Raw content of Bio::Expression::FeatureGroup
<![CDATA[# $Id: FeatureGroup.pm,v 1.1.2.2 2003/09/17 09:19:21 allenday Exp $
# BioPerl module for Bio::Expression::FeatureGroup
#
# Copyright Allen Day <allenday@ucla.edu>, Stanley Nelson <snelson@ucla.edu>
# Human Genetics, UCLA Medical School, University of California, Los Angeles
# POD documentation - main docs before the code
=head1 NAME
Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA
Bio::Expression::FeatureI
=head1 SYNOPSIS
#
=head1 DESCRIPTION
A set of DNA/RNA features.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Allen Day E<lt>allenday@ucla.eduE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Expression::FeatureGroup;
use strict;
use base qw(Bio::Root::Root Bio::Expression::FeatureI);
use vars qw($DEBUG);
=head2 new
Title : new
Usage : $featuregroup = Bio::Expression::FeatureGroup->new(%args);
Function: create a new featuregroup object
Returns : a Bio::Expression::FeatureGroup object
Args : an optional hash of parameters to be used in initialization:
-id -- the featuregroup ID
-type -- the featuregroup type
=cut
sub new {
my($class,@args) = @_;
my $self = bless {}, $class;
$self->_initialize(@args);
return $self;
}
=head2 _initialize
Title : _initialize
Usage : $featuregroup->_initialize(@args);
Function: initialize the featuregroup object
Returns : nothing
Args : @args
=cut
sub _initialize{
my ($self,@args) = @_;
my %param = @args;
$self->type($param{-type});
$self->id($param{-id} );
$self->SUPER::_initialize(@args);
$DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
}
=head2 type
Title : type
Usage : $featuregroup->type($optional_arg);
Function: get/set the type of the featuregroup
Comments: this is probably going to be a string like
"quality control", "mismatch blah blah", etc.
Returns : the featuregroup type
Args : a new value for the featuregroup type
=cut
sub type {
my $self = shift;
$self->{type} = shift if @_;
return $self->{type};
}
=head2 id
Title : id
Usage : $featuregroup->id($optional_arg);
Function: get/set the id of the featuregroup
Returns : the featuregroup id
Args : a new value for the featuregroup id
=cut
sub id {
my $self = shift;
$self->{id} = shift if @_;
return $self->{id};
}
=head2 standard_deviation
Title : standard_deviation
Usage : $featuregroup->standard_deviation($optional_arg);
Function: get/set the standard deviation of the featuregroup value
Returns : the featuregroup standard deviation
Args : a new value for the featuregroup standard deviation
Notes : this method does no calculation, it merely holds a value
=cut
sub standard_deviation {
my $self = shift;
$self->{standard_deviation} = shift if @_;
return $self->{standard_deviation};
}
=head2 quantitation
Title : quantitation
Usage : $featuregroup->quantitation($optional_arg);
Function: get/set the quantitation of the featuregroup
Returns : the featuregroup's quantitated value
Args : a new value for the featuregroup's quantitated value
Notes : this method does no calculation, it merely holds a value
=cut
sub quantitation {
my $self = shift;
$self->{quantitation} = shift if @_;
return $self->{quantitation};
}
=head2 quantitation_units
Title : quantitation_units
Usage : $featuregroup->quantitation_units($optional_arg);
Function: get/set the quantitation units of the featuregroup
Returns : the featuregroup's quantitated value units
Args : a new value for the featuregroup's quantitated value units
=cut
sub quantitation_units {
my $self = shift;
$self->{quantitation_units} = shift if @_;
return $self->{quantitation_units};
}
=head2 presence
Title : presence
Usage : $featuregroup->presence($optional_arg);
Function: get/set the presence call of the featuregroup
Returns : the featuregroup's presence call
Args : a new value for the featuregroup's presence call
=cut
sub presence {
my $self = shift;
$self->{presence} = shift if @_;
return $self->{presence};
}
=head2 add_feature
Title : add_feature
Usage : $feature_copy = $featuregroup->add_feature($feature);
Function: add a feature to the featuregroup
Returns : see this_feature()
Args : a Bio::Expression::FeatureI compliant object
=cut
sub add_feature {
my($self,@args) = @_;
foreach my $feature (@args){
$self->throw('Features must be Bio::Expression::FeatureI compliant') unless $feature->isa('Bio::Expression::FeatureI');
push @{$self->{features}}, $feature;
}
return $self->{features} ? $self->{features}->[-1] : undef;
}
=head2 this_feature
Title : this_feature
Usage : $feature = $featuregroup->this_feature
Function: access the last feature added to the featuregroup
Returns : the last feature added to the featuregroup
Args : none
=cut
sub this_feature {
my $self = shift;
return $self->{features} ? $self->{features}->[-1] : undef;
}
=head2 each_feature
Title : each_feature
Usage : @features = $featuregroup->each_feature
Function: returns a list of Bio::Expression::FeatureI compliant
objects
Returns : a list of objects
Args : none
=cut
sub each_feature {
my $self = shift;
return @{$self->{features}} if defined($self->{features});
return ();
}
=head2 each_feature_quantitation
Title : each_feature_quantitation
Usage : @featurequantitions = $featuregroup->each_feature_quantitation;
Function: returns an list of quantitations of the features in the featuregroup
Returns : a list of numeric values
Args : none
=cut
sub each_feature_quantitation {
my $self = shift;
my @values = ();
push @values, $_->value foreach $self->each_feature;
return @values;
}
=head2 is_qc
Title : is_qc
Usage : $is_quality_control = $featuregroup->is_qc
Function: get/set whether or not the featuregroup is used for quality control purposes
Returns : a boolean (equivalent)
Args : a new value
=cut
sub is_qc {
my $self = shift;
$self->{is_qc} = shift if defined @_;
return $self->{is_qc};
}
1;
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