Bio::Expression
FeatureSet
Summary
Bio::Expression::FeatureSet - 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 : new
Usage : $featureset = Bio::Expression::FeatureSet->new(%args);
Function: create a new featureset object
Returns : a Bio::Expression::FeatureSet object
Args : an optional hash of parameters to be used in initialization:
-id -- the featureset ID
-type -- the featureset type |
Title : _initialize
Usage : $featureset->_initialize(@args);
Function: initialize the featureset object
Returns : nothing
Args : @args |
Title : type
Usage : $featureset->type($optional_arg);
Function: get/set the type of the featureset
Comments: this is probably going to be a string like
"quality control", "mismatch blah blah", etc.
Returns : the featureset type
Args : a new value for the featureset type |
Title : id
Usage : $featureset->id($optional_arg);
Function: get/set the id of the featureset
Returns : the featureset id
Args : a new value for the featureset id |
Title : standard_deviation
Usage : $featureset->standard_deviation($optional_arg);
Function: get/set the standard deviation of the featureset value
Returns : the featureset standard deviation
Args : a new value for the featureset standard deviation
Notes : this method does no calculation, it merely holds a value |
Title : quantitation
Usage : $featureset->quantitation($optional_arg);
Function: get/set the quantitation of the featureset
Returns : the featureset's quantitated value
Args : a new value for the featureset's quantitated value
Notes : this method does no calculation, it merely holds a value |
Title : quantitation_units
Usage : $featureset->quantitation_units($optional_arg);
Function: get/set the quantitation units of the featureset
Returns : the featureset's quantitated value units
Args : a new value for the featureset's quantitated value units |
Title : presence
Usage : $featureset->presence($optional_arg);
Function: get/set the presence call of the featureset
Returns : the featureset's presence call
Args : a new value for the featureset's presence call |
Title : add_feature
Usage : $feature_copy = $featureset->add_feature($feature);
Function: add a feature to the featureset
Returns : see this_feature()
Args : a Bio::Expression::FeatureI compliant object |
Title : this_feature
Usage : $feature = $featureset->this_feature
Function: access the last feature added to the featureset
Returns : the last feature added to the featureset
Args : none |
Title : each_feature
Usage : @features = $featureset->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 = $featureset->each_feature_quantitation;
Function: returns an list of quantitations of the features in the featureset
Returns : a list of numeric values
Args : none |
Title : is_qc
Usage : $is_quality_control = $featureset->is_qc
Function: get/set whether or not the featureset is used for quality control purposes
Returns : a boolean (equivalent)
Args : a new value |
Methods code
sub new
{ my($class,@args) = @_;
my $self = bless {}, $class;
$self->_initialize(@args);
return $self;} | sub _initialize
{ my ($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 type
{ my $self = shift;
$self->{type} = shift if @_;
return $self->{type};} | sub id
{ my $self = shift;
$self->{id} = shift if @_;
return $self->{id};} | sub standard_deviation
{ my $self = shift;
$self->{standard_deviation} = shift if @_;
return $self->{standard_deviation};} | 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 presence
{ my $self = shift;
$self->{presence} = shift if @_;
return $self->{presence};} | sub add_feature
{ my($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 this_feature
{ my $self = shift;
return $self->{features} ? $self->{features}->[-1] : undef;} | sub each_feature
{ my $self = shift;
return @{$self->{features}};} | sub each_feature_quantitation
{ my $self = shift;
my @values = ();
push @values, $_->value foreach $self->each_feature;
return @values; } | sub is_qc
{ my $self = shift;
$self->{is_qc} = shift if defined @_;
return $self->{is_qc};} | General documentation
User feedback is an integral part of the evolution of this and other
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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 _