Bio/Search/BlastStatistics.pm

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