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1 # $Id: AvWithinCoordPolicy.pm,v 1.4 2002/12/01 00:05:20 jason Exp $
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2 #
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3 # BioPerl module for Bio::Location::AvWithinCoordPolicy
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4 #
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5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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6 # and Jason Stajich <jason@bioperl.org>
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7 #
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8 # Copyright Hilmar Lapp, Jason Stajich
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9 #
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10 # You may distribute this module under the same terms as perl itself
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Location::AvWithinCoordPolicy - class implementing
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16 Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
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17
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18 =head1 SYNOPSIS
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19
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20 See Bio::Location::CoordinatePolicyI
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21
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22 =head1 DESCRIPTION
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23
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24 CoordinatePolicyI implementing objects are used by Bio::LocationI
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25 implementing objects to determine integer-valued coordinates when
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26 asked for it.
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27
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28 This class will compute the coordinates such that for fuzzy locations
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29 of type WITHIN and BETWEEN the average of the two limits will be
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30 returned, and for all other locations it will return the widest
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31 possible range, but by using some common sense. This means that
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32 e.g. locations like "E<lt>5..100" (start before position 5) will return 5
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33 as start (returned values have to be positive integers).
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34
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35 =head1 FEEDBACK
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36
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37 User feedback is an integral part of the evolution of this and other
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38 Bioperl modules. Send your comments and suggestions preferably to one
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39 of the Bioperl mailing lists. Your participation is much appreciated.
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40
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41 bioperl-l@bioperl.org - General discussion
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42 http://bio.perl.org/MailList.html - About the mailing lists
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43
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44 =head2 Reporting Bugs
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45
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46 Report bugs to the Bioperl bug tracking system to help us keep track
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47 the bugs and their resolution. Bug reports can be submitted via email
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48 or the web:
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49
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50 bioperl-bugs@bio.perl.org
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51 http://bugzilla.bioperl.org/
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52
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53 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
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54
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55 Email E<lt>hlapp@gmx.netE<gt>, E<lt>jason@bioperl.orgE<gt>
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56
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57 =head1 APPENDIX
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58
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59 The rest of the documentation details each of the object
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60 methods. Internal methods are usually preceded with a _
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61
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62 =cut
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63
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64 # Let the code begin...
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65
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66
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67 package Bio::Location::AvWithinCoordPolicy;
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68 use vars qw(@ISA);
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69 use strict;
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70
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71 use Bio::Location::WidestCoordPolicy;
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72
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73 @ISA = qw(Bio::Location::WidestCoordPolicy);
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74
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75 sub new {
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76 my ($class, @args) = @_;
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77 my $self = $class->SUPER::new(@args);
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78
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79 return $self;
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80 }
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81
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82
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83
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84 =head2 start
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85
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86 Title : start
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87 Usage : $start = $policy->start($location);
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88 Function: Get the integer-valued start coordinate of the given location as
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89 computed by this computation policy.
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90 Returns : A positive integer number.
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91 Args : A Bio::LocationI implementing object.
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92
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93 =cut
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94
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95 sub start {
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96 my ($self,$loc) = @_;
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97
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98 if(($loc->start_pos_type() eq 'WITHIN') ||
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99 ($loc->start_pos_type() eq 'BETWEEN')) {
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100 my ($min, $max) = ($loc->min_start(), $loc->max_start());
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101 return int(($min+$max)/2) if($min && $max);
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102 }
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103 return $self->SUPER::start($loc);
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104 }
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105
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106 =head2 end
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107
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108 Title : end
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109 Usage : $end = $policy->end($location);
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110 Function: Get the integer-valued end coordinate of the given location as
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111 computed by this computation policy.
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112 Returns : A positive integer number.
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113 Args : A Bio::LocationI implementing object.
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114
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115 =cut
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116
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117 sub end {
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118 my ($self,$loc) = @_;
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119
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120 if(($loc->end_pos_type() eq 'WITHIN') ||
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121 ($loc->end_pos_type() eq 'BETWEEN')) {
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122 my ($min, $max) = ($loc->min_end(), $loc->max_end());
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123 return int(($min+$max)/2) if($min && $max);
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124 }
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125 return $self->SUPER::end($loc);
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126 }
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127
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128 1;
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129
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