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Summary

Bio::SeqI [Developers] - Abstract Interface of Sequence (with features)

Package variables

Included modules

Inherit

Bio::AnnotatableI Bio::FeatureHolderI Bio::PrimarySeqI

Synopsis

    # Bio::SeqI is the interface class for sequences.

    # If you are a newcomer to bioperl, you should
    # start with Bio::Seq documentation. This
    # documentation is mainly for developers using
    # Bioperl.

    # Bio::SeqI implements Bio::PrimarySeqI
    $seq      = $seqobj->seq(); # actual sequence as a string
    $seqstr   = $seqobj->subseq(10,50);

    # Bio::SeqI has annotationcollections

    $ann      = $seqobj->annotation(); # annotation object

    # Bio::SeqI has sequence features
    # features must implement Bio::SeqFeatureI

    @features = $seqobj->get_SeqFeatures(); # just top level
    @features = $seqobj->get_all_SeqFeatures(); # descend into sub features

Description

Bio::SeqI is the abstract interface of annotated Sequences. These
methods are those which you can be guarenteed to get for any Bio::SeqI
- for most users of the package the documentation (and methods) in
this class are not at useful - this is a developers only class which
defines what methods have to be implmented by other Perl objects to
comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man
Bio::Seq" for more information.
There aren't many here, because too many complicated functions here
prevent implementations which are just wrappers around a database or
similar delayed mechanisms.
Most of the clever stuff happens inside the SeqFeatureI system.
A good reference implementation is Bio::Seq which is a pure perl
implementation of this class with alot of extra pieces for extra
manipulation. However, if you want to be able to use any sequence
object in your analysis, if you can do it just using these methods,
then you know you will be future proof and compatible with other
implementations of Seq.

Methods

Methods description

 Title   : primary_seq
 Usage   : $obj->primary_seq($newval)
 Function: Retrieve the underlying Bio::PrimarySeqI object if available.
           This is in the event one has a sequence with lots of features
           but want to be able to narrow the object to just one with
           the basics of a sequence (no features or annotations).
 Returns : Bio::PrimarySeqI
 Args    : Bio::PrimarySeqI or none;

 Title   : seq
 Usage   : my $string = $seq->seq();
 Function: Retrieves the sequence string for the sequence object
 Returns : string
 Args    : none

 Title   : species
 Usage   :
 Function: Gets or sets the species
 Example : $species = $self->species();
 Returns : Bio::Species object
 Args    : Bio::Species object or none;

 Title   : write_GFF
 Usage   : $seq->write_GFF(\*FILEHANDLE);
 Function: Convience method to write out all the sequence features
           in GFF format to the provided filehandle (STDOUT by default)
 Returns : none
 Args    : [optional] filehandle to write to (default is STDOUT)

Methods code

sub primary_seq {

    my ($self) = @_;
    $self->throw_not_implemented;
}

1;

}

sub seq {

   my ($self) = @_;
   $self->throw_not_implemented();

}

sub species {

    my ($self) = @_;
    $self->throw_not_implemented();

}

sub write_GFF {

   my ($self,$fh) = @_;

   $fh || do { $fh =\* STDOUT; };

   foreach my $sf ( $self->get_all_SeqFeatures() ) {
       print $fh $sf->gff_string, "\n";
   }

}

General documentation

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

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/

Email birney@sanger.ac.uk

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

 Title   : get_SeqFeatures
 Usage   : my @feats = $seq->get_SeqFeatures();
 Function: retrieve just the toplevel sequence features attached to this seq
 Returns : array of Bio::SeqFeatureI objects
 Args    : none

This method comes through extension of Bio::FeatureHolderI. See
Bio::FeatureHolderI and Bio::SeqFeatureI for more information.

 Title   : get_all_SeqFeatures
 Usage   : @features = $annseq->get_all_SeqFeatures()
 Function: returns all SeqFeatures, included sub SeqFeatures
 Returns : an array of Bio::SeqFeatureI objects
 Args    : none

This method comes through extension of Bio::FeatureHolderI. See
Bio::FeatureHolderI and Bio::SeqFeatureI for more information.

 Title   : feature_count
 Usage   : $seq->feature_count()
 Function: Return the number of SeqFeatures attached to a sequence
 Returns : integer representing the number of SeqFeatures
 Args    : none

This method comes through extension of Bio::FeatureHolderI. See
Bio::FeatureHolderI for more information.

 Title   : annotation
 Usage   : $obj->annotation($seq_obj)
 Function: retrieve the attached annotation object
 Returns : Bio::AnnotationCollectionI or none;

See Bio::AnnotationCollectionI and Bio::Annotation::Collection
for more information. This method comes through extension from
Bio::AnnotatableI.