Bio/Expression/FeatureGroup.pm

   1 # $Id$
   2 # BioPerl module for Bio::Expression::FeatureGroup
   3 #
   4 # Copyright Allen Day <allenday@ucla.edu>, Stanley Nelson <snelson@ucla.edu>
   5 # Human Genetics, UCLA Medical School, University of California, Los Angeles
   6
   7 # POD documentation - main docs before the code
   8
   9 =head1 NAME
  10
  11 Bio::Expression::FeatureGroup - a set of DNA/RNA features.  ISA
  12 Bio::Expression::FeatureI
  13
  14 =head1 SYNOPSIS
  15
  16 #
  17
  18 =head1 DESCRIPTION
  19
  20 A set of DNA/RNA features.
  21
  22 =head1 FEEDBACK
  23
  24 =head2 Mailing Lists
  25
  26 User feedback is an integral part of the evolution of this and other
  27 Bioperl modules. Send your comments and suggestions preferably to one
  28 of the Bioperl mailing lists.  Your participation is much appreciated.
  29
  30   bioperl-l@bioperl.org                  - General discussion
  31   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  32
  33 =head2 Reporting Bugs
  34
  35 Report bugs to the Bioperl bug tracking system to help us keep track
  36 the bugs and their resolution.  Bug reports can be submitted via the
  37 web:
  38
  39   http://bugzilla.open-bio.org/
  40
  41 =head1 AUTHOR
  42
  43 Allen Day E<lt>allenday@ucla.eduE<gt>
  44
  45 =head1 APPENDIX
  46
  47 The rest of the documentation details each of the object
  48 methods. Internal methods are usually preceded with a _
  49
  50 =cut
  51
  52 # Let the code begin...
  53 package Bio::Expression::FeatureGroup;
  54
  55 use strict;
  56
  57 use base qw(Bio::Root::Root Bio::Expression::FeatureI);
  58 use vars qw($DEBUG);
  59
  60 =head2 new
  61
  62  Title   : new
  63  Usage   : $featuregroup = Bio::Expression::FeatureGroup->new(%args);
  64  Function: create a new featuregroup object
  65  Returns : a Bio::Expression::FeatureGroup object
  66  Args    : an optional hash of parameters to be used in initialization:
  67            -id    --  the featuregroup ID
  68            -type  --  the featuregroup type
  69
  70 =cut
  71
  72 sub new {
  73   my($class,@args) = @_;
  74   my $self = bless {}, $class;
  75   $self->_initialize(@args);
  76   return $self;
  77 }
  78
  79 =head2 _initialize
  80
  81  Title   : _initialize
  82  Usage   : $featuregroup->_initialize(@args);
  83  Function: initialize the featuregroup object
  84  Returns : nothing
  85  Args    : @args
  86
  87 =cut
  88
  89 sub _initialize{
  90   my ($self,@args) = @_;
  91   my %param = @args;
  92
  93   $self->type($param{-type});
  94   $self->id($param{-id}    );
  95
  96   $self->SUPER::_initialize(@args);
  97   $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
  98 }
  99
 100 =head2 type
 101
 102  Title   : type
 103  Usage   : $featuregroup->type($optional_arg);
 104  Function: get/set the type of the featuregroup
 105  Comments: this is probably going to be a string like
 106            "quality control", "mismatch blah blah", etc.
 107  Returns : the featuregroup type
 108  Args    : a new value for the featuregroup type
 109
 110 =cut
 111
 112 sub type {
 113   my $self = shift;
 114   $self->{type} = shift if @_;
 115   return $self->{type};
 116 }
 117
 118 =head2 id
 119
 120  Title   : id
 121  Usage   : $featuregroup->id($optional_arg);
 122  Function: get/set the id of the featuregroup
 123  Returns : the featuregroup id
 124  Args    : a new value for the featuregroup id
 125
 126 =cut
 127
 128 sub id {
 129   my $self = shift;
 130   $self->{id} = shift if @_;
 131   return $self->{id};
 132 }
 133
 134
 135 =head2 standard_deviation
 136
 137  Title   : standard_deviation
 138  Usage   : $featuregroup->standard_deviation($optional_arg);
 139  Function: get/set the standard deviation of the featuregroup value
 140  Returns : the featuregroup standard deviation
 141  Args    : a new value for the featuregroup standard deviation
 142  Notes   : this method does no calculation, it merely holds a value
 143
 144 =cut
 145
 146 sub standard_deviation {
 147   my $self = shift;
 148   $self->{standard_deviation} = shift if @_;
 149   return $self->{standard_deviation};
 150 }
 151
 152 =head2 quantitation
 153
 154  Title   : quantitation
 155  Usage   : $featuregroup->quantitation($optional_arg);
 156  Function: get/set the quantitation of the featuregroup
 157  Returns : the featuregroup's quantitated value
 158  Args    : a new value for the featuregroup's quantitated value
 159  Notes   : this method does no calculation, it merely holds a value
 160
 161 =cut
 162
 163 sub quantitation {
 164   my $self = shift;
 165   $self->{quantitation} = shift if @_;
 166   return $self->{quantitation};
 167 }
 168
 169 =head2 quantitation_units
 170
 171  Title   : quantitation_units
 172  Usage   : $featuregroup->quantitation_units($optional_arg);
 173  Function: get/set the quantitation units of the featuregroup
 174  Returns : the featuregroup's quantitated value units
 175  Args    : a new value for the featuregroup's quantitated value units
 176
 177 =cut
 178
 179 sub quantitation_units {
 180   my $self = shift;
 181   $self->{quantitation_units} = shift if @_;
 182   return $self->{quantitation_units};
 183 }
 184
 185 =head2 presence
 186
 187  Title   : presence
 188  Usage   : $featuregroup->presence($optional_arg);
 189  Function: get/set the presence call of the featuregroup
 190  Returns : the featuregroup's presence call
 191  Args    : a new value for the featuregroup's presence call
 192
 193 =cut
 194
 195 sub presence {
 196   my $self = shift;
 197   $self->{presence} = shift if @_;
 198   return $self->{presence};
 199 }
 200
 201 =head2 add_feature
 202
 203  Title   : add_feature
 204  Usage   : $feature_copy = $featuregroup->add_feature($feature);
 205  Function: add a feature to the featuregroup
 206  Returns : see this_feature()
 207  Args    : a Bio::Expression::FeatureI compliant object
 208
 209 =cut
 210
 211 sub add_feature {
 212   my($self,@args) = @_;
 213   foreach my $feature (@args){
 214         $self->throw('Features must be Bio::Expression::FeatureI compliant') unless $feature->isa('Bio::Expression::FeatureI');
 215     push @{$self->{features}}, $feature;
 216   }
 217
 218   return $self->{features} ? $self->{features}->[-1] : undef;
 219 }
 220
 221 =head2 this_feature
 222
 223  Title   : this_feature
 224  Usage   : $feature = $featuregroup->this_feature
 225  Function: access the last feature added to the featuregroup
 226  Returns : the last feature added to the featuregroup
 227  Args    : none
 228
 229 =cut
 230
 231 sub this_feature {
 232   my $self = shift;
 233   return $self->{features} ? $self->{features}->[-1] : undef;
 234 }
 235
 236 =head2 each_feature
 237
 238  Title   : each_feature
 239  Usage   : @features = $featuregroup->each_feature
 240  Function: returns a list of Bio::Expression::FeatureI compliant
 241            objects
 242  Returns : a list of objects
 243  Args    : none
 244
 245 =cut
 246
 247 sub each_feature {
 248   my $self = shift;
 249   return @{$self->{features}} if defined($self->{features});
 250   return ();
 251 }
 252
 253 =head2 each_feature_quantitation
 254
 255  Title   : each_feature_quantitation
 256  Usage   : @featurequantitions = $featuregroup->each_feature_quantitation;
 257  Function: returns an list of quantitations of the features in the featuregroup
 258  Returns : a list of numeric values
 259  Args    : none
 260
 261 =cut
 262
 263 sub each_feature_quantitation {
 264   my $self = shift;
 265   my @values = ();
 266   push @values, $_->value foreach $self->each_feature;
 267   return @values;
 268 }
 269
 270 =head2 is_qc
 271
 272  Title   : is_qc
 273  Usage   : $is_quality_control = $featuregroup->is_qc
 274  Function: get/set whether or not the featuregroup is used for quality control purposes
 275  Returns : a boolean (equivalent)
 276  Args    : a new value
 277
 278 =cut
 279
 280 sub is_qc {
 281   my $self = shift;
 282   $self->{is_qc} = shift if defined @_;
 283   return $self->{is_qc};
 284 }
 285
 286 1;