Bio/Location/NarrowestCoordPolicy.pm

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