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

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Location::CoordinatePolicyI
   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::CoordinatePolicyI - Abstract interface for objects implementing
  17 a certain policy of computing integer-valued coordinates of a Location
  18
  19 =head1 SYNOPSIS
  20
  21     # get a location, e.g., from a SeqFeature
  22     $location = $feature->location();
  23     # examine its coordinate computation policy
  24     print "Location of feature ", $feature->primary_tag(), " employs a ",
  25           ref($location->coordinate_policy()),
  26           " instance for coordinate computation\n";
  27     # change the policy, e.g. because the user chose to do so
  28     $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
  29
  30 =head1 DESCRIPTION
  31
  32 Objects implementing this interface are used by Bio::LocationI
  33 implementing objects to determine integer-valued coordinates when
  34 asked for it. While this may seem trivial for simple locations, there
  35 are different ways to do it for fuzzy or compound (split)
  36 locations. Classes implementing this interface implement a certain
  37 policy, like 'always widest range', 'always smallest range', 'mean for
  38 BETWEEN locations', etc. By installing a different policy object in a
  39 Location object, the behaviour of coordinate computation can be changed
  40 on-the-fly, and with a single line of code client-side.
  41
  42 =head1 FEEDBACK
  43
  44 User feedback is an integral part of the evolution of this and other
  45 Bioperl modules. Send your comments and suggestions preferably to one
  46 of the Bioperl mailing lists.  Your participation is much appreciated.
  47
  48   bioperl-l@bioperl.org                  - General discussion
  49   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  50
  51 =head2 Support
  52
  53 Please direct usage questions or support issues to the mailing list:
  54
  55 I<bioperl-l@bioperl.org>
  56
  57 rather than to the module maintainer directly. Many experienced and
  58 reponsive experts will be able look at the problem and quickly
  59 address it. Please include a thorough description of the problem
  60 with code and data examples if at all possible.
  61
  62 =head2 Reporting Bugs
  63
  64 Report bugs to the Bioperl bug tracking system to help us keep track
  65 the bugs and their resolution.  Bug reports can be submitted via the
  66 web:
  67
  68   http://bugzilla.open-bio.org/
  69
  70 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  71
  72 Email hlapp@gmx.net, jason@bioperl.org
  73
  74 =head1 APPENDIX
  75
  76 The rest of the documentation details each of the object
  77 methods. Internal methods are usually preceded with a _
  78
  79 =cut
  80
  81 # Let the code begin...
  82
  83
  84 package Bio::Location::CoordinatePolicyI;
  85 use strict;
  86
  87 use base qw(Bio::Root::RootI);
  88
  89 =head2 start
  90
  91   Title   : start
  92   Usage   : $start = $policy->start($location);
  93   Function: Get the integer-valued start coordinate of the given location as
  94             computed by this computation policy.
  95   Returns : A positive integer number.
  96   Args    : A Bio::LocationI implementing object.
  97
  98 =cut
  99
 100 sub start {
 101     my ($self) = @_;
 102     $self->throw_not_implemented();
 103 }
 104
 105 =head2 end
 106
 107   Title   : end
 108   Usage   : $end = $policy->end($location);
 109   Function: Get the integer-valued end coordinate of the given location as
 110             computed by this computation policy.
 111   Returns : A positive integer number.
 112   Args    : A Bio::LocationI implementing object.
 113
 114 =cut
 115
 116 sub end {
 117     my ($self) = @_;
 118     $self->throw_not_implemented();
 119 }
 120
 121 1;