Bio::DB SeqI
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Summary
Bio::DB::SeqI - Abstract Interface for Sequence databases
Package variables
No package variables defined.
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_all_primary_idsDescriptionCode
get_Seq_by_primary_idDescriptionCode
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_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
may be 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
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 $db->get_all_primary_ids.
There is no other way to get (or guess) the primary_ids
in a database.
The other possibility is to get Bio::PrimarySeqI objects via the get_PrimarySeq_stream and the primary_id field on these objects are specified as the ids to use here. Returns : A Bio::Seq object Args : accession number (as a string) Throws : "acc does not exist" exception
Methods code
get_PrimarySeq_streamdescriptionprevnextTop
sub get_PrimarySeq_stream {
   my ($self,@args) = @_;
   $self->throw("Object did not provide a PrimarySeq stream object");
}
get_all_primary_idsdescriptionprevnextTop
sub get_all_primary_ids {
   my ($self,@args) = @_;
   $self->throw("Object did not provide a get_all_ids method");
}
get_Seq_by_primary_iddescriptionprevnextTop
sub get_Seq_by_primary_id {
   my ($self,@args) = @_;
   $self->throw("Abstract database call of get_Seq_by_primary_id. Your database".
       " has not implemented this method!");

}

1;
}
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Methods inherited 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
get_Seq_by_versionTop
 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 [that were] specific for Bio::DB::SeqITop