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MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

=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.

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

    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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

    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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

    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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

    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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

    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

MAGE/QuantitationType/DerivedSignal.pm  view on Meta::CPAN

  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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

=head1 NAME

Bio::MAGE::QuantitationType::MeasuredSignal - Class for the MAGE-OM API

=head1 SYNOPSIS

  use Bio::MAGE::QuantitationType::MeasuredSignal

  # creating an empty instance
  my $measuredsignal = Bio::MAGE::QuantitationType::MeasuredSignal->new();

  # creating an instance with existing data
  my $measuredsignal = Bio::MAGE::QuantitationType::MeasuredSignal->new(
        name=>$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 = $measuredsignal->name(); # getter
  $measuredsignal->name($value); # setter

  # 'isBackground' attribute
  my $isBackground_val = $measuredsignal->isBackground(); # getter
  $measuredsignal->isBackground($value); # setter

  # 'identifier' attribute
  my $identifier_val = $measuredsignal->identifier(); # getter
  $measuredsignal->identifier($value); # setter


  # 'dataType' association
  my $ontologyentry_ref = $measuredsignal->dataType(); # getter
  $measuredsignal->dataType($ontologyentry_ref); # setter

  # 'auditTrail' association
  my $audit_array_ref = $measuredsignal->auditTrail(); # getter
  $measuredsignal->auditTrail(\@audit_list); # setter

  # 'channel' association
  my $channel_ref = $measuredsignal->channel(); # getter
  $measuredsignal->channel($channel_ref); # setter

  # 'propertySets' association
  my $namevaluetype_array_ref = $measuredsignal->propertySets(); # getter
  $measuredsignal->propertySets(\@namevaluetype_list); # setter

  # 'confidenceIndicators' association
  my $confidenceindicator_array_ref = $measuredsignal->confidenceIndicators(); # getter
  $measuredsignal->confidenceIndicators(\@confidenceindicator_list); # setter

  # 'descriptions' association
  my $description_array_ref = $measuredsignal->descriptions(); # getter
  $measuredsignal->descriptions(\@description_list); # setter

  # 'scale' association
  my $ontologyentry_ref = $measuredsignal->scale(); # getter
  $measuredsignal->scale($ontologyentry_ref); # setter

  # 'security' association
  my $security_ref = $measuredsignal->security(); # getter
  $measuredsignal->security($security_ref); # setter

  # 'quantitationTypeMaps' association
  my $quantitationtypemap_array_ref = $measuredsignal->quantitationTypeMaps(); # getter
  $measuredsignal->quantitationTypeMaps(\@quantitationtypemap_list); # setter



=head1 DESCRIPTION

From the MAGE-OM documentation for the C<MeasuredSignal> class:

Best measure from feature extraction as to the presence and intensity of the signal.  Of type float.

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

The potentially ambiguous common identifier.


=over


=item $val = $measuredsignal->setName($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

Indicates whether the quantitation has been measured from the background or from the feature itself.


=over


=item $val = $measuredsignal->setIsBackground($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

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 = $measuredsignal->setIdentifier($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

The specific type for the quantitations.  From a controlled vocabulary of {float, int, boolean, etc.}


=over


=item $val = $measuredsignal->setDataType($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

A list of Audit instances that track changes to the instance of Describable.


=over


=item $array_ref = $measuredsignal->setAuditTrail($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

    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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  my $self = shift;
  croak(__PACKAGE__ . "::getAuditTrail: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__AUDITTRAIL};
}




=item $val = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

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 = $measuredsignal->setPropertySets($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

    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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  my $self = shift;
  croak(__PACKAGE__ . "::getPropertySets: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__PROPERTYSETS};
}




=item $val = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

The optional channel associated with the QuantitationType.


=over


=item $val = $measuredsignal->setChannel($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.


=over


=item $array_ref = $measuredsignal->setConfidenceIndicators($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

    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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  my $self = shift;
  croak(__PACKAGE__ . "::getConfidenceIndicators: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__CONFIDENCEINDICATORS};
}




=item $val = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

Free hand text descriptions.  Makes available the associations of Description to an instance of Describable.


=over


=item $array_ref = $measuredsignal->setDescriptions($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

    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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  my $self = shift;
  croak(__PACKAGE__ . "::getDescriptions: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__DESCRIPTIONS};
}




=item $val = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

From the MAGE-OM documentation:

Information on the security for the instance of the class.


=over


=item $val = $measuredsignal->setSecurity($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

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 = $measuredsignal->setScale($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

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 = $measuredsignal->setQuantitationTypeMaps($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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

    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 = $measuredsignal->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

MAGE/QuantitationType/MeasuredSignal.pm  view on Meta::CPAN

  my $self = shift;
  croak(__PACKAGE__ . "::getQuantitationTypeMaps: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__QUANTITATIONTYPEMAPS};
}




=item $val = $measuredsignal->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

t/DerivedSignal.t  view on Meta::CPAN

use Bio::MAGE::BioAssayData::QuantitationTypeMap;
use Bio::MAGE::Description::OntologyEntry;
use Bio::MAGE::NameValueType;
use Bio::MAGE::BioAssay::Channel;
use Bio::MAGE::AuditAndSecurity::Audit;
use Bio::MAGE::AuditAndSecurity::Security;
use Bio::MAGE::Description::Description;


# we test the new() method
my $derivedsignal;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $derivedsignal = Bio::MAGE::QuantitationType::DerivedSignal->new();
}
isa_ok($derivedsignal, 'Bio::MAGE::QuantitationType::DerivedSignal');

# test the package_name class method
is($derivedsignal->package_name(), q[QuantitationType],
  'package');

# test the class_name class method
is($derivedsignal->class_name(), q[Bio::MAGE::QuantitationType::DerivedSignal],
  'class_name');

# set the attribute values in the call to new()
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $derivedsignal = Bio::MAGE::QuantitationType::DerivedSignal->new(isBackground => '1',
identifier => '2',
name => '3');
}


#
# testing attribute isBackground
#

# test attribute values can be set in new()
is($derivedsignal->getIsBackground(), '1',
  'isBackground new');

# test getter/setter
$derivedsignal->setIsBackground('1');
is($derivedsignal->getIsBackground(), '1',
  'isBackground getter/setter');

# test getter throws exception with argument
eval {$derivedsignal->getIsBackground(1)};
ok($@, 'isBackground getter throws exception with argument');

# test setter throws exception with no argument
eval {$derivedsignal->setIsBackground()};
ok($@, 'isBackground setter throws exception with no argument');

# test setter throws exception with too many argument
eval {$derivedsignal->setIsBackground('1', '1')};
ok($@, 'isBackground setter throws exception with too many argument');

# test setter accepts undef
eval {$derivedsignal->setIsBackground(undef)};
ok((!$@ and not defined $derivedsignal->getIsBackground()),
   'isBackground setter accepts undef');



#
# testing attribute identifier
#

# test attribute values can be set in new()
is($derivedsignal->getIdentifier(), '2',
  'identifier new');

# test getter/setter
$derivedsignal->setIdentifier('2');
is($derivedsignal->getIdentifier(), '2',
  'identifier getter/setter');

# test getter throws exception with argument
eval {$derivedsignal->getIdentifier(1)};
ok($@, 'identifier getter throws exception with argument');

# test setter throws exception with no argument
eval {$derivedsignal->setIdentifier()};
ok($@, 'identifier setter throws exception with no argument');

# test setter throws exception with too many argument
eval {$derivedsignal->setIdentifier('2', '2')};
ok($@, 'identifier setter throws exception with too many argument');

# test setter accepts undef
eval {$derivedsignal->setIdentifier(undef)};
ok((!$@ and not defined $derivedsignal->getIdentifier()),
   'identifier setter accepts undef');



#
# testing attribute name
#

# test attribute values can be set in new()
is($derivedsignal->getName(), '3',
  'name new');

# test getter/setter
$derivedsignal->setName('3');
is($derivedsignal->getName(), '3',
  'name getter/setter');

# test getter throws exception with argument
eval {$derivedsignal->getName(1)};
ok($@, 'name getter throws exception with argument');

# test setter throws exception with no argument
eval {$derivedsignal->setName()};
ok($@, 'name setter throws exception with no argument');

# test setter throws exception with too many argument
eval {$derivedsignal->setName('3', '3')};
ok($@, 'name setter throws exception with too many argument');

# test setter accepts undef
eval {$derivedsignal->setName(undef)};
ok((!$@ and not defined $derivedsignal->getName()),
   'name setter accepts undef');



# retrieve the list of association meta-data
my %assns = Bio::MAGE::QuantitationType::DerivedSignal->associations();

# set the association values in the call to new()
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $derivedsignal = Bio::MAGE::QuantitationType::DerivedSignal->new(dataType => Bio::MAGE::Description::OntologyEntry->new(),
descriptions => [Bio::MAGE::Description::Description->new()],
scale => Bio::MAGE::Description::OntologyEntry->new(),
security => Bio::MAGE::AuditAndSecurity::Security->new(),
auditTrail => [Bio::MAGE::AuditAndSecurity::Audit->new()],
channel => Bio::MAGE::BioAssay::Channel->new(),
propertySets => [Bio::MAGE::NameValueType->new()],
confidenceIndicators => [Bio::MAGE::QuantitationType::ConfidenceIndicator->new()],
quantitationTypeMaps => [Bio::MAGE::BioAssayData::QuantitationTypeMap->new()]);
}

t/DerivedSignal.t  view on Meta::CPAN

# testing association dataType
my $datatype_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $datatype_assn = Bio::MAGE::Description::OntologyEntry->new();
}


isa_ok($derivedsignal->getDataType, q[Bio::MAGE::Description::OntologyEntry]);

is($derivedsignal->setDataType($datatype_assn), $datatype_assn,
  'setDataType returns value');

ok($derivedsignal->getDataType() == $datatype_assn,
   'getDataType fetches correct value');

# test setDataType throws exception with bad argument
eval {$derivedsignal->setDataType(1)};
ok($@, 'setDataType throws exception with bad argument');


# test getDataType throws exception with argument
eval {$derivedsignal->getDataType(1)};
ok($@, 'getDataType throws exception with argument');

# test setDataType throws exception with no argument
eval {$derivedsignal->setDataType()};
ok($@, 'setDataType throws exception with no argument');

# test setDataType throws exception with too many argument
eval {$derivedsignal->setDataType(1,2)};
ok($@, 'setDataType throws exception with too many argument');

# test setDataType accepts undef
eval {$derivedsignal->setDataType(undef)};
ok((!$@ and not defined $derivedsignal->getDataType()),
   'setDataType accepts undef');

# test the meta-data for the assoication
$assn = $assns{dataType};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association descriptions
my $descriptions_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $descriptions_assn = Bio::MAGE::Description::Description->new();
}


ok((UNIVERSAL::isa($derivedsignal->getDescriptions,'ARRAY')
 and scalar @{$derivedsignal->getDescriptions} == 1
 and UNIVERSAL::isa($derivedsignal->getDescriptions->[0], q[Bio::MAGE::Description::Description])),
  'descriptions set in new()');

ok(eq_array($derivedsignal->setDescriptions([$descriptions_assn]), [$descriptions_assn]),
   'setDescriptions returns correct value');

ok((UNIVERSAL::isa($derivedsignal->getDescriptions,'ARRAY')
 and scalar @{$derivedsignal->getDescriptions} == 1
 and $derivedsignal->getDescriptions->[0] == $descriptions_assn),
   'getDescriptions fetches correct value');

is($derivedsignal->addDescriptions($descriptions_assn), 2,
  'addDescriptions returns number of items in list');

ok((UNIVERSAL::isa($derivedsignal->getDescriptions,'ARRAY')
 and scalar @{$derivedsignal->getDescriptions} == 2
 and $derivedsignal->getDescriptions->[0] == $descriptions_assn
 and $derivedsignal->getDescriptions->[1] == $descriptions_assn),
  'addDescriptions adds correct value');

# test setDescriptions throws exception with non-array argument
eval {$derivedsignal->setDescriptions(1)};
ok($@, 'setDescriptions throws exception with non-array argument');

# test setDescriptions throws exception with bad argument array
eval {$derivedsignal->setDescriptions([1])};
ok($@, 'setDescriptions throws exception with bad argument array');

# test addDescriptions throws exception with no arguments
eval {$derivedsignal->addDescriptions()};
ok($@, 'addDescriptions throws exception with no arguments');

# test addDescriptions throws exception with bad argument
eval {$derivedsignal->addDescriptions(1)};
ok($@, 'addDescriptions throws exception with bad array');

# test setDescriptions accepts empty array ref
eval {$derivedsignal->setDescriptions([])};
ok((!$@ and defined $derivedsignal->getDescriptions()
    and UNIVERSAL::isa($derivedsignal->getDescriptions, 'ARRAY')
    and scalar @{$derivedsignal->getDescriptions} == 0),
   'setDescriptions accepts empty array ref');


# test getDescriptions throws exception with argument
eval {$derivedsignal->getDescriptions(1)};
ok($@, 'getDescriptions throws exception with argument');

# test setDescriptions throws exception with no argument
eval {$derivedsignal->setDescriptions()};
ok($@, 'setDescriptions throws exception with no argument');

# test setDescriptions throws exception with too many argument
eval {$derivedsignal->setDescriptions(1,2)};
ok($@, 'setDescriptions throws exception with too many argument');

# test setDescriptions accepts undef
eval {$derivedsignal->setDescriptions(undef)};
ok((!$@ and not defined $derivedsignal->getDescriptions()),
   'setDescriptions accepts undef');

# test the meta-data for the assoication
$assn = $assns{descriptions};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association scale
my $scale_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $scale_assn = Bio::MAGE::Description::OntologyEntry->new();
}


isa_ok($derivedsignal->getScale, q[Bio::MAGE::Description::OntologyEntry]);

is($derivedsignal->setScale($scale_assn), $scale_assn,
  'setScale returns value');

ok($derivedsignal->getScale() == $scale_assn,
   'getScale fetches correct value');

# test setScale throws exception with bad argument
eval {$derivedsignal->setScale(1)};
ok($@, 'setScale throws exception with bad argument');


# test getScale throws exception with argument
eval {$derivedsignal->getScale(1)};
ok($@, 'getScale throws exception with argument');

# test setScale throws exception with no argument
eval {$derivedsignal->setScale()};
ok($@, 'setScale throws exception with no argument');

# test setScale throws exception with too many argument
eval {$derivedsignal->setScale(1,2)};
ok($@, 'setScale throws exception with too many argument');

# test setScale accepts undef
eval {$derivedsignal->setScale(undef)};
ok((!$@ and not defined $derivedsignal->getScale()),
   'setScale accepts undef');

# test the meta-data for the assoication
$assn = $assns{scale};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association security
my $security_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $security_assn = Bio::MAGE::AuditAndSecurity::Security->new();
}


isa_ok($derivedsignal->getSecurity, q[Bio::MAGE::AuditAndSecurity::Security]);

is($derivedsignal->setSecurity($security_assn), $security_assn,
  'setSecurity returns value');

ok($derivedsignal->getSecurity() == $security_assn,
   'getSecurity fetches correct value');

# test setSecurity throws exception with bad argument
eval {$derivedsignal->setSecurity(1)};
ok($@, 'setSecurity throws exception with bad argument');


# test getSecurity throws exception with argument
eval {$derivedsignal->getSecurity(1)};
ok($@, 'getSecurity throws exception with argument');

# test setSecurity throws exception with no argument
eval {$derivedsignal->setSecurity()};
ok($@, 'setSecurity throws exception with no argument');

# test setSecurity throws exception with too many argument
eval {$derivedsignal->setSecurity(1,2)};
ok($@, 'setSecurity throws exception with too many argument');

# test setSecurity accepts undef
eval {$derivedsignal->setSecurity(undef)};
ok((!$@ and not defined $derivedsignal->getSecurity()),
   'setSecurity accepts undef');

# test the meta-data for the assoication
$assn = $assns{security};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association auditTrail
my $audittrail_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $audittrail_assn = Bio::MAGE::AuditAndSecurity::Audit->new();
}


ok((UNIVERSAL::isa($derivedsignal->getAuditTrail,'ARRAY')
 and scalar @{$derivedsignal->getAuditTrail} == 1
 and UNIVERSAL::isa($derivedsignal->getAuditTrail->[0], q[Bio::MAGE::AuditAndSecurity::Audit])),
  'auditTrail set in new()');

ok(eq_array($derivedsignal->setAuditTrail([$audittrail_assn]), [$audittrail_assn]),
   'setAuditTrail returns correct value');

ok((UNIVERSAL::isa($derivedsignal->getAuditTrail,'ARRAY')
 and scalar @{$derivedsignal->getAuditTrail} == 1
 and $derivedsignal->getAuditTrail->[0] == $audittrail_assn),
   'getAuditTrail fetches correct value');

is($derivedsignal->addAuditTrail($audittrail_assn), 2,
  'addAuditTrail returns number of items in list');

ok((UNIVERSAL::isa($derivedsignal->getAuditTrail,'ARRAY')
 and scalar @{$derivedsignal->getAuditTrail} == 2
 and $derivedsignal->getAuditTrail->[0] == $audittrail_assn
 and $derivedsignal->getAuditTrail->[1] == $audittrail_assn),
  'addAuditTrail adds correct value');

# test setAuditTrail throws exception with non-array argument
eval {$derivedsignal->setAuditTrail(1)};
ok($@, 'setAuditTrail throws exception with non-array argument');

# test setAuditTrail throws exception with bad argument array
eval {$derivedsignal->setAuditTrail([1])};
ok($@, 'setAuditTrail throws exception with bad argument array');

# test addAuditTrail throws exception with no arguments
eval {$derivedsignal->addAuditTrail()};
ok($@, 'addAuditTrail throws exception with no arguments');

# test addAuditTrail throws exception with bad argument
eval {$derivedsignal->addAuditTrail(1)};
ok($@, 'addAuditTrail throws exception with bad array');

# test setAuditTrail accepts empty array ref
eval {$derivedsignal->setAuditTrail([])};
ok((!$@ and defined $derivedsignal->getAuditTrail()
    and UNIVERSAL::isa($derivedsignal->getAuditTrail, 'ARRAY')
    and scalar @{$derivedsignal->getAuditTrail} == 0),
   'setAuditTrail accepts empty array ref');


# test getAuditTrail throws exception with argument
eval {$derivedsignal->getAuditTrail(1)};
ok($@, 'getAuditTrail throws exception with argument');

# test setAuditTrail throws exception with no argument
eval {$derivedsignal->setAuditTrail()};
ok($@, 'setAuditTrail throws exception with no argument');

# test setAuditTrail throws exception with too many argument
eval {$derivedsignal->setAuditTrail(1,2)};
ok($@, 'setAuditTrail throws exception with too many argument');

# test setAuditTrail accepts undef
eval {$derivedsignal->setAuditTrail(undef)};
ok((!$@ and not defined $derivedsignal->getAuditTrail()),
   'setAuditTrail accepts undef');

# test the meta-data for the assoication
$assn = $assns{auditTrail};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association channel
my $channel_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $channel_assn = Bio::MAGE::BioAssay::Channel->new();
}


isa_ok($derivedsignal->getChannel, q[Bio::MAGE::BioAssay::Channel]);

is($derivedsignal->setChannel($channel_assn), $channel_assn,
  'setChannel returns value');

ok($derivedsignal->getChannel() == $channel_assn,
   'getChannel fetches correct value');

# test setChannel throws exception with bad argument
eval {$derivedsignal->setChannel(1)};
ok($@, 'setChannel throws exception with bad argument');


# test getChannel throws exception with argument
eval {$derivedsignal->getChannel(1)};
ok($@, 'getChannel throws exception with argument');

# test setChannel throws exception with no argument
eval {$derivedsignal->setChannel()};
ok($@, 'setChannel throws exception with no argument');

# test setChannel throws exception with too many argument
eval {$derivedsignal->setChannel(1,2)};
ok($@, 'setChannel throws exception with too many argument');

# test setChannel accepts undef
eval {$derivedsignal->setChannel(undef)};
ok((!$@ and not defined $derivedsignal->getChannel()),
   'setChannel accepts undef');

# test the meta-data for the assoication
$assn = $assns{channel};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association propertySets
my $propertysets_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $propertysets_assn = Bio::MAGE::NameValueType->new();
}


ok((UNIVERSAL::isa($derivedsignal->getPropertySets,'ARRAY')
 and scalar @{$derivedsignal->getPropertySets} == 1
 and UNIVERSAL::isa($derivedsignal->getPropertySets->[0], q[Bio::MAGE::NameValueType])),
  'propertySets set in new()');

ok(eq_array($derivedsignal->setPropertySets([$propertysets_assn]), [$propertysets_assn]),
   'setPropertySets returns correct value');

ok((UNIVERSAL::isa($derivedsignal->getPropertySets,'ARRAY')
 and scalar @{$derivedsignal->getPropertySets} == 1
 and $derivedsignal->getPropertySets->[0] == $propertysets_assn),
   'getPropertySets fetches correct value');

is($derivedsignal->addPropertySets($propertysets_assn), 2,
  'addPropertySets returns number of items in list');

ok((UNIVERSAL::isa($derivedsignal->getPropertySets,'ARRAY')
 and scalar @{$derivedsignal->getPropertySets} == 2
 and $derivedsignal->getPropertySets->[0] == $propertysets_assn
 and $derivedsignal->getPropertySets->[1] == $propertysets_assn),
  'addPropertySets adds correct value');

# test setPropertySets throws exception with non-array argument
eval {$derivedsignal->setPropertySets(1)};
ok($@, 'setPropertySets throws exception with non-array argument');

# test setPropertySets throws exception with bad argument array
eval {$derivedsignal->setPropertySets([1])};
ok($@, 'setPropertySets throws exception with bad argument array');

# test addPropertySets throws exception with no arguments
eval {$derivedsignal->addPropertySets()};
ok($@, 'addPropertySets throws exception with no arguments');

# test addPropertySets throws exception with bad argument
eval {$derivedsignal->addPropertySets(1)};
ok($@, 'addPropertySets throws exception with bad array');

# test setPropertySets accepts empty array ref
eval {$derivedsignal->setPropertySets([])};
ok((!$@ and defined $derivedsignal->getPropertySets()
    and UNIVERSAL::isa($derivedsignal->getPropertySets, 'ARRAY')
    and scalar @{$derivedsignal->getPropertySets} == 0),
   'setPropertySets accepts empty array ref');


# test getPropertySets throws exception with argument
eval {$derivedsignal->getPropertySets(1)};
ok($@, 'getPropertySets throws exception with argument');

# test setPropertySets throws exception with no argument
eval {$derivedsignal->setPropertySets()};
ok($@, 'setPropertySets throws exception with no argument');

# test setPropertySets throws exception with too many argument
eval {$derivedsignal->setPropertySets(1,2)};
ok($@, 'setPropertySets throws exception with too many argument');

# test setPropertySets accepts undef
eval {$derivedsignal->setPropertySets(undef)};
ok((!$@ and not defined $derivedsignal->getPropertySets()),
   'setPropertySets accepts undef');

# test the meta-data for the assoication
$assn = $assns{propertySets};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association confidenceIndicators
my $confidenceindicators_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $confidenceindicators_assn = Bio::MAGE::QuantitationType::ConfidenceIndicator->new();
}


ok((UNIVERSAL::isa($derivedsignal->getConfidenceIndicators,'ARRAY')
 and scalar @{$derivedsignal->getConfidenceIndicators} == 1
 and UNIVERSAL::isa($derivedsignal->getConfidenceIndicators->[0], q[Bio::MAGE::QuantitationType::ConfidenceIndicator])),
  'confidenceIndicators set in new()');

ok(eq_array($derivedsignal->setConfidenceIndicators([$confidenceindicators_assn]), [$confidenceindicators_assn]),
   'setConfidenceIndicators returns correct value');

ok((UNIVERSAL::isa($derivedsignal->getConfidenceIndicators,'ARRAY')
 and scalar @{$derivedsignal->getConfidenceIndicators} == 1
 and $derivedsignal->getConfidenceIndicators->[0] == $confidenceindicators_assn),
   'getConfidenceIndicators fetches correct value');

is($derivedsignal->addConfidenceIndicators($confidenceindicators_assn), 2,
  'addConfidenceIndicators returns number of items in list');

ok((UNIVERSAL::isa($derivedsignal->getConfidenceIndicators,'ARRAY')
 and scalar @{$derivedsignal->getConfidenceIndicators} == 2
 and $derivedsignal->getConfidenceIndicators->[0] == $confidenceindicators_assn
 and $derivedsignal->getConfidenceIndicators->[1] == $confidenceindicators_assn),
  'addConfidenceIndicators adds correct value');

# test setConfidenceIndicators throws exception with non-array argument
eval {$derivedsignal->setConfidenceIndicators(1)};
ok($@, 'setConfidenceIndicators throws exception with non-array argument');

# test setConfidenceIndicators throws exception with bad argument array
eval {$derivedsignal->setConfidenceIndicators([1])};
ok($@, 'setConfidenceIndicators throws exception with bad argument array');

# test addConfidenceIndicators throws exception with no arguments
eval {$derivedsignal->addConfidenceIndicators()};
ok($@, 'addConfidenceIndicators throws exception with no arguments');

# test addConfidenceIndicators throws exception with bad argument
eval {$derivedsignal->addConfidenceIndicators(1)};
ok($@, 'addConfidenceIndicators throws exception with bad array');

# test setConfidenceIndicators accepts empty array ref
eval {$derivedsignal->setConfidenceIndicators([])};
ok((!$@ and defined $derivedsignal->getConfidenceIndicators()
    and UNIVERSAL::isa($derivedsignal->getConfidenceIndicators, 'ARRAY')
    and scalar @{$derivedsignal->getConfidenceIndicators} == 0),
   'setConfidenceIndicators accepts empty array ref');


# test getConfidenceIndicators throws exception with argument
eval {$derivedsignal->getConfidenceIndicators(1)};
ok($@, 'getConfidenceIndicators throws exception with argument');

# test setConfidenceIndicators throws exception with no argument
eval {$derivedsignal->setConfidenceIndicators()};
ok($@, 'setConfidenceIndicators throws exception with no argument');

# test setConfidenceIndicators throws exception with too many argument
eval {$derivedsignal->setConfidenceIndicators(1,2)};
ok($@, 'setConfidenceIndicators throws exception with too many argument');

# test setConfidenceIndicators accepts undef
eval {$derivedsignal->setConfidenceIndicators(undef)};
ok((!$@ and not defined $derivedsignal->getConfidenceIndicators()),
   'setConfidenceIndicators accepts undef');

# test the meta-data for the assoication
$assn = $assns{confidenceIndicators};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

# testing association quantitationTypeMaps
my $quantitationtypemaps_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $quantitationtypemaps_assn = Bio::MAGE::BioAssayData::QuantitationTypeMap->new();
}


ok((UNIVERSAL::isa($derivedsignal->getQuantitationTypeMaps,'ARRAY')
 and scalar @{$derivedsignal->getQuantitationTypeMaps} == 1
 and UNIVERSAL::isa($derivedsignal->getQuantitationTypeMaps->[0], q[Bio::MAGE::BioAssayData::QuantitationTypeMap])),
  'quantitationTypeMaps set in new()');

ok(eq_array($derivedsignal->setQuantitationTypeMaps([$quantitationtypemaps_assn]), [$quantitationtypemaps_assn]),
   'setQuantitationTypeMaps returns correct value');

ok((UNIVERSAL::isa($derivedsignal->getQuantitationTypeMaps,'ARRAY')
 and scalar @{$derivedsignal->getQuantitationTypeMaps} == 1
 and $derivedsignal->getQuantitationTypeMaps->[0] == $quantitationtypemaps_assn),
   'getQuantitationTypeMaps fetches correct value');

is($derivedsignal->addQuantitationTypeMaps($quantitationtypemaps_assn), 2,
  'addQuantitationTypeMaps returns number of items in list');

ok((UNIVERSAL::isa($derivedsignal->getQuantitationTypeMaps,'ARRAY')
 and scalar @{$derivedsignal->getQuantitationTypeMaps} == 2
 and $derivedsignal->getQuantitationTypeMaps->[0] == $quantitationtypemaps_assn
 and $derivedsignal->getQuantitationTypeMaps->[1] == $quantitationtypemaps_assn),
  'addQuantitationTypeMaps adds correct value');

# test setQuantitationTypeMaps throws exception with non-array argument
eval {$derivedsignal->setQuantitationTypeMaps(1)};
ok($@, 'setQuantitationTypeMaps throws exception with non-array argument');

# test setQuantitationTypeMaps throws exception with bad argument array
eval {$derivedsignal->setQuantitationTypeMaps([1])};
ok($@, 'setQuantitationTypeMaps throws exception with bad argument array');

# test addQuantitationTypeMaps throws exception with no arguments
eval {$derivedsignal->addQuantitationTypeMaps()};
ok($@, 'addQuantitationTypeMaps throws exception with no arguments');

# test addQuantitationTypeMaps throws exception with bad argument
eval {$derivedsignal->addQuantitationTypeMaps(1)};
ok($@, 'addQuantitationTypeMaps throws exception with bad array');

# test setQuantitationTypeMaps accepts empty array ref
eval {$derivedsignal->setQuantitationTypeMaps([])};
ok((!$@ and defined $derivedsignal->getQuantitationTypeMaps()
    and UNIVERSAL::isa($derivedsignal->getQuantitationTypeMaps, 'ARRAY')
    and scalar @{$derivedsignal->getQuantitationTypeMaps} == 0),
   'setQuantitationTypeMaps accepts empty array ref');


# test getQuantitationTypeMaps throws exception with argument
eval {$derivedsignal->getQuantitationTypeMaps(1)};
ok($@, 'getQuantitationTypeMaps throws exception with argument');

# test setQuantitationTypeMaps throws exception with no argument
eval {$derivedsignal->setQuantitationTypeMaps()};
ok($@, 'setQuantitationTypeMaps throws exception with no argument');

# test setQuantitationTypeMaps throws exception with too many argument
eval {$derivedsignal->setQuantitationTypeMaps(1,2)};
ok($@, 'setQuantitationTypeMaps throws exception with too many argument');

# test setQuantitationTypeMaps accepts undef
eval {$derivedsignal->setQuantitationTypeMaps(undef)};
ok((!$@ and not defined $derivedsignal->getQuantitationTypeMaps()),
   'setQuantitationTypeMaps accepts undef');

# test the meta-data for the assoication
$assn = $assns{quantitationTypeMaps};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/DerivedSignal.t  view on Meta::CPAN

{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};

  # create a superclass
  $standardquantitationtype = Bio::MAGE::QuantitationType::StandardQuantitationType->new();
}

# testing superclass StandardQuantitationType
isa_ok($standardquantitationtype, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);
isa_ok($derivedsignal, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);

t/MeasuredSignal.t  view on Meta::CPAN

use Bio::MAGE::BioAssayData::QuantitationTypeMap;
use Bio::MAGE::Description::OntologyEntry;
use Bio::MAGE::NameValueType;
use Bio::MAGE::BioAssay::Channel;
use Bio::MAGE::AuditAndSecurity::Audit;
use Bio::MAGE::AuditAndSecurity::Security;
use Bio::MAGE::Description::Description;


# we test the new() method
my $measuredsignal;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $measuredsignal = Bio::MAGE::QuantitationType::MeasuredSignal->new();
}
isa_ok($measuredsignal, 'Bio::MAGE::QuantitationType::MeasuredSignal');

# test the package_name class method
is($measuredsignal->package_name(), q[QuantitationType],
  'package');

# test the class_name class method
is($measuredsignal->class_name(), q[Bio::MAGE::QuantitationType::MeasuredSignal],
  'class_name');

# set the attribute values in the call to new()
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $measuredsignal = Bio::MAGE::QuantitationType::MeasuredSignal->new(isBackground => '1',
identifier => '2',
name => '3');
}


#
# testing attribute isBackground
#

# test attribute values can be set in new()
is($measuredsignal->getIsBackground(), '1',
  'isBackground new');

# test getter/setter
$measuredsignal->setIsBackground('1');
is($measuredsignal->getIsBackground(), '1',
  'isBackground getter/setter');

# test getter throws exception with argument
eval {$measuredsignal->getIsBackground(1)};
ok($@, 'isBackground getter throws exception with argument');

# test setter throws exception with no argument
eval {$measuredsignal->setIsBackground()};
ok($@, 'isBackground setter throws exception with no argument');

# test setter throws exception with too many argument
eval {$measuredsignal->setIsBackground('1', '1')};
ok($@, 'isBackground setter throws exception with too many argument');

# test setter accepts undef
eval {$measuredsignal->setIsBackground(undef)};
ok((!$@ and not defined $measuredsignal->getIsBackground()),
   'isBackground setter accepts undef');



#
# testing attribute identifier
#

# test attribute values can be set in new()
is($measuredsignal->getIdentifier(), '2',
  'identifier new');

# test getter/setter
$measuredsignal->setIdentifier('2');
is($measuredsignal->getIdentifier(), '2',
  'identifier getter/setter');

# test getter throws exception with argument
eval {$measuredsignal->getIdentifier(1)};
ok($@, 'identifier getter throws exception with argument');

# test setter throws exception with no argument
eval {$measuredsignal->setIdentifier()};
ok($@, 'identifier setter throws exception with no argument');

# test setter throws exception with too many argument
eval {$measuredsignal->setIdentifier('2', '2')};
ok($@, 'identifier setter throws exception with too many argument');

# test setter accepts undef
eval {$measuredsignal->setIdentifier(undef)};
ok((!$@ and not defined $measuredsignal->getIdentifier()),
   'identifier setter accepts undef');



#
# testing attribute name
#

# test attribute values can be set in new()
is($measuredsignal->getName(), '3',
  'name new');

# test getter/setter
$measuredsignal->setName('3');
is($measuredsignal->getName(), '3',
  'name getter/setter');

# test getter throws exception with argument
eval {$measuredsignal->getName(1)};
ok($@, 'name getter throws exception with argument');

# test setter throws exception with no argument
eval {$measuredsignal->setName()};
ok($@, 'name setter throws exception with no argument');

# test setter throws exception with too many argument
eval {$measuredsignal->setName('3', '3')};
ok($@, 'name setter throws exception with too many argument');

# test setter accepts undef
eval {$measuredsignal->setName(undef)};
ok((!$@ and not defined $measuredsignal->getName()),
   'name setter accepts undef');



# retrieve the list of association meta-data
my %assns = Bio::MAGE::QuantitationType::MeasuredSignal->associations();

# set the association values in the call to new()
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $measuredsignal = Bio::MAGE::QuantitationType::MeasuredSignal->new(dataType => Bio::MAGE::Description::OntologyEntry->new(),
descriptions => [Bio::MAGE::Description::Description->new()],
scale => Bio::MAGE::Description::OntologyEntry->new(),
security => Bio::MAGE::AuditAndSecurity::Security->new(),
auditTrail => [Bio::MAGE::AuditAndSecurity::Audit->new()],
channel => Bio::MAGE::BioAssay::Channel->new(),
propertySets => [Bio::MAGE::NameValueType->new()],
confidenceIndicators => [Bio::MAGE::QuantitationType::ConfidenceIndicator->new()],
quantitationTypeMaps => [Bio::MAGE::BioAssayData::QuantitationTypeMap->new()]);
}

t/MeasuredSignal.t  view on Meta::CPAN

# testing association dataType
my $datatype_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $datatype_assn = Bio::MAGE::Description::OntologyEntry->new();
}


isa_ok($measuredsignal->getDataType, q[Bio::MAGE::Description::OntologyEntry]);

is($measuredsignal->setDataType($datatype_assn), $datatype_assn,
  'setDataType returns value');

ok($measuredsignal->getDataType() == $datatype_assn,
   'getDataType fetches correct value');

# test setDataType throws exception with bad argument
eval {$measuredsignal->setDataType(1)};
ok($@, 'setDataType throws exception with bad argument');


# test getDataType throws exception with argument
eval {$measuredsignal->getDataType(1)};
ok($@, 'getDataType throws exception with argument');

# test setDataType throws exception with no argument
eval {$measuredsignal->setDataType()};
ok($@, 'setDataType throws exception with no argument');

# test setDataType throws exception with too many argument
eval {$measuredsignal->setDataType(1,2)};
ok($@, 'setDataType throws exception with too many argument');

# test setDataType accepts undef
eval {$measuredsignal->setDataType(undef)};
ok((!$@ and not defined $measuredsignal->getDataType()),
   'setDataType accepts undef');

# test the meta-data for the assoication
$assn = $assns{dataType};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association descriptions
my $descriptions_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $descriptions_assn = Bio::MAGE::Description::Description->new();
}


ok((UNIVERSAL::isa($measuredsignal->getDescriptions,'ARRAY')
 and scalar @{$measuredsignal->getDescriptions} == 1
 and UNIVERSAL::isa($measuredsignal->getDescriptions->[0], q[Bio::MAGE::Description::Description])),
  'descriptions set in new()');

ok(eq_array($measuredsignal->setDescriptions([$descriptions_assn]), [$descriptions_assn]),
   'setDescriptions returns correct value');

ok((UNIVERSAL::isa($measuredsignal->getDescriptions,'ARRAY')
 and scalar @{$measuredsignal->getDescriptions} == 1
 and $measuredsignal->getDescriptions->[0] == $descriptions_assn),
   'getDescriptions fetches correct value');

is($measuredsignal->addDescriptions($descriptions_assn), 2,
  'addDescriptions returns number of items in list');

ok((UNIVERSAL::isa($measuredsignal->getDescriptions,'ARRAY')
 and scalar @{$measuredsignal->getDescriptions} == 2
 and $measuredsignal->getDescriptions->[0] == $descriptions_assn
 and $measuredsignal->getDescriptions->[1] == $descriptions_assn),
  'addDescriptions adds correct value');

# test setDescriptions throws exception with non-array argument
eval {$measuredsignal->setDescriptions(1)};
ok($@, 'setDescriptions throws exception with non-array argument');

# test setDescriptions throws exception with bad argument array
eval {$measuredsignal->setDescriptions([1])};
ok($@, 'setDescriptions throws exception with bad argument array');

# test addDescriptions throws exception with no arguments
eval {$measuredsignal->addDescriptions()};
ok($@, 'addDescriptions throws exception with no arguments');

# test addDescriptions throws exception with bad argument
eval {$measuredsignal->addDescriptions(1)};
ok($@, 'addDescriptions throws exception with bad array');

# test setDescriptions accepts empty array ref
eval {$measuredsignal->setDescriptions([])};
ok((!$@ and defined $measuredsignal->getDescriptions()
    and UNIVERSAL::isa($measuredsignal->getDescriptions, 'ARRAY')
    and scalar @{$measuredsignal->getDescriptions} == 0),
   'setDescriptions accepts empty array ref');


# test getDescriptions throws exception with argument
eval {$measuredsignal->getDescriptions(1)};
ok($@, 'getDescriptions throws exception with argument');

# test setDescriptions throws exception with no argument
eval {$measuredsignal->setDescriptions()};
ok($@, 'setDescriptions throws exception with no argument');

# test setDescriptions throws exception with too many argument
eval {$measuredsignal->setDescriptions(1,2)};
ok($@, 'setDescriptions throws exception with too many argument');

# test setDescriptions accepts undef
eval {$measuredsignal->setDescriptions(undef)};
ok((!$@ and not defined $measuredsignal->getDescriptions()),
   'setDescriptions accepts undef');

# test the meta-data for the assoication
$assn = $assns{descriptions};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association scale
my $scale_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $scale_assn = Bio::MAGE::Description::OntologyEntry->new();
}


isa_ok($measuredsignal->getScale, q[Bio::MAGE::Description::OntologyEntry]);

is($measuredsignal->setScale($scale_assn), $scale_assn,
  'setScale returns value');

ok($measuredsignal->getScale() == $scale_assn,
   'getScale fetches correct value');

# test setScale throws exception with bad argument
eval {$measuredsignal->setScale(1)};
ok($@, 'setScale throws exception with bad argument');


# test getScale throws exception with argument
eval {$measuredsignal->getScale(1)};
ok($@, 'getScale throws exception with argument');

# test setScale throws exception with no argument
eval {$measuredsignal->setScale()};
ok($@, 'setScale throws exception with no argument');

# test setScale throws exception with too many argument
eval {$measuredsignal->setScale(1,2)};
ok($@, 'setScale throws exception with too many argument');

# test setScale accepts undef
eval {$measuredsignal->setScale(undef)};
ok((!$@ and not defined $measuredsignal->getScale()),
   'setScale accepts undef');

# test the meta-data for the assoication
$assn = $assns{scale};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association security
my $security_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $security_assn = Bio::MAGE::AuditAndSecurity::Security->new();
}


isa_ok($measuredsignal->getSecurity, q[Bio::MAGE::AuditAndSecurity::Security]);

is($measuredsignal->setSecurity($security_assn), $security_assn,
  'setSecurity returns value');

ok($measuredsignal->getSecurity() == $security_assn,
   'getSecurity fetches correct value');

# test setSecurity throws exception with bad argument
eval {$measuredsignal->setSecurity(1)};
ok($@, 'setSecurity throws exception with bad argument');


# test getSecurity throws exception with argument
eval {$measuredsignal->getSecurity(1)};
ok($@, 'getSecurity throws exception with argument');

# test setSecurity throws exception with no argument
eval {$measuredsignal->setSecurity()};
ok($@, 'setSecurity throws exception with no argument');

# test setSecurity throws exception with too many argument
eval {$measuredsignal->setSecurity(1,2)};
ok($@, 'setSecurity throws exception with too many argument');

# test setSecurity accepts undef
eval {$measuredsignal->setSecurity(undef)};
ok((!$@ and not defined $measuredsignal->getSecurity()),
   'setSecurity accepts undef');

# test the meta-data for the assoication
$assn = $assns{security};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association auditTrail
my $audittrail_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $audittrail_assn = Bio::MAGE::AuditAndSecurity::Audit->new();
}


ok((UNIVERSAL::isa($measuredsignal->getAuditTrail,'ARRAY')
 and scalar @{$measuredsignal->getAuditTrail} == 1
 and UNIVERSAL::isa($measuredsignal->getAuditTrail->[0], q[Bio::MAGE::AuditAndSecurity::Audit])),
  'auditTrail set in new()');

ok(eq_array($measuredsignal->setAuditTrail([$audittrail_assn]), [$audittrail_assn]),
   'setAuditTrail returns correct value');

ok((UNIVERSAL::isa($measuredsignal->getAuditTrail,'ARRAY')
 and scalar @{$measuredsignal->getAuditTrail} == 1
 and $measuredsignal->getAuditTrail->[0] == $audittrail_assn),
   'getAuditTrail fetches correct value');

is($measuredsignal->addAuditTrail($audittrail_assn), 2,
  'addAuditTrail returns number of items in list');

ok((UNIVERSAL::isa($measuredsignal->getAuditTrail,'ARRAY')
 and scalar @{$measuredsignal->getAuditTrail} == 2
 and $measuredsignal->getAuditTrail->[0] == $audittrail_assn
 and $measuredsignal->getAuditTrail->[1] == $audittrail_assn),
  'addAuditTrail adds correct value');

# test setAuditTrail throws exception with non-array argument
eval {$measuredsignal->setAuditTrail(1)};
ok($@, 'setAuditTrail throws exception with non-array argument');

# test setAuditTrail throws exception with bad argument array
eval {$measuredsignal->setAuditTrail([1])};
ok($@, 'setAuditTrail throws exception with bad argument array');

# test addAuditTrail throws exception with no arguments
eval {$measuredsignal->addAuditTrail()};
ok($@, 'addAuditTrail throws exception with no arguments');

# test addAuditTrail throws exception with bad argument
eval {$measuredsignal->addAuditTrail(1)};
ok($@, 'addAuditTrail throws exception with bad array');

# test setAuditTrail accepts empty array ref
eval {$measuredsignal->setAuditTrail([])};
ok((!$@ and defined $measuredsignal->getAuditTrail()
    and UNIVERSAL::isa($measuredsignal->getAuditTrail, 'ARRAY')
    and scalar @{$measuredsignal->getAuditTrail} == 0),
   'setAuditTrail accepts empty array ref');


# test getAuditTrail throws exception with argument
eval {$measuredsignal->getAuditTrail(1)};
ok($@, 'getAuditTrail throws exception with argument');

# test setAuditTrail throws exception with no argument
eval {$measuredsignal->setAuditTrail()};
ok($@, 'setAuditTrail throws exception with no argument');

# test setAuditTrail throws exception with too many argument
eval {$measuredsignal->setAuditTrail(1,2)};
ok($@, 'setAuditTrail throws exception with too many argument');

# test setAuditTrail accepts undef
eval {$measuredsignal->setAuditTrail(undef)};
ok((!$@ and not defined $measuredsignal->getAuditTrail()),
   'setAuditTrail accepts undef');

# test the meta-data for the assoication
$assn = $assns{auditTrail};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association channel
my $channel_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $channel_assn = Bio::MAGE::BioAssay::Channel->new();
}


isa_ok($measuredsignal->getChannel, q[Bio::MAGE::BioAssay::Channel]);

is($measuredsignal->setChannel($channel_assn), $channel_assn,
  'setChannel returns value');

ok($measuredsignal->getChannel() == $channel_assn,
   'getChannel fetches correct value');

# test setChannel throws exception with bad argument
eval {$measuredsignal->setChannel(1)};
ok($@, 'setChannel throws exception with bad argument');


# test getChannel throws exception with argument
eval {$measuredsignal->getChannel(1)};
ok($@, 'getChannel throws exception with argument');

# test setChannel throws exception with no argument
eval {$measuredsignal->setChannel()};
ok($@, 'setChannel throws exception with no argument');

# test setChannel throws exception with too many argument
eval {$measuredsignal->setChannel(1,2)};
ok($@, 'setChannel throws exception with too many argument');

# test setChannel accepts undef
eval {$measuredsignal->setChannel(undef)};
ok((!$@ and not defined $measuredsignal->getChannel()),
   'setChannel accepts undef');

# test the meta-data for the assoication
$assn = $assns{channel};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association propertySets
my $propertysets_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $propertysets_assn = Bio::MAGE::NameValueType->new();
}


ok((UNIVERSAL::isa($measuredsignal->getPropertySets,'ARRAY')
 and scalar @{$measuredsignal->getPropertySets} == 1
 and UNIVERSAL::isa($measuredsignal->getPropertySets->[0], q[Bio::MAGE::NameValueType])),
  'propertySets set in new()');

ok(eq_array($measuredsignal->setPropertySets([$propertysets_assn]), [$propertysets_assn]),
   'setPropertySets returns correct value');

ok((UNIVERSAL::isa($measuredsignal->getPropertySets,'ARRAY')
 and scalar @{$measuredsignal->getPropertySets} == 1
 and $measuredsignal->getPropertySets->[0] == $propertysets_assn),
   'getPropertySets fetches correct value');

is($measuredsignal->addPropertySets($propertysets_assn), 2,
  'addPropertySets returns number of items in list');

ok((UNIVERSAL::isa($measuredsignal->getPropertySets,'ARRAY')
 and scalar @{$measuredsignal->getPropertySets} == 2
 and $measuredsignal->getPropertySets->[0] == $propertysets_assn
 and $measuredsignal->getPropertySets->[1] == $propertysets_assn),
  'addPropertySets adds correct value');

# test setPropertySets throws exception with non-array argument
eval {$measuredsignal->setPropertySets(1)};
ok($@, 'setPropertySets throws exception with non-array argument');

# test setPropertySets throws exception with bad argument array
eval {$measuredsignal->setPropertySets([1])};
ok($@, 'setPropertySets throws exception with bad argument array');

# test addPropertySets throws exception with no arguments
eval {$measuredsignal->addPropertySets()};
ok($@, 'addPropertySets throws exception with no arguments');

# test addPropertySets throws exception with bad argument
eval {$measuredsignal->addPropertySets(1)};
ok($@, 'addPropertySets throws exception with bad array');

# test setPropertySets accepts empty array ref
eval {$measuredsignal->setPropertySets([])};
ok((!$@ and defined $measuredsignal->getPropertySets()
    and UNIVERSAL::isa($measuredsignal->getPropertySets, 'ARRAY')
    and scalar @{$measuredsignal->getPropertySets} == 0),
   'setPropertySets accepts empty array ref');


# test getPropertySets throws exception with argument
eval {$measuredsignal->getPropertySets(1)};
ok($@, 'getPropertySets throws exception with argument');

# test setPropertySets throws exception with no argument
eval {$measuredsignal->setPropertySets()};
ok($@, 'setPropertySets throws exception with no argument');

# test setPropertySets throws exception with too many argument
eval {$measuredsignal->setPropertySets(1,2)};
ok($@, 'setPropertySets throws exception with too many argument');

# test setPropertySets accepts undef
eval {$measuredsignal->setPropertySets(undef)};
ok((!$@ and not defined $measuredsignal->getPropertySets()),
   'setPropertySets accepts undef');

# test the meta-data for the assoication
$assn = $assns{propertySets};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association confidenceIndicators
my $confidenceindicators_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $confidenceindicators_assn = Bio::MAGE::QuantitationType::ConfidenceIndicator->new();
}


ok((UNIVERSAL::isa($measuredsignal->getConfidenceIndicators,'ARRAY')
 and scalar @{$measuredsignal->getConfidenceIndicators} == 1
 and UNIVERSAL::isa($measuredsignal->getConfidenceIndicators->[0], q[Bio::MAGE::QuantitationType::ConfidenceIndicator])),
  'confidenceIndicators set in new()');

ok(eq_array($measuredsignal->setConfidenceIndicators([$confidenceindicators_assn]), [$confidenceindicators_assn]),
   'setConfidenceIndicators returns correct value');

ok((UNIVERSAL::isa($measuredsignal->getConfidenceIndicators,'ARRAY')
 and scalar @{$measuredsignal->getConfidenceIndicators} == 1
 and $measuredsignal->getConfidenceIndicators->[0] == $confidenceindicators_assn),
   'getConfidenceIndicators fetches correct value');

is($measuredsignal->addConfidenceIndicators($confidenceindicators_assn), 2,
  'addConfidenceIndicators returns number of items in list');

ok((UNIVERSAL::isa($measuredsignal->getConfidenceIndicators,'ARRAY')
 and scalar @{$measuredsignal->getConfidenceIndicators} == 2
 and $measuredsignal->getConfidenceIndicators->[0] == $confidenceindicators_assn
 and $measuredsignal->getConfidenceIndicators->[1] == $confidenceindicators_assn),
  'addConfidenceIndicators adds correct value');

# test setConfidenceIndicators throws exception with non-array argument
eval {$measuredsignal->setConfidenceIndicators(1)};
ok($@, 'setConfidenceIndicators throws exception with non-array argument');

# test setConfidenceIndicators throws exception with bad argument array
eval {$measuredsignal->setConfidenceIndicators([1])};
ok($@, 'setConfidenceIndicators throws exception with bad argument array');

# test addConfidenceIndicators throws exception with no arguments
eval {$measuredsignal->addConfidenceIndicators()};
ok($@, 'addConfidenceIndicators throws exception with no arguments');

# test addConfidenceIndicators throws exception with bad argument
eval {$measuredsignal->addConfidenceIndicators(1)};
ok($@, 'addConfidenceIndicators throws exception with bad array');

# test setConfidenceIndicators accepts empty array ref
eval {$measuredsignal->setConfidenceIndicators([])};
ok((!$@ and defined $measuredsignal->getConfidenceIndicators()
    and UNIVERSAL::isa($measuredsignal->getConfidenceIndicators, 'ARRAY')
    and scalar @{$measuredsignal->getConfidenceIndicators} == 0),
   'setConfidenceIndicators accepts empty array ref');


# test getConfidenceIndicators throws exception with argument
eval {$measuredsignal->getConfidenceIndicators(1)};
ok($@, 'getConfidenceIndicators throws exception with argument');

# test setConfidenceIndicators throws exception with no argument
eval {$measuredsignal->setConfidenceIndicators()};
ok($@, 'setConfidenceIndicators throws exception with no argument');

# test setConfidenceIndicators throws exception with too many argument
eval {$measuredsignal->setConfidenceIndicators(1,2)};
ok($@, 'setConfidenceIndicators throws exception with too many argument');

# test setConfidenceIndicators accepts undef
eval {$measuredsignal->setConfidenceIndicators(undef)};
ok((!$@ and not defined $measuredsignal->getConfidenceIndicators()),
   'setConfidenceIndicators accepts undef');

# test the meta-data for the assoication
$assn = $assns{confidenceIndicators};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

# testing association quantitationTypeMaps
my $quantitationtypemaps_assn;
{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};
  $quantitationtypemaps_assn = Bio::MAGE::BioAssayData::QuantitationTypeMap->new();
}


ok((UNIVERSAL::isa($measuredsignal->getQuantitationTypeMaps,'ARRAY')
 and scalar @{$measuredsignal->getQuantitationTypeMaps} == 1
 and UNIVERSAL::isa($measuredsignal->getQuantitationTypeMaps->[0], q[Bio::MAGE::BioAssayData::QuantitationTypeMap])),
  'quantitationTypeMaps set in new()');

ok(eq_array($measuredsignal->setQuantitationTypeMaps([$quantitationtypemaps_assn]), [$quantitationtypemaps_assn]),
   'setQuantitationTypeMaps returns correct value');

ok((UNIVERSAL::isa($measuredsignal->getQuantitationTypeMaps,'ARRAY')
 and scalar @{$measuredsignal->getQuantitationTypeMaps} == 1
 and $measuredsignal->getQuantitationTypeMaps->[0] == $quantitationtypemaps_assn),
   'getQuantitationTypeMaps fetches correct value');

is($measuredsignal->addQuantitationTypeMaps($quantitationtypemaps_assn), 2,
  'addQuantitationTypeMaps returns number of items in list');

ok((UNIVERSAL::isa($measuredsignal->getQuantitationTypeMaps,'ARRAY')
 and scalar @{$measuredsignal->getQuantitationTypeMaps} == 2
 and $measuredsignal->getQuantitationTypeMaps->[0] == $quantitationtypemaps_assn
 and $measuredsignal->getQuantitationTypeMaps->[1] == $quantitationtypemaps_assn),
  'addQuantitationTypeMaps adds correct value');

# test setQuantitationTypeMaps throws exception with non-array argument
eval {$measuredsignal->setQuantitationTypeMaps(1)};
ok($@, 'setQuantitationTypeMaps throws exception with non-array argument');

# test setQuantitationTypeMaps throws exception with bad argument array
eval {$measuredsignal->setQuantitationTypeMaps([1])};
ok($@, 'setQuantitationTypeMaps throws exception with bad argument array');

# test addQuantitationTypeMaps throws exception with no arguments
eval {$measuredsignal->addQuantitationTypeMaps()};
ok($@, 'addQuantitationTypeMaps throws exception with no arguments');

# test addQuantitationTypeMaps throws exception with bad argument
eval {$measuredsignal->addQuantitationTypeMaps(1)};
ok($@, 'addQuantitationTypeMaps throws exception with bad array');

# test setQuantitationTypeMaps accepts empty array ref
eval {$measuredsignal->setQuantitationTypeMaps([])};
ok((!$@ and defined $measuredsignal->getQuantitationTypeMaps()
    and UNIVERSAL::isa($measuredsignal->getQuantitationTypeMaps, 'ARRAY')
    and scalar @{$measuredsignal->getQuantitationTypeMaps} == 0),
   'setQuantitationTypeMaps accepts empty array ref');


# test getQuantitationTypeMaps throws exception with argument
eval {$measuredsignal->getQuantitationTypeMaps(1)};
ok($@, 'getQuantitationTypeMaps throws exception with argument');

# test setQuantitationTypeMaps throws exception with no argument
eval {$measuredsignal->setQuantitationTypeMaps()};
ok($@, 'setQuantitationTypeMaps throws exception with no argument');

# test setQuantitationTypeMaps throws exception with too many argument
eval {$measuredsignal->setQuantitationTypeMaps(1,2)};
ok($@, 'setQuantitationTypeMaps throws exception with too many argument');

# test setQuantitationTypeMaps accepts undef
eval {$measuredsignal->setQuantitationTypeMaps(undef)};
ok((!$@ and not defined $measuredsignal->getQuantitationTypeMaps()),
   'setQuantitationTypeMaps accepts undef');

# test the meta-data for the assoication
$assn = $assns{quantitationTypeMaps};
isa_ok($assn, 'Bio::MAGE::Association');
$end = $assn->other();
isa_ok($end, 'Bio::MAGE::Association::End');
ok((defined $end
   and defined $end->documentation(),
   and defined $end->cardinality(),

t/MeasuredSignal.t  view on Meta::CPAN

{
  # silence the abstract class warnings
  local $SIG{__WARN__} = sub {'IGNORE'};

  # create a superclass
  $standardquantitationtype = Bio::MAGE::QuantitationType::StandardQuantitationType->new();
}

# testing superclass StandardQuantitationType
isa_ok($standardquantitationtype, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);
isa_ok($measuredsignal, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);

t/StandardQuantitationType.t  view on Meta::CPAN

   and ($end->is_ref() == 0 or $end->is_ref() == 1),
   and defined $end->class_name(),
   and $end->class_name()),
   'quantitationTypeMaps->self() is a valid Bio::MAGE::Association::End'
  );




# create a subclass
my $derivedsignal = Bio::MAGE::QuantitationType::DerivedSignal->new();

# testing subclass DerivedSignal
isa_ok($derivedsignal, q[Bio::MAGE::QuantitationType::DerivedSignal]);
isa_ok($derivedsignal, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);


# create a subclass
my $measuredsignal = Bio::MAGE::QuantitationType::MeasuredSignal->new();

# testing subclass MeasuredSignal
isa_ok($measuredsignal, q[Bio::MAGE::QuantitationType::MeasuredSignal]);
isa_ok($measuredsignal, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);


# create a subclass
my $ratio = Bio::MAGE::QuantitationType::Ratio->new();

# testing subclass Ratio
isa_ok($ratio, q[Bio::MAGE::QuantitationType::Ratio]);
isa_ok($ratio, q[Bio::MAGE::QuantitationType::StandardQuantitationType]);