Bio::Expression FeatureGroup
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Summary
Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA
Bio::Expression::FeatureI
Package variables
No package variables defined.
Inherit
Bio::Expression::FeatureI Bio::Root::Root
Synopsis
#
Description
A set of DNA/RNA features.
Methods
newDescriptionCode
_initializeDescriptionCode
typeDescriptionCode
idDescriptionCode
standard_deviationDescriptionCode
quantitationDescriptionCode
quantitation_unitsDescriptionCode
presenceDescriptionCode
add_featureDescriptionCode
this_featureDescriptionCode
each_featureDescriptionCode
each_feature_quantitationDescriptionCode
is_qcDescriptionCode
Methods description
newcode    nextTop
 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
_initializecodeprevnextTop
 Title   : _initialize
Usage : $featuregroup->_initialize(@args);
Function: initialize the featuregroup object
Returns : nothing
Args : @args
typecodeprevnextTop
 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
idcodeprevnextTop
 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
standard_deviationcodeprevnextTop
 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
quantitationcodeprevnextTop
 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
quantitation_unitscodeprevnextTop
 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
presencecodeprevnextTop
 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
add_featurecodeprevnextTop
 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
this_featurecodeprevnextTop
 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
each_featurecodeprevnextTop
 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
each_feature_quantitationcodeprevnextTop
 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
is_qccodeprevnextTop
 Title   : is_qc
Usage : $is_quality_control = $featuregroup->is_qc
Function: get/set whether or not the featuregroup is used for quality control purposes
Returns : a boolean (equivalent)
Args : a new value
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = bless {}, $class;
  $self->_initialize(@args);
  return $self;
}
_initializedescriptionprevnextTop
sub _initialize {
  my ($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);
}
typedescriptionprevnextTop
sub type {
  my $self = shift;
  $self->{type} = shift if @_;
  return $self->{type};
}
iddescriptionprevnextTop
sub id {
  my $self = shift;
  $self->{id} = shift if @_;
  return $self->{id};
}
standard_deviationdescriptionprevnextTop
sub standard_deviation {
  my $self = shift;
  $self->{standard_deviation} = shift if @_;
  return $self->{standard_deviation};
}
quantitationdescriptionprevnextTop
sub quantitation {
  my $self = shift;
  $self->{quantitation} = shift if @_;
  return $self->{quantitation};
}
quantitation_unitsdescriptionprevnextTop
sub quantitation_units {
  my $self = shift;
  $self->{quantitation_units} = shift if @_;
  return $self->{quantitation_units};
}
presencedescriptionprevnextTop
sub presence {
  my $self = shift;
  $self->{presence} = shift if @_;
  return $self->{presence};
}
add_featuredescriptionprevnextTop
sub add_feature {
  my($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;
}
this_featuredescriptionprevnextTop
sub this_feature {
  my $self = shift;
  return $self->{features} ? $self->{features}->[-1] : undef;
}
each_featuredescriptionprevnextTop
sub each_feature {
  my $self = shift;
  return @{$self->{features}} if defined($self->{features});
  return ();
}
each_feature_quantitationdescriptionprevnextTop
sub each_feature_quantitation {
  my $self = shift;
  my @values = ();
  push @values, $_->value foreach $self->each_feature;
  return @values;
}
is_qcdescriptionprevnextTop
sub is_qc {
  my $self = shift;
  $self->{is_qc} = shift if defined @_;
  return $self->{is_qc};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
AUTHORTop
Allen Day <allenday@ucla.edu>
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _