Raw content of Bio::FeatureHolderI # $Id: FeatureHolderI.pm,v 1.2 2002/11/19 07:04:22 lapp Exp $ # # BioPerl module for Bio::FeatureHolderI # # Cared for by Hilmar Lapp <hlapp at gmx.net> # # Copyright Hilmar Lapp # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::FeatureHolderI - the base interface an object with features must implement =head1 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 } } =head1 DESCRIPTION This is the base interface that all feature-holding objects must implement. Popular feature-holders are for instance L<Bio::Seq> objects. Since L<Bio::SeqFeatureI> defines a sub_SeqFeature() method, most Bio::SeqFeatureI implementations like L<Bio::SeqFeature::Generic> will implement the feature holder interface as well. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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/ =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::FeatureHolderI; use vars qw(@ISA); use strict; use Carp; use Bio::Root::RootI; @ISA = qw( Bio::Root::RootI ); =head2 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. =cut sub get_SeqFeatures{ shift->throw_not_implemented(); } =head2 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(). =cut sub feature_count { return scalar(shift->get_SeqFeatures(@_)); } =head2 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(). =cut sub get_all_SeqFeatures{ my $self = shift; my @flatarr; foreach my $feat ( $self->get_SeqFeatures(@_) ){ push(@flatarr,$feat); &_add_flattened_SeqFeatures(\@flatarr,$feat,@_); } return @flatarr; } sub _add_flattened_SeqFeatures { my ($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); } } 1;