Bio::SeqI(3pm)						User Contributed Perl Documentation					    Bio::SeqI(3pm)

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 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 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	: @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.

   feature_count
	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.

   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: 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)

   annotation
	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.

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

       See Bio::Species for more information

   primary_seq
	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;

       See Bio::PrimarySeqI for more information

perl v5.14.2							    2012-03-02							    Bio::SeqI(3pm)