lib/Bio/Location/CoordinatePolicyI.pm

   1 #
   2 # BioPerl module for Bio::Location::CoordinatePolicyI
   3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   4 #
   5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   6 #          and Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Hilmar Lapp, Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing
  16 a certain policy of computing integer-valued coordinates of a Location
  17
  18 =head1 SYNOPSIS
  19
  20     # get a location, e.g., from a SeqFeature
  21     $location = $feature->location();
  22     # examine its coordinate computation policy
  23     print "Location of feature ", $feature->primary_tag(), " employs a ",
  24           ref($location->coordinate_policy()),
  25           " instance for coordinate computation\n";
  26     # change the policy, e.g. because the user chose to do so
  27     $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
  28
  29 =head1 DESCRIPTION
  30
  31 Objects implementing this interface are used by Bio::LocationI
  32 implementing objects to determine integer-valued coordinates when
  33 asked for it. While this may seem trivial for simple locations, there
  34 are different ways to do it for fuzzy or compound (split)
  35 locations. Classes implementing this interface implement a certain
  36 policy, like 'always widest range', 'always smallest range', 'mean for
  37 BETWEEN locations', etc. By installing a different policy object in a
  38 Location object, the behaviour of coordinate computation can be changed
  39 on-the-fly, and with a single line of code client-side.
  40
  41 =head1 FEEDBACK
  42
  43 User feedback is an integral part of the evolution of this and other
  44 Bioperl modules. Send your comments and suggestions preferably to one
  45 of the Bioperl mailing lists.  Your participation is much appreciated.
  46
  47   bioperl-l@bioperl.org                  - General discussion
  48   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  49
  50 =head2 Support
  51
  52 Please direct usage questions or support issues to the mailing list:
  53
  54 I<bioperl-l@bioperl.org>
  55
  56 rather than to the module maintainer directly. Many experienced and
  57 reponsive experts will be able look at the problem and quickly
  58 address it. Please include a thorough description of the problem
  59 with code and data examples if at all possible.
  60
  61 =head2 Reporting Bugs
  62
  63 Report bugs to the Bioperl bug tracking system to help us keep track
  64 the bugs and their resolution.  Bug reports can be submitted via the
  65 web:
  66
  67   https://github.com/bioperl/bioperl-live/issues
  68
  69 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  70
  71 Email hlapp@gmx.net, jason@bioperl.org
  72
  73 =head1 APPENDIX
  74
  75 The rest of the documentation details each of the object
  76 methods. Internal methods are usually preceded with a _
  77
  78 =cut
  79
  80 # Let the code begin...
  81
  82
  83 package Bio::Location::CoordinatePolicyI;
  84 use strict;
  85
  86 use base qw(Bio::Root::RootI);
  87
  88 =head2 start
  89
  90   Title   : start
  91   Usage   : $start = $policy->start($location);
  92   Function: Get the integer-valued start coordinate of the given location as
  93             computed by this computation policy.
  94   Returns : A positive integer number.
  95   Args    : A Bio::LocationI implementing object.
  96
  97 =cut
  98
  99 sub start {
 100     my ($self) = @_;
 101     $self->throw_not_implemented();
 102 }
 103
 104 =head2 end
 105
 106   Title   : end
 107   Usage   : $end = $policy->end($location);
 108   Function: Get the integer-valued end coordinate of the given location as
 109             computed by this computation policy.
 110   Returns : A positive integer number.
 111   Args    : A Bio::LocationI implementing object.
 112
 113 =cut
 114
 115 sub end {
 116     my ($self) = @_;
 117     $self->throw_not_implemented();
 118 }
 119
 120 1;