Bio/Search/Result/hmmer3Result.pm

   1 # $Id: bioperl.lisp 15559 2009-02-23 12:11:20Z maj $
   2 #
   3 # BioPerl module for Bio::Search::Result::hmmer3Result
   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::Result::hmmer3Result - 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::Result::hmmer3Result;
  79 use strict;
  80
  81 use base qw(Bio::Search::Result::GenericResult);
  82
  83 =head2 new
  84
  85  Title   : new
  86  Usage   : my $obj = new Bio::Search::Result::hmmer3Result.pm();
  87  Function: Builds a new Bio::Search::Result::hmmer3Result.pm object
  88  Returns : an instance of Bio::Search::Result::hmmer3Result.pm
  89  Args    : -hmm_name => string, name of hmm file
  90            -sequence_file => name of the sequence file
  91
  92 =cut
  93
  94 sub new {
  95   my($class,@args) = @_;
  96   my $self = $class->SUPER::new(@args);
  97
  98   my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
  99                                          @args);
 100   defined( $seqfile ) && $self->sequence_file( $seqfile );
 101   defined( $hmm ) && $self->hmm_name( $hmm );
 102
 103   return $self;
 104 }
 105
 106 =head2 hmm_name
 107
 108  Title   : hmm_name
 109  Usage   : $obj->hmm_name($newval)
 110  Function: Get/Set the value of hmm_name
 111  Returns : value of hmm_name
 112  Args    : newvalue (optional)
 113
 114
 115 =cut
 116
 117 sub hmm_name{
 118    my ($self,$value) = @_;
 119    if( defined $value) {
 120       $self->{'_hmm_name'} = $value;
 121     }
 122     return $self->{'_hmm_name'};
 123 }
 124
 125 =head2 sequence_file
 126
 127  Title   : sequence_file
 128  Usage   : $obj->sequence_file($newval)
 129  Function: Get/Set the value of sequence_file
 130  Returns : value of sequence_file
 131  Args    : newvalue (optional)
 132
 133
 134 =cut
 135
 136 sub sequence_file{
 137    my ($self,$value) = @_;
 138    if( defined $value) {
 139       $self->{'_sequence_file'} = $value;
 140     }
 141     return $self->{'_sequence_file'};
 142
 143 }
 144
 145 =head2 next_model
 146
 147  Title   : next_model
 148  Usage   : my $domain = $result->next_model
 149  Function: Returns the next domain - this
 150            is an alias for next_hit
 151  Returns : L<Bio::Search::Hit::HitI> object
 152  Args    : none
 153
 154
 155 =cut
 156
 157 sub next_model{ shift->next_hit }
 158
 159 =head2 models
 160
 161  Title   : models
 162  Usage   : my @domains = $result->models;
 163  Function: Returns the list of HMM models seen - this
 164            is an alias for hits()
 165  Returns : Array of L<Bio::Search::Hit::HitI> objects
 166  Args    : none
 167
 168
 169 =cut
 170
 171 sub models{ shift->hits }
 172
 173 =head2 rewind
 174
 175  Title   : rewind
 176  Usage   : $result->rewind;
 177  Function: Allow one to reset the Hit iteration to the beginning
 178            Since this is an in-memory implementation
 179  Returns : none
 180  Args    : none
 181
 182 =cut
 183
 184 sub rewind{
 185    my ($self) = @_;
 186    $self->{'_hitindex'} = 0;
 187 }
 188
 189
 190
 191 1;