Summary

Bio::FeatureHolderI - the base interface an object with features must implement

Package variables

Included modules

Inherit

Bio::Root::RootI

Synopsis

    use Bio::SeqIO;
    # get a feature-holding object somehow: for example, Bio::SeqI objects
    # have features
    my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank);
    while (my $seq = $seqio->next_seq()) {
        # $seq is-a Bio::FeatureHolderI, hence:
        my @feas = $seq->get_SeqFeatures();
        # each element is-a Bio::SeqFeatureI
        foreach my $fea (@feas) {
            # do something with the feature objects
        }
    }

Description

This is the base interface that all feature-holding objects must
implement.
Popular feature-holders are for instance Bio::Seq objects. Since
Bio::SeqFeatureI defines a sub_SeqFeature() method, most
Bio::SeqFeatureI implementations like Bio::SeqFeature::Generic will
implement the feature holder interface as well.

Methods

Methods description

 Title   : get_SeqFeatures
 Usage   :
 Function: Get the feature objects held by this feature holder.
 Example :
 Returns : an array of Bio::SeqFeatureI implementing objects
 Args    : none

 Title   : feature_count
 Usage   : $obj->feature_count()
 Function: Return the number of SeqFeatures attached to a feature holder.

           This is before flattening a possible sub-feature tree.

           We provide a default implementation here that just counts
           the number of objects returned by get_SeqFeatures().
           Implementors may want to override this with a more
           efficient implementation.

 Returns : integer representing the number of SeqFeatures
 Args    : None

 Title   : get_all_SeqFeatures
 Usage   :
 Function: Get the flattened tree of feature objects held by this
           feature holder. The difference to get_SeqFeatures is that
           the entire tree of sub-features will be flattened out.

           We provide a default implementation here, so implementors
           don''t necessarily need to implement this method.

 Example :
 Returns : an array of Bio::SeqFeatureI implementing objects
 Args    : none

Methods code

sub get_SeqFeatures {

    shift->throw_not_implemented();

}

sub feature_count {

    return scalar(shift->get_SeqFeatures(@_));

}

sub get_all_SeqFeatures {

    my $self = shift;
    my @flatarr;

    foreach my $feat ( $self->get_SeqFeatures(@_) ){
	push(@flatarr,$feat);
	&_add_flattened_SeqFeatures(\@flatarr,$feat,@_);
    }
    return @flatarr;

}

sub _add_flattened_SeqFeatures {

    my ($arrayref,$feat,@args) = @_;
    my @subs = ();

    if($feat->isa("Bio::FeatureHolderI")) {
	@subs = $feat->get_SeqFeatures(@args);
    } elsif($feat->isa("Bio::SeqFeatureI")) {
	@subs = $feat->sub_SeqFeature();
    } else {
	confess ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ".
	    "Don't know how to flatten.";
    }
    foreach my $sub (@subs) {
	push(@$arrayref,$sub);
	&_add_flattened_SeqFeatures($arrayref,$sub);
    }

}

General documentation

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