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

Bio::MAGE::BioMaterial::BioMaterial

SYNOPSIS

  use Bio::MAGE::BioMaterial::BioMaterial;

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

    # creating an already populated instance
  my $biomaterial = Bio::MAGE::BioMaterial::BioMaterial->new(characteristics=>$characteristics_value,
                        treatments=>$treatments_value,
                        qualityControlStatistics=>$qualityControlStatistics_value,
                        materialType=>$materialType_value);

    # setting and retrieving object associations
  my $characteristics_val = $biomaterial->characteristics();
  $biomaterial->characteristics($value);

  my $treatments_val = $biomaterial->treatments();
  $biomaterial->treatments($value);

  my $qualityControlStatistics_val = $biomaterial->qualityControlStatistics();
  $biomaterial->qualityControlStatistics($value);

  my $materialType_val = $biomaterial->materialType();
  $biomaterial->materialType($value);

DESCRIPTION

From the MAGE-OM documentation for the BioMaterial class:

BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... Biomaterials can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)).

INHERITANCE

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

• Bio::MAGE::Identifiable
  

Bio::MAGE::BioMaterial::BioMaterial has the following subclasses

• Bio::MAGE::BioMaterial::LabeledExtract
  
• Bio::MAGE::BioMaterial::BioSource
  
• Bio::MAGE::BioMaterial::BioSample
  

CLASS METHODS

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

new()

new(%args)

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

• characteristics
  Sets the value of the characteristics association (from Bio::MAGE::BioMaterial::BioMaterial).

• treatments
  Sets the value of the treatments association (from Bio::MAGE::BioMaterial::BioMaterial).

• qualityControlStatistics
  Sets the value of the qualityControlStatistics association (from Bio::MAGE::BioMaterial::BioMaterial).

• materialType
  Sets the value of the materialType association (from Bio::MAGE::BioMaterial::BioMaterial).

• 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::BioMaterial::BioMaterial.

$package_name = package()

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

@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::BioMaterial::BioMaterial: has the following attribute accessor methods:

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::BioMaterial::BioMaterial: has the following association accessor methods:

characteristics

From the MAGE-OM documentation for the characteristics association:

Innate properties of the biosource, such as genotype, cultivar, tissue type, cell type, ploidy, etc.

$array_ref = $biomaterial->setCharacteristics($array_ref)

The restricted setter method for the characteristics association.

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

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

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::OntologyEntry instances

$array_ref = $biomaterial->getCharacteristics()

The restricted getter method for the characteristics association.

Input parameters: none

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

Side effects: none

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

$biomaterial->addCharacteristics(@vals)

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

Input parameters: the list of values @vals to add to the characteristics 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::OntologyEntry

treatments

From the MAGE-OM documentation for the treatments association:

This association is one way from BioMaterial to Treatment. From this a BioMaterial can discover the amount and type of BioMaterial that was part of the treatment that produced it.

$array_ref = $biomaterial->setTreatments($array_ref)

The restricted setter method for the treatments association.

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

Return value: the current value of the treatments association : a reference to an array of objects of type Bio::MAGE::BioMaterial::Treatment

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::BioMaterial::Treatment instances

$array_ref = $biomaterial->getTreatments()

The restricted getter method for the treatments association.

Input parameters: none

Return value: the current value of the treatments association : a reference to an array of objects of type Bio::MAGE::BioMaterial::Treatment

Side effects: none

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

$biomaterial->addTreatments(@vals)

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

Input parameters: the list of values @vals to add to the treatments 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::BioMaterial::Treatment

qualityControlStatistics

From the MAGE-OM documentation for the qualityControlStatistics association:

Measures of the quality of the BioMaterial.

$array_ref = $biomaterial->setQualityControlStatistics($array_ref)

The restricted setter method for the qualityControlStatistics association.

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

Return value: the current value of the qualityControlStatistics 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 = $biomaterial->getQualityControlStatistics()

The restricted getter method for the qualityControlStatistics association.

Input parameters: none

Return value: the current value of the qualityControlStatistics 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

$biomaterial->addQualityControlStatistics(@vals)

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

Input parameters: the list of values @vals to add to the qualityControlStatistics 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

materialType

From the MAGE-OM documentation for the materialType association:

The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.

$val = $biomaterial->setMaterialType($val)

The restricted setter method for the materialType association.

Input parameters: the value to which the materialType association will be set : an instance of type Bio::MAGE::Description::OntologyEntry.

Return value: the current value of the materialType association : an instance of type Bio::MAGE::Description::OntologyEntry.

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::Description::OntologyEntry

$val = $biomaterial->getMaterialType()

The restricted getter method for the materialType association.

Input parameters: none

Return value: the current value of the materialType association : an instance of type Bio::MAGE::Description::OntologyEntry.

Side effects: none

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

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).