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.\" ========================================================================
.\"
.IX Title "MAGE 3"
.TH MAGE 3 "2003-11-12" "perl v5.22.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::MAGE \- Container module for classes in the MAGE MAGE package
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::MAGE;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a \fIpackage\fR module that encapsulates a number of classes in
the Bio::MAGE hierarchy. These classes belong to the
\&\s-1MAGE\s0 package of the MAGE-OM object model.
.SH "CLASSES"
.IX Header "CLASSES"
The Bio::MAGE module contains the following
Bio::MAGE classes:
.IP "\(bu" 4
Extendable
.IP "\(bu" 4
Identifiable
.IP "\(bu" 4
Describable
.IP "\(bu" 4
NameValueType
.SH "CLASS METHODS"
.IX Header "CLASS METHODS"
.ie n .IP "@class_list = \fIBio::MAGE::classes()\fR;" 4
.el .IP "\f(CW@class_list\fR = \fIBio::MAGE::classes()\fR;" 4
.IX Item "@class_list = Bio::MAGE::classes();"
This method returns a list of non-fully qualified class names
(i.e. they do not have 'Bio::MAGE::' as a prefix) in this package.
.ie n .IP "$obj_ref = Bio::MAGE\->new(%parameters)" 4
.el .IP "\f(CW$obj_ref\fR = Bio::MAGE\->new(%parameters)" 4
.IX Item "$obj_ref = Bio::MAGE->new(%parameters)"
.PD 0
.ie n .IP "$obj_ref_copy = $obj_ref\->\fInew()\fR" 4
.el .IP "\f(CW$obj_ref_copy\fR = \f(CW$obj_ref\fR\->\fInew()\fR" 4
.IX Item "$obj_ref_copy = $obj_ref->new()"
.PD
The \f(CW\*(C`new()\*(C'\fR method is the class constructor. If invoked with an
existing object instance, it is a copy constructor.
.Sp
\&\fBReturn value\fR: It returns a reference to an object of class
\&\f(CW\*(C`Bio::MAGE\*(C'\fR.
.Sp
\&\fBSide effects\fR: It invokes the \f(CW\*(C`initialize()\*(C'\fR method if it is defined
by the class.
.ie n .IP "@list_names = \fIBio::MAGE::mageml_packages()\fR;" 4
.el .IP "\f(CW@list_names\fR = \fIBio::MAGE::mageml_packages()\fR;" 4
.IX Item "@list_names = Bio::MAGE::mageml_packages();"
This method returns an ordered list of the MAGE-ML packages that exist
in the top level MAGE-ML element.
.ie n .IP "$hash_ref = \fIBio::MAGE::class2fullclass()\fR;" 4
.el .IP "\f(CW$hash_ref\fR = \fIBio::MAGE::class2fullclass()\fR;" 4
.IX Item "$hash_ref = Bio::MAGE::class2fullclass();"
This method returns a hash table that specifies the fully-delimited
class name of a class given the abbreviated name.
.SH "INSTANCE METHODS"
.IX Header "INSTANCE METHODS"
.ie n .IP "$mage\->add_objects(@list)" 4
.el .IP "\f(CW$mage\fR\->add_objects(@list)" 4
.IX Item "$mage->add_objects(@list)"
The objects in \f(CW@list\fR are added to the \s-1MAGE\s0
object. This method will recursively descend that association hierarcy
of each object and place all Identifiable objects in their appropriate
lists for writing as MAGE-ML.
.ie n .IP "$pkg_obj = $mage\->\fIgetAuditAndSecurity_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetAuditAndSecurity_package()\fR" 4
.IX Item "$pkg_obj = $mage->getAuditAndSecurity_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::AuditAndSecurity\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetDescription_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetDescription_package()\fR" 4
.IX Item "$pkg_obj = $mage->getDescription_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::Description\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetMeasurement_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetMeasurement_package()\fR" 4
.IX Item "$pkg_obj = $mage->getMeasurement_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::Measurement\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetBQS_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetBQS_package()\fR" 4
.IX Item "$pkg_obj = $mage->getBQS_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::BQS\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetBioEvent_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetBioEvent_package()\fR" 4
.IX Item "$pkg_obj = $mage->getBioEvent_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::BioEvent\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetProtocol_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetProtocol_package()\fR" 4
.IX Item "$pkg_obj = $mage->getProtocol_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::Protocol\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetBioMaterial_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetBioMaterial_package()\fR" 4
.IX Item "$pkg_obj = $mage->getBioMaterial_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::BioMaterial\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetBioSequence_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetBioSequence_package()\fR" 4
.IX Item "$pkg_obj = $mage->getBioSequence_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::BioSequence\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetDesignElement_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetDesignElement_package()\fR" 4
.IX Item "$pkg_obj = $mage->getDesignElement_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::DesignElement\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetArrayDesign_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetArrayDesign_package()\fR" 4
.IX Item "$pkg_obj = $mage->getArrayDesign_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::ArrayDesign\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetArray_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetArray_package()\fR" 4
.IX Item "$pkg_obj = $mage->getArray_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::Array\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetBioAssay_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetBioAssay_package()\fR" 4
.IX Item "$pkg_obj = $mage->getBioAssay_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::BioAssay\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetQuantitationType_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetQuantitationType_package()\fR" 4
.IX Item "$pkg_obj = $mage->getQuantitationType_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::QuantitationType\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetBioAssayData_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetBioAssayData_package()\fR" 4
.IX Item "$pkg_obj = $mage->getBioAssayData_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::BioAssayData\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetExperiment_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetExperiment_package()\fR" 4
.IX Item "$pkg_obj = $mage->getExperiment_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::Experiment\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$pkg_obj = $mage\->\fIgetHigherLevelAnalysis_package()\fR" 4
.el .IP "\f(CW$pkg_obj\fR = \f(CW$mage\fR\->\fIgetHigherLevelAnalysis_package()\fR" 4
.IX Item "$pkg_obj = $mage->getHigherLevelAnalysis_package()"
This method manages the handling of the singleton class object for the
\&\f(CW\*(C`Bio::MAGE::HigherLevelAnalysis\*(C'\fR class. When called it will return
the object, creating one if it has not already been created.
.Sp
This is useful when retrieving data from parsed MAGE-ML file.
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.PD 0
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
The \f(CW\*(C`set_slots()\*(C'\fR method is used to set a number of slots at the same
time. It has two different invocation methods. The first takes a named
parameter list, and the second takes two array references.
.Sp
\&\fBReturn value\fR: none
.Sp
\&\fBSide effects\fR: will call \f(CW\*(C`croak()\*(C'\fR if a slot_name is used that the class
does not define.
.ie n .IP "$obj\->get_slots(@name_list)" 4
.el .IP "\f(CW$obj\fR\->get_slots(@name_list)" 4
.IX Item "$obj->get_slots(@name_list)"
The \f(CW\*(C`get_slots()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a list of instance objects
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
The \f(CW\*(C`set_slot()\*(C'\fR method sets the slot \f(CW$name\fR to the value \f(CW$val\fR
.Sp
\&\fBReturn value\fR: the new value of the slot, i.e. \f(CW$val\fR
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
The \f(CW\*(C`get_slot()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "@names = $obj\->\fIget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = \f(CW$obj\fR\->\fIget_slot_names()\fR" 4
.IX Item "@names = $obj->get_slot_names()"
The \f(CW\*(C`get_slot_names()\*(C'\fR method is used to retrieve the name of all
slots defined for a given object.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $mage\->\fIobjects()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->\fIobjects()\fR" 4
.IX Item "$val = $mage->objects()"
.PD 0
.ie n .IP "$val = $mage\->objects($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->objects($val)" 4
.IX Item "$val = $mage->objects($val)"
.PD
This is the unified setter/getter method for the objects slot. If
\&\f(CW$val\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$val\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the objects
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $mage\->\fItagname()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->\fItagname()\fR" 4
.IX Item "$val = $mage->tagname()"
.PD 0
.ie n .IP "$val = $mage\->tagname($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->tagname($val)" 4
.IX Item "$val = $mage->tagname($val)"
.PD
This is the unified setter/getter method for the tagname slot. If
\&\f(CW$val\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$val\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the tagname
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $mage\->\fIidentifier()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->\fIidentifier()\fR" 4
.IX Item "$val = $mage->identifier()"
.PD 0
.ie n .IP "$val = $mage\->identifier($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->identifier($val)" 4
.IX Item "$val = $mage->identifier($val)"
.PD
This is the unified setter/getter method for the identifier slot. If
\&\f(CW$val\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$val\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the identifier
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $mage\->\fIregistered_objects()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->\fIregistered_objects()\fR" 4
.IX Item "$val = $mage->registered_objects()"
.PD 0
.ie n .IP "$val = $mage\->registered_objects($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->registered_objects($val)" 4
.IX Item "$val = $mage->registered_objects($val)"
.PD
This is the unified setter/getter method for the registered_objects slot. If
\&\f(CW$val\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$val\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the registered_objects
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $mage\->\fIidentifiers()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->\fIidentifiers()\fR" 4
.IX Item "$val = $mage->identifiers()"
.PD 0
.ie n .IP "$val = $mage\->identifiers($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->identifiers($val)" 4
.IX Item "$val = $mage->identifiers($val)"
.PD
This is the unified setter/getter method for the identifiers slot. If
\&\f(CW$val\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$val\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the identifiers
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.ie n .IP "$val = $mage\->\fIpackages()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->\fIpackages()\fR" 4
.IX Item "$val = $mage->packages()"
.PD 0
.ie n .IP "$val = $mage\->packages($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$mage\fR\->packages($val)" 4
.IX Item "$val = $mage->packages($val)"
.PD
This is the unified setter/getter method for the packages slot. If
\&\f(CW$val\fR is specified, the setter method is invoked, with no
parameters, the getter method is invoked.
.Sp
Input parameters: the optional \f(CW$val\fR will invoke the setter method.
.Sp
Return value: for both setter and getter the current value of the packages
slot
.Sp
Side effects: none
.Sp
Exceptions: none
.SH "BUGS"
.IX Header "BUGS"
Please send bug reports to mged\-mage@lists.sf.net
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason E. Stewart (www.openinformatics.com)
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fIperl\fR\|(1).