/ 
bioperl-1.2.3
/ Bio::Seq::RichSeq

NAME

Bio::Seq::RichSeq - Module implementing a sequence created from a rich sequence database entry

SYNOPSIS

See Bio::Seq::RichSeqI and documentation of methods.

DESCRIPTION

This module implements Bio::Seq::RichSeqI, an interface for sequences created from or created for entries from/of rich sequence databanks, like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI interface therefore focus on databank-specific information. Note that not every rich databank format may use all of the properties provided.

Implemented Interfaces

This class implementes the following interfaces.

Bio::Seq::RichSeqI

Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI.

Bio::IdentifiableI
Bio::DescribableI
Bio::AnnotatableI

FEEDBACK

Mailing Lists

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 Bugs

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 Birney

Email birney@ebi.ac.uk

Describe contact details here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $seq    = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
                                             -id  => 'human_id',
				             -accession_number => 'AL000012',
				            );

 Function: Returns a new seq object from
           basic constructors, being a string for the sequence
           and strings for id and accession_number
 Returns : a new Bio::Seq::RichSeq object

division

Title   : division
Usage   : $obj->division($newval)
Function: 
Returns : value of division
Args    : newvalue (optional)

molecule

Title   : molecule
Usage   : $obj->molecule($newval)
Function: 
Returns : type of molecule (DNA, mRNA)
Args    : newvalue (optional)

add_date

Title   : add_date
Usage   : $self->add_date($datestr)
Function: adds a date
Example :
Returns : a date string or an array of such strings
Args    :

get_dates

Title   : get_dates
Usage   :
Function:
Example :
Returns : an array of date strings
Args    :

pid

Title   : pid
Usage   :
Function: Get (and set, depending on the implementation) the PID property
          for the sequence.
Example :
Returns : a string
Args    :

accession

Title   : accession
Usage   : $obj->accession($newval)
Function: Whilst the underlying sequence object does not 
          have an accession, so we need one here.

          In this implementation this is merely a synonym for
          accession_number().
Example : 
Returns : value of accession
Args    : newvalue (optional)

add_secondary_accession

Title   : add_secondary_accession
Usage   : $self->add_domment($ref)
Function: adds a secondary_accession
Example :
Returns : 
Args    : a string or an array of strings

get_secondary_accessions

Title   : get_secondary_accessions
Usage   :
Function:
Example :
Returns : An array of strings
Args    :

seq_version

Title   : seq_version
Usage   : $obj->seq_version($newval)
Function: 
Example : 
Returns : value of seq_version
Args    : newvalue (optional)

keywords

Title   : keywords
Usage   : $obj->keywords($newval)
Function: 
Returns : value of keywords (a string)
Args    : newvalue (optional) (a string)