Bio::Seq RichSeqI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
Package variables
No package variables defined.
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->get_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
get_secondary_accessionsDescriptionCode
divisionDescriptionCode
moleculeDescriptionCode
pidDescriptionCode
get_datesDescriptionCode
seq_versionDescriptionCode
get_keywordsDescriptionCode
Methods description
get_secondary_accessionscode    nextTop
 Title   : get_secondary_accessions
 Usage   : 
 Function: Get the secondary accessions for a sequence.

           An implementation that allows modification of this array
           property should provide the methods add_secondary_accession
           and remove_secondary_accessions, with obvious purpose.

 Example :
 Returns : an array of strings
 Args    : none
divisioncodeprevnextTop
 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    :
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    :
get_datescodeprevnextTop
 Title   : get_dates
 Usage   :
 Function: Get (and set, depending on the implementation) the dates the
           databank entry specified for the sequence

           An implementation that allows modification of this array
           property should provide the methods add_date and
           remove_dates, with obvious purpose.

 Example :
 Returns : an array of strings
 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    :
get_keywordscodeprevnextTop
 Title   : get_keywords
 Usage   : $obj->get_keywords()
 Function: Get the keywords for this sequence object.

           An implementation that allows modification of this array
           property should provide the methods add_keyword and
           remove_keywords, with obvious purpose.

 Returns : an array of strings
 Args    :
Methods code
get_secondary_accessionsdescriptionprevnextTop
sub get_secondary_accessions {
   my ($self,@args) = @_;

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

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

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

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

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

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

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:
  http://bugzilla.open-bio.org/
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 _