Bio/Tools/Run/GenericParameters.pm

   1 #
   2 # BioPerl module for wrapping runtime parameters
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com)
   7 #
   8 # Copyright Chad Matsalla
   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::Tools::Run::GenericParameters - An object for the parameters used to run programs
  17
  18 =head1 SYNOPSIS
  19
  20   my $void   = $obj->set_parameter("parameter_name","parameter_value");
  21   my $value  = $obj->get_parameter("parameter_name");
  22
  23 =head1 DESCRIPTION
  24
  25 This is a basic container to hold the parameters used to run a
  26 program.  This module may get incorporated into the more generic
  27 Bio::Tools::Run framework in bioperl-run distribution.
  28
  29 =head1 FEEDBACK
  30
  31 =head2 Mailing Lists
  32
  33 User feedback is an integral part of the evolution of this and other
  34 Bioperl modules. Send your comments and suggestions preferably to
  35 the Bioperl mailing list.  Your participation is much appreciated.
  36
  37   bioperl-l@bioperl.org                  - General discussion
  38   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  39
  40 =head2 Support
  41
  42 Please direct usage questions or support issues to the mailing list:
  43
  44 I<bioperl-l@bioperl.org>
  45
  46 rather than to the module maintainer directly. Many experienced and
  47 reponsive experts will be able look at the problem and quickly
  48 address it. Please include a thorough description of the problem
  49 with code and data examples if at all possible.
  50
  51 =head2 Reporting Bugs
  52
  53 Report bugs to the Bioperl bug tracking system to help us keep track
  54 of the bugs and their resolution. Bug reports can be submitted via the
  55 web:
  56
  57   https://github.com/bioperl/bioperl-live/issues
  58
  59 =head1 AUTHOR - Chad Matsalla
  60
  61 Email bioinformatics1 at dieselwurks dot com
  62
  63 =head1 CONTRIBUTORS
  64
  65 Sendu Bala, bix@sendu.me.uk
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74 # Let the code begin...
  75
  76 package Bio::Tools::Run::GenericParameters;
  77 use strict;
  78
  79 use base qw(Bio::Root::Root Bio::Tools::Run::ParametersI);
  80
  81 sub new {
  82     my ($class, @args) = @_;
  83     my $self = $class->SUPER::new(@args);
  84     return $self;
  85 }
  86
  87 =head2 get_parameter
  88
  89  Title   : get_parameter
  90  Usage   : $parameter_object->get_parameter($param_name);
  91  Function: Get the value of a parameter named $param_name
  92  Returns : A scalar that should be a string
  93  Args    : A scalar that should be a string
  94
  95 =cut
  96
  97 sub get_parameter {
  98     my ($self,$arg) = @_;
  99     return $self->{params}->{$arg};
 100 }
 101
 102 =head2 set_parameter
 103
 104  Title   : set_parameter
 105  Usage   : $parameter_object->set_parameter($param_name => $param_value);
 106  Function: Set the value of a parameter named $param_name to $param_value
 107  Returns : Void
 108  Args    : A hash containing name=>value pairs
 109
 110 =cut
 111
 112 sub set_parameter {
 113     my ($self,$name,$value) = @_;
 114     $self->{params}->{$name} = $value;
 115 }
 116
 117 =head2 available_parameters
 118
 119  Title   : available_parameters
 120  Usage   : my @paramnames = $parameter_object->available_parameters
 121  Function: Returns the names of the available parameters
 122  Returns : list of available parameter names
 123  Args    : none
 124
 125 =cut
 126
 127 sub available_parameters {
 128     my $self = shift;
 129     return keys %{$self->{params}};
 130 }
 131
 132 1;