Bio::Expression
FeatureGroup
Toolbar
Summary
Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA
Bio::Expression::FeatureI
Package variables
No package variables defined.
Inherit
Synopsis
#
Description
A set of DNA/RNA features.
Methods
Methods description
Title : _initialize
Usage : $featuregroup->_initialize(@args);
Function: initialize the featuregroup object
Returns : nothing
Args : @args |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Methods code
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 && $self->verbose > 0);} | sub add_feature
{ my($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;} | sub each_feature
{ my $self = shift;
return @{$self->{features}} if defined($self->{features});
return ();} | sub each_feature_quantitation
{ my $self = shift;
my @values = ();
push @values, $_->value foreach $self->each_feature;
return @values; } | sub id
{ my $self = shift;
$self->{id} = shift if @_;
return $self->{id};} | sub is_qc
{ my $self = shift;
$self->{is_qc} = shift if defined @_;
return $self->{is_qc};
}
1;} | sub new
{ my($class,@args) = @_;
my $self = bless {}, $class;
$self->_initialize(@args);
return $self;} | sub presence
{ my $self = shift;
$self->{presence} = shift if @_;
return $self->{presence};} | sub quantitation
{ my $self = shift;
$self->{quantitation} = shift if @_;
return $self->{quantitation};} | sub quantitation_units
{ my $self = shift;
$self->{quantitation_units} = shift if @_;
return $self->{quantitation_units};} | sub standard_deviation
{ my $self = shift;
$self->{standard_deviation} = shift if @_;
return $self->{standard_deviation};} | sub this_feature
{ my $self = shift;
return $self->{features} ? $self->{features}->[-1] : undef;} | sub type
{ my $self = shift;
$self->{type} = shift if @_;
return $self->{type};} | General documentation
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
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/
Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _