Bio/Search/Result/INFERNALResult.pm

   1 #
   2 # BioPerl module for Bio::Search::Result::INFERNALResult.pm
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Paul Cantalupo
   7 #
   8 # Copyright Paul Cantalupo
   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::Search::Result::INFERNALResult - A Result object for INFERNAL results
  17
  18 =head1 SYNOPSIS
  19
  20     # typically one gets Results from a SearchIO stream
  21     use Bio::SearchIO;
  22     my $io = Bio::SearchIO->new(-format => 'infernal',
  23                                 -file   => 't/data/cmsearch_output.txt');
  24     while( my $result = $io->next_result ) {
  25         while( my $hit = $result->next_hit ) {
  26           print join(" ", $result->query_name, $result->algorithm, $result->num_hits), "\n";
  27         }
  28     }
  29
  30 =head1 DESCRIPTION
  31
  32 This object is a specialization of L<Bio::Search::Result::GenericResult>. There
  33 is one extra method called L<cm_name>.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 of the bugs and their resolution. Bug reports can be submitted via the
  61 web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Paul Cantalupo
  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::Search::Result::INFERNALResult;
  77 use strict;
  78 use warnings;
  79
  80 use base qw(Bio::Search::Result::GenericResult);
  81
  82 =head2 new
  83
  84  Title   : new
  85  Usage   : my $obj = Bio::Search::Result::INFERNALResult->new();
  86  Function: Builds a new Bio::Search::Result::INFERNALResult object
  87  Returns : Bio::Search::Result::INFERNALResult
  88  Args    : -cm_name    => string, name of covariance model (CM) file.
  89            plus Bio::Search::Result::GenericResult parameters
  90
  91 =cut
  92
  93 sub new {
  94   my ($class, @args) = @_;
  95   my $self = $class->SUPER::new(@args);
  96
  97   my ($cm) = $self->_rearrange([qw(CM_NAME)], @args);
  98   if (defined $cm) { $self->cm_name($cm) }
  99
 100   return $self;
 101 }
 102
 103 =head2 cm_name
 104
 105  Title   : cm_name
 106  Usage   : $obj->cm_name($newvalue)
 107  Function: Get/Set value of the covariance model file name (cm_name)
 108  Returns : value of cm_name
 109  Args    : newvalue (optional)
 110
 111 =cut
 112
 113 sub cm_name {
 114   my ($self, $value) = @_;
 115   if (defined $value) {
 116     $self->{'_cm_name'} = $value;
 117   }
 118   return $self->{'_cm_name'};
 119 }
 120
 121 1;