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

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://github.com/bioperl/bioperl-live/issues

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

perl v5.32.1			  2019-12-07			  Bio::SeqI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney | APPENDIX

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