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1 # $Id: CoordinatePolicyI.pm,v 1.4 2002/10/22 07:38:34 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Location::CoordinatePolicyI
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4 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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5 # and Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Hilmar Lapp, Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10 # POD documentation - main docs before the code
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11
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12 =head1 NAME
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13
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14 Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing
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15 a certain policy of computing integer-valued coordinates of a Location
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16
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17 =head1 SYNOPSIS
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18
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19 # get a location, e.g., from a SeqFeature
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20 $location = $feature->location();
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21 # examine its coordinate computation policy
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22 print "Location of feature ", $feature->primary_tag(), " employs a ",
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23 ref($location->coordinate_policy()),
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24 " instance for coordinate computation\n";
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25 # change the policy, e.g. because the user chose to do so
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26 $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
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27
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28 =head1 DESCRIPTION
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29
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30 Objects implementing this interface are used by Bio::LocationI
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31 implementing objects to determine integer-valued coordinates when
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32 asked for it. While this may seem trivial for simple locations, there
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33 are different ways to do it for fuzzy or compound (split)
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34 locations. Classes implementing this interface implement a certain
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35 policy, like 'always widest range', 'always smallest range', 'mean for
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36 BETWEEN locations', etc. By installing a different policy object in a
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37 Location object, the behaviour of coordinate computation can be changed
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38 on-the-fly, and with a single line of code client-side.
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39
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40 =head1 FEEDBACK
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41
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42 User feedback is an integral part of the evolution of this and other
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43 Bioperl modules. Send your comments and suggestions preferably to one
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44 of the Bioperl mailing lists. Your participation is much appreciated.
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45
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46 bioperl-l@bioperl.org - General discussion
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47 http://bio.perl.org/MailList.html - About the mailing lists
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48
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49 =head2 Reporting Bugs
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50
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51 Report bugs to the Bioperl bug tracking system to help us keep track
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52 the bugs and their resolution. Bug reports can be submitted via email
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53 or the web:
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54
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55 bioperl-bugs@bio.perl.org
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56 http://bugzilla.bioperl.org/
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57
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58 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
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59
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60 Email hlapp@gmx.net, jason@bioperl.org
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61
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62 =head1 APPENDIX
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63
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64 The rest of the documentation details each of the object
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65 methods. Internal methods are usually preceded with a _
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66
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67 =cut
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::Location::CoordinatePolicyI;
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73 use vars qw(@ISA);
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74 use strict;
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75 use Bio::Root::RootI;
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76
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77 @ISA = qw(Bio::Root::RootI);
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78
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79 =head2 start
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80
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81 Title : start
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82 Usage : $start = $policy->start($location);
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83 Function: Get the integer-valued start coordinate of the given location as
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84 computed by this computation policy.
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85 Returns : A positive integer number.
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86 Args : A Bio::LocationI implementing object.
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87
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88 =cut
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89
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90 sub start {
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91 my ($self) = @_;
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92 $self->throw_not_implemented();
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93 }
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94
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95 =head2 end
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96
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97 Title : end
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98 Usage : $end = $policy->end($location);
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99 Function: Get the integer-valued end coordinate of the given location as
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100 computed by this computation policy.
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101 Returns : A positive integer number.
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102 Args : A Bio::LocationI implementing object.
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103
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104 =cut
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105
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106 sub end {
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107 my ($self) = @_;
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108 $self->throw_not_implemented();
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109 }
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110
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111 1;
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