/ 
bioperl-1.4
/ Bio::SeqFeatureI

NAME

Bio::SeqFeatureI - Abstract interface of a Sequence Feature

SYNOPSIS

    # get a seqfeature somehow, eg, from a Sequence with Features attached

    foreach $feat ( $seq->get_SeqFeatures() ) {
            print "Feature from ", $feat->start, "to ", 
	          $feat->end, " Primary tag  ", $feat->primary_tag, 
	          ", produced by ", $feat->source_tag(), "\n";

            if( $feat->strand == 0 ) {
		print "Feature applicable to either strand\n";
            } else {
                print "Feature on strand ", $feat->strand,"\n"; # -1,1
            }
            print "feature location is ",$feat->start, "..",
                  $feat->end, " on strand ", $feat->strand, "\n";
            print "easy utility to print locations in GenBank/EMBL way ",
                  $feat->location->to_FTstring(), "\n";

            foreach $tag ( $feat->get_all_tags() ) {
		print "Feature has tag ", $tag, " with values, ",
		      join(' ',$feat->get_tag_values($tag)), "\n";
            }
	    print "new feature\n" if $feat->has_tag('new');
	    # features can have sub features
	    my @subfeat = $feat->get_SeqFeatures();
	}

DESCRIPTION

This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implemention, it just provides the definitions of what methods one can call. See Bio::SeqFeature::Generic for a good standard implementation of this object

FEEDBACK

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

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

APPENDIX

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

SeqFeatureI specific methods

New method interfaces.

get_SeqFeatures

Title   : get_SeqFeatures
Usage   : @feats = $feat->get_SeqFeatures();
Function: Returns an array of sub Sequence Features
Returns : An array
Args    : none

display_name

Title   : display_name
Usage   : $name = $feat->display_name()
Function: Returns the human-readable name of the feature for displays.
Returns : a string
Args    : none

primary_tag

Title   : primary_tag
Usage   : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
          eg 'exon'
Returns : a string 
Args    : none

source_tag

Title   : source_tag
Usage   : $tag = $feat->source_tag()
Function: Returns the source tag for a feature,
          eg, 'genscan' 
Returns : a string 
Args    : none

has_tag

Title   : has_tag
Usage   : $tag_exists = $self->has_tag('some_tag')
Function: 
Returns : TRUE if the specified tag exists, and FALSE otherwise
Args    :

get_tag_values

Title   : get_tag_values
Usage   : @values = $self->get_tag_values('some_tag')
Function: 
Returns : An array comprising the values of the specified tag.
Args    : a string

throws an exception if there is no such tag

get_tagset_values

Title   : get_tagset_values
Usage   : @values = $self->get_tagset_values(qw(label transcript_id product))
Function: 
Returns : An array comprising the values of the specified tags, in order of tags
Args    : An array of strings

does NOT throw an exception if none of the tags are not present

this method is useful for getting a human-readable label for a SeqFeatureI; not all tags can be assumed to be present, so a list of possible tags in preferential order is provided

get_all_tags

Title   : get_all_tags
Usage   : @tags = $feat->get_all_tags()
Function: gives all tags for this feature
Returns : an array of strings
Args    : none

attach_seq

Title   : attach_seq
Usage   : $sf->attach_seq($seq)
Function: Attaches a Bio::Seq object to this feature. This
          Bio::Seq object is for the *entire* sequence: ie
          from 1 to 10000

          Note that it is not guaranteed that if you obtain a feature from
          an object in bioperl, it will have a sequence attached. Also,
          implementors of this interface can choose to provide an empty
          implementation of this method. I.e., there is also no guarantee 
          that if you do attach a sequence, seq() or entire_seq() will not
          return undef.

          The reason that this method is here on the interface is to enable
          you to call it on every SeqFeatureI compliant object, and
          that it will be implemented in a useful way and set to a useful 
          value for the great majority of use cases. Implementors who choose
          to ignore the call are encouraged to specifically state this in
          their documentation.

Example :
Returns : TRUE on success
Args    : a Bio::PrimarySeqI compliant object

seq

Title   : seq
Usage   : $tseq = $sf->seq()
Function: returns the truncated sequence (if there is a sequence attached) 
          for this feature
Example :
Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
          bounded by start & end, or undef if there is no sequence attached
Args    : none

entire_seq

Title   : entire_seq
Usage   : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
          sequence attached
Args    : none

seq_id

Title   : seq_id
Usage   : $obj->seq_id($newval)
Function: There are many cases when you make a feature that you
          do know the sequence name, but do not know its actual
          sequence. This is an attribute such that you can store
          the ID (e.g., display_id) of the sequence.

          This attribute should *not* be used in GFF dumping, as
          that should come from the collection in which the seq
          feature was found.
Returns : value of seq_id
Args    : newvalue (optional)

gff_string

Title   : gff_string
Usage   : $str = $feat->gff_string;
          $str = $feat->gff_string($gff_formatter);
Function: Provides the feature information in GFF format.

          The implementation provided here returns GFF2 by default. If you
          want a different version, supply an object implementing a method
          gff_string() accepting a SeqFeatureI object as argument. E.g., to
          obtain GFF1 format, do the following:

               my $gffio = Bio::Tools::GFF->new(-gff_version => 1);
               $gff1str = $feat->gff_string($gff1io);

Returns : A string
Args    : Optionally, an object implementing gff_string().

_static_gff_formatter

Title   : _static_gff_formatter
Usage   :
Function:
Example :
Returns : 
Args    :

Bio::RangeI methods

List of interfaces inherited from Bio::RangeI (see Bio::RangeI for details).

start

Title   : start
Usage   : $start = $feat->start
Function: Returns the start coordinate of the feature
Returns : integer
Args    : none

end

Title   : end
Usage   : $end = $feat->end
Function: Returns the end coordinate of the feature
Returns : integer
Args    : none

strand

Title   : strand
Usage   : $strand = $feat->strand()
Function: Returns strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args    : none

Decorating methods

These methods have an implementation provided by Bio::SeqFeatureI, but can be validly overwritten by subclasses

spliced_seq

Title   : spliced_seq

Usage   : $seq = $feature->spliced_seq()
          $seq = $feature_with_remote_locations->spliced_seq($db_for_seqs)

Function: Provides a sequence of the feature which is the most
          semantically "relevant" feature for this sequence. A default
          implementation is provided which for simple cases returns just
          the sequence, but for split cases, loops over the split location
          to return the sequence. In the case of split locations with
          remote locations, eg

          join(AB000123:5567-5589,80..1144)

          in the case when a database object is passed in, it will attempt
          to retrieve the sequence from the database object, and "Do the right thing",
          however if no database object is provided, it will generate the correct
          number of N's (DNA) or X's (protein, though this is unlikely).

          This function is deliberately "magical" attempting to second guess
          what a user wants as "the" sequence for this feature

          Implementing classes are free to override this method with their
          own magic if they have a better idea what the user wants

Args    : [optional] A Bio::DB::RandomAccessI compliant object
Returns : A Bio::Seq

RangeI methods

These methods are inherited from RangeI and can be used directly from a SeqFeatureI interface. Remember that a SeqFeature is-a RangeI, and so wherever you see RangeI you can use a feature ($r in the below documentation).

overlaps

Title   : overlaps
Usage   : if($feat->overlaps($r)) { do stuff }
          if($feat->overlaps(200)) { do stuff }
Function: tests if $feat overlaps $r
Args    : a RangeI to test for overlap with, or a point
Returns : true if the Range overlaps with the feature, false otherwise

contains

Title   : contains
Usage   : if($feat->contains($r) { do stuff }
Function: tests whether $feat totally contains $r
Args    : a RangeI to test for being contained
Returns : true if the argument is totaly contained within this range

equals

Title   : equals
Usage   : if($feat->equals($r))
Function: test whether $feat has the same start, end, strand as $r
Args    : a RangeI to test for equality
Returns : true if they are describing the same range

Geometrical methods

These methods do things to the geometry of ranges, and return triplets (start, stop, strand) from which new ranges could be built.

intersection

Title   : intersection
Usage   : ($start, $stop, $strand) = $feat->intersection($r)
Function: gives the range that is contained by both ranges
Args    : a RangeI to compare this one to
Returns : nothing if they do not overlap, or the range that they do overlap

union

Title   : union
Usage   : ($start, $stop, $strand) = $feat->union($r);
        : ($start, $stop, $strand) = Bio::RangeI->union(@ranges);
Function: finds the minimal range that contains all of the ranges
Args    : a range or list of ranges to find the union of
Returns : the range containing all of the ranges

location

 Title   : location
 Usage   : my $location = $seqfeature->location()
 Function: returns a location object suitable for identifying location 
	   of feature on sequence or parent feature  
 Returns : Bio::LocationI object
 Args    : none

primary_id

Title   : primary_id
Usage   : $obj->primary_id($newval)
Function: 
Example : 
Returns : value of primary_id (a scalar)
Args    : on set, new value (a scalar or undef, optional)