Bio/Search/HSP/hmmer3HSP.pm

   1 #
   2 # BioPerl module for Bio::Search::HSP::hmmer3HSP
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Thomas Sharpton <thomas.sharpton@gmail.com>
   7 #
   8 # Copyright Thomas Sharpton
   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::HSP::hmmer3HSP - DESCRIPTION of Object
  17
  18 =head1 SYNOPSIS
  19
  20 Give standard usage here
  21
  22 =head1 DESCRIPTION
  23
  24 Describe the object here
  25
  26 =head1 FEEDBACK
  27
  28 =head2 Mailing Lists
  29
  30 User feedback is an integral part of the evolution of this and other
  31 Bioperl modules. Send your comments and suggestions preferably to
  32 the Bioperl mailing list.  Your participation is much appreciated.
  33
  34   bioperl-l@bioperl.org                  - General discussion
  35   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  36
  37 =head2 Support
  38
  39 Please direct usage questions or support issues to the mailing list:
  40
  41 L<bioperl-l@bioperl.org>
  42
  43 rather than to the module maintainer directly. Many experienced and
  44 reponsive experts will be able look at the problem and quickly
  45 address it. Please include a thorough description of the problem
  46 with code and data examples if at all possible.
  47
  48 =head2 Reporting Bugs
  49
  50 Report bugs to the Bioperl bug tracking system to help us keep track
  51 of the bugs and their resolution. Bug reports can be submitted via
  52 the web:
  53
  54   https://redmine.open-bio.org/projects/bioperl/
  55
  56 =head1 AUTHOR - Thomas Sharpton
  57
  58 Email thomas.sharpton@gmail.com
  59
  60 Describe contact details here
  61
  62 =head1 CONTRIBUTORS
  63
  64 Additional contributors names and emails here
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::Search::HSP::hmmer3HSP;
  78 use strict;
  79
  80 use base qw(Bio::Search::HSP::GenericHSP);
  81
  82 =head2 new
  83
  84  Title   : new
  85  Usage   : my $obj = new Bio::Search::HSP::hmmer3HSP();
  86  Function: Builds a new Bio::Search::HSP::hmmer3HSP object
  87  Returns : an instance of Bio::Search::HSP::hmmer3HSP
  88  Args    :
  89
  90 =cut
  91
  92 sub new {
  93   my($class,@args) = @_;
  94
  95   my $self = $class->SUPER::new(@args);
  96   return $self;
  97 }
  98
  99 =head2 get_aln
 100
 101  Title   : get_aln
 102  Usage   : my $aln = $hsp->gel_aln
 103  Function: Returns a Bio::SimpleAlign representing the HSP alignment
 104  Returns : Bio::SimpleAlign
 105  Args    : none
 106
 107 =cut
 108
 109 sub get_aln {
 110     my ($self) = shift;
 111     $self->warn("Inappropriate to build a Bio::SimpleAlign from a HMMER HSP object");
 112     return;
 113 }
 114
 115 1;