• Bio::MAGE::ArrayDesign::ArrayDesign
• SYNOPSIS
• DESCRIPTION
• INHERITANCE
• CLASS METHODS
• ATTRIBUTES
• ASSOCIATIONS
• BUGS
• AUTHOR
• SEE ALSO

Bio::MAGE::ArrayDesign::ArrayDesign

SYNOPSIS

  use Bio::MAGE::ArrayDesign::ArrayDesign;

    # creating an empty instance
  my $arraydesign = Bio::MAGE::ArrayDesign::ArrayDesign->new();

    # creating an already populated instance
  my $arraydesign = Bio::MAGE::ArrayDesign::ArrayDesign->new(numberOfFeatures=>$numberOfFeatures_value,
                        version=>$version_value,
                        reporterGroups=>$reporterGroups_value,
                        protocolApplications=>$protocolApplications_value,
                        featureGroups=>$featureGroups_value,
                        compositeGroups=>$compositeGroups_value,
                        designProviders=>$designProviders_value);

    # setting and retrieving object attributes
  my $numberOfFeatures_val = $arraydesign->numberOfFeatures();
  $arraydesign->numberOfFeatures($value);

  my $version_val = $arraydesign->version();
  $arraydesign->version($value);

    # setting and retrieving object associations
  my $reporterGroups_val = $arraydesign->reporterGroups();
  $arraydesign->reporterGroups($value);

  my $protocolApplications_val = $arraydesign->protocolApplications();
  $arraydesign->protocolApplications($value);

  my $featureGroups_val = $arraydesign->featureGroups();
  $arraydesign->featureGroups($value);

  my $compositeGroups_val = $arraydesign->compositeGroups();
  $arraydesign->compositeGroups($value);

  my $designProviders_val = $arraydesign->designProviders();
  $arraydesign->designProviders($value);

DESCRIPTION

From the MAGE-OM documentation for the ArrayDesign class:

Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.

INHERITANCE

Bio::MAGE::ArrayDesign::ArrayDesign has the following super classes

• Bio::MAGE::Identifiable
  

Bio::MAGE::ArrayDesign::ArrayDesign has the following subclasses

• Bio::MAGE::ArrayDesign::PhysicalArrayDesign
  

CLASS METHODS

The following methods can all be called without first having an instance of the class via the Bio::MAGE::ArrayDesign::ArrayDesign->methodname() syntax.

new()

new(%args)

The object constructor new() accepts the following optional named-value style arguments:

• numberOfFeatures
  Sets the value of the numberOfFeatures attribute (from Bio::MAGE::ArrayDesign::ArrayDesign).

• version
  Sets the value of the version attribute (from Bio::MAGE::ArrayDesign::ArrayDesign).

• reporterGroups
  Sets the value of the reporterGroups association (from Bio::MAGE::ArrayDesign::ArrayDesign).

• protocolApplications
  Sets the value of the protocolApplications association (from Bio::MAGE::ArrayDesign::ArrayDesign).

• featureGroups
  Sets the value of the featureGroups association (from Bio::MAGE::ArrayDesign::ArrayDesign).

• compositeGroups
  Sets the value of the compositeGroups association (from Bio::MAGE::ArrayDesign::ArrayDesign).

• designProviders
  Sets the value of the designProviders association (from Bio::MAGE::ArrayDesign::ArrayDesign).

• identifier
  Sets the value of the identifier attribute (from Bio::MAGE::Identifiable).

• name
  Sets the value of the name attribute (from Bio::MAGE::Identifiable).

• security
  Sets the value of the security association (from Bio::MAGE::Describable).

• auditTrail
  Sets the value of the auditTrail association (from Bio::MAGE::Describable).

• descriptions
  Sets the value of the descriptions association (from Bio::MAGE::Describable).

• propertySets
  Sets the value of the propertySets association (from Bio::MAGE::Extendable).

$obj->set_slots(%parameters)

$obj->set_slots(\@name_list, \@value_list)

The set_slots() method is used to set a number of slots at the same time. It has two different invocation methods. The first takes a named parameter list, and the second takes two array references.

Return value: none

Side effects: will call croak() if a slot_name is used that the class does not define.

$obj->get_slots(@name_list)

The get_slots() method is used to get the values of a number of slots at the same time.

Return value: a list of instance objects

Side effects: none

$val = $obj->set_slot($name,$val)

The set_slot() method sets the slot $name to the value $val

Return value: the new value of the slot, i.e. $val

Side effects: none

$val = $obj->get_slot($name)

The get_slot() method is used to get the values of a number of slots at the same time.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

@names = $obj->get_slot_names()

The get_slot_names() method is used to retrieve the name of all slots defined for a given object.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

$name = class_name()

Returns the full class name for this class, Bio::MAGE::ArrayDesign::ArrayDesign.

$package_name = package()

Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the package that contains class, Bio::MAGE::ArrayDesign::ArrayDesign.

@classes = subclasses()

returns the list of subclasses for this class.

@classes = superclasses()

returns the list of superclasses for this class.

@methods = attribute_methods()

returns the list of attribute accessor methods for this class.

@methods = association_methods()

returns the list of association accessor methods for this class.

%assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are Bio::MAGE::Association objects that provide the meta-information for the association.

ATTRIBUTES

Attributes are simple data types that belong to a single instance of a class. In the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute.

Bio::MAGE::ArrayDesign::ArrayDesign: has the following attribute accessor methods:

numberOfFeatures

From the MAGE-OM documentation for the numberOfFeatures attribute:

The number of features for this array

$val = $arraydesign->setNumberOfFeatures($val)

The restricted setter method for the numberOfFeatures attribute.

Input parameters: the value to which the numberOfFeatures attribute will be set

Return value: the current value of the numberOfFeatures attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $arraydesign->getNumberOfFeatures()

The restricted getter method for the numberOfFeatures attribute.

Input parameters: none

Return value: the current value of the numberOfFeatures attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

version

From the MAGE-OM documentation for the version attribute:

The version of this design.

$val = $arraydesign->setVersion($val)

The restricted setter method for the version attribute.

Input parameters: the value to which the version attribute will be set

Return value: the current value of the version attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $arraydesign->getVersion()

The restricted getter method for the version attribute.

Input parameters: none

Return value: the current value of the version attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

Attributes Inherited from Bio::MAGE::Identifiable

identifier

From the MAGE-OM documentation for the identifier attribute:

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.

$val = $identifiable->setIdentifier($val)

The restricted setter method for the identifier attribute.

Input parameters: the value to which the identifier attribute will be set

Return value: the current value of the identifier attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $identifiable->getIdentifier()

The restricted getter method for the identifier attribute.

Input parameters: none

Return value: the current value of the identifier attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

name

From the MAGE-OM documentation for the name attribute:

The potentially ambiguous common identifier.

$val = $identifiable->setName($val)

The restricted setter method for the name attribute.

Input parameters: the value to which the name attribute will be set

Return value: the current value of the name attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $identifiable->getName()

The restricted getter method for the name attribute.

Input parameters: none

Return value: the current value of the name attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

ASSOCIATIONS

Associations are references to other class objects which can be shared by multiple class instances at the same time. In the Perl implementation of MAGE-OM classes, associations are implemented using three separate methods:

get*

Retrieves the current value. If the association has list cardinality, an array reference is returned.

set*

Sets the current value replacing any existing value. If the association has list cardinality, the argument must be an array reference. Unless you know what you are doing, you probably should be using the add* methods.

add*

This method exists only for associations with list cardinality. It appends a list of objects to any values that may already be stored in the association.

Bio::MAGE::ArrayDesign::ArrayDesign: has the following association accessor methods:

reporterGroups

From the MAGE-OM documentation for the reporterGroups association:

The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.

$array_ref = $arraydesign->setReporterGroups($array_ref)

The restricted setter method for the reporterGroups association.

Input parameters: the value to which the reporterGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup

Return value: the current value of the reporterGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::ArrayDesign::ReporterGroup instances

$array_ref = $arraydesign->getReporterGroups()

The restricted getter method for the reporterGroups association.

Input parameters: none

Return value: the current value of the reporterGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$arraydesign->addReporterGroups(@vals)

Because the reporterGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the reporterGroups association.

Input parameters: the list of values @vals to add to the reporterGroups association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::ArrayDesign::ReporterGroup

protocolApplications

From the MAGE-OM documentation for the protocolApplications association:

Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.

$array_ref = $arraydesign->setProtocolApplications($array_ref)

The restricted setter method for the protocolApplications association.

Input parameters: the value to which the protocolApplications association will be set : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication

Return value: the current value of the protocolApplications association : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::Protocol::ProtocolApplication instances

$array_ref = $arraydesign->getProtocolApplications()

The restricted getter method for the protocolApplications association.

Input parameters: none

Return value: the current value of the protocolApplications association : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$arraydesign->addProtocolApplications(@vals)

Because the protocolApplications association has list cardinality, it may store more than one value. This method adds the current list of objects in the protocolApplications association.

Input parameters: the list of values @vals to add to the protocolApplications association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::Protocol::ProtocolApplication

featureGroups

From the MAGE-OM documentation for the featureGroups association:

The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types.

$array_ref = $arraydesign->setFeatureGroups($array_ref)

The restricted setter method for the featureGroups association.

Input parameters: the value to which the featureGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup

Return value: the current value of the featureGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::ArrayDesign::FeatureGroup instances

$array_ref = $arraydesign->getFeatureGroups()

The restricted getter method for the featureGroups association.

Input parameters: none

Return value: the current value of the featureGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$arraydesign->addFeatureGroups(@vals)

Because the featureGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the featureGroups association.

Input parameters: the list of values @vals to add to the featureGroups association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::ArrayDesign::FeatureGroup

compositeGroups

From the MAGE-OM documentation for the compositeGroups association:

The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types.

$array_ref = $arraydesign->setCompositeGroups($array_ref)

The restricted setter method for the compositeGroups association.

Input parameters: the value to which the compositeGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup

Return value: the current value of the compositeGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::ArrayDesign::CompositeGroup instances

$array_ref = $arraydesign->getCompositeGroups()

The restricted getter method for the compositeGroups association.

Input parameters: none

Return value: the current value of the compositeGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$arraydesign->addCompositeGroups(@vals)

Because the compositeGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the compositeGroups association.

Input parameters: the list of values @vals to add to the compositeGroups association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::ArrayDesign::CompositeGroup

designProviders

From the MAGE-OM documentation for the designProviders association:

The primary contact for information on the array design

$array_ref = $arraydesign->setDesignProviders($array_ref)

The restricted setter method for the designProviders association.

Input parameters: the value to which the designProviders association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact

Return value: the current value of the designProviders association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Contact instances

$array_ref = $arraydesign->getDesignProviders()

The restricted getter method for the designProviders association.

Input parameters: none

Return value: the current value of the designProviders association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$arraydesign->addDesignProviders(@vals)

Because the designProviders association has list cardinality, it may store more than one value. This method adds the current list of objects in the designProviders association.

Input parameters: the list of values @vals to add to the designProviders association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Contact

Associations Inherited from Bio::MAGE::Describable

security

From the MAGE-OM documentation for the security association:

Information on the security for the instance of the class.

$val = $describable->setSecurity($val)

The restricted setter method for the security association.

Input parameters: the value to which the security association will be set : an instance of type Bio::MAGE::AuditAndSecurity::Security.

Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security

$val = $describable->getSecurity()

The restricted getter method for the security association.

Input parameters: none

Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.

Side effects: none

Exceptions: will call croak() if any input parameters are specified

auditTrail

From the MAGE-OM documentation for the auditTrail association:

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

$array_ref = $describable->setAuditTrail($array_ref)

The restricted setter method for the auditTrail association.

Input parameters: the value to which the auditTrail association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit

Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit instances

$array_ref = $describable->getAuditTrail()

The restricted getter method for the auditTrail association.

Input parameters: none

Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$describable->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 @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit

descriptions

From the MAGE-OM documentation for the descriptions association:

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

$array_ref = $describable->setDescriptions($array_ref)

The restricted setter method for the descriptions association.

Input parameters: the value to which the descriptions association will be set : a reference to an array of objects of type Bio::MAGE::Description::Description

Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::Description::Description instances

$array_ref = $describable->getDescriptions()

The restricted getter method for the descriptions association.

Input parameters: none

Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$describable->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 @vals to add to the descriptions association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description

Associations Inherited from Bio::MAGE::Extendable

propertySets

From the MAGE-OM documentation for the propertySets association:

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.

$array_ref = $extendable->setPropertySets($array_ref)

The restricted setter method for the propertySets association.

Input parameters: the value to which the propertySets association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType

Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances

$array_ref = $extendable->getPropertySets()

The restricted getter method for the propertySets association.

Input parameters: none

Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$extendable->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 @vals to add to the propertySets association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType

BUGS

Please send bug reports to mged-mage@lists.sf.net

AUTHOR

Jason E. Stewart (www.openinformatics.com)

SEE ALSO

perl(1).