Bio::MAGE::DesignElement::MismatchInformation

SYNOPSIS

  use Bio::MAGE::DesignElement::MismatchInformation;
    # creating an empty instance
  my $mismatchinformation = Bio::MAGE::DesignElement::MismatchInformation->new();
    # creating an already populated instance
  my $mismatchinformation = Bio::MAGE::DesignElement::MismatchInformation->new(replacedLength=>$replacedLength_value,
                        startCoord=>$startCoord_value,
                        newSequence=>$newSequence_value);
    # setting and retrieving object attributes
  my $replacedLength_val = $mismatchinformation->replacedLength();
  $mismatchinformation->replacedLength($value);
  my $startCoord_val = $mismatchinformation->startCoord();
  $mismatchinformation->startCoord($value);
  my $newSequence_val = $mismatchinformation->newSequence();
  $mismatchinformation->newSequence($value);

DESCRIPTION

From the MAGE-OM documentation for the MismatchInformation class:

Describes how a reporter varies from its ReporterCharacteristics sequence(s) or how a Feature varies from its Reporter sequence.

INHERITANCE

Bio::MAGE::DesignElement::MismatchInformation has the following super classes

CLASS METHODS

The following methods can all be called without first having an instance of the class via the Bio::MAGE::DesignElement::MismatchInformation->methodname() syntax.

new()
new(%args)
The object constructor new() accepts the following optional named-value style arguments:
$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::DesignElement::MismatchInformation.

$package_name = package()
Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the package that contains class, Bio::MAGE::DesignElement::MismatchInformation.

@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::DesignElement::MismatchInformation: has the following attribute accessor methods:

replacedLength
From the MAGE-OM documentation for the replacedLength attribute:

Length of the original sequence that is replaced. A deletion is specified when the length of the newSequence is less than the replacedLength.

$val = $mismatchinformation->setReplacedLength($val)
The restricted setter method for the replacedLength attribute.

Input parameters: the value to which the replacedLength attribute will be set

Return value: the current value of the replacedLength attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $mismatchinformation->getReplacedLength()
The restricted getter method for the replacedLength attribute.

Input parameters: none

Return value: the current value of the replacedLength attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

startCoord
From the MAGE-OM documentation for the startCoord attribute:

Offset into the sequence that the mismatch occurs.

$val = $mismatchinformation->setStartCoord($val)
The restricted setter method for the startCoord attribute.

Input parameters: the value to which the startCoord attribute will be set

Return value: the current value of the startCoord attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $mismatchinformation->getStartCoord()
The restricted getter method for the startCoord attribute.

Input parameters: none

Return value: the current value of the startCoord attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

newSequence
From the MAGE-OM documentation for the newSequence attribute:

The sequence that replaces the specified sequence starting at start_coord.

$val = $mismatchinformation->setNewSequence($val)
The restricted setter method for the newSequence attribute.

Input parameters: the value to which the newSequence attribute will be set

Return value: the current value of the newSequence attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $mismatchinformation->getNewSequence()
The restricted getter method for the newSequence attribute.

Input parameters: none

Return value: the current value of the newSequence 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).