lib/Bio/Search/BlastStatistics.pm

   1 #
   2 #
   3 # BioPerl module for wrapping Blast statistics
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com)
   8 #
   9 # Copyright Chad Matsalla
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Search::BlastStatistics - An object for Blast statistics
  18
  19 =head1 SYNOPSIS
  20
  21           # this is a wrapper to hold the statistics from a Blast report
  22      my $bs = $result->get_statistics();
  23           # you can get a statistic generically, like this:
  24      my $kappa  = $bs->get_statistic("kappa");
  25           # or specifically, like this:
  26      my $kappa2 = $bs->get_kappa();
  27
  28
  29 =head1 DESCRIPTION
  30
  31 This is a basic container to hold the statistics returned from a Blast.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Support
  45
  46 Please direct usage questions or support issues to the mailing list:
  47
  48 I<bioperl-l@bioperl.org>
  49
  50 rather than to the module maintainer directly. Many experienced and
  51 reponsive experts will be able look at the problem and quickly
  52 address it. Please include a thorough description of the problem
  53 with code and data examples if at all possible.
  54
  55 =head2 Reporting Bugs
  56
  57 Report bugs to the Bioperl bug tracking system to help us keep track
  58 of the bugs and their resolution. Bug reports can be submitted via the
  59 web:
  60
  61   https://github.com/bioperl/bioperl-live/issues
  62
  63 =head1 AUTHOR - Chad Matsalla
  64
  65 Email bioinformatics1 at dieselwurks dot com
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::Search::BlastStatistics;
  79 use strict;
  80
  81 # Object preamble - inherits from Bio::Root::Root
  82
  83
  84 use base qw(Bio::Root::RootI Bio::Search::StatisticsI);
  85
  86
  87
  88
  89
  90 sub new {
  91     my ($class, @args) = @_;
  92           # really, don't bother with any initial initialization
  93     my $self = $class->SUPER::new(@args);
  94     return $self;
  95 }
  96
  97
  98 =head2 get_statistic
  99
 100  Title   : get_statistic
 101  Usage   : $statistic_object->get_statistic($statistic_name);
 102  Function: Get the value of a statistic named $statistic_name
 103  Returns : A scalar that should be a string
 104  Args    : A scalar that should be a string
 105
 106 =cut
 107
 108 sub get_statistic {
 109    my ($self,$arg) = @_;
 110      return $self->{$arg};
 111 }
 112
 113
 114 =head2 set_statistic
 115
 116  Title   : set_statistic
 117  Usage   : $statistic_object->set_statistic($statistic_name => $statistic_value);
 118  Function: Set the value of a statistic named $statistic_name to $statistic_value
 119  Returns : Void
 120  Args    : A hash containing name=>value pairs
 121
 122 =cut
 123
 124 sub set_statistic {
 125    my ($self,%args) = @_;
 126      foreach (keys %args) {
 127           $self->{$_} = $args{$_};
 128      }
 129 }
 130
 131
 132
 133 1;