Other packages in the module: Bio::DB::Fasta Bio::PrimarySeq::Fasta

Package variables

Synopsis

No synopsis!

Description

No description!

Methods

Methods description

None available.

Methods code

sub new {

  my $class = shift;
  $class = ref($class) if ref $class;
  my ($db,$id,$start,$stop) = @_;
  return bless { db    => $db,
		 id    => $id,
		 start => $start || 1,
		 stop  => $stop  || $db->length($id)
	       },$class;

}

sub seq {

  my $self = shift;
  return $self->{db}->seq($self->{id},$self->{start},$self->{stop});

}

sub subseq {

  my $self = shift;
  $self->trunc(@_)->seq();

}

sub trunc {

  my $self = shift;
  my ($start,$stop) = @_;
  $self->throw("Stop cannot be smaller than start")  unless $start <= $stop;
  return $self->{start} <= $self->{stop} ?  $self->new($self->{db},
						       $self->{id},
						       $self->{start}+$start-1,
						       $self->{start}+$stop-1)
                                         :  $self->new($self->{db},
						       $self->{id},
						       $self->{start}-($start-1),
						       $self->{start}-($stop-1)
						      );

}

sub display_id {

  my $self = shift;
  return $self->{id};

}

sub accession_number {

  my $self = shift;
  return "unknown";

}

sub primary_id {

  my $self = shift;
  return overload::StrVal($self);

}

sub can_call_new {

 return 0

}

sub alphabet {

  my $self = shift;
  return $self->{db}->alphabet($self->{id});

}

sub revcom {

  my $self = shift;
  return $self->new(@{$self}{'db','id','stop','start'});

}

sub length {

  my $self = shift;
  return $self->{db}->length($self->{id});

}

sub description {

     my $self = shift;
    return '';

}

General documentation