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 = $bs->get_kappa();
  27
  28
  29 =head1 DESCRIPTION
  30
  31 This is a basic container to hold the statistics returned from a Blast.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Support
  45
  46 Please direct usage questions or support issues to the mailing list:
  47
  48 I<bioperl-l@bioperl.org>
  49
  50 rather than to the module maintainer directly. Many experienced and
  51 reponsive experts will be able look at the problem and quickly
  52 address it. Please include a thorough description of the problem
  53 with code and data examples if at all possible.
  54
  55 =head2 Reporting Bugs
  56
  57 Report bugs to the Bioperl bug tracking system to help us keep track
  58 of the bugs and their resolution. Bug reports can be submitted via the
  59 web:
  60
  61   https://github.com/bioperl/bioperl-live/issues
  62
  63 =head1 AUTHOR - Chad Matsalla
  64
  65 Email bioinformatics1 at dieselwurks dot com
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::Search::BlastStatistics;
  79
  80 use strict;
  81
  82 # Object preamble - inherits from Bio::Root::Root
  83
  84
  85 use base qw(Bio::Root::RootI Bio::Search::StatisticsI);
  86
  87
  88
  89
  90
  91 sub new {
  92     my ($class, @args) = @_;
  93           # really, don't bother with any initial initialization
  94     my $self = $class->SUPER::new(@args);
  95     return $self;
  96 }
  97
  98
  99 =head2 get_statistic
 100
 101  Title   : get_statistic
 102  Usage   : $statistic_object->get_statistic($statistic_name);
 103  Function: Get the value of a statistic named $statistic_name
 104  Returns : A scalar that should be a string
 105  Args    : A scalar that should be a string
 106
 107 =cut
 108
 109 sub get_statistic {
 110    my ($self,$arg) = @_;
 111      return $self->{$arg};
 112 }
 113
 114
 115 =head2 set_statistic
 116
 117  Title   : set_statistic
 118  Usage   : $statistic_object->set_statistic($statistic_name => $statistic_value);
 119  Function: Set the value of a statistic named $statistic_name to $statistic_value
 120  Returns : Void
 121  Args    : A hash containing name=>value pairs
 122
 123 =cut
 124
 125 sub set_statistic {
 126    my ($self,%args) = @_;
 127      foreach (keys %args) {
 128           $self->{$_} = $args{$_};
 129      }
 130 }
 131
 132
 133
 134 1;