Bio::DB SeqI
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Summary
Bio::DB::SeqI - Abstract Interface for Sequence databases
Package variables
No package variables defined.
Included modules
Bio::DB::RandomAccessI
Inherit
Bio::DB::RandomAccessI
Synopsis
   # get a Bio::DB::SeqI somehow

   $seq = $seqdb->get_Seq_by_id('some-id');
   $seq = $seqdb->get_Seq_by_acc('some-accession-number');

   @ids = $seqdb->get_all_ids();
   $stream = $seqdb->get_PrimarySeq_stream();
   while((my $seq = $stream->next_seq()) {
      # $seq is a PrimarySeqI compliant object
   }
Description
Abstract interface for a sequence database
Methods
get_PrimarySeq_streamDescriptionCode
get_Seq_by_primary_idDescriptionCode
get_all_primary_idsDescriptionCode
Methods description
get_PrimarySeq_streamcode    nextTop
 Title   : get_PrimarySeq_stream
 Usage   : $stream = get_PrimarySeq_stream
 Function: Makes a Bio::SeqIO compliant object
           which provides a single method, next_seq
 Returns : Bio::SeqIO
 Args    : none
get_Seq_by_primary_idcodeprevnextTop
 Title   : get_Seq_by_primary_id
 Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
 Function: Gets a Bio::Seq object by the primary id. The primary
           id in these cases has to come from $db->get_all_primary_ids.
           There is no other way to get (or guess) the primary_ids
           in a database.

           The other possibility is to get Bio::PrimarySeqI objects
           via the get_PrimarySeq_stream and the primary_id field
           on these objects are specified as the ids to use here.
 Returns : A Bio::Seq object
 Args    : accession number (as a string)
 Throws  : "acc does not exist" exception
get_all_primary_idscodeprevnextTop
 Title   : get_all_ids
 Usage   : @ids = $seqdb->get_all_primary_ids()
 Function: gives an array of all the primary_ids of the 
           sequence objects in the database. These
           maybe ids (display style) or accession numbers
           or something else completely different - they
           *are not* meaningful outside of this database
           implementation.
 Example :
 Returns : an array of strings
 Args    : none
Methods code
get_PrimarySeq_streamdescriptionprevnextTop
sub get_PrimarySeq_stream {
   my ($self,@args) = @_;

   $self->throw("Object did not provide a PrimarySeq stream object");
}
get_Seq_by_primary_iddescriptionprevnextTop
sub get_Seq_by_primary_id {
   my ($self,@args) = @_;

   $self->throw("Abstract database call of get_Seq_by_primary_id. Your database has not implemented this method!");

}

1;
}
get_all_primary_idsdescriptionprevnextTop
sub get_all_primary_ids {
   my ($self,@args) = @_;
   $self->throw("Object did not provide a get_all_ids method");
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
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/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
Describe contact details here
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Methods inherieted from Bio::DB::RandomAccessITop
get_Seq_by_idTop
 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
 Args    : the id (as a string) of a sequence
 Throws  : "id does not exist" exception
get_Seq_by_accTop
 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc('X77802');
 Function: Gets a Bio::Seq object by accession number
 Returns : A Bio::Seq object
 Args    : accession number (as a string)
 Throws  : "acc does not exist" exception
Methods [that were] specific for Bio::DB::SeqITop