Bio LocatableSeq
Other packages in the module: Bio::Search::Tiling::MapTileUtils Bio::Search::HSP::HSPI
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Methods
get_SeqFeaturesDescriptionCode
feature_countDescriptionCode
add_SeqFeatureDescriptionCode
remove_SeqFeaturesDescriptionCode
Methods description
get_SeqFeaturescode    nextTop
 Title   : get_SeqFeatures
 Usage   :
 Function: Get the feature objects held by this feature holder.

           Features which are not top-level are subfeatures of one or
           more of the returned feature objects, which means that you
           must traverse the subfeature arrays of each top-level
           feature object in order to traverse all features associated
           with this sequence.

           Top-level features can be obtained by tag, specified in 
           the argument.

           Use get_all_SeqFeatures() if you want the feature tree
           flattened into one single array.

 Example :
 Returns : an array of Bio::SeqFeatureI implementing objects
 Args    : [optional] scalar string (feature tag)
feature_countcodeprevnextTop
 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
add_SeqFeaturecodeprevnextTop
 Title   : add_SeqFeature
 Usage   : $seq->add_SeqFeature($feat);
           $seq->add_SeqFeature(@feat);
 Function: Adds the given feature object (or each of an array of feature
           objects to the feature array of this
           sequence. The object passed is required to implement the
           Bio::SeqFeatureI interface.
 Returns : 1 on success
 Args    : A Bio::SeqFeatureI implementing object, or an array of such objects.
remove_SeqFeaturescodeprevnextTop
 Title   : remove_SeqFeatures
 Usage   : $seq->remove_SeqFeatures();
 Function: Flushes all attached SeqFeatureI objects.

           To remove individual feature objects, delete those from the returned
           array and re-add the rest.
 Example :
 Returns : The array of Bio::SeqFeatureI objects removed from this seq.
 Args    : None
Methods code
get_SeqFeaturesdescriptionprevnextTop
sub get_SeqFeatures {
   my $self = shift;
   my $tag = shift;

   if( !defined $self->{'_as_feat'} ) {
       $self->{'_as_feat'} = [];
   }
   if ($tag) {
       return map { $_->primary_tag eq $tag ? $_ : () } @{$self->{'_as_feat'}};
   }
   else {
       return @{$self->{'_as_feat'}};
   }
}
feature_countdescriptionprevnextTop
sub feature_count {
    my ($self) = @_;
    if (defined($self->{'_as_feat'})) {
	return ($#{$self->{'_as_feat'}} + 1);
    } else {
	return 0;
    }
}
add_SeqFeaturedescriptionprevnextTop
sub add_SeqFeature {
   my ($self,@feat) = @_;
   $self->{'_as_feat'} = [] unless $self->{'_as_feat'};
   foreach my $feat ( @feat ) {
       if( !$feat->isa("Bio::SeqFeatureI") ) {
	   $self->throw("$feat is not a SeqFeatureI and that's what we expect...");
       }
       $feat->attach_seq($self);
       push(@{$self->{'_as_feat'}},$feat);
   }
   return 1;
}
remove_SeqFeaturesdescriptionprevnextTop
sub remove_SeqFeatures {
    my $self = shift;

    return () unless $self->{'_as_feat'};
    my @feats = @{$self->{'_as_feat'}};
    $self->{'_as_feat'} = [];
    return @feats;
}

1;
}
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