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Bio::MAGE::DesignElement::ReporterPosition - Class for the MAGE-OM API |
Bio::MAGE::DesignElement::ReporterPosition - Class for the MAGE-OM API
use Bio::MAGE::DesignElement::ReporterPosition
# creating an empty instance my $reporterposition = Bio::MAGE::DesignElement::ReporterPosition->new();
# creating an instance with existing data
my $reporterposition = Bio::MAGE::DesignElement::ReporterPosition->new(
end=>$end_val,
start=>$start_val,
propertySets=>\@namevaluetype_list,
reporter=>$reporter_ref,
mismatchInformation=>\@mismatchinformation_list,
);
# 'end' attribute my $end_val = $reporterposition->end(); # getter $reporterposition->end($value); # setter
# 'start' attribute my $start_val = $reporterposition->start(); # getter $reporterposition->start($value); # setter
# 'propertySets' association my $namevaluetype_array_ref = $reporterposition->propertySets(); # getter $reporterposition->propertySets(\@namevaluetype_list); # setter
# 'reporter' association my $reporter_ref = $reporterposition->reporter(); # getter $reporterposition->reporter($reporter_ref); # setter
# 'mismatchInformation' association my $mismatchinformation_array_ref = $reporterposition->mismatchInformation(); # getter $reporterposition->mismatchInformation(\@mismatchinformation_list); # setter
From the MAGE-OM documentation for the ReporterPosition class:
The location in the composite target's sequence to which a source reporter maps. The association to MismatchInformation allows the specification, usually for control purposes, of deviations from the CompositeSequence's BioMaterial.
Bio::MAGE::DesignElement::ReporterPosition has the following superclasses:
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::DesignElement::ReporterPosition->methodname() syntax.
new()new(%args)new() accepts the following optional
named-value style arguments:
end attribute (this attribute was inherited from class Bio::MAGE::BioSequence::SequencePosition).
start attribute (this attribute was inherited from class Bio::MAGE::BioSequence::SequencePosition).
propertySets association (this association was inherited from class Bio::MAGE::Extendable).
The value must be of type: array of Bio::MAGE::NameValueType.
reporter association
The value must be of type: instance of Bio::MAGE::DesignElement::Reporter.
mismatchInformation association
The value must be of type: array of Bio::MAGE::DesignElement::MismatchInformation.
new(%parameters)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.
get_slot_names()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
get_attribute_names()get_association_names()get_superclasses()get_subclasses()class_name()package_name()associations()Association objects that
provide the meta-information for the association.
new()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.
set_slots(%parameters)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.
get_slots(@name_list)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
set_slot($name,$val)set_slot() method sets the slot $name to the value $val
Return value: the new value of the slot, i.e. $val
Side effects: none
get_slot($name)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 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::DesignElement::ReporterPosition has the following attribute accessor methods:
end attribute.
From the MAGE-OM documentation:
The location of the base, for nucleotides, that the SeqFeature ends.
setEnd($val)end attribute.
Input parameters: the value to which the end attribute will be set
Return value: the current value of the end attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or
if too many input parameters are specified
getEnd()end attribute.
Input parameters: none
Return value: the current value of the end attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified
start attribute.
From the MAGE-OM documentation:
The location of the base, for nucleotides, that the SeqFeature starts.
setStart($val)start attribute.
Input parameters: the value to which the start attribute will be set
Return value: the current value of the start attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or
if too many input parameters are specified
getStart()start attribute.
Input parameters: none
Return value: the current value of the start attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified
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:
Bio::MAGE::DesignElement::ReporterPosition has the following association accessor methods:
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.
setPropertySets($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances
getPropertySets()propertySets association.
Input parameters: none
Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addPropertySets(@vals)Input parameters: the list of values @vals to add to the propertySets association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType
reporter association.
From the MAGE-OM documentation:
A reporter that comprises part of a CompositeSequence.
setReporter($val)reporter association.
Input parameters: the value to which the reporter association will be set : one of the accepted enumerated values.
Return value: the current value of the reporter 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 $val is not an instance of class Bio::MAGE::DesignElement::Reporter
getReporter()reporter association.
Input parameters: none
Return value: the current value of the reporter association : an instance of type Bio::MAGE::DesignElement::Reporter.
Side effects: none
Exceptions: will call croak() if any input parameters are specified
mismatchInformation association.
From the MAGE-OM documentation:
Differences in how the reporter matches its compositeSequence's sequence.
setMismatchInformation($array_ref)mismatchInformation association.
Input parameters: the value to which the mismatchInformation association will be set : a reference to an array of objects of type Bio::MAGE::DesignElement::MismatchInformation
Return value: the current value of the mismatchInformation association : a reference to an array of objects of type Bio::MAGE::DesignElement::MismatchInformation
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::DesignElement::MismatchInformation instances
getMismatchInformation()mismatchInformation association.
Input parameters: none
Return value: the current value of the mismatchInformation association : a reference to an array of objects of type Bio::MAGE::DesignElement::MismatchInformation
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addMismatchInformation(@vals)Input parameters: the list of values @vals to add to the mismatchInformation 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::DesignElement::MismatchInformation
sub initialize {
my $self = shift; return 1;
}
In the Perl implementation of MAGE-OM classes, there are
three types of class data members: slots, attributes, and
associations.
This API uses the term slot to indicate a data member of the class
that was not present in the UML model and is used for mainly internal
purposes - use only if you understand the inner workings of the
API. Most often slots are used by generic methods such as those in the
XML writing and reading classes.
Slots are implemented using unified getter/setter methods:
get_slot_names()DATA CHECKING: No data type checking is made for these methods.
The terms attribute and association indicate data members of the
class that were specified directly from the UML model.
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
NOTE: For associations, if the association has list cardinality, an array reference is returned.
DATA CHECKING: Ensure that no argument is provided.
NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.
DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.
Appends a list of objects to any values that may already be stored in the association.
DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.
The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that
will operate on slots, attributes, and associations:
get_slot($name)set_slot($name,$val)set_slots(%parameters)
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
Jason E. Stewart (jasons 'at' cpan 'dot' org)
perl(1).
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Bio::MAGE::DesignElement::ReporterPosition - Class for the MAGE-OM API |