lib/Bio/Location/AvWithinCoordPolicy.pm

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