branch-1-6/Bio/Location/AvWithinCoordPolicy.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Location::AvWithinCoordPolicy
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   8 #          and Jason Stajich <jason@bioperl.org>
   9 #
  10 # Copyright Hilmar Lapp, Jason Stajich
  11 #
  12 # You may distribute this module under the same terms as perl itself
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Location::AvWithinCoordPolicy - class implementing
  18 Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
  19
  20 =head1 SYNOPSIS
  21
  22 See Bio::Location::CoordinatePolicyI
  23
  24 =head1 DESCRIPTION
  25
  26 CoordinatePolicyI implementing objects are used by Bio::LocationI
  27 implementing objects to determine integer-valued coordinates when
  28 asked for it.
  29
  30 This class will compute the coordinates such that for fuzzy locations
  31 of type WITHIN and BETWEEN the average of the two limits will be
  32 returned, and for all other locations it will return the widest
  33 possible range, but by using some common sense. This means that
  34 e.g. locations like "E<lt>5..100" (start before position 5) will return 5
  35 as start (returned values have to be positive integers).
  36
  37 =head1 FEEDBACK
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to one
  41 of the Bioperl mailing lists.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.  Bug reports can be submitted via the
  61 web:
  62
  63   http://bugzilla.open-bio.org/
  64
  65 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  66
  67 Email E<lt>hlapp-at-gmx-dot-netE<gt>, E<lt>jason-at-bioperl-dot-orgE<gt>
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object
  72 methods. Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76 # Let the code begin...
  77
  78
  79 package Bio::Location::AvWithinCoordPolicy;
  80 use strict;
  81
  82
  83 use base qw(Bio::Location::WidestCoordPolicy);
  84
  85 sub new {
  86     my ($class, @args) = @_;
  87     my $self = $class->SUPER::new(@args);
  88
  89     return $self;
  90 }
  91
  92
  93
  94 =head2 start
  95
  96   Title   : start
  97   Usage   : $start = $policy->start($location);
  98   Function: Get the integer-valued start coordinate of the given location as
  99             computed by this computation policy.
 100   Returns : A positive integer number.
 101   Args    : A Bio::LocationI implementing object.
 102
 103 =cut
 104
 105 sub start {
 106     my ($self,$loc) = @_;
 107
 108     if(($loc->start_pos_type() eq 'WITHIN') ||
 109        ($loc->start_pos_type() eq 'BETWEEN')) {
 110         my ($min, $max) = ($loc->min_start(), $loc->max_start());
 111         return int(($min+$max)/2) if($min && $max);
 112     }
 113     return $self->SUPER::start($loc);
 114 }
 115
 116 =head2 end
 117
 118   Title   : end
 119   Usage   : $end = $policy->end($location);
 120   Function: Get the integer-valued end coordinate of the given location as
 121             computed by this computation policy.
 122   Returns : A positive integer number.
 123   Args    : A Bio::LocationI implementing object.
 124
 125 =cut
 126
 127 sub end {
 128     my ($self,$loc) = @_;
 129
 130     if(($loc->end_pos_type() eq 'WITHIN') ||
 131        ($loc->end_pos_type() eq 'BETWEEN')) {
 132         my ($min, $max) = ($loc->min_end(), $loc->max_end());
 133         return int(($min+$max)/2) if($min && $max);
 134     }
 135     return $self->SUPER::end($loc);
 136 }
 137
 138 1;
 139