Bio/Search/Hit/hmmer3Hit.pm

   1 # $Id: bioperl.lisp 15559 2009-02-23 12:11:20Z maj $
   2 #
   3 # BioPerl module for Bio::Search::Hit::hmmer3Hit
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Thomas Sharpton <thomas.sharpton@gmail.com>
   8 #
   9 # Copyright Thomas Sharpton
  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::Hit::hmmer3Hit - DESCRIPTION of Object
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Describe the object here
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 L<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 of the bugs and their resolution. Bug reports can be submitted via
  53 the web:
  54
  55   https://github.com/bioperl/bioperl-live/issues
  56
  57 =head1 AUTHOR - Thomas Sharpton
  58
  59 Email thomas.sharpton@gmail.com
  60
  61 Describe contact details here
  62
  63 =head1 CONTRIBUTORS
  64
  65 Additional contributors names and emails here
  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::Hit::hmmer3Hit;
  79 use strict;
  80
  81
  82 use base qw(Bio::Search::Hit::GenericHit);
  83
  84 =head2 new
  85
  86  Title   : new
  87  Usage   : my $obj = Bio::Search::Hit::HMMERHit->new();
  88  Function: Builds a new Bio::Search::Hit::HMMERHit object
  89  Returns : Bio::Search::Hit::HMMERHit
  90  Args    :
  91
  92  Plus the Bio::Search::Hit::GenericHit inherited params
  93            -name         => Name of Hit (required)
  94            -description  => Description (optional)
  95            -accession    => Accession number (optional)
  96            -length       => Length of the Hit (optional)
  97            -score        => Raw Score for the Hit (optional)
  98            -significance => Significance value for the Hit (optional)
  99            -algorithm    => Algorithm used (BLASTP, FASTX, etc...)
 100            -hsps         => Array ref of HSPs for this Hit.
 101
 102
 103 =cut
 104
 105
 106 =head2 next_domain
 107
 108  Title   : next_domain
 109  Usage   : my $domain = $hit->next_domain();
 110  Function: An alias for L<next_hsp()>, this will return the next HSP
 111  Returns : L<Bio::Search::HSP::HSPI> object
 112  Args    : none
 113
 114
 115 =cut
 116
 117 sub next_domain{ shift->next_hsp }
 118
 119 =head2 domains
 120
 121  Title   : domains
 122  Usage   : my @domains = $hit->domains();
 123  Function: An alias for L<hsps()>, this will return the full list of hsps
 124  Returns : array of L<Bio::Search::HSP::HSPI> objects
 125  Args    : none
 126
 127
 128 =cut
 129
 130 sub domains{ shift->hsps() }
 131
 132 =head2 bits
 133
 134  Usage     : $hit_object->bits();
 135  Purpose   : Gets the bit score of the best HSP for the current hit.
 136  Example   : $bits = $hit_object->bits();
 137  Returns   : Integer or undef if bit score is not set
 138  Argument  : n/a
 139
 140 See Also   : L<score()|score>
 141
 142 =cut
 143
 144 sub bits { return 0 }
 145
 146 =head2 iteration
 147
 148  Title   : iteration
 149  Usage   : $obj->iteration($newval)
 150  Function: PSI-BLAST iteration
 151  Returns : value of iteration
 152  Args    : newvalue (optional)
 153
 154
 155 =cut
 156
 157 sub iteration { return 0 }
 158
 159 1;