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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Location/AvWithinCoordPolicy.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: AvWithinCoordPolicy.pm,v 1.4 2002/12/01 00:05:20 jason Exp $
+#
+# BioPerl module for Bio::Location::AvWithinCoordPolicy
+#
+# 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::AvWithinCoordPolicy - class implementing 
+Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
+
+=head1 SYNOPSIS
+
+See Bio::Location::CoordinatePolicyI
+
+=head1 DESCRIPTION
+
+CoordinatePolicyI implementing objects are used by Bio::LocationI
+implementing objects to determine integer-valued coordinates when
+asked for it.
+
+This class will compute the coordinates such that for fuzzy locations
+of type WITHIN and BETWEEN the average of the two limits will be
+returned, and for all other locations it will return the widest
+possible range, but by using some common sense. This means that
+e.g. locations like "E<lt>5..100" (start before position 5) will return 5
+as start (returned values have to be positive integers).
+
+=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<lt>[e-mail]<gt>, E<lt>[e-mail]<gt>
+
+=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::AvWithinCoordPolicy;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Location::WidestCoordPolicy;
+
+@ISA = qw(Bio::Location::WidestCoordPolicy);
+
+sub new { 
+    my ($class, @args) = @_;
+    my $self = $class->SUPER::new(@args);
+
+    return $self;
+}
+
+
+
+=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 ($self,$loc) = @_;
+
+    if(($loc->start_pos_type() eq 'WITHIN') ||
+       ($loc->start_pos_type() eq 'BETWEEN')) {
+	my ($min, $max) = ($loc->min_start(), $loc->max_start());
+	return int(($min+$max)/2) if($min && $max);
+    }
+    return $self->SUPER::start($loc);
+}
+
+=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 ($self,$loc) = @_;
+
+    if(($loc->end_pos_type() eq 'WITHIN') ||
+       ($loc->end_pos_type() eq 'BETWEEN')) {
+	my ($min, $max) = ($loc->min_end(), $loc->max_end());
+	return int(($min+$max)/2) if($min && $max);
+    }
+    return $self->SUPER::end($loc);
+}
+
+1;
+