Bio::FeatureHolderI

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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://github.com/bioperl/bioperl-live/issues

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: 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()

 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().