/usr/share/perl5/Bio/Search/BlastStatistics.pm is in libbio-perl-perl 1.6.924-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 | #
#
# BioPerl module for wrapping Blast statistics
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chad Matsalla (bioinformatics1 at dieselwurks dot com)
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::BlastStatistics - An object for Blast statistics
=head1 SYNOPSIS
# this is a wrapper to hold the statistics from a Blast report
my $bs = $result->get_statistics();
# you can get a statistic generically, like this:
my $kappa = $bs->get_statistic("kappa");
# or specifically, like this:
my $kappa2 = $bs->get_kappa();
=head1 DESCRIPTION
This is a basic container to hold the statistics returned from a Blast.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Chad Matsalla
Email bioinformatics1 at dieselwurks dot com
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::BlastStatistics;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::RootI Bio::Search::StatisticsI);
sub new {
my ($class, @args) = @_;
# really, don't bother with any initial initialization
my $self = $class->SUPER::new(@args);
return $self;
}
=head2 get_statistic
Title : get_statistic
Usage : $statistic_object->get_statistic($statistic_name);
Function: Get the value of a statistic named $statistic_name
Returns : A scalar that should be a string
Args : A scalar that should be a string
=cut
sub get_statistic {
my ($self,$arg) = @_;
return $self->{$arg};
}
=head2 set_statistic
Title : set_statistic
Usage : $statistic_object->set_statistic($statistic_name => $statistic_value);
Function: Set the value of a statistic named $statistic_name to $statistic_value
Returns : Void
Args : A hash containing name=>value pairs
=cut
sub set_statistic {
my ($self,%args) = @_;
foreach (keys %args) {
$self->{$_} = $args{$_};
}
}
1;
|