• Bio::MAGE::BioSequence::SequencePosition
• SYNOPSIS
• DESCRIPTION
• INHERITANCE
• CLASS METHODS
• ATTRIBUTES
• BUGS
• AUTHOR
• SEE ALSO

Bio::MAGE::BioSequence::SequencePosition

SYNOPSIS

  use Bio::MAGE::BioSequence::SequencePosition;

    # creating an empty instance
  my $sequenceposition = Bio::MAGE::BioSequence::SequencePosition->new();

    # creating an already populated instance
  my $sequenceposition = Bio::MAGE::BioSequence::SequencePosition->new(end=>$end_value,
                        start=>$start_value);

    # setting and retrieving object attributes
  my $end_val = $sequenceposition->end();
  $sequenceposition->end($value);

  my $start_val = $sequenceposition->start();
  $sequenceposition->start($value);

DESCRIPTION

From the MAGE-OM documentation for the SequencePosition class:

Designates the position of the Feature in its BioSequence.

INHERITANCE

Bio::MAGE::BioSequence::SequencePosition has the following super classes

• Bio::MAGE::Extendable
  

Bio::MAGE::BioSequence::SequencePosition has the following subclasses

• Bio::MAGE::DesignElement::CompositePosition
  
• Bio::MAGE::DesignElement::ReporterPosition
  

CLASS METHODS

The following methods can all be called without first having an instance of the class via the Bio::MAGE::BioSequence::SequencePosition->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 (from Bio::MAGE::BioSequence::SequencePosition).

• start
  Sets the value of the start attribute (from Bio::MAGE::BioSequence::SequencePosition).

• propertySets
  Sets the value of the propertySets association (from Bio::MAGE::Extendable).

$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

$name = class_name()

Returns the full class name for this class, Bio::MAGE::BioSequence::SequencePosition.

$package_name = package()

Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the package that contains class, Bio::MAGE::BioSequence::SequencePosition.

@classes = subclasses()

returns the list of subclasses for this class.

@classes = superclasses()

returns the list of superclasses for this class.

@methods = attribute_methods()

returns the list of attribute accessor methods for this class.

@methods = association_methods()

returns the list of association accessor methods for this class.

%assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are Bio::MAGE::Association objects that provide the meta-information for the association.

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::BioSequence::SequencePosition: has the following attribute accessor methods:

end

From the MAGE-OM documentation for the end attribute:

The location of the base, for nucleotides, that the SeqFeature ends.

$val = $sequenceposition->setEnd($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 = $sequenceposition->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

From the MAGE-OM documentation for the start attribute:

The location of the base, for nucleotides, that the SeqFeature starts.

$val = $sequenceposition->setStart($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 = $sequenceposition->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

BUGS

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

AUTHOR

Jason E. Stewart (www.openinformatics.com)

SEE ALSO

perl(1).