diff variant_effect_predictor/Bio/SeqFeature/CollectionI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/CollectionI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,144 @@
+# $Id: CollectionI.pm,v 1.2 2002/10/22 07:45:20 lapp Exp $
+#
+# BioPerl module for Bio::SeqFeature::CollectionI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects. 
+
+=head1 SYNOPSIS
+
+
+# get a Bio::SeqFeature::CollectionI somehow
+# perhaps a Bio::SeqFeature::Collection
+
+
+    use Bio::SeqFeature::Collection;
+    my $collection = new Bio::SeqFeature::Collection;
+    $collection->add_features(\@featurelist);
+
+
+    $collection->features(-attributes => 
+			  [ { 'location' => new Bio::Location::Simple
+				  (-start=> 1, -end => 300) ,
+				  'overlaps' }]);
+
+=head1 DESCRIPTION
+
+This interface describes the basic methods needed for a collection of Sequence Features.  
+
+=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://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+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::SeqFeature::CollectionI;
+use vars qw(@ISA);
+use strict;
+use Carp;
+use Bio::Root::RootI;
+
+@ISA = qw( Bio::Root::RootI );
+
+
+=head2 add_features
+
+ Title   : add_features
+ Usage   : $collection->add_features(\@features);
+ Function:
+ Returns : number of features added
+ Args    : arrayref of Bio::SeqFeatureI objects to index
+
+=cut
+
+sub add_features{
+    shift->throw_not_implemented();
+}
+
+
+=head2 features
+
+ Title   : features
+ Usage   : my @f = $collection->features(@args);
+ Returns : a list of Bio::SeqFeatureI objects
+ Args    : see below
+ Status  : public
+
+This routine will retrieve features associated with this collection
+object.  It can be used to return all features, or a subset based on
+their type, location, or attributes.
+
+  -types     List of feature types to return.  Argument is an array
+             of Bio::Das::FeatureTypeI objects or a set of strings
+             that can be converted into FeatureTypeI objects.
+
+  -callback   A callback to invoke on each feature.  The subroutine
+              will be passed to each Bio::SeqFeatureI object in turn.
+
+  -attributes A hash reference containing attributes to match.
+
+The -attributes argument is a hashref containing one or more attributes
+to match against:
+
+  -attributes => { Gene => 'abc-1',
+                   Note => 'confirmed' }
+
+Attribute matching is simple exact string matching, and multiple
+attributes are ANDed together.  See L<Bio::DB::ConstraintsI> for a
+more sophisticated take on this.
+
+If one provides a callback, it will be invoked on each feature in
+turn.  If the callback returns a false value, iteration will be
+interrupted.  When a callback is provided, the method returns undef.
+
+=cut
+
+sub features{
+    shift->throw_not_implemented();
+}
+
+1;