branch-1-6/Bio/Tools/HMMER/Set.pm

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