MAGE::...quence(3pm)

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

okay bestie, buckle UP, because this is the MAGE::...quence(3pm) page from the User Contributed Perl Documentation and it's giving long. It comes in 4 parts, this is part 1, so don't go anywhere 💅

✨ NAME ✨

Bio::MAGE::BioSequence::BioSequence — the class for the MAGE-OM API. that's it, that's the name, iconic 🎀

🌸 SYNOPSIS 🌸

here's the whole vibe in code, no cap:

  use Bio::MAGE::BioSequence::BioSequence

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

  # creating an instance with existing data
  my $biosequence = Bio::MAGE::BioSequence::BioSequence->new(
        identifier=>$identifier_val,
        isApproximateLength=>$isapproximatelength_val,
        length=>$length_val,
        sequence=>$sequence_val,
        name=>$name_val,
        isCircular=>$iscircular_val,
        sequenceDatabases=>\@databaseentry_list,
        auditTrail=>\@audit_list,
        polymerType=>$ontologyentry_ref,
        species=>$ontologyentry_ref,
        propertySets=>\@namevaluetype_list,
        ontologyEntries=>\@ontologyentry_list,
        descriptions=>\@description_list,
        seqFeatures=>\@seqfeature_list,
        security=>$security_ref,
        type=>$ontologyentry_ref,
  );

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

  # 'isApproximateLength' attribute
  my $isApproximateLength_val = $biosequence->isApproximateLength(); # getter
  $biosequence->isApproximateLength($value); # setter

  # 'length' attribute
  my $length_val = $biosequence->length(); # getter
  $biosequence->length($value); # setter

  # 'sequence' attribute
  my $sequence_val = $biosequence->sequence(); # getter
  $biosequence->sequence($value); # setter

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

  # 'isCircular' attribute
  my $isCircular_val = $biosequence->isCircular(); # getter
  $biosequence->isCircular($value); # setter

  # 'sequenceDatabases' association
  my $databaseentry_array_ref = $biosequence->sequenceDatabases(); # getter
  $biosequence->sequenceDatabases(\@databaseentry_list); # setter

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

  # 'polymerType' association
  my $ontologyentry_ref = $biosequence->polymerType(); # getter
  $biosequence->polymerType($ontologyentry_ref); # setter

  # 'species' association
  my $ontologyentry_ref = $biosequence->species(); # getter
  $biosequence->species($ontologyentry_ref); # setter

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

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

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

  # 'seqFeatures' association
  my $seqfeature_array_ref = $biosequence->seqFeatures(); # getter
  $biosequence->seqFeatures(\@seqfeature_list); # setter

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

  # 'type' association
  my $ontologyentry_ref = $biosequence->type(); # getter
  $biosequence->type($ontologyentry_ref); # setter

🦋 DESCRIPTION 🦋

straight from the MAGE-OM documentation for the "BioSequence" class:

A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.

so like... DNA, RNA, or protein? it's the sequence representation. Clone, Gene, or the literal sequence itself. lowkey obsessed 🧬✨

🌈 INHERITANCE 🌈

Bio::MAGE::BioSequence::BioSequence has the following superclasses:

Bio::MAGE::Identifiable

that's the whole family tree for now, bestie 💜

👑 CLASS METHODS 👑

okay so these are the methods you can call without even having an instance first — like, you don't need an object, you just do Bio::MAGE::BioSequence::BioSequence->methodname(). main character energy, honestly ✨

🍓 `new()`

🍓 `new(%args)`

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

identifier — sets the value of the "identifier" attribute. and psst, this attribute was inherited from class "Bio::MAGE::Identifiable". iykyk 💅
isApproximateLength — sets the value of the "isApproximateLength" attribute.
length — sets the value of the "length" attribute.
sequence — sets the value of the "sequence" attribute.
name — sets the value of the "name" attribute. inherited from class "Bio::MAGE::Identifiable" 💜
isCircular — sets the value of the "isCircular" attribute.
sequenceDatabases — sets the value of the "sequenceDatabases" association. The value must be of type: array of "Bio::MAGE::Description::DatabaseEntry".
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. inherited from class "Bio::MAGE::Extendable" ✨ The value must be of type: array of "Bio::MAGE::NameValueType".
species — sets the value of the "species" association. The value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".
polymerType — sets the value of the "polymerType" association. The value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".
ontologyEntries — sets the value of the "ontologyEntries" association. The value must be of type: array of "Bio::MAGE::Description::OntologyEntry".
seqFeatures — sets the value of the "seqFeatures" association. The value must be of type: array of "Bio::MAGE::BioSequence::SeqFeature".
descriptions — sets the value of the "descriptions" association. inherited from class "Bio::MAGE::Describable" 💜 The value must be of type: array of "Bio::MAGE::Description::Description".
security — sets the value of the "security" association. inherited from class "Bio::MAGE::Describable". The value must be of type: instance of "Bio::MAGE::AuditAndSecurity::Security".
type — sets the value of the "type" association. The value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".

💖 `$obj = class->new(%parameters)`

The "new()" method is the class constructor. it builds the thing, 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. so don't come for it asking for those 🙈

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. slay.

💖 `@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. very meta, very demure 💅

🎀 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. copy-paste but make it official ✨

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. pick your fighter 🫶

Return value: none.
Side effects: will call "croak()" if a slot_name is used that the class does not define. so like... don't do that 💀

💜 `@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 to put the value in, one to get it back out. iconic duo behavior 🔥

"Bio::MAGE::BioSequence::BioSequence" 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 = $biosequence->setIdentifier($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 = $biosequence->getIdentifier() — the restricted getter method for the identifier attribute. Bestie this one just reads, it does not write 💅

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

🌸 isApproximateLength

Methods for the isApproximateLength attribute, babes ✨

Straight from the MAGE-OM documentation:

If length not positively known will be true

$val = $biosequence->setIsApproximateLength($val) — the restricted setter method for the isApproximateLength attribute.

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

$val = $biosequence->getIsApproximateLength() — the restricted getter method for the isApproximateLength attribute.

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

🦋 length

Methods for the length attribute 💖

From the MAGE-OM documentation:

The number of residues in the biosequence.

$val = $biosequence->setLength($val) — the restricted setter method for the length attribute.

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

$val = $biosequence->getLength() — the restricted getter method for the length attribute.

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

🎀 sequence

Methods for the sequence attribute, okurrr 🌈

From the MAGE-OM documentation:

The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G.

The attribute is optional and instead of specified here, can be found through the DatabaseEntry.

⚠️ Heads up bestie: that second line is doing a lot of heavy lifting — this thing is optional, and if it's not chilling here, it's living inside the DatabaseEntry instead. Lowkey iconic of it.

$val = $biosequence->setSequence($val) — the restricted setter method for the sequence attribute.

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

$val = $biosequence->getSequence() — the restricted getter method for the sequence attribute.

Input parameters: none
Return value: the current value of the sequence 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 = $biosequence->setName($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 = $biosequence->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

🔥 isCircular

Methods for the isCircular attribute 🫶

From the MAGE-OM documentation:

Indicates if the BioSequence is circular in nature.

$val = $biosequence->setIsCircular($val) — the restricted setter method for the isCircular attribute.

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

$val = $biosequence->getIsCircular() — the restricted getter method for the isCircular attribute.

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

🦋 ASSOCIATIONS 🦋

Okay so associations are just references to other classes, bestie — it's giving networking but for data 💅 And every association in MAGE-OM has a cardinality, which decides the minimum and maximum number of instances of the other class that may be included in the association:

exactly one item — There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1 — There may be one item in the association, i.e. this is an optional data field.
1..N — There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
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::BioSequence::BioSequence has the following association accessor methods 👑

🍓 sequenceDatabases

Methods for the sequenceDatabases association.

From the MAGE-OM documentation:

References an entry in a species database, like GenBank, UniGene, etc.

$array_ref = $biosequence->setSequenceDatabases($array_ref) — the restricted setter method for the sequenceDatabases association.

Input parameters: the value to which the sequenceDatabases association will be set : a reference to an array of objects of type Bio::MAGE::Description::DatabaseEntry
Return value: the current value of the sequenceDatabases association : a reference to an array of objects of type Bio::MAGE::Description::DatabaseEntry
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::DatabaseEntry instances

$array_ref = $biosequence->getSequenceDatabases() — the restricted getter method for the sequenceDatabases association.

Input parameters: none
Return value: the current value of the sequenceDatabases association : a reference to an array of objects of type Bio::MAGE::Description::DatabaseEntry
Side effects: none
Exceptions: will call croak() if any input parameters are specified

$val = $biosequence->addSequenceDatabases(@vals) — because the sequenceDatabases association has list cardinality, it may store more than one value. This method adds the current list of objects in the sequenceDatabases association. Not me casually dropping multiple objects at once 😌

Input parameters: the list of values @vals to add to the sequenceDatabases 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::DatabaseEntry

🧚 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 = $biosequence->setAuditTrail($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 = $biosequence->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 = $biosequence->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. Receipts, but make them audit records 🧾

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 💖

Bestie, these are the 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 = $biosequence->setPropertySets($array_ref) — the restricted setter for the propertySets association. She sets, she doesn't guess. 💅
- 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 = $biosequence->getPropertySets() — the restricted getter for the propertySets association. Just reading, minding her business. ✨
- 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 = $biosequence->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. She's a collector, fr fr. 🫶
- 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

🌸 species 🌸

Methods for the species association. Biology girlies rise. 🧚

From the MAGE-OM documentation:

The organism from which this sequence was obtained.

$val = $biosequence->setSpecies($val) — the restricted setter for the species association.
- Input parameters: the value to which the species association will be set : one of the accepted enumerated values.
- Return value: the current value of the species 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::OntologyEntry
$val = $biosequence->getSpecies() — the restricted getter for the species association. No arguments, no drama. 💅
- Input parameters: none
- Return value: the current value of the species association : an instance of type Bio::MAGE::Description::OntologyEntry.
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified

🦋 polymerType 🦋

Methods for the polymerType association.

From the MAGE-OM documentation:

A choice of protein, RNA, or DNA.

$val = $biosequence->setPolymerType($val) — the restricted setter for the polymerType association.
- Input parameters: the value to which the polymerType association will be set : one of the accepted enumerated values.
- Return value: the current value of the polymerType 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::OntologyEntry
$val = $biosequence->getPolymerType() — the restricted getter for the polymerType association.
- Input parameters: none
- Return value: the current value of the polymerType association : an instance of type Bio::MAGE::Description::OntologyEntry.
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified

🌈 ontologyEntries 🌈

Methods for the ontologyEntries association.

From the MAGE-OM documentation:

Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.

$array_ref = $biosequence->setOntologyEntries($array_ref) — the restricted setter for the ontologyEntries association.
- Input parameters: the value to which the ontologyEntries association will be set : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
- Return value: the current value of the ontologyEntries 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 = $biosequence->getOntologyEntries() — the restricted getter for the ontologyEntries association. ✨
- Input parameters: none
- Return value: the current value of the ontologyEntries 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 = $biosequence->addOntologyEntries(@vals) — because the ontologyEntries association has list cardinality, it may store more than one value. This method adds the current list of objects in the ontologyEntries association. Stack 'em up bestie, she can hold them all. 🫶
- Input parameters: the list of values @vals to add to the ontologyEntries 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

🔥 seqFeatures 🔥

Methods for the seqFeatures association.

From the MAGE-OM documentation:

Association to annotations for subsequences. Corresponds to the GenBank Frame Table.

$array_ref = $biosequence->setSeqFeatures($array_ref) — the restricted setter for the seqFeatures association.
- Input parameters: the value to which the seqFeatures association will be set : a reference to an array of objects of type Bio::MAGE::BioSequence::SeqFeature
- Return value: the current value of the seqFeatures association : a reference to an array of objects of type Bio::MAGE::BioSequence::SeqFeature
- 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::BioSequence::SeqFeature instances
$array_ref = $biosequence->getSeqFeatures() — the restricted getter for the seqFeatures association. She's just peeking, respectfully. 🙈
- Input parameters: none
- Return value: the current value of the seqFeatures association : a reference to an array of objects of type Bio::MAGE::BioSequence::SeqFeature
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $biosequence->addSeqFeatures(@vals) — because the seqFeatures association has list cardinality, it may store more than one value. This method adds the current list of objects in the seqFeatures association. The way she just keeps adding... iconic. 👑
- Input parameters: the list of values @vals to add to the seqFeatures 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::BioSequence::SeqFeature

🎀 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 = $biosequence->setDescriptions($array_ref) — the restricted setter 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 = $biosequence->getDescriptions() — the restricted getter 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 = $biosequence->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.

So for that method that adds to the descriptions association, here's the breakdown:

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

✨ security ✨

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $biosequence->setSecurity($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 = $biosequence->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

✨ type ✨

Methods for the type association.

From the MAGE-OM documentation:

The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.

$val = $biosequence->setType($val)
- The restricted setter method for the type association.
- Input parameters: the value to which the type association will be set : one of the accepted enumerated values.
- Return value: the current value of the type 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::OntologyEntry
$val = $biosequence->getType()
- The restricted getter method for the type association.
- Input parameters: none
- Return value: the current value of the type association : an instance of type Bio::MAGE::Description::OntologyEntry.
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified

           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. Periodt.

✨ 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 550: '=item' outside of any '=over'
Around line 635: You forgot a '=back' before '=head2'
Around line 1097: Expected '=item 2'
Around line 1102: Expected '=item 3'
Around line 1107: Expected '=item 4'

Source/version: perl v5.32.0, date: 2020-11-27. MAGE::...quence(3pm) — and that's the tea, bestie! 💖✨

📦 where this page comes from

debian bookworm: libbio-mage-perl 20030502.3-6 · MIT
debian trixie: libbio-mage-perl 20030502.3-6 · MIT
ubuntu jammy: libbio-mage-perl 20030502.3-6 · MIT
ubuntu noble: libbio-mage-perl 20030502.3-6 · MIT
ubuntu resolute: libbio-mage-perl 20030502.3-6 · MIT
ubuntu stonking: libbio-mage-perl 20030502.3-6 · MIT
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms

MAGE::...quence(3pm)

✨ NAME ✨

🌸 SYNOPSIS 🌸

🦋 DESCRIPTION 🦋

🌈 INHERITANCE 🌈

👑 CLASS METHODS 👑

🍓 new()

🍓 new(%args)

💖 $obj = class->new(%parameters)

💖 @names = class->get_slot_names()

💖 @name_list = get_attribute_names()

💖 @name_list = get_association_names()

💖 @class_list = get_superclasses()

💖 @class_list = get_subclasses()

💖 $name = class_name()

💖 $package_name = package_name()

💖 %assns = associations()

🎀 INSTANCE METHODS 🎀

💜 $obj_copy = $obj->new()

💜 $obj->set_slots(%parameters)

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

💜 @obj_list = $obj->get_slots(@name_list)

💜 $val = $obj->set_slot($name,$val)

💜 $val = $obj->get_slot($name)

🧚 ATTRIBUTES 🧚

🌸 identifier

⭐ $val = $biosequence->setIdentifier($val)

🌸 isApproximateLength

🦋 length

🎀 sequence

💜 name

🔥 isCircular

🦋 ASSOCIATIONS 🦋

🍓 sequenceDatabases

🧚 auditTrail

💖 propertySets 💖

🌸 species 🌸

🦋 polymerType 🦋

🌈 ontologyEntries 🌈

🔥 seqFeatures 🔥

🎀 descriptions 🎀

✨ security ✨

✨ type ✨

🌸 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌸

✨ SLOTS ✨

✨ ATTRIBUTES AND ASSOCIATIONS ✨

✨ GENERIC METHODS ✨

🐞 BUGS 🐞

👑 AUTHOR 👑

🌈 SEE ALSO 🌈

💀 POD ERRORS 💀

🍓 `new()`

🍓 `new(%args)`

💖 `$obj = class->new(%parameters)`

💖 `@names = class->get_slot_names()`

💖 `@name_list = get_attribute_names()`

💖 `@name_list = get_association_names()`

💖 `@class_list = get_superclasses()`

💖 `@class_list = get_subclasses()`

💖 `$name = class_name()`

💖 `$package_name = package_name()`

💖 `%assns = associations()`

💜 `$obj_copy = $obj->new()`

💜 `$obj->set_slots(%parameters)`

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

💜 `@obj_list = $obj->get_slots(@name_list)`

💜 `$val = $obj->set_slot($name,$val)`

💜 `$val = $obj->get_slot($name)`

🌸 `identifier`

⭐ `$val = $biosequence->setIdentifier($val)`