Bio::Seq RichSeqI
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Summary
Bio::Seq::RichSeqI - RichSeq interface, mainly for database orientated sequences
Package variables
No package variables defined.
Included modules
Bio::SeqI
Inherit
Bio::SeqI
Synopsis
    @secondary   = $richseq->get_secondary_accessions;
    $division    = $richseq->division;
    $mol         = $richseq->molecule;
    @dates       = $richseq->get_dates; 
    $seq_version = $richseq->seq_version;  
    $pid         = $richseq->pid;
    $keywords    = $richseq->keywords;
Description
This interface extends the Bio::SeqI interface to give additional functionality
to sequences with richer data sources, in particular from database sequences
(EMBL, GenBank and Swissprot).
Methods
divisionDescriptionCode
get_datesDescriptionCode
get_secondary_accessionsDescriptionCode
keywordsDescriptionCode
moleculeDescriptionCode
pidDescriptionCode
seq_versionDescriptionCode
Methods description
divisioncode    nextTop
 Title   : division
 Usage   :
 Function: Get (and set, depending on the implementation) the divison for
           a sequence.

           Examples from GenBank are PLN (plants), PRI (primates), etc.
 Example :
 Returns : a string
 Args    :
get_datescodeprevnextTop
 Title   : get_dates
 Usage   :
 Function: Get (and set, depending on the implementation) the dates the
           databank entry specified for the sequence
 Example :
 Returns : an array of strings
 Args    :
get_secondary_accessionscodeprevnextTop
 Title   : get_secondary_accessions
 Usage   : 
 Function: Get the secondary accessions for a sequence.
 Example :
 Returns : an array of strings
 Args    : none
keywordscodeprevnextTop
 Title   : keywords
 Usage   : $obj->keywords($newval)
 Function: 
 Returns : value of keywords (a string)
 Args    : newvalue (optional) (a string)
moleculecodeprevnextTop
 Title   : molecule
 Usage   :
 Function: Get (and set, depending on the implementation) the molecule
           type for the sequence.

           This is not necessarily the same as Bio::PrimarySeqI::alphabet(),
           because it is databank-specific.
 Example :
 Returns : a string
 Args    :
pidcodeprevnextTop
 Title   : pid
 Usage   :
 Function: Get (and set, depending on the implementation) the PID property
           for the sequence.
 Example :
 Returns : a string
 Args    :
seq_versioncodeprevnextTop
 Title   : seq_version
 Usage   :
 Function: Get (and set, depending on the implementation) the version string
           of the sequence.
 Example :
 Returns : a string
 Args    :
Methods code
divisiondescriptionprevnextTop
sub division {
   my ($self,@args) = @_;

   $self->throw("hit division in interface definition - error");
}
get_datesdescriptionprevnextTop
sub get_dates {
   my ($self,@args) = @_;

   $self->throw("hit get_dates in interface definition - error");
}
get_secondary_accessionsdescriptionprevnextTop
sub get_secondary_accessions {
   my ($self,@args) = @_;

   $self->throw("hit get_secondary_accessions in interface definition - error");
}
keywordsdescriptionprevnextTop
sub keywords {
   my ($self) = @_;
   $self->throw("hit keywords in interface definition - error");
}

1;
}
moleculedescriptionprevnextTop
sub molecule {
   my ($self,@args) = @_;

   $self->throw("hit molecule in interface definition - error");
}
piddescriptionprevnextTop
sub pid {
   my ($self,@args) = @_;

   $self->throw("hit pid in interface definition - error");
}
seq_versiondescriptionprevnextTop
sub seq_version {
   my ($self,@args) = @_;

   $self->throw("hit seq_version in interface definition - error");
}
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://bio.perl.org/MailList.html             - 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 _