NAME

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

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 guaranteed 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 implemented 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 method here, because too many complicated functions here would 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 a lot 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.

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       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 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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney

       Email birney@ebi.ac.uk

APPENDIX

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

   get_SeqFeatures
        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.

   get_all_SeqFeatures
        Title   : get_all_SeqFeatures
        Usage   : my @feats = $seq->get_all_SeqFeatures();
        Function: returns all SeqFeatures, including 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.

   feature_count
        Title   : feature_count
        Usage   : my $count = $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.

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

   write_GFF
        Title   : write_GFF
        Usage   : $seq->write_GFF(\*FILEHANDLE);
        Function: Convenience 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)

   annotation
        Title   : annotation
        Usage   : my $ann = $seq->annotation($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.

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

       See Bio::Species for more information

   primary_seq
        Title   : primary_seq
        Usage   : my $primaryseq = $seq->primary_seq($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;

       See Bio::PrimarySeqI for more information