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1 # $Id: NarrowestCoordPolicy.pm,v 1.7 2002/12/01 00:05:20 jason Exp $
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2 #
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3 # BioPerl module for Bio::Location::NarrowestCoordPolicy
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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::NarrowestCoordPolicy - class implementing
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16 Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
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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 always the narrowest possible
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29 range is returned, but by using some common sense. This means that e.g.
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30 locations like "E<gt>5..100" (start before position 5) will return 5 as start
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31 (returned values have to be positive integers).
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32
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33 =head1 FEEDBACK
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to one
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37 of the Bioperl mailing lists. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bio.perl.org/MailList.html - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 the bugs and their resolution. Bug reports can be submitted via email
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46 or the web:
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47
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48 bioperl-bugs@bio.perl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
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52
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53 Email hlapp@gmx.net, jason@bioperl.org
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54
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55 =head1 APPENDIX
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56
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57 The rest of the documentation details each of the object
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58 methods. Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62 # Let the code begin...
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63
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64
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65 package Bio::Location::NarrowestCoordPolicy;
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66 use vars qw(@ISA);
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67 use strict;
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68
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69 use Bio::Root::Root;
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70 use Bio::Location::CoordinatePolicyI;
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71
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72 @ISA = qw(Bio::Root::Root Bio::Location::CoordinatePolicyI);
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73
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74 sub new {
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75 my ($class, @args) = @_;
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76 my $self = $class->SUPER::new(@args);
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77
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78 return $self;
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79 }
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80
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81
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82
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83 =head2 start
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84
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85 Title : start
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86 Usage : $start = $policy->start($location);
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87 Function: Get the integer-valued start coordinate of the given location as
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88 computed by this computation policy.
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89 Returns : A positive integer number.
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90 Args : A Bio::LocationI implementing object.
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91
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92 =cut
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93
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94 sub start {
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95 my ($self,$loc) = @_;
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96
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97 # For performance reasons we don't check that it's indeed a Bio::LocationI
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98 # object. Hopefully, Location-object programmers are smart enough.
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99 my $pos = $loc->max_start();
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100 # if max is not defined or equals 0 we resort to min
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101 $pos = $loc->min_start() if(! $pos);
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102 return $pos;
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103 }
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104
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105 =head2 end
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106
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107 Title : end
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108 Usage : $end = $policy->end($location);
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109 Function: Get the integer-valued end coordinate of the given location as
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110 computed by this computation policy.
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111 Returns : A positive integer number.
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112 Args : A Bio::LocationI implementing object.
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113
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114 =cut
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115
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116 sub end {
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117 my ($self,$loc) = @_;
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118
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119 # For performance reasons we don't check that it's indeed a Bio::LocationI
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120 # object. Hopefully, Location-object programmers are smart enough.
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121 my $pos = $loc->min_end();
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122 # if min is not defined or equals 0 we resort to max
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123 $pos = $loc->max_end() if(! $pos);
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124 return $pos;
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125 }
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126
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127 1;
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128
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