NAME

Bio::MAGE::DesignElement - Container module for classes in the MAGE DesignElement package

SYNOPSIS

use Bio::MAGE::DesignElement;

DESCRIPTION

This is a package module that encapsulates a number of classes in the Bio::MAGE hierarchy. These classes belong to the DesignElement package of the MAGE-OM object model.

CLASSES

The Bio::MAGE::DesignElement module contains the following Bio::MAGE classes:

• DesignElement

• Position

• Reporter

• ReporterPosition

• CompositePosition

• CompositeSequence

• Feature

• MismatchInformation

• FeatureInformation

• CompositeCompositeMap

• FeatureReporterMap

• ReporterCompositeMap

• FeatureLocation

CLASS METHODS

@class_list = Bio::MAGE::DesignElement::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.

$obj_ref = Bio::MAGE::DesignElement->new(%parameters)

$obj_ref_copy = $obj_ref->new()

The new() method is the class constructor. If invoked with an existing object instance, it is a copy constructor.

Return value: It returns a reference to an object of class Bio::MAGE::DesignElement.

Side effects: It invokes the initialize() method if it is defined by the class.

INSTANCE METHODS

$array_ref = $designelement->getCompositeSequence_list()

This method handles the list for the Bio::MAGE::DesignElement::CompositeSequence class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from parsed MAGE-ML file.

$designelement->addCompositeSequence(@vals)

This method is an interface for adding Bio::MAGE::DesignElement::CompositeSequence objects to the compositesequence_list list. It is generally used by generic methods such as those in the XMLWriter.

Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not a subclass of class Bio::MAGE::DesignElement::CompositeSequence

$array_ref = $designelement->getReporter_list()

This method handles the list for the Bio::MAGE::DesignElement::Reporter class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from parsed MAGE-ML file.

$designelement->addReporter(@vals)

This method is an interface for adding Bio::MAGE::DesignElement::Reporter objects to the reporter_list list. It is generally used by generic methods such as those in the XMLWriter.

Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not a subclass of class Bio::MAGE::DesignElement::Reporter

$array_ref = $designelement->getCompositeCompositeMap_list()

This method handles the list for the Bio::MAGE::DesignElement::CompositeCompositeMap class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from parsed MAGE-ML file.

$designelement->addCompositeCompositeMap(@vals)

This method is an interface for adding Bio::MAGE::DesignElement::CompositeCompositeMap objects to the compositecompositemap_list list. It is generally used by generic methods such as those in the XMLWriter.

Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not a subclass of class Bio::MAGE::DesignElement::CompositeCompositeMap

$array_ref = $designelement->getReporterCompositeMap_list()

This method handles the list for the Bio::MAGE::DesignElement::ReporterCompositeMap class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from parsed MAGE-ML file.

$designelement->addReporterCompositeMap(@vals)

This method is an interface for adding Bio::MAGE::DesignElement::ReporterCompositeMap objects to the reportercompositemap_list list. It is generally used by generic methods such as those in the XMLWriter.

Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not a subclass of class Bio::MAGE::DesignElement::ReporterCompositeMap

$array_ref = $designelement->getFeatureReporterMap_list()

This method handles the list for the Bio::MAGE::DesignElement::FeatureReporterMap class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from parsed MAGE-ML file.

$designelement->addFeatureReporterMap(@vals)

This method is an interface for adding Bio::MAGE::DesignElement::FeatureReporterMap objects to the featurereportermap_list list. It is generally used by generic methods such as those in the XMLWriter.

Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted.

Return value: none

Side effects: none

Exceptions: will call croak() if no input parameters are specified , or if any of the objects in @vals is not a subclass of class Bio::MAGE::DesignElement::FeatureReporterMap

$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->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

@names = $obj->get_slot_names()

The get_slot_names() method is used to retrieve the name of all slots defined for a given object.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

$val = $designelement->compositesequence_list()

$val = $designelement->compositesequence_list($val)

This is the unified setter/getter method for the compositesequence_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the compositesequence_list slot

Side effects: none

Exceptions: none

$val = $designelement->reporter_list()

$val = $designelement->reporter_list($val)

This is the unified setter/getter method for the reporter_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the reporter_list slot

Side effects: none

Exceptions: none

$val = $designelement->compositecompositemap_list()

$val = $designelement->compositecompositemap_list($val)

This is the unified setter/getter method for the compositecompositemap_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the compositecompositemap_list slot

Side effects: none

Exceptions: none

$val = $designelement->reportercompositemap_list()

$val = $designelement->reportercompositemap_list($val)

This is the unified setter/getter method for the reportercompositemap_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the reportercompositemap_list slot

Side effects: none

Exceptions: none

$val = $designelement->featurereportermap_list()

$val = $designelement->featurereportermap_list($val)

This is the unified setter/getter method for the featurereportermap_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the featurereportermap_list slot

Side effects: none

Exceptions: none

$val = $designelement->mageml_lists()

$val = $designelement->mageml_lists($val)

This is the unified setter/getter method for the mageml_lists slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the mageml_lists slot

Side effects: none

Exceptions: none

$val = $designelement->tagname()

$val = $designelement->tagname($val)

This is the unified setter/getter method for the tagname slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the tagname slot

Side effects: none

Exceptions: none

BUGS

Please send bug reports to mged-mage@lists.sf.net

AUTHOR

Jason E. Stewart (www.openinformatics.com)

SEE ALSO

perl(1).