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

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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 email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Email hlapp at gmx.net Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_SeqFeatures
Title : get_SeqFeatures Usage : Function: Get the feature objects held by this feature holder. 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.

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().