/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqI

NAME

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

SYNOPSIS

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

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

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

# FAST::Bio::SeqI has annotationcollections

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

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

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

DESCRIPTION

FAST::Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guarenteed to get for any FAST::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 FAST::Bio::SeqI interface. Go "perldoc FAST::Bio::Seq" or "man FAST::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 FAST::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 FAST::Bio::SeqFeatureI objects
Args    : none

This method comes through extension of FAST::Bio::FeatureHolderI. See FAST::Bio::FeatureHolderI and FAST::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 FAST::Bio::SeqFeatureI objects
Args    : none

This method comes through extension of FAST::Bio::FeatureHolderI. See FAST::Bio::FeatureHolderI and FAST::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 FAST::Bio::FeatureHolderI. See FAST::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 : FAST::Bio::AnnotationCollectionI or none;

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

species

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

See FAST::Bio::Species for more information

primary_seq

Title   : primary_seq
Usage   : $obj->primary_seq($newval)
Function: Retrieve the underlying FAST::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 : FAST::Bio::PrimarySeqI
Args    : FAST::Bio::PrimarySeqI or none;

See FAST::Bio::PrimarySeqI for more information