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MAGE/BioSequence/BioSequence.pm  view on Meta::CPAN

                                        '__ORDERED' => undef
                                      }, 'Bio::MAGE::Association::End' ),
                   '__OTHER' => bless( {
                                         '__NAME' => 'sequenceDatabases',
                                         '__IS_REF' => 1,
                                         '__CARDINALITY' => '0..N',
                                         '__DOCUMENTATION' => 'References an entry in a species database, like GenBank, UniGene, etc.',
                                         '__CLASS_NAME' => 'DatabaseEntry',
                                         '__RANK' => '1',
                                         '__ORDERED' => 0
                                       }, 'Bio::MAGE::Association::End' )
                 }, 'Bio::MAGE::Association' ),
          'ontologyEntries',
          bless( {
                   '__SELF' => bless( {
                                        '__NAME' => undef,
                                        '__IS_REF' => 0,
                                        '__CARDINALITY' => '1',
                                        '__DOCUMENTATION' => 'Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.',
                                        '__CLASS_NAME' => 'BioSequence',
                                        '__RANK' => undef,
                                        '__ORDERED' => undef
                                      }, 'Bio::MAGE::Association::End' ),
                   '__OTHER' => bless( {
                                         '__NAME' => 'ontologyEntries',
                                         '__IS_REF' => 1,
                                         '__CARDINALITY' => '0..N',
                                         '__DOCUMENTATION' => 'Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.',
                                         '__CLASS_NAME' => 'OntologyEntry',
                                         '__RANK' => '2',
                                         '__ORDERED' => 0
                                       }, 'Bio::MAGE::Association::End' )
                 }, 'Bio::MAGE::Association' ),
          'polymerType',
          bless( {
                   '__SELF' => bless( {
                                        '__NAME' => undef,
                                        '__IS_REF' => 0,
                                        '__CARDINALITY' => '1',
                                        '__DOCUMENTATION' => 'A choice of protein, RNA, or DNA.',
                                        '__CLASS_NAME' => 'BioSequence',
                                        '__RANK' => undef,
                                        '__ORDERED' => undef
                                      }, 'Bio::MAGE::Association::End' ),
                   '__OTHER' => bless( {
                                         '__NAME' => 'polymerType',
                                         '__IS_REF' => 1,
                                         '__CARDINALITY' => '1',
                                         '__DOCUMENTATION' => 'A choice of protein, RNA, or DNA.',
                                         '__CLASS_NAME' => 'OntologyEntry',
                                         '__RANK' => '3',
                                         '__ORDERED' => 0
                                       }, 'Bio::MAGE::Association::End' )
                 }, 'Bio::MAGE::Association' ),
          'type',
          bless( {
                   '__SELF' => bless( {
                                        '__NAME' => undef,
                                        '__IS_REF' => 0,
                                        '__CARDINALITY' => '1',
                                        '__DOCUMENTATION' => 'The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.',
                                        '__CLASS_NAME' => 'BioSequence',
                                        '__RANK' => undef,
                                        '__ORDERED' => undef
                                      }, 'Bio::MAGE::Association::End' ),
                   '__OTHER' => bless( {
                                         '__NAME' => 'type',
                                         '__IS_REF' => 1,
                                         '__CARDINALITY' => '1',
                                         '__DOCUMENTATION' => 'The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.',
                                         '__CLASS_NAME' => 'OntologyEntry',
                                         '__RANK' => '4',
                                         '__ORDERED' => 0
                                       }, 'Bio::MAGE::Association::End' )
                 }, 'Bio::MAGE::Association' ),
          'species',
          bless( {
                   '__SELF' => bless( {
                                        '__NAME' => undef,
                                        '__IS_REF' => 0,
                                        '__CARDINALITY' => '1',
                                        '__DOCUMENTATION' => 'The organism from which this sequence was obtained.',
                                        '__CLASS_NAME' => 'BioSequence',
                                        '__RANK' => undef,
                                        '__ORDERED' => undef
                                      }, 'Bio::MAGE::Association::End' ),
                   '__OTHER' => bless( {
                                         '__NAME' => 'species',
                                         '__IS_REF' => 1,
                                         '__CARDINALITY' => '0..1',
                                         '__DOCUMENTATION' => 'The organism from which this sequence was obtained.',
                                         '__CLASS_NAME' => 'OntologyEntry',
                                         '__RANK' => '5',
                                         '__ORDERED' => 0
                                       }, 'Bio::MAGE::Association::End' )
                 }, 'Bio::MAGE::Association' ),
          'seqFeatures',
          bless( {
                   '__SELF' => bless( {
                                        '__NAME' => undef,
                                        '__IS_REF' => 0,
                                        '__CARDINALITY' => '1',
                                        '__DOCUMENTATION' => 'Association to annotations for subsequences.  Corresponds to the GenBank Frame Table.',
                                        '__CLASS_NAME' => 'BioSequence',
                                        '__RANK' => undef,
                                        '__ORDERED' => undef
                                      }, 'Bio::MAGE::Association::End' ),
                   '__OTHER' => bless( {
                                         '__NAME' => 'seqFeatures',
                                         '__IS_REF' => 1,
                                         '__CARDINALITY' => '0..N',
                                         '__DOCUMENTATION' => 'Association to annotations for subsequences.  Corresponds to the GenBank Frame Table.',
                                         '__CLASS_NAME' => 'SeqFeature',
                                         '__RANK' => '6',
                                         '__ORDERED' => 0
                                       }, 'Bio::MAGE::Association::End' )
                 }, 'Bio::MAGE::Association' )
        ]

}

=head1 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.

=over

=item new()

MAGE/BioSequence/BioSequence.pm  view on Meta::CPAN

Return value: the current value of the C<security> association : one of the accepted enumerated values.

Side effects: none

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

=cut


sub setSecurity {
  my $self = shift;
  croak(__PACKAGE__ . "::setSecurity: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setSecurity: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
  croak(__PACKAGE__ . "::setSecurity: wrong type: " . ref($val) . " expected Bio::MAGE::AuditAndSecurity::Security") unless (not defined $val) or UNIVERSAL::isa($val,'Bio::MAGE::AuditAndSecurity::Security');
  return $self->{__SECURITY} = $val;
}


=item $val = $biosequence->getSecurity()

The restricted getter method for the C<security> association.

Input parameters: none

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

Side effects: none

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

=cut


sub getSecurity {
  my $self = shift;
  croak(__PACKAGE__ . "::getSecurity: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__SECURITY};
}





=back


=item type

Methods for the C<type> association.


From the MAGE-OM documentation:

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


=over


=item $val = $biosequence->setType($val)

The restricted setter method for the C<type> association.


Input parameters: the value to which the C<type> association will be set : one of the accepted enumerated values.

Return value: the current value of the C<type> association : one of the accepted enumerated values.

Side effects: none

Exceptions: will call C<croak()> if no input parameters are specified, or
if too many input parameters are specified, or if C<$val> is not an instance of class C<Bio::MAGE::Description::OntologyEntry>

=cut


sub setType {
  my $self = shift;
  croak(__PACKAGE__ . "::setType: no arguments passed to setter")
    unless @_;
  croak(__PACKAGE__ . "::setType: too many arguments passed to setter")
    if @_ > 1;
  my $val = shift;
  croak(__PACKAGE__ . "::setType: wrong type: " . ref($val) . " expected Bio::MAGE::Description::OntologyEntry") unless (not defined $val) or UNIVERSAL::isa($val,'Bio::MAGE::Description::OntologyEntry');
  return $self->{__TYPE} = $val;
}


=item $val = $biosequence->getType()

The restricted getter method for the C<type> association.

Input parameters: none

Return value: the current value of the C<type> association : an instance of type C<Bio::MAGE::Description::OntologyEntry>.

Side effects: none

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

=cut


sub getType {
  my $self = shift;
  croak(__PACKAGE__ . "::getType: arguments passed to getter")
    if @_;
  my $val = shift;
  return $self->{__TYPE};
}