Provided by: libbio-mage-perl_20030502.3-3_all 
NAME
Bio::MAGE::DesignElement::CompositePosition - Class for the MAGE-OM API
SYNOPSIS
use Bio::MAGE::DesignElement::CompositePosition
# creating an empty instance
my $compositeposition = Bio::MAGE::DesignElement::CompositePosition->new();
# creating an instance with existing data
my $compositeposition = Bio::MAGE::DesignElement::CompositePosition->new(
end=>$end_val,
start=>$start_val,
composite=>$compositesequence_ref,
propertySets=>\@namevaluetype_list,
mismatchInformation=>\@mismatchinformation_list,
);
# 'end' attribute
my $end_val = $compositeposition->end(); # getter
$compositeposition->end($value); # setter
# 'start' attribute
my $start_val = $compositeposition->start(); # getter
$compositeposition->start($value); # setter
# 'composite' association
my $compositesequence_ref = $compositeposition->composite(); # getter
$compositeposition->composite($compositesequence_ref); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $compositeposition->propertySets(); # getter
$compositeposition->propertySets(\@namevaluetype_list); # setter
# 'mismatchInformation' association
my $mismatchinformation_array_ref = $compositeposition->mismatchInformation(); # getter
$compositeposition->mismatchInformation(\@mismatchinformation_list); # setter
DESCRIPTION
From the MAGE-OM documentation for the "CompositePosition" class:
The location in the compositeSequence target's sequence to which a source compositeSequence maps. The
association to MismatchInformation allows the specification, usually for control purposes, of deviations
from the CompositeSequence's BioMaterial.
INHERITANCE
Bio::MAGE::DesignElement::CompositePosition has the following superclasses:
• Bio::MAGE::BioSequence::SequencePosition
CLASS METHODS
The following methods can all be called without first having an instance of the class via the
Bio::MAGE::DesignElement::CompositePosition->methodname() syntax.
new()
new(%args)
The object constructor "new()" accepts the following optional named-value style arguments:
• end
Sets the value of the "end" attribute (this attribute was inherited from class
"Bio::MAGE::BioSequence::SequencePosition").
• start
Sets the value of the "start" attribute (this attribute was inherited from class
"Bio::MAGE::BioSequence::SequencePosition").
• composite
Sets the value of the "composite" association
The value must be of type: instance of "Bio::MAGE::DesignElement::CompositeSequence".
• 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".
• mismatchInformation
Sets the value of the "mismatchInformation" association
The value must be of type: array of "Bio::MAGE::DesignElement::MismatchInformation".
$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::DesignElement::CompositePosition" has the following attribute accessor methods:
end Methods for the "end" attribute.
From the MAGE-OM documentation:
The location of the base, for nucleotides, that the SeqFeature ends.
$val = $compositeposition->setEnd($val)
The restricted setter method for the "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
$val = $compositeposition->getEnd()
The restricted getter method for the "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
Methods for the "start" attribute.
From the MAGE-OM documentation:
The location of the base, for nucleotides, that the SeqFeature starts.
$val = $compositeposition->setStart($val)
The restricted setter method for the "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
$val = $compositeposition->getStart()
The restricted getter method for the "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
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::DesignElement::CompositePosition has the following association accessor methods:
composite
Methods for the "composite" association.
From the MAGE-OM documentation:
A source CompositeSequence that is part of a target CompositeSequence
$val = $compositeposition->setComposite($val)
The restricted setter method for the "composite" association.
Input parameters: the value to which the "composite" association will be set : one of the
accepted enumerated values.
Return value: the current value of the "composite" 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::CompositeSequence"
$val = $compositeposition->getComposite()
The restricted getter method for the "composite" association.
Input parameters: none
Return value: the current value of the "composite" association : an instance of type
"Bio::MAGE::DesignElement::CompositeSequence".
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
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 = $compositeposition->setPropertySets($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 = $compositeposition->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 = $compositeposition->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"
mismatchInformation
Methods for the "mismatchInformation" association.
From the MAGE-OM documentation:
Differences in how the contained compositeSequence matches its target compositeSequence's sequence.
$array_ref = $compositeposition->setMismatchInformation($array_ref)
The restricted setter method for the "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
$array_ref = $compositeposition->getMismatchInformation()
The restricted getter method for the "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
$val = $compositeposition->addMismatchInformation(@vals)
Because the mismatchInformation association has list cardinality, it may store more than one
value. This method adds the current list of objects in the mismatchInformation association.
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;
}
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
Hey! The above document had some coding errors, which are explained below:
Around line 343:
'=item' outside of any '=over'
Around line 428:
You forgot a '=back' before '=head2'
Around line 600:
Expected '=item 2'
Around line 605:
Expected '=item 3'
Around line 610:
Expected '=item 4'