Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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


       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.

       For more information, please see the relevant

Implemented Interfaces

       This class implementes the following interfaces.

           Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI, specifically via
           Bio::Seq and Bio::PrimarySeq. Please review the documentation for those modules on
           implementation details relevant to those interfaces, as well as the ones below.



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AUTHOR - Ewan Birney



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

        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

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

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

        Title   : add_date
        Usage   : $self->add_date($datestr)
        Function: adds one or more dates

                  This implementation stores dates as keyed annotation, the
                  key being 'date_changed'. You can take advantage of this
                  fact when accessing the annotation collection directly.

        Example :
        Returns :
        Args    : a date string or an array of such strings

        Title   : get_dates
        Usage   : my @dates = $seq->get_dates;
        Function: Get the dates of the sequence (usually, when it was created and
        Returns : an array of date strings
        Args    :

        Title   : pid
        Usage   : my $pid = $seq->pid();
        Function: Get (and set, depending on the implementation) the PID property
                  for the sequence.
        Returns : a string
        Args    :

        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
        Example :
        Returns : value of accession
        Args    : newvalue (optional)

        Title   : add_secondary_accession
        Usage   : $self->add_domment($ref)
        Function: adds a secondary_accession

                  This implementation stores secondary accession numbers as
                  keyed annotation, the key being 'secondary_accession'. You
                  can take advantage of this fact when accessing the
                  annotation collection directly.

        Example :
        Returns :
        Args    : a string or an array of strings

        Title   : get_secondary_accessions
        Usage   : my @acc = $seq->get_secondary_accessions();
        Function: Get the secondary accession numbers as strings.
        Returns : An array of strings
        Args    : none

        Title   : seq_version
        Usage   : $obj->seq_version($newval)
        Function: Get/set the sequence version
        Returns : value of seq_version (a scalar)
        Args    : on set, new value (a scalar or undef, optional)
        Note    : this differs from Bio::PrimarySeq version() in that this explicitly
                  refers to the sequence record version one would find in a typical
                  sequence file.

        Title   : add_keyword
        Usage   : $obj->add_keyword($newval)
        Function: Add a new keyword to the annotation of the sequence.

                  This implementation stores keywords as keyed annotation,
                  the key being 'keyword'. You can take advantage of this
                  fact when accessing the annotation collection directly.

        Returns :
        Args    : value to be added (optional) (a string)

        Title   : get_keywords
        Usage   : $obj->get_keywords($newval)
        Function: Get the keywords for this sequence as an array of strings.
        Returns : an array of strings
        Args    :

Private methods and synonyms for backward compatibility

        Title   : _add_annotation_value
        Usage   :
        Function: Adds a value to the annotation collection under the specified
                  key. Note that this is not a public method.
        Returns :
        Args    : key (a string), value(s) (one or more scalars)

        Title   : _get_annotation_values
        Usage   :
        Function: Gets the values of a specific annotation as identified by the
                  key from the annotation collection. Note that this is not a
                  public method.
        Example :
        Returns : an array of strings
        Args    : the key (a string)