diff variant_effect_predictor/Bio/Location/CoordinatePolicyI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Location/CoordinatePolicyI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: CoordinatePolicyI.pm,v 1.4 2002/10/22 07:38:34 lapp Exp $
+#
+# BioPerl module for Bio::Location::CoordinatePolicyI
+# Cared for by Hilmar Lapp <[e-mail]>
+#          and Jason Stajich <[e-mail]>
+#
+# Copyright Hilmar Lapp, Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing
+a certain policy of computing integer-valued coordinates of a Location
+
+=head1 SYNOPSIS
+
+    # get a location, e.g., from a SeqFeature
+    $location = $feature->location();
+    # examine its coordinate computation policy
+    print "Location of feature ", $feature->primary_tag(), " employs a ",
+          ref($location->coordinate_policy()), 
+          " instance for coordinate computation\n";
+    # change the policy, e.g. because the user chose to do so
+    $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
+
+=head1 DESCRIPTION
+
+Objects implementing this interface are used by Bio::LocationI
+implementing objects to determine integer-valued coordinates when
+asked for it. While this may seem trivial for simple locations, there
+are different ways to do it for fuzzy or compound (split)
+locations. Classes implementing this interface implement a certain
+policy, like 'always widest range', 'always smallest range', 'mean for
+BETWEEN locations', etc. By installing a different policy object in a
+Location object, the behaviour of coordinate computation can be changed
+on-the-fly, and with a single line of code client-side.
+
+=head1 FEEDBACK
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]             - General discussion
+  http://bio.perl.org/MailList.html - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp, Jason Stajich
+
+Email [e-mail], [e-mail]
+
+=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::Location::CoordinatePolicyI;
+use vars qw(@ISA);
+use strict;
+use Bio::Root::RootI;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 start
+
+  Title   : start
+  Usage   : $start = $policy->start($location);
+  Function: Get the integer-valued start coordinate of the given location as
+            computed by this computation policy.
+  Returns : A positive integer number.
+  Args    : A Bio::LocationI implementing object.
+
+=cut
+
+sub start {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 end
+
+  Title   : end
+  Usage   : $end = $policy->end($location);
+  Function: Get the integer-valued end coordinate of the given location as
+            computed by this computation policy.
+  Returns : A positive integer number.
+  Args    : A Bio::LocationI implementing object.
+
+=cut
+
+sub end {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+1;