Provided by: libbio-mage-perl_20030502.3-4_all bug

NAME

       Bio::MAGE::BioSequence::BioSequence - Class for the MAGE-OM API

SYNOPSIS

         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

       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.

INHERITANCE

       Bio::MAGE::BioSequence::BioSequence 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::BioSequence::BioSequence->methodname() syntax.

       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").

           ·   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 (this attribute was 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 (this association was 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 (this association was 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 (this association was 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.

           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.

           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.

           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.

       "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.

               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.

           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.

           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.

           $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
       Associations are references to other classes. Associations in MAGE-OM have a cardinality
       that determines the minimum and maximum number of instances of the 'other' class that
       maybe included in the association:

       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::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.

               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.

               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 = $biosequence->setPropertySets($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 = $biosequence->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 = $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.

               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.

           From the MAGE-OM documentation:

           The organism from which this sequence was obtained.

           $val = $biosequence->setSpecies($val)
               The restricted setter method 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 method for the "species" association.

               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 method 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 method 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 method 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 method 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.

               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 method 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 method for the "seqFeatures" association.

               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.

               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 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 = $biosequence->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 = $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.

               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".

   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

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       Around line 550:
           '=item' outside of any '=over'

       Around line 635:
           You forgot a '=back' before '=head2'

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