Bio::DB RandomAccessI
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Summary
Bio::DB::RandomAccessI - Abstract interface for a sequence database
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Root::RootI
Inherit
Bio::Root::Root
Synopsis
  #
  # get a database object somehow using a concrete class
  #

  $seq = $db->get_Seq_by_id('ROA1_HUMAN');

  #
  # $seq is a Bio::Seq object
  #
Description
This is a pure interface class - in other words, all this does is define
methods which other (concrete) classes will actually implement.
The Bio::DB::RandomAccessI class defines what methods a generic database class
should have. At the moment it is just the ability to make Bio::Seq objects
from a name (id) or a accession number.
Methods
get_Seq_by_accDescriptionCode
get_Seq_by_idDescriptionCode
get_Seq_by_versionDescriptionCode
Methods description
get_Seq_by_acccode    nextTop
 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc('X77802');
           $seq = $db->get_Seq_by_acc(Locus => 'X77802');
 Function: Gets a Bio::Seq object by accession number
 Returns : A Bio::Seq object or undef if not found
 Args    : accession number (as a string), or a two
               element list consisting of namespace=>accession
 Throws  : "more than one sequences correspond to this accession"
            if the accession maps to multiple primary ids and
            method is called in a scalar context
NOTE: The two-element form allows you to choose the namespace for the
accession number.
get_Seq_by_idcodeprevnextTop
 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
 Function: Gets a Bio::Seq object by its name
 Returns : a Bio::Seq object or undef if not found
 Args    : the id (as a string) of a sequence,
get_Seq_by_versioncodeprevnextTop
 Title   : get_Seq_by_version
 Usage   : $seq = $db->get_Seq_by_version('X77802.1');
 Function: Gets a Bio::Seq object by sequence version
 Returns : A Bio::Seq object
 Args    : accession.version (as a string)
 Throws  : "acc.version does not exist" exception
Methods code
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
get_Seq_by_versiondescriptionprevnextTop
sub get_Seq_by_version {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}



## End of Package

1;
}
General documentation
CONTACTTop
Ewan Birney originally wrote this class.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
    bioperl-bugs@bio.perl.org                   
    http://bugzilla.bioperl.org/
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _