Bio::FeatureHolderI(3pm) User Contributed Perl Documentation Bio::FeatureHolderI(3pm)
NAME
Bio::FeatureHolderI - the base interface an object with features must implement
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.
FEEDBACK
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
Support
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 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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
CONTRIBUTORS
Steffen Grossmann [SG], grossman-at-molgen.mpg.de Mark A. Jensen, maj -at- fortinbras -dot- us
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
add_SeqFeature()
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($subfeat,'EXPAND')
Function: adds 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, the parent''s start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature
Example :
Returns : nothing
Args : a Bio::SeqFeatureI object
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
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().
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().
perl v5.14.2 2012-03-02 Bio::FeatureHolderI(3pm)