diff variant_effect_predictor/Bio/FeatureHolderI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/FeatureHolderI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,194 @@
+# $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.
+
+  [e-mail]              - 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:
+
+  [e-mail]
+  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;