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

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Location::NarrowestCoordPolicy
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   8 #          and Jason Stajich <jason@bioperl.org>
   9 #
  10 # Copyright Hilmar Lapp, Jason Stajich
  11 #
  12 # You may distribute this module under the same terms as perl itself
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Location::NarrowestCoordPolicy - class implementing
  18 Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
  19
  20 =head1 SYNOPSIS
  21
  22 See Bio::Location::CoordinatePolicyI
  23
  24 =head1 DESCRIPTION
  25
  26 CoordinatePolicyI implementing objects are used by Bio::LocationI
  27 implementing objects to determine integer-valued coordinates when
  28 asked for it.
  29
  30 This class will compute the coordinates such that always the narrowest possible
  31 range is returned, but by using some common sense. This means that e.g.
  32 locations like "E<gt>5..100" (start before position 5) will return 5 as start
  33 (returned values have to be positive integers).
  34
  35 =head1 FEEDBACK
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to one
  39 of the Bioperl mailing lists.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Support
  45
  46 Please direct usage questions or support issues to the mailing list:
  47
  48 I<bioperl-l@bioperl.org>
  49
  50 rather than to the module maintainer directly. Many experienced and
  51 reponsive experts will be able look at the problem and quickly
  52 address it. Please include a thorough description of the problem
  53 with code and data examples if at all possible.
  54
  55 =head2 Reporting Bugs
  56
  57 Report bugs to the Bioperl bug tracking system to help us keep track
  58 the bugs and their resolution.  Bug reports can be submitted via the
  59 web:
  60
  61   http://bugzilla.open-bio.org/
  62
  63 =head1 AUTHOR - Hilmar Lapp, Jason Stajich
  64
  65 Email E<lt>hlapp-at-gmx.netE<gt>, E<lt>jason@bioperl.orgE<gt>
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object
  70 methods. Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::Location::NarrowestCoordPolicy;
  78 use strict;
  79
  80
  81 use base qw(Bio::Root::Root Bio::Location::CoordinatePolicyI);
  82
  83 sub new {
  84     my ($class, @args) = @_;
  85     my $self = $class->SUPER::new(@args);
  86
  87     return $self;
  88 }
  89
  90
  91 =head2 start
  92
  93   Title   : start
  94   Usage   : $start = $policy->start($location);
  95   Function: Get the integer-valued start coordinate of the given location as
  96             computed by this computation policy.
  97   Returns : A positive integer number.
  98   Args    : A Bio::LocationI implementing object.
  99
 100 =cut
 101
 102 sub start {
 103     my ($self,$loc) = @_;
 104
 105     # For performance reasons we don't check that it's indeed a Bio::LocationI
 106     # object. Hopefully, Location-object programmers are smart enough.
 107     my $pos = $loc->max_start();
 108     # if max is not defined or equals 0 we resort to min
 109     $pos = $loc->min_start() if(! $pos);
 110     return $pos;
 111 }
 112
 113 =head2 end
 114
 115   Title   : end
 116   Usage   : $end = $policy->end($location);
 117   Function: Get the integer-valued end coordinate of the given location as
 118             computed by this computation policy.
 119   Returns : A positive integer number.
 120   Args    : A Bio::LocationI implementing object.
 121
 122 =cut
 123
 124 sub end {
 125     my ($self,$loc) = @_;
 126
 127     # For performance reasons we don't check that it's indeed a Bio::LocationI
 128     # object. Hopefully, Location-object programmers are smart enough.
 129     my $pos = $loc->min_end();
 130     # if min is not defined or equals 0 we resort to max
 131     $pos = $loc->max_end() if(! $pos);
 132     return $pos;
 133 }
 134
 135 1;
 136