• Bio::MAGE::DesignElement::MismatchInformation
• SYNOPSIS
• DESCRIPTION
• INHERITANCE
• CLASS METHODS
• ATTRIBUTES
• BUGS
• AUTHOR
• SEE ALSO

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

• Bio::MAGE::Extendable
  

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:

• replacedLength
  Sets the value of the replacedLength attribute (from Bio::MAGE::DesignElement::MismatchInformation).

• startCoord
  Sets the value of the startCoord attribute (from Bio::MAGE::DesignElement::MismatchInformation).

• newSequence
  Sets the value of the newSequence attribute (from Bio::MAGE::DesignElement::MismatchInformation).

• 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::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).