Bio FeatureHolderI
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Summary
Bio::FeatureHolderI - the base interface an object with features must implement
Package variables
No package variables defined.
Included modules
Carp
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
get_SeqFeaturesDescriptionCode
add_SeqFeatureDescriptionCode
remove_SeqFeaturesDescriptionCode
feature_countDescriptionCode
get_all_SeqFeaturesDescriptionCode
_add_flattened_SeqFeatures
No description
Code
set_ParentIDs_from_hierarchy()
No description
Code
create_hierarchy_from_ParentIDs()
No description
Code
Methods description
get_SeqFeatures()code    nextTop
 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)
add_SeqFeature()codeprevnextTop
 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
remove_SeqFeatures()codeprevnextTop
 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
feature_countcodeprevnextTop
 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().
get_all_SeqFeaturescodeprevnextTop
 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().
Methods code
get_SeqFeaturesdescriptionprevnextTop
sub get_SeqFeatures {
  shift->throw_not_implemented();
}
add_SeqFeaturedescriptionprevnextTop
sub add_SeqFeature {
  shift->throw_not_implemented();
}
remove_SeqFeaturesdescriptionprevnextTop
sub remove_SeqFeatures {
  shift->throw_not_implemented();
}
feature_countdescriptionprevnextTop
sub feature_count {
    return scalar(shift->get_SeqFeatures(@_));
}
get_all_SeqFeaturesdescriptionprevnextTop
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;
}
_add_flattened_SeqFeaturesdescriptionprevnextTop
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);
    }
}
set_ParentIDs_from_hierarchy()descriptionprevnextTop
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);
}
create_hierarchy_from_ParentIDs()descriptionprevnextTop
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); } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
CONTRIBUTORSTop
Steffen Grossmann [SG], grossman-at-molgen.mpg.de
Mark A. Jensen, maj -at- fortinbras -dot- us
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _