MAGE::...ompound(3pm)

📦 version 20030502.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

🌸 MAGE::...ompound(3pm) — User Contributed Perl Documentation 💅

okay bestie, sit down, hydrate, and let me tell you about Bio::MAGE::BioMaterial::Compound — this is the 3pm manpage, the User Contributed Perl Documentation one, and it is long, so we're doing this in parts. Part 1 starts now. no sign-off, we're just getting started 🫶

✨ NAME ✨

Bio::MAGE::BioMaterial::Compound — the class for the MAGE-OM API. that's it, that's the name, she's iconic 👑

🦋 SYNOPSIS 🦋

  use Bio::MAGE::BioMaterial::Compound

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

  # creating an instance with existing data
  my $compound = Bio::MAGE::BioMaterial::Compound->new(
        identifier=>$identifier_val,
        name=>$name_val,
        isSolvent=>$issolvent_val,
        auditTrail=>\@audit_list,
        propertySets=>\@namevaluetype_list,
        compoundIndices=>\@ontologyentry_list,
        componentCompounds=>\@compoundmeasurement_list,
        descriptions=>\@description_list,
        externalLIMS=>$databaseentry_ref,
        security=>$security_ref,
  );

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

  # 'name' attribute
  my $name_val = $compound->name(); # getter
  $compound->name($value); # setter

  # 'isSolvent' attribute
  my $isSolvent_val = $compound->isSolvent(); # getter
  $compound->isSolvent($value); # setter

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

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

  # 'compoundIndices' association
  my $ontologyentry_array_ref = $compound->compoundIndices(); # getter
  $compound->compoundIndices(\@ontologyentry_list); # setter

  # 'componentCompounds' association
  my $compoundmeasurement_array_ref = $compound->componentCompounds(); # getter
  $compound->componentCompounds(\@compoundmeasurement_list); # setter

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

  # 'externalLIMS' association
  my $databaseentry_ref = $compound->externalLIMS(); # getter
  $compound->externalLIMS($databaseentry_ref); # setter

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

💖 DESCRIPTION 💖

straight from the MAGE-OM documentation for the "Compound" class, no cap:

A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). It may also be made of other Compounds in proportions using CompoundMeasurements to enumerate the Compounds and their amounts such as LB (Luria Broth) Media. ✨

like. she can be a lil simple girlie OR a whole composite situation. range. 💅

🌈 INHERITANCE 🌈

Bio::MAGE::BioMaterial::Compound has the following superclasses:

  • Bio::MAGE::Identifiable

👑 CLASS METHODS 👑

The following methods can all be called without first having an instance of the class, via the Bio::MAGE::BioMaterial::Compound->methodname() syntax. yes bestie, class methods. you don't need an object to slide in here 🫶

🌸 new()

🌸 new(%args)

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

  • identifier — Sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
  • name — Sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
  • isSolvent — Sets the value of the "isSolvent" attribute
  • auditTrail — Sets the value of the "auditTrail" association (this association was inherited from class "Bio::MAGE::Describable").

The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Audit".

  • propertySets — Sets the value of the "propertySets" association (this association was inherited from class "Bio::MAGE::Extendable").

The value must be of type: array of "Bio::MAGE::NameValueType".

  • compoundIndices — Sets the value of the "compoundIndices" association

The value must be of type: array of "Bio::MAGE::Description::OntologyEntry".

  • descriptions — Sets the value of the "descriptions" association (this association was inherited from class "Bio::MAGE::Describable").

The value must be of type: array of "Bio::MAGE::Description::Description".

  • componentCompounds — Sets the value of the "componentCompounds" association

The value must be of type: array of "Bio::MAGE::BioMaterial::CompoundMeasurement".

  • security — Sets the value of the "security" association (this association was inherited from class "Bio::MAGE::Describable").

The value must be of type: instance of "Bio::MAGE::AuditAndSecurity::Security".

  • externalLIMS — Sets the value of the "externalLIMS" association

The value must be of type: instance of "Bio::MAGE::Description::DatabaseEntry".

🎀 $obj = class->new(%parameters) 🎀

The "new()" method is the class constructor. the main character fr fr.

  • Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.
  • Return value: It returns a reference to an object of the class.
  • Side effects: It invokes the "initialize()" method if it is defined by the class.

🎀 @names = class->get_slot_names() 🎀

The "get_slot_names()" method is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. ok so it's slots only, don't come for me 🙈
  • Return value: A list of the names of all slots defined for this class.
  • Side effects: none

🎀 @name_list = get_attribute_names() 🎀

returns the list of attribute data members for this class.

🎀 @name_list = get_association_names() 🎀

returns the list of association data members for this class.

🎀 @class_list = get_superclasses() 🎀

returns the list of superclasses for this class.

🎀 @class_list = get_subclasses() 🎀

returns the list of subclasses for this class.

🎀 $name = class_name() 🎀

Returns the full class name for this class.

🎀 $package_name = package_name() 🎀

Returns the base package name (i.e. no 'namespace::') of the package that contains this class.

🎀 %assns = associations() 🎀

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

🧚 INSTANCE METHODS 🧚

💜 $obj_copy = $obj->new() 💜

When invoked with an existing object reference and not a class name, the "new()" method acts as a copy constructor — with the new object's initial values set to be those of the existing object. it's giving clone era 🔥

  • Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.
  • Return value: It returns a reference to an object of the class.
  • Side effects: It invokes the "initialize()" method if it is defined by the class.

💜 $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_list = $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

🎀 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. one for putting the vibe in, one for getting the vibe out 💅

"Bio::MAGE::BioMaterial::Compound" has the following attribute accessor methods:

🌸 identifier

Methods for the "identifier" attribute.

From the MAGE-OM documentation:

An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.

$val = $compound->setIdentifier($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 = $compound->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

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $compound->setName($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 = $compound->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

🌸 isSolvent

Methods for the "isSolvent" attribute.

From the MAGE-OM documentation:

A Compound may be a special case Solvent.

$val = $compound->setIsSolvent($val)

The restricted setter method for the "isSolvent" attribute.

  • Input parameters: the value to which the isSolvent attribute will be set
  • Return value: the current value of the isSolvent attribute
  • Side effects: none
  • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

💅 $val = $compound->getIsSolvent()

The restricted getter method for the isSolvent attribute. She only gives, never takes, bestie 🫶

  • Input parameters: none
  • Return value: the current value of the isSolvent attribute
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified

🦋 ASSOCIATIONS 🦋

okay so associations are literally just references to other classes — like, this class knows a guy who knows a guy ✨. And every association in MAGE-OM comes with a cardinality, which is just the rule for the minimum and maximum number of instances of the 'other' class that can be in there:

  1. There must be exactly one item in the association, i.e. this is a mandatory data field.
  2. 0..1 There may be one item in the association, i.e. this is an optional data field.
  3. 1..N There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
  4. 0..N There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

Bio::MAGE::BioMaterial::Compound has the following association accessor methods:

🫶 auditTrail

Methods for the auditTrail association.

From the MAGE-OM documentation:

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

💖 $array_ref = $compound->setAuditTrail($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 = $compound->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

✨ $val = $compound->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. Stack 'em up, no cap 🧚

  • Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals
  • 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

🍓 propertySets

Methods for the propertySets association.

From the MAGE-OM documentation:

Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

💜 $array_ref = $compound->setPropertySets($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 = $compound->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

⭐ $val = $compound->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: the number of items stored in the slot after adding @vals
  • 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

🔥 compoundIndices

Methods for the compoundIndices association.

From the MAGE-OM documentation:

Indices into common Compound Indices, such as the Merck Index, for this Compound.

👑 $array_ref = $compound->setCompoundIndices($array_ref)

The restricted setter method for the compoundIndices association.

  • Input parameters: the value to which the compoundIndices association will be set : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
  • Return value: the current value of the compoundIndices 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 = $compound->getCompoundIndices()

The restricted getter method for the compoundIndices association.

  • Input parameters: none
  • Return value: the current value of the compoundIndices 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

🎀 $val = $compound->addCompoundIndices(@vals)

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

  • Input parameters: the list of values @vals to add to the compoundIndices association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals
  • 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

🌸 descriptions

Methods for the descriptions association.

From the MAGE-OM documentation:

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

💅 $array_ref = $compound->setDescriptions($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 = $compound->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

💜 $val = $compound->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: the number of items stored in the slot after adding @vals
  • 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

🫶 componentCompounds

Methods for the componentCompounds association.

From the MAGE-OM documentation:

The Compounds and their amounts used to create this Compound.

💖 $array_ref = $compound->setComponentCompounds($array_ref)

The restricted setter method for the componentCompounds association.

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

Return value: the current value of the componentCompounds association — a reference to an array of objects of type Bio::MAGE::BioMaterial::CompoundMeasurement. ✨

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::CompoundMeasurement instances. 💀

$array_ref = $compound->getComponentCompounds()

The restricted getter method for the componentCompounds association. 💖

  • Input parameters: none.
  • Return value: the current value of the componentCompounds association — a reference to an array of objects of type Bio::MAGE::BioMaterial::CompoundMeasurement.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

$val = $compound->addComponentCompounds(@vals)

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

  • Input parameters: the list of values @vals to add to the componentCompounds association. NOTE: submitting a single value is permitted.
  • Return value: the number of items stored in the slot after adding @vals.
  • 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::CompoundMeasurement.

security

Methods for the security association. 🔐

From the MAGE-OM documentation:

Information on the security for the instance of the class.

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

The restricted setter method for the security association.

  • Input parameters: the value to which the security association will be set : one of the accepted enumerated values.
  • Return value: the current value of the security association : one of the accepted enumerated values.
  • 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 = $compound->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.

externalLIMS

Methods for the externalLIMS association. 🧬

From the MAGE-OM documentation:

Reference to an entry in an external LIMS data source.

$val = $compound->setExternalLIMS($val)

The restricted setter method for the externalLIMS association.

  • Input parameters: the value to which the externalLIMS association will be set : one of the accepted enumerated values.
  • Return value: the current value of the externalLIMS association : one of the accepted enumerated values.
  • 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::DatabaseEntry.

$val = $compound->getExternalLIMS()

The restricted getter method for the externalLIMS association.

  • Input parameters: none.
  • Return value: the current value of the externalLIMS association : an instance of type Bio::MAGE::Description::DatabaseEntry.
  • Side effects: none.
  • Exceptions: will call croak() if any input parameters are specified.

And here’s a lil initialize method that just returns 1 — iconic, no notes:

sub initialize {

  my $self = shift;
  return 1;

}

SLOTS, ATTRIBUTES, AND ASSOCIATIONS

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. 💅

SLOTS

This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes — use only if you understand the inner workings of the API. Most often slots are used by generic methods such as those in the XML writing and reading classes. 🫣

Slots are implemented using unified getter/setter methods:

$var = $obj->slot_name();

Retrieves the current value of the slot.

$new_var = $obj->slot_name($new_var);

Store $new_var in the slot — the return value is also $new_var.

@names = $obj->get_slot_names()

Returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods. 🚨

ATTRIBUTES AND ASSOCIATIONS

The terms attribute and association indicate data members of the class that were specified directly from the UML model. 🌟

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

get*

Retrieves the current value.

NOTE: For associations, if the association has list cardinality, an array reference is returned.

DATA CHECKING: Ensure that no argument is provided.

set*

Sets the current value, replacing any existing value.

NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.

DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.

add*

NOTE: Only present in associations with list cardinality.

Appends a list of objects to any values that may already be stored in the association.

DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

GENERIC METHODS

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods. 👀

BUGS

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) 🐛

AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org) 👑

SEE ALSO

perl(1). 📚

POD ERRORS

Hey! The above document had some coding errors, which are explained below: 😭

Around line 424: '=item' outside of any '=over'

Around line 509: You forgot a '=back' before '=head2'

Around line 753: Expected '=item 2'

Around line 758: Expected '=item 3'

Around line 763: Expected '=item 4'

Signing off from MAGE::...ompound(3pm) — this was perl v5.32.0, dated 2020-11-27. Bye bestie! 🦋💖

📦 where this page comes from