Bio/Expression/FeatureI.pm

   1 # $Id$
   2 # BioPerl module for Bio::Expression::FeatureI
   3 #
   4 # Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
   5 # Human Genetics, UCLA Medical School, University of California, Los Angeles
   6
   7 # POD documentation - main docs before the code
   8
   9 =head1 NAME
  10
  11 Bio::Expression::FeatureI - an interface class for DNA/RNA features
  12
  13 =head1 SYNOPSIS
  14
  15 Do not use this module directly
  16
  17 =head1 DESCRIPTION
  18
  19 This provides a standard bioperl interface class for representing
  20 DNA and RNA features.  It cannot be instantiated directly, but serves
  21 as an abstract base class for implementors.
  22
  23 =head1 FEEDBACK
  24
  25 =head2 Mailing Lists
  26
  27 User feedback is an integral part of the evolution of this and other
  28 Bioperl modules. Send your comments and suggestions preferably to one
  29 of the Bioperl mailing lists.  Your participation is much appreciated.
  30
  31   bioperl-l@bioperl.org                  - General discussion
  32   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  33
  34 =head2 Reporting Bugs
  35
  36 Report bugs to the Bioperl bug tracking system to help us keep track
  37 the bugs and their resolution.  Bug reports can be submitted via the
  38 web:
  39
  40   http://bugzilla.open-bio.org/
  41
  42 =head1 AUTHOR
  43
  44 Allen Day E<lt>allenday@ucla.eduE<gt>
  45
  46 =head1 APPENDIX
  47
  48 The rest of the documentation details each of the object
  49 methods. Internal methods are usually preceded with a _
  50
  51 =cut
  52
  53 # Let the code begin...
  54 package Bio::Expression::FeatureI;
  55
  56 use strict;
  57 use Bio::Root::RootI;
  58
  59 use base qw(Bio::Root::RootI Bio::PrimarySeqI);
  60 use vars qw($DEBUG);
  61
  62 =head2 quantitation()
  63
  64   Title   : value
  65   Usage   : $val = $ftr->quantitation()
  66   Function: get/set the feature's quantitation
  67   Returns : A numeric value
  68   Args    : a new numeric value (optional)
  69
  70 =cut
  71
  72 sub quantitation {
  73   shift->throw_not_implemented();
  74 }
  75
  76 =head2 quantitation_units()
  77
  78   Title   : quantitation_units
  79   Usage   : $units = $ftr->quantitation_units()
  80   Function: get/set the units of the feature's quantitation
  81   Returns : A string or undef
  82   Args    : a new string (optional)
  83
  84 =cut
  85
  86 sub quantitation_units {
  87   shift->throw_not_implemented();
  88 }
  89
  90 =head2 standard_deviation()
  91
  92   Title   : standard_deviation
  93   Usage   : $std_dev = $ftr->standard_deviation()
  94   Function: get/set the feature's standard deviation of quantitation()
  95   Returns : A numeric value
  96   Args    : a new numeric value (optional)
  97   Comments: no calculation is done here
  98
  99 =cut
 100
 101 sub standard_deviation {
 102   shift->throw_not_implemented();
 103 }
 104
 105 =head2 sample_count()
 106
 107   Title   : sample_count
 108   Usage   : $sample_count = $ftr->sample_count()
 109   Function: get/set the number of samples used to calculate
 110             quantitation()
 111   Returns : An integer
 112   Args    : a new integer (optional)
 113
 114 =cut
 115
 116 sub sample_count {
 117   shift->throw_not_implemented();
 118 }
 119
 120 1;