag)) {
      $sth->execute($id,$tagid,$value) or $self->throw($sth->errstr);
    }
  }
  $sth->finish;
}

sub _genericid {
  my $self = shift;
  my ($table,$namefield,$name,$add_if_missing) = @_;
  my $qualified_table = $self->_qualify($table);
  my $sth = $self->_prepare(<<END);

lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm  view on Meta::CPAN

  print $fh join("\t",$id,$dbh->quote($_),1),"\n" foreach @$names;
  print $fh join("\t",$id,$dbh->quote($_),0),"\n" foreach @$aliases;
}

sub _dump_update_attribute_index {
  my $self = shift;
  my ($obj,$id) = @_;
  my $fh        = $self->dump_filehandle('attribute');
  my $dbh       = $self->dbh;
  for my $tag ($obj->all_tags) {
    my $tagid = $self->_attributeid($tag);
    for my $value ($obj->each_tag_value($tag)) {
      print $fh join("\t",$id,$tagid,$dbh->quote($value)),"\n";
    }
  }
}

sub coverage_array {
    my $self = shift;
    my ($seq_name,$start,$end,$types,$bins) = 
	rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],
		   ['TYPES','TYPE','PRIMARY_TAG'],'BINS'],@_);

lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm  view on Meta::CPAN

  $sth->finish;
}


sub _dump_update_attribute_index {
  my $self = shift;
  my ($obj,$id) = @_;
  my $fh        = $self->dump_filehandle('attribute');
  my $dbh       = $self->dbh;
  for my $tag ($obj->all_tags) {
    my $tagid = $self->_attributeid($tag);
    for my $value ($obj->each_tag_value($tag)) {
      # unlike DBI::mysql, don't quote, as quotes will be quoted when loaded
      print $fh join("\t",$id,$tagid,$value),"\n";
    }
  }
}

sub _update_indexes {
    my $self = shift;
    my $obj  = shift;
    defined (my $id   = $obj->primary_id) or return;
    $self->SUPER::_update_indexes($obj);

lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm  view on Meta::CPAN

}

sub _update_attribute_index {
  my $self = shift;
  my ($obj,$id) = @_;
  my $attribute = $self->_attribute_table;
  $self->_delete_index($attribute,$id);

  my $sth = $self->_prepare("INSERT INTO $attribute (id,attribute_id,attribute_value) VALUES (?,?,?)");
  for my $tag ($obj->get_all_tags) {
    my $tagid = $self->_attributeid($tag);
    for my $value ($obj->get_tag_values($tag)) {
      $sth->execute($id,$tagid,$value) or $self->throw($sth->errstr);
    }
  }
  $sth->finish;
}

sub _genericid {
  my $self = shift;
  my ($table,$namefield,$name,$add_if_missing) = @_;
  my $qualified_table = $self->_qualify($table);
  my $sth = $self->_prepare(<<END);

lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm  view on Meta::CPAN

  print $fh join("\t",$id,$dbh->quote($_),1),"\n" foreach @$names;
  print $fh join("\t",$id,$dbh->quote($_),0),"\n" foreach @$aliases;
}

sub _dump_update_attribute_index {
  my $self = shift;
  my ($obj,$id) = @_;
  my $fh        = $self->dump_filehandle('attribute');
  my $dbh       = $self->dbh;
  for my $tag ($obj->all_tags) {
    my $tagid = $self->_attributeid($tag);
    for my $value ($obj->each_tag_value($tag)) {
      print $fh join("\t",$id,$tagid,$dbh->quote($value)),"\n";
    }
  }
}

sub coverage_array {
    my $self = shift;
    my ($seq_name,$start,$end,$types,$bins) = 
	rearrange([['SEQID','SEQ_ID','REF'],'START',['STOP','END'],
		   ['TYPES','TYPE','PRIMARY_TAG'],'BINS'],@_);