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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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
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().
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
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().
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.