lib/Bio/SeqFeature/Gene/NC_Feature.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Gene::NC_Feature.pm
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
   7 #
   8 # Copyright David Block
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqFeature::Gene::NC_Feature.pm - superclass for non-coding features
  17
  18 =head1 SYNOPSIS
  19
  20 Give standard usage here
  21
  22 =head1 DESCRIPTION
  23
  24 Describe the object here
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to
  32 the Bioperl mailing list.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Support
  38
  39 Please direct usage questions or support issues to the mailing list:
  40
  41 I<bioperl-l@bioperl.org>
  42
  43 rather than to the module maintainer directly. Many experienced and
  44 reponsive experts will be able look at the problem and quickly
  45 address it. Please include a thorough description of the problem
  46 with code and data examples if at all possible.
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 of the bugs and their resolution. Bug reports can be submitted via the
  52 web:
  53
  54   https://github.com/bioperl/bioperl-live/issues
  55
  56 =head1 AUTHOR - David Block
  57
  58 Email dblock@gnf.org
  59
  60 =head1 APPENDIX
  61
  62 The rest of the documentation details each of the object methods.
  63 Internal methods are usually preceded with a _
  64
  65 =cut
  66
  67
  68 # Let the code begin...
  69
  70 package Bio::SeqFeature::Gene::NC_Feature;
  71 use strict;
  72
  73 # Object preamble - inherits from Bio::Root::Root
  74
  75
  76 use base qw(Bio::SeqFeature::Generic);
  77
  78 sub new {
  79     my($class,@args) = @_;
  80
  81     my $self = $class->SUPER::new(@args);
  82
  83     my ($is_coding) =
  84         $self->_rearrange([qw(IS_CODING)],@args);
  85     # default is non-coding
  86     $self->is_coding(defined($is_coding) ? $is_coding : 0);
  87
  88     return $self;
  89 }
  90
  91
  92
  93 =head2 is_coding
  94
  95  Title   : is_coding
  96  Usage   : if ($feature->is_coding()) {
  97                      #do something
  98             }
  99  Function: Whether or not the feature codes for amino acid.
 100  Returns : FALSE
 101  Args    : none
 102
 103 =cut
 104
 105 sub is_coding{
 106     my $self = shift;
 107
 108     return $self->{'is_coding'} = shift if @_;
 109     return $self->{'is_coding'};
 110 }
 111
 112 =head2 cds
 113
 114  Title   : cds
 115  Usage   : $cds=$feature->cds();
 116  Function: get the coding sequence of this feature
 117  Returns : undef
 118  Args    : none
 119
 120
 121 =cut
 122
 123 sub cds {
 124    my ($self,@args) = @_;
 125    return;
 126
 127 }
 128
 129
 130 1;