#
# BioPerl module for Bio::FeatureHolderI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

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

=head1 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
        }
    }

=head1 DESCRIPTION

This is the base interface that all feature-holding objects must
implement.

Popular feature-holders are for instance L<Bio::Seq> objects. Since
L<Bio::SeqFeatureI> defines a sub_SeqFeature() method, most
Bio::SeqFeatureI implementations like L<Bio::SeqFeature::Generic> will
implement the feature holder interface as well.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

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

=head1 AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

=head1 CONTRIBUTORS

Steffen Grossmann [SG], grossman-at-molgen.mpg.de
Mark A. Jensen, maj -at- fortinbras -dot- us

=head1 APPENDIX

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

=cut


# Let the code begin...



package Bio::FeatureHolderI;
$Bio::FeatureHolderI::VERSION = '1.7.8';
use strict;
use Carp;

use base qw(Bio::Root::RootI);

=head2 get_SeqFeatures()

 Usage   : @feats = $obj->get_SeqFeatures()
 Function: Get the feature objects held by this feature holder.
 Example :
 Returns : an array of Bio::SeqFeatureI implementing objects
           if tag specified, return features having that tag
 Args    : [optional] scalar string (feature tag)

=cut

sub get_SeqFeatures {
  shift->throw_not_implemented();
}

=head2 add_SeqFeature()

 Usage   : $feat->add_SeqFeature($subfeat);
           $feat->add_SeqFeature($subfeat,'EXPAND')
 Function: Add a SeqFeature into the subSeqFeature array.
           with no 'EXPAND' qualifer, subfeat will be tested
           as to whether it lies inside the parent, and throw
           an exception if not.

           If EXPAND is used and the object implements Bio::RangeI
           (which is not guaranteed), the parent''s start/end/strand
           will be extended so that the new subFeature can be accomodated.
 Example :
 Returns : nothing
 Args    : a Bio::SeqFeatureI object

=cut

sub add_SeqFeature {
  shift->throw_not_implemented();
}


=head2 remove_SeqFeatures()

 Usage   : $obj->remove_SeqFeatures
 Function: Removes all sub SeqFeatures.  If you want to remove only a subset,
           remove that subset from the returned array, and add back the rest.
 Returns : The array of Bio::SeqFeatureI implementing sub-features that was
           deleted from this feature.
 Args    : none

=cut

sub remove_SeqFeatures {
  shift->throw_not_implemented();
}

=head2 feature_count

 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

At some day we may want to expand this method to allow for a feature
filter to be passed in.

Our default implementation allows for any number of additional
arguments and will pass them on to get_SeqFeatures(). I.e., in order to
support filter arguments, just support them in get_SeqFeatures().

=cut

sub feature_count {
    return scalar(shift->get_SeqFeatures(@_));
}

=head2 get_all_SeqFeatures

 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

At some day we may want to expand this method to allow for a feature
filter to be passed in.

Our default implementation allows for any number of additional
arguments and will pass them on to any invocation of
get_SeqFeatures(), wherever a component of the tree implements
FeatureHolderI. I.e., in order to support filter arguments, just
support them in get_SeqFeatures().

=cut

sub get_all_SeqFeatures{
    my $self = shift;
    my @flatarr;

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

    # needed to deal with subfeatures which appear more than once in the hierarchy [SG]
    my %seen = ();
    my @uniq_flatarr = ();
    foreach my $feat (@flatarr) {
	push(@uniq_flatarr, $feat) unless $seen{$feat}++;
    }
    return @uniq_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);
    }

}

sub set_ParentIDs_from_hierarchy(){
    # DEPRECATED - use IDHandler
    my $self = shift;
    require "Bio/SeqFeature/Tools/IDHandler.pm";
    Bio::SeqFeature::Tools::IDHandler->new->set_ParentIDs_from_hierarchy($self);
}

sub create_hierarchy_from_ParentIDs(){
    # DEPRECATED - use IDHandler
    my $self = shift;
    require "Bio/SeqFeature/Tools/IDHandler.pm";
    Bio::SeqFeature::Tools::IDHandler->new->create_hierarchy_from_ParentIDs($self);
}



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