Bio-MAGE
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MAGE/QuantitationType/DerivedSignal.pm view on Meta::CPAN
##############################
#
# Bio::MAGE::QuantitationType::DerivedSignal
#
##############################
# C O P Y R I G H T N O T I C E
# Copyright (c) 2001-2006 by:
# * The MicroArray Gene Expression Database Society (MGED)
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
package Bio::MAGE::QuantitationType::DerivedSignal;
use strict;
use Carp;
use base qw(Bio::MAGE::QuantitationType::StandardQuantitationType);
use Bio::MAGE::Association;
use vars qw($__ASSOCIATIONS
$__CLASS_NAME
$__PACKAGE_NAME
$__SUBCLASSES
$__SUPERCLASSES
$__ATTRIBUTE_NAMES
$__ASSOCIATION_NAMES
);
=head1 NAME
Bio::MAGE::QuantitationType::DerivedSignal - Class for the MAGE-OM API
=head1 SYNOPSIS
use Bio::MAGE::QuantitationType::DerivedSignal
# creating an empty instance
my $derivedsignal = Bio::MAGE::QuantitationType::DerivedSignal->new();
# creating an instance with existing data
my $derivedsignal = Bio::MAGE::QuantitationType::DerivedSignal->new(
name=>$name_val,
isBackground=>$isbackground_val,
identifier=>$identifier_val,
dataType=>$ontologyentry_ref,
auditTrail=>\@audit_list,
channel=>$channel_ref,
propertySets=>\@namevaluetype_list,
confidenceIndicators=>\@confidenceindicator_list,
descriptions=>\@description_list,
scale=>$ontologyentry_ref,
security=>$security_ref,
quantitationTypeMaps=>\@quantitationtypemap_list,
);
# 'name' attribute
my $name_val = $derivedsignal->name(); # getter
$derivedsignal->name($value); # setter
# 'isBackground' attribute
my $isBackground_val = $derivedsignal->isBackground(); # getter
$derivedsignal->isBackground($value); # setter
# 'identifier' attribute
my $identifier_val = $derivedsignal->identifier(); # getter
$derivedsignal->identifier($value); # setter
# 'dataType' association
my $ontologyentry_ref = $derivedsignal->dataType(); # getter
$derivedsignal->dataType($ontologyentry_ref); # setter
# 'auditTrail' association
my $audit_array_ref = $derivedsignal->auditTrail(); # getter
$derivedsignal->auditTrail(\@audit_list); # setter
# 'channel' association
my $channel_ref = $derivedsignal->channel(); # getter
$derivedsignal->channel($channel_ref); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $derivedsignal->propertySets(); # getter
$derivedsignal->propertySets(\@namevaluetype_list); # setter
# 'confidenceIndicators' association
my $confidenceindicator_array_ref = $derivedsignal->confidenceIndicators(); # getter
$derivedsignal->confidenceIndicators(\@confidenceindicator_list); # setter
# 'descriptions' association
my $description_array_ref = $derivedsignal->descriptions(); # getter
$derivedsignal->descriptions(\@description_list); # setter
# 'scale' association
my $ontologyentry_ref = $derivedsignal->scale(); # getter
$derivedsignal->scale($ontologyentry_ref); # setter
# 'security' association
my $security_ref = $derivedsignal->security(); # getter
$derivedsignal->security($security_ref); # setter
# 'quantitationTypeMaps' association
my $quantitationtypemap_array_ref = $derivedsignal->quantitationTypeMaps(); # getter
$derivedsignal->quantitationTypeMaps(\@quantitationtypemap_list); # setter
=head1 DESCRIPTION
From the MAGE-OM documentation for the C<DerivedSignal> class:
A calculated measurement of the intensity of a signal, for example, after a transformation involving normalization and/or replicate DesignElements. Of type float.
=cut
=head1 INHERITANCE
Bio::MAGE::QuantitationType::DerivedSignal has the following superclasses:
=over
=item * Bio::MAGE::QuantitationType::StandardQuantitationType
=back
=cut
BEGIN {
$__CLASS_NAME = q[Bio::MAGE::QuantitationType::DerivedSignal];
$__PACKAGE_NAME = q[QuantitationType];
$__SUBCLASSES = [];
$__SUPERCLASSES = ['Bio::MAGE::QuantitationType::StandardQuantitationType'];
$__ATTRIBUTE_NAMES = ['name', 'isBackground', 'identifier'];
$__ASSOCIATION_NAMES = ['dataType', 'auditTrail', 'propertySets', 'channel', 'confidenceIndicators', 'descriptions', 'security', 'scale', 'quantitationTypeMaps'];
$__ASSOCIATIONS = []
}
=head1 CLASS METHODS
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::QuantitationType::DerivedSignal->methodname() syntax.
=over
=item new()
=item new(%args)
The object constructor C<new()> accepts the following optional
named-value style arguments:
=over
=item * name
MAGE/QuantitationType/DerivedSignal.pm view on Meta::CPAN
#
# code for get_slots() inherited from Base.pm
#
=item $val = $obj->set_slot($name,$val)
The C<set_slot()> method sets the slot C<$name> to the value C<$val>
B<Return value>: the new value of the slot, i.e. C<$val>
B<Side effects>: none
=cut
#
# code for set_slot() inherited from Base.pm
#
=item $val = $obj->get_slot($name)
The C<get_slot()> method is used to get the values of a number of
slots at the same time.
B<Return value>: a single slot value, or undef if the slot has not been
initialized.
B<Side effects>: none
=cut
#
# code for get_slot() inherited from Base.pm
#
=head2 ATTRIBUTES
Attributes are simple data types that belong to a single instance of a
class. In the Perl implementation of the MAGE-OM classes, the
interface to attributes is implemented using separate setter and
getter methods for each attribute.
C<Bio::MAGE::QuantitationType::DerivedSignal> has the following attribute accessor methods:
=over
=item name
Methods for the C<name> attribute.
From the MAGE-OM documentation:
The potentially ambiguous common identifier.
=over
=item $val = $derivedsignal->setName($val)
The restricted setter method for the C<name> attribute.
Input parameters: the value to which the C<name> attribute will be set
Return value: the current value of the C<name> attribute
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified
=cut
sub setName {
my $self = shift;
croak(__PACKAGE__ . "::setName: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setName: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
return $self->{__NAME} = $val;
}
=item $val = $derivedsignal->getName()
The restricted getter method for the C<name> attribute.
Input parameters: none
Return value: the current value of the C<name> attribute
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getName {
my $self = shift;
croak(__PACKAGE__ . "::getName: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__NAME};
}
=back
=item isBackground
Methods for the C<isBackground> attribute.
From the MAGE-OM documentation:
Indicates whether the quantitation has been measured from the background or from the feature itself.
=over
=item $val = $derivedsignal->setIsBackground($val)
The restricted setter method for the C<isBackground> attribute.
Input parameters: the value to which the C<isBackground> attribute will be set
Return value: the current value of the C<isBackground> attribute
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified
=cut
sub setIsBackground {
my $self = shift;
croak(__PACKAGE__ . "::setIsBackground: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setIsBackground: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
return $self->{__ISBACKGROUND} = $val;
}
=item $val = $derivedsignal->getIsBackground()
The restricted getter method for the C<isBackground> attribute.
Input parameters: none
Return value: the current value of the C<isBackground> attribute
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getIsBackground {
my $self = shift;
croak(__PACKAGE__ . "::getIsBackground: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__ISBACKGROUND};
}
=back
=item identifier
Methods for the C<identifier> attribute.
From the MAGE-OM documentation:
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
=over
=item $val = $derivedsignal->setIdentifier($val)
The restricted setter method for the C<identifier> attribute.
Input parameters: the value to which the C<identifier> attribute will be set
Return value: the current value of the C<identifier> attribute
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified
=cut
sub setIdentifier {
my $self = shift;
croak(__PACKAGE__ . "::setIdentifier: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setIdentifier: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
return $self->{__IDENTIFIER} = $val;
}
=item $val = $derivedsignal->getIdentifier()
The restricted getter method for the C<identifier> attribute.
Input parameters: none
Return value: the current value of the C<identifier> attribute
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getIdentifier {
my $self = shift;
croak(__PACKAGE__ . "::getIdentifier: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__IDENTIFIER};
}
=back
=back
=head2 ASSOCIATIONS
Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and
maximum number of instances of the 'other' class that maybe included
in the association:
=over
=item 1
There B<must> be exactly one item in the association, i.e. this is a
mandatory data field.
=item 0..1
There B<may> be one item in the association, i.e. this is an optional
data field.
=item 1..N
There B<must> be one or more items in the association, i.e. this is a
mandatory data field, with list cardinality.
=item 0..N
There B<may> be one or more items in the association, i.e. this is an
optional data field, with list cardinality.
=back
Bio::MAGE::QuantitationType::DerivedSignal has the following association accessor methods:
=over
=item dataType
Methods for the C<dataType> association.
From the MAGE-OM documentation:
The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}
=over
=item $val = $derivedsignal->setDataType($val)
The restricted setter method for the C<dataType> association.
Input parameters: the value to which the C<dataType> association will be set : one of the accepted enumerated values.
Return value: the current value of the C<dataType> association : one of the accepted enumerated values.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$val> is not an instance of class C<Bio::MAGE::Description::OntologyEntry>
=cut
sub setDataType {
my $self = shift;
croak(__PACKAGE__ . "::setDataType: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setDataType: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setDataType: wrong type: " . ref($val) . " expected Bio::MAGE::Description::OntologyEntry") unless (not defined $val) or UNIVERSAL::isa($val,'Bio::MAGE::Description::OntologyEntry');
return $self->{__DATATYPE} = $val;
}
=item $val = $derivedsignal->getDataType()
The restricted getter method for the C<dataType> association.
Input parameters: none
Return value: the current value of the C<dataType> association : an instance of type C<Bio::MAGE::Description::OntologyEntry>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getDataType {
my $self = shift;
croak(__PACKAGE__ . "::getDataType: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__DATATYPE};
}
=back
=item auditTrail
Methods for the C<auditTrail> association.
From the MAGE-OM documentation:
A list of Audit instances that track changes to the instance of Describable.
=over
=item $array_ref = $derivedsignal->setAuditTrail($array_ref)
The restricted setter method for the C<auditTrail> association.
Input parameters: the value to which the C<auditTrail> association will be set : a reference to an array of objects of type C<Bio::MAGE::AuditAndSecurity::Audit>
Return value: the current value of the C<auditTrail> association : a reference to an array of objects of type C<Bio::MAGE::AuditAndSecurity::Audit>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$array_ref> is not a reference to an array class C<Bio::MAGE::AuditAndSecurity::Audit> instances
=cut
sub setAuditTrail {
my $self = shift;
croak(__PACKAGE__ . "::setAuditTrail: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setAuditTrail: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setAuditTrail: expected array reference, got $self")
unless (not defined $val) or UNIVERSAL::isa($val,'ARRAY');
if (defined $val) {
foreach my $val_ent (@{$val}) {
croak(__PACKAGE__ . "::setAuditTrail: wrong type: " . ref($val_ent) . " expected Bio::MAGE::AuditAndSecurity::Audit")
unless UNIVERSAL::isa($val_ent,'Bio::MAGE::AuditAndSecurity::Audit');
}
}
return $self->{__AUDITTRAIL} = $val;
}
=item $array_ref = $derivedsignal->getAuditTrail()
The restricted getter method for the C<auditTrail> association.
Input parameters: none
Return value: the current value of the C<auditTrail> association : a reference to an array of objects of type C<Bio::MAGE::AuditAndSecurity::Audit>
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getAuditTrail {
my $self = shift;
croak(__PACKAGE__ . "::getAuditTrail: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__AUDITTRAIL};
}
=item $val = $derivedsignal->addAuditTrail(@vals)
Because the auditTrail association has list cardinality, it may store more
than one value. This method adds the current list of objects in the auditTrail association.
Input parameters: the list of values C<@vals> to add to the auditTrail association. B<NOTE>: submitting a single value is permitted.
Return value: the number of items stored in the slot B<after> adding C<@vals>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or if any of the objects in @vals is not an instance of class C<Bio::MAGE::AuditAndSecurity::Audit>
=cut
sub addAuditTrail {
my $self = shift;
croak(__PACKAGE__ . "::addAuditTrail: no arguments passed to adder")
unless @_;
my @vals = @_;
foreach my $val (@vals) {
croak(__PACKAGE__ . "::addAuditTrail: wrong type: " . ref($val) . " expected Bio::MAGE::AuditAndSecurity::Audit")
unless UNIVERSAL::isa($val,'Bio::MAGE::AuditAndSecurity::Audit');
}
return push(@{$self->{__AUDITTRAIL}},@vals);
}
=back
=item propertySets
Methods for the C<propertySets> association.
From the MAGE-OM documentation:
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
=over
=item $array_ref = $derivedsignal->setPropertySets($array_ref)
The restricted setter method for the C<propertySets> association.
Input parameters: the value to which the C<propertySets> association will be set : a reference to an array of objects of type C<Bio::MAGE::NameValueType>
Return value: the current value of the C<propertySets> association : a reference to an array of objects of type C<Bio::MAGE::NameValueType>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$array_ref> is not a reference to an array class C<Bio::MAGE::NameValueType> instances
=cut
sub setPropertySets {
my $self = shift;
croak(__PACKAGE__ . "::setPropertySets: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setPropertySets: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setPropertySets: expected array reference, got $self")
unless (not defined $val) or UNIVERSAL::isa($val,'ARRAY');
if (defined $val) {
foreach my $val_ent (@{$val}) {
croak(__PACKAGE__ . "::setPropertySets: wrong type: " . ref($val_ent) . " expected Bio::MAGE::NameValueType")
unless UNIVERSAL::isa($val_ent,'Bio::MAGE::NameValueType');
}
}
return $self->{__PROPERTYSETS} = $val;
}
=item $array_ref = $derivedsignal->getPropertySets()
The restricted getter method for the C<propertySets> association.
Input parameters: none
Return value: the current value of the C<propertySets> association : a reference to an array of objects of type C<Bio::MAGE::NameValueType>
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getPropertySets {
my $self = shift;
croak(__PACKAGE__ . "::getPropertySets: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__PROPERTYSETS};
}
=item $val = $derivedsignal->addPropertySets(@vals)
Because the propertySets association has list cardinality, it may store more
than one value. This method adds the current list of objects in the propertySets association.
Input parameters: the list of values C<@vals> to add to the propertySets association. B<NOTE>: submitting a single value is permitted.
Return value: the number of items stored in the slot B<after> adding C<@vals>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or if any of the objects in @vals is not an instance of class C<Bio::MAGE::NameValueType>
=cut
sub addPropertySets {
my $self = shift;
croak(__PACKAGE__ . "::addPropertySets: no arguments passed to adder")
unless @_;
my @vals = @_;
foreach my $val (@vals) {
croak(__PACKAGE__ . "::addPropertySets: wrong type: " . ref($val) . " expected Bio::MAGE::NameValueType")
unless UNIVERSAL::isa($val,'Bio::MAGE::NameValueType');
}
return push(@{$self->{__PROPERTYSETS}},@vals);
}
=back
=item channel
Methods for the C<channel> association.
From the MAGE-OM documentation:
The optional channel associated with the QuantitationType.
=over
=item $val = $derivedsignal->setChannel($val)
The restricted setter method for the C<channel> association.
Input parameters: the value to which the C<channel> association will be set : one of the accepted enumerated values.
Return value: the current value of the C<channel> association : one of the accepted enumerated values.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$val> is not an instance of class C<Bio::MAGE::BioAssay::Channel>
=cut
sub setChannel {
my $self = shift;
croak(__PACKAGE__ . "::setChannel: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setChannel: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setChannel: wrong type: " . ref($val) . " expected Bio::MAGE::BioAssay::Channel") unless (not defined $val) or UNIVERSAL::isa($val,'Bio::MAGE::BioAssay::Channel');
return $self->{__CHANNEL} = $val;
}
=item $val = $derivedsignal->getChannel()
The restricted getter method for the C<channel> association.
Input parameters: none
Return value: the current value of the C<channel> association : an instance of type C<Bio::MAGE::BioAssay::Channel>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getChannel {
my $self = shift;
croak(__PACKAGE__ . "::getChannel: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__CHANNEL};
}
=back
=item confidenceIndicators
Methods for the C<confidenceIndicators> association.
From the MAGE-OM documentation:
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
=over
=item $array_ref = $derivedsignal->setConfidenceIndicators($array_ref)
The restricted setter method for the C<confidenceIndicators> association.
Input parameters: the value to which the C<confidenceIndicators> association will be set : a reference to an array of objects of type C<Bio::MAGE::QuantitationType::ConfidenceIndicator>
Return value: the current value of the C<confidenceIndicators> association : a reference to an array of objects of type C<Bio::MAGE::QuantitationType::ConfidenceIndicator>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$array_ref> is not a reference to an array class C<Bio::MAGE::QuantitationType::ConfidenceIndicator> instances
=cut
sub setConfidenceIndicators {
my $self = shift;
croak(__PACKAGE__ . "::setConfidenceIndicators: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setConfidenceIndicators: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setConfidenceIndicators: expected array reference, got $self")
unless (not defined $val) or UNIVERSAL::isa($val,'ARRAY');
if (defined $val) {
foreach my $val_ent (@{$val}) {
croak(__PACKAGE__ . "::setConfidenceIndicators: wrong type: " . ref($val_ent) . " expected Bio::MAGE::QuantitationType::ConfidenceIndicator")
unless UNIVERSAL::isa($val_ent,'Bio::MAGE::QuantitationType::ConfidenceIndicator');
}
}
return $self->{__CONFIDENCEINDICATORS} = $val;
}
=item $array_ref = $derivedsignal->getConfidenceIndicators()
The restricted getter method for the C<confidenceIndicators> association.
Input parameters: none
Return value: the current value of the C<confidenceIndicators> association : a reference to an array of objects of type C<Bio::MAGE::QuantitationType::ConfidenceIndicator>
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getConfidenceIndicators {
my $self = shift;
croak(__PACKAGE__ . "::getConfidenceIndicators: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__CONFIDENCEINDICATORS};
}
=item $val = $derivedsignal->addConfidenceIndicators(@vals)
Because the confidenceIndicators association has list cardinality, it may store more
than one value. This method adds the current list of objects in the confidenceIndicators association.
Input parameters: the list of values C<@vals> to add to the confidenceIndicators association. B<NOTE>: submitting a single value is permitted.
Return value: the number of items stored in the slot B<after> adding C<@vals>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or if any of the objects in @vals is not an instance of class C<Bio::MAGE::QuantitationType::ConfidenceIndicator>
=cut
sub addConfidenceIndicators {
my $self = shift;
croak(__PACKAGE__ . "::addConfidenceIndicators: no arguments passed to adder")
unless @_;
my @vals = @_;
foreach my $val (@vals) {
croak(__PACKAGE__ . "::addConfidenceIndicators: wrong type: " . ref($val) . " expected Bio::MAGE::QuantitationType::ConfidenceIndicator")
unless UNIVERSAL::isa($val,'Bio::MAGE::QuantitationType::ConfidenceIndicator');
}
return push(@{$self->{__CONFIDENCEINDICATORS}},@vals);
}
=back
=item descriptions
Methods for the C<descriptions> association.
From the MAGE-OM documentation:
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
=over
=item $array_ref = $derivedsignal->setDescriptions($array_ref)
The restricted setter method for the C<descriptions> association.
Input parameters: the value to which the C<descriptions> association will be set : a reference to an array of objects of type C<Bio::MAGE::Description::Description>
Return value: the current value of the C<descriptions> association : a reference to an array of objects of type C<Bio::MAGE::Description::Description>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$array_ref> is not a reference to an array class C<Bio::MAGE::Description::Description> instances
=cut
sub setDescriptions {
my $self = shift;
croak(__PACKAGE__ . "::setDescriptions: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setDescriptions: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setDescriptions: expected array reference, got $self")
unless (not defined $val) or UNIVERSAL::isa($val,'ARRAY');
if (defined $val) {
foreach my $val_ent (@{$val}) {
croak(__PACKAGE__ . "::setDescriptions: wrong type: " . ref($val_ent) . " expected Bio::MAGE::Description::Description")
unless UNIVERSAL::isa($val_ent,'Bio::MAGE::Description::Description');
}
}
return $self->{__DESCRIPTIONS} = $val;
}
=item $array_ref = $derivedsignal->getDescriptions()
The restricted getter method for the C<descriptions> association.
Input parameters: none
Return value: the current value of the C<descriptions> association : a reference to an array of objects of type C<Bio::MAGE::Description::Description>
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getDescriptions {
my $self = shift;
croak(__PACKAGE__ . "::getDescriptions: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__DESCRIPTIONS};
}
=item $val = $derivedsignal->addDescriptions(@vals)
Because the descriptions association has list cardinality, it may store more
than one value. This method adds the current list of objects in the descriptions association.
Input parameters: the list of values C<@vals> to add to the descriptions association. B<NOTE>: submitting a single value is permitted.
Return value: the number of items stored in the slot B<after> adding C<@vals>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or if any of the objects in @vals is not an instance of class C<Bio::MAGE::Description::Description>
=cut
sub addDescriptions {
my $self = shift;
croak(__PACKAGE__ . "::addDescriptions: no arguments passed to adder")
unless @_;
my @vals = @_;
foreach my $val (@vals) {
croak(__PACKAGE__ . "::addDescriptions: wrong type: " . ref($val) . " expected Bio::MAGE::Description::Description")
unless UNIVERSAL::isa($val,'Bio::MAGE::Description::Description');
}
return push(@{$self->{__DESCRIPTIONS}},@vals);
}
=back
=item security
Methods for the C<security> association.
From the MAGE-OM documentation:
Information on the security for the instance of the class.
=over
=item $val = $derivedsignal->setSecurity($val)
The restricted setter method for the C<security> association.
Input parameters: the value to which the C<security> association will be set : one of the accepted enumerated values.
Return value: the current value of the C<security> association : one of the accepted enumerated values.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$val> is not an instance of class C<Bio::MAGE::AuditAndSecurity::Security>
=cut
sub setSecurity {
my $self = shift;
croak(__PACKAGE__ . "::setSecurity: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setSecurity: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setSecurity: wrong type: " . ref($val) . " expected Bio::MAGE::AuditAndSecurity::Security") unless (not defined $val) or UNIVERSAL::isa($val,'Bio::MAGE::AuditAndSecurity::Security');
return $self->{__SECURITY} = $val;
}
=item $val = $derivedsignal->getSecurity()
The restricted getter method for the C<security> association.
Input parameters: none
Return value: the current value of the C<security> association : an instance of type C<Bio::MAGE::AuditAndSecurity::Security>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getSecurity {
my $self = shift;
croak(__PACKAGE__ . "::getSecurity: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__SECURITY};
}
=back
=item scale
Methods for the C<scale> association.
From the MAGE-OM documentation:
Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}
=over
=item $val = $derivedsignal->setScale($val)
The restricted setter method for the C<scale> association.
Input parameters: the value to which the C<scale> association will be set : one of the accepted enumerated values.
Return value: the current value of the C<scale> association : one of the accepted enumerated values.
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$val> is not an instance of class C<Bio::MAGE::Description::OntologyEntry>
=cut
sub setScale {
my $self = shift;
croak(__PACKAGE__ . "::setScale: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setScale: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setScale: wrong type: " . ref($val) . " expected Bio::MAGE::Description::OntologyEntry") unless (not defined $val) or UNIVERSAL::isa($val,'Bio::MAGE::Description::OntologyEntry');
return $self->{__SCALE} = $val;
}
=item $val = $derivedsignal->getScale()
The restricted getter method for the C<scale> association.
Input parameters: none
Return value: the current value of the C<scale> association : an instance of type C<Bio::MAGE::Description::OntologyEntry>.
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getScale {
my $self = shift;
croak(__PACKAGE__ . "::getScale: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__SCALE};
}
=back
=item quantitationTypeMaps
Methods for the C<quantitationTypeMaps> association.
From the MAGE-OM documentation:
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
=over
=item $array_ref = $derivedsignal->setQuantitationTypeMaps($array_ref)
The restricted setter method for the C<quantitationTypeMaps> association.
Input parameters: the value to which the C<quantitationTypeMaps> association will be set : a reference to an array of objects of type C<Bio::MAGE::BioAssayData::QuantitationTypeMap>
Return value: the current value of the C<quantitationTypeMaps> association : a reference to an array of objects of type C<Bio::MAGE::BioAssayData::QuantitationTypeMap>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$array_ref> is not a reference to an array class C<Bio::MAGE::BioAssayData::QuantitationTypeMap> instances
=cut
sub setQuantitationTypeMaps {
my $self = shift;
croak(__PACKAGE__ . "::setQuantitationTypeMaps: no arguments passed to setter")
unless @_;
croak(__PACKAGE__ . "::setQuantitationTypeMaps: too many arguments passed to setter")
if @_ > 1;
my $val = shift;
croak(__PACKAGE__ . "::setQuantitationTypeMaps: expected array reference, got $self")
unless (not defined $val) or UNIVERSAL::isa($val,'ARRAY');
if (defined $val) {
foreach my $val_ent (@{$val}) {
croak(__PACKAGE__ . "::setQuantitationTypeMaps: wrong type: " . ref($val_ent) . " expected Bio::MAGE::BioAssayData::QuantitationTypeMap")
unless UNIVERSAL::isa($val_ent,'Bio::MAGE::BioAssayData::QuantitationTypeMap');
}
}
return $self->{__QUANTITATIONTYPEMAPS} = $val;
}
=item $array_ref = $derivedsignal->getQuantitationTypeMaps()
The restricted getter method for the C<quantitationTypeMaps> association.
Input parameters: none
Return value: the current value of the C<quantitationTypeMaps> association : a reference to an array of objects of type C<Bio::MAGE::BioAssayData::QuantitationTypeMap>
Side effects: none
Exceptions: will call C<croak()> if any input parameters are specified
=cut
sub getQuantitationTypeMaps {
my $self = shift;
croak(__PACKAGE__ . "::getQuantitationTypeMaps: arguments passed to getter")
if @_;
my $val = shift;
return $self->{__QUANTITATIONTYPEMAPS};
}
=item $val = $derivedsignal->addQuantitationTypeMaps(@vals)
Because the quantitationTypeMaps association has list cardinality, it may store more
than one value. This method adds the current list of objects in the quantitationTypeMaps association.
Input parameters: the list of values C<@vals> to add to the quantitationTypeMaps association. B<NOTE>: submitting a single value is permitted.
Return value: the number of items stored in the slot B<after> adding C<@vals>
Side effects: none
Exceptions: will call C<croak()> if no input parameters are specified, or if any of the objects in @vals is not an instance of class C<Bio::MAGE::BioAssayData::QuantitationTypeMap>
=cut
sub addQuantitationTypeMaps {
my $self = shift;
croak(__PACKAGE__ . "::addQuantitationTypeMaps: no arguments passed to adder")
unless @_;
my @vals = @_;
foreach my $val (@vals) {
croak(__PACKAGE__ . "::addQuantitationTypeMaps: wrong type: " . ref($val) . " expected Bio::MAGE::BioAssayData::QuantitationTypeMap")
unless UNIVERSAL::isa($val,'Bio::MAGE::BioAssayData::QuantitationTypeMap');
}
return push(@{$self->{__QUANTITATIONTYPEMAPS}},@vals);
}
=back
sub initialize {
my $self = shift;
return 1;
}
=back
=cut
=head1 SLOTS, ATTRIBUTES, AND ASSOCIATIONS
In the Perl implementation of MAGE-OM classes, there are
three types of class data members: C<slots>, C<attributes>, and
C<associations>.
=head2 SLOTS
This API uses the term C<slot> to indicate a data member of the class
that was not present in the UML model and is used for mainly internal
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