Bio/Tools/HMMER/Set.pm

   1 #
   2 # BioPerl module for Bio::Tools::HMMER::Set
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@sanger.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   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::Tools::HMMER::Set - Set of identical domains from HMMER matches
  17
  18 =head1 SYNOPSIS
  19
  20     # get a Set object probably from the results object
  21     print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";
  22
  23     foreach $domain ( $set->each_Domain ) {
  24         print "Domain start ",$domain->start," end ",$domain->end,"\n";
  25     }
  26
  27 =head1 DESCRIPTION
  28
  29 Represents a set of HMMER domains hitting one sequence. HMMER reports two
  30 different scores, a per sequence total score (and evalue) and a per
  31 domain score and evalue. This object represents a collection of the same
  32 domain with the sequence bits score and evalue. (these attributes are also
  33 on the per domain scores, which you can get there).
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to one
  41 of the Bioperl mailing lists.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.Bug reports can be submitted via the
  61 web:
  62
  63  https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Ewan Birney
  66
  67 Email birney-at-ebi.ac.uk
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object
  72 methods. Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79
  80 package Bio::Tools::HMMER::Set;
  81 use strict;
  82
  83 use Bio::Tools::HMMER::Domain;
  84
  85 use base qw(Bio::Root::Root);
  86
  87 sub new {
  88     my($class,@args) = @_;
  89     my $self = $class->SUPER::new(@args);
  90     my ($name,$acc,$desc) = $self->_rearrange([qw(NAME ACCESSION DESC)],
  91                                               @args);
  92     $name && $self->name($name);
  93     $acc  && $self->accession($acc);
  94     $desc && $self->desc($desc);
  95
  96
  97     $self->{'domains'} = [];
  98     $self->{'domainnames'} = {};
  99     return $self;
 100 }
 101
 102 =head2 add_Domain
 103
 104  Title   : add_Domain
 105  Usage   : $set->add_Domain($domain)
 106  Function: adds the domain to the list
 107  Returns : nothing
 108  Args    : A Bio::Tools::HMMER::Domain object
 109
 110 =cut
 111
 112 sub add_Domain{
 113    my ($self,$domain) = @_;
 114
 115
 116    if( ! defined $domain || ! $domain->isa("Bio::Tools::HMMER::Domain") ) {
 117        $self->throw("[$domain] is not a Bio::Tools::HMMER::Domain. aborting");
 118    }
 119    return if $self->{'domainnames'}->{$domain->get_nse}++;
 120    push(@{$self->{'domains'}},$domain);
 121
 122 }
 123
 124 =head2 each_Domain
 125
 126  Title   : each_Domain
 127  Usage   : foreach $domain ( $set->each_Domain() )
 128  Function: returns an array of domain objects in this set
 129  Returns : array
 130  Args    : none
 131
 132
 133 =cut
 134
 135 sub each_Domain{
 136    my ($self,@args) = @_;
 137
 138    return @{$self->{'domains'}};
 139 }
 140
 141 =head2 name
 142
 143  Title   : name
 144  Usage   : $obj->name($newval)
 145  Function:
 146  Example :
 147  Returns : value of name
 148  Args    : newvalue (optional)
 149
 150
 151 =cut
 152
 153 sub name{
 154    my ($obj,$value) = @_;
 155    if( defined $value) {
 156       $obj->{'name'} = $value;
 157     }
 158     return $obj->{'name'};
 159
 160 }
 161
 162 =head2 desc
 163
 164  Title   : desc
 165  Usage   : $obj->desc($newval)
 166  Function:
 167  Example :
 168  Returns : value of desc
 169  Args    : newvalue (optional)
 170
 171 =cut
 172
 173 sub desc{
 174    my ($self,$value) = @_;
 175    if( defined $value) {
 176       $self->{'desc'} = $value;
 177     }
 178     return $self->{'desc'};
 179
 180 }
 181
 182 =head2 accession
 183
 184  Title   : accession
 185  Usage   : $obj->accession($newval)
 186  Function:
 187  Example :
 188  Returns : value of accession
 189  Args    : newvalue (optional)
 190
 191
 192 =cut
 193
 194 sub accession{
 195    my ($self,$value) = @_;
 196    if( defined $value) {
 197       $self->{'accession'} = $value;
 198     }
 199     return $self->{'accession'};
 200 }
 201
 202
 203 =head2 bits
 204
 205  Title   : bits
 206  Usage   : $obj->bits($newval)
 207  Function:
 208  Example :
 209  Returns : value of bits
 210  Args    : newvalue (optional)
 211
 212
 213 =cut
 214
 215 sub bits{
 216    my ($obj,$value) = @_;
 217
 218    if( defined $value) {
 219       $obj->{'bits'} = $value;
 220     }
 221     return $obj->{'bits'};
 222
 223 }
 224
 225 =head2 evalue
 226
 227  Title   : evalue
 228  Usage   : $obj->evalue($newval)
 229  Function:
 230  Example :
 231  Returns : value of evalue
 232  Args    : newvalue (optional)
 233
 234
 235 =cut
 236
 237 sub evalue{
 238    my ($obj,$value) = @_;
 239    if( defined $value) {
 240       $obj->{'evalue'} = $value;
 241     }
 242     return $obj->{'evalue'};
 243
 244 }
 245
 246
 247 sub addHMMUnit {
 248     my $self = shift;
 249     my $unit = shift;
 250
 251     $self->warn("Using old addHMMUnit call on Bio::Tools::HMMER::Set. Should replace with add_Domain");
 252     return $self->add_Domain($unit);
 253 }
 254
 255 sub eachHMMUnit {
 256     my $self = shift;
 257     $self->warn("Using old eachHMMUnit call on Bio::Tools::HMMER::Set. Should replace with each_Domain");
 258     return $self->each_Domain();
 259 }
 260
 261 1;  # says use was ok
 262 __END__
 263