• Bio::MAGE::Array::Array
• SYNOPSIS
• DESCRIPTION
• INHERITANCE
• CLASS METHODS
• ATTRIBUTES
• ASSOCIATIONS
• BUGS
• AUTHOR
• SEE ALSO

Bio::MAGE::Array::Array

SYNOPSIS

  use Bio::MAGE::Array::Array;

    # creating an empty instance
  my $array = Bio::MAGE::Array::Array->new();

    # creating an already populated instance
  my $array = Bio::MAGE::Array::Array->new(arrayXOrigin=>$arrayXOrigin_value,
                        arrayYOrigin=>$arrayYOrigin_value,
                        arrayIdentifier=>$arrayIdentifier_value,
                        originRelativeTo=>$originRelativeTo_value,
                        arrayGroup=>$arrayGroup_value,
                        arrayDesign=>$arrayDesign_value,
                        information=>$information_value,
                        arrayManufactureDeviations=>$arrayManufactureDeviations_value);

    # setting and retrieving object attributes
  my $arrayXOrigin_val = $array->arrayXOrigin();
  $array->arrayXOrigin($value);

  my $arrayYOrigin_val = $array->arrayYOrigin();
  $array->arrayYOrigin($value);

  my $arrayIdentifier_val = $array->arrayIdentifier();
  $array->arrayIdentifier($value);

  my $originRelativeTo_val = $array->originRelativeTo();
  $array->originRelativeTo($value);

    # setting and retrieving object associations
  my $arrayGroup_val = $array->arrayGroup();
  $array->arrayGroup($value);

  my $arrayDesign_val = $array->arrayDesign();
  $array->arrayDesign($value);

  my $information_val = $array->information();
  $array->information($value);

  my $arrayManufactureDeviations_val = $array->arrayManufactureDeviations();
  $array->arrayManufactureDeviations($value);

DESCRIPTION

From the MAGE-OM documentation for the Array class:

The physical substrate along with its features and their annotation

INHERITANCE

Bio::MAGE::Array::Array has the following super classes

• Bio::MAGE::Identifiable
  

CLASS METHODS

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

new()

new(%args)

The object constructor new() accepts the following optional named-value style arguments:

• arrayXOrigin
  Sets the value of the arrayXOrigin attribute (from Bio::MAGE::Array::Array).

• arrayYOrigin
  Sets the value of the arrayYOrigin attribute (from Bio::MAGE::Array::Array).

• arrayIdentifier
  Sets the value of the arrayIdentifier attribute (from Bio::MAGE::Array::Array).

• originRelativeTo
  Sets the value of the originRelativeTo attribute (from Bio::MAGE::Array::Array).

• arrayGroup
  Sets the value of the arrayGroup association (from Bio::MAGE::Array::Array).

• arrayDesign
  Sets the value of the arrayDesign association (from Bio::MAGE::Array::Array).

• information
  Sets the value of the information association (from Bio::MAGE::Array::Array).

• arrayManufactureDeviations
  Sets the value of the arrayManufactureDeviations association (from Bio::MAGE::Array::Array).

• identifier
  Sets the value of the identifier attribute (from Bio::MAGE::Identifiable).

• name
  Sets the value of the name attribute (from Bio::MAGE::Identifiable).

• security
  Sets the value of the security association (from Bio::MAGE::Describable).

• auditTrail
  Sets the value of the auditTrail association (from Bio::MAGE::Describable).

• descriptions
  Sets the value of the descriptions association (from Bio::MAGE::Describable).

• 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::Array::Array.

$package_name = package()

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

@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::Array::Array: has the following attribute accessor methods:

arrayXOrigin

From the MAGE-OM documentation for the arrayXOrigin attribute:

This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

$val = $array->setArrayXOrigin($val)

The restricted setter method for the arrayXOrigin attribute.

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

Return value: the current value of the arrayXOrigin attribute

Side effects: none

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

$val = $array->getArrayXOrigin()

The restricted getter method for the arrayXOrigin attribute.

Input parameters: none

Return value: the current value of the arrayXOrigin attribute

Side effects: none

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

arrayYOrigin

From the MAGE-OM documentation for the arrayYOrigin attribute:

This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

$val = $array->setArrayYOrigin($val)

The restricted setter method for the arrayYOrigin attribute.

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

Return value: the current value of the arrayYOrigin attribute

Side effects: none

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

$val = $array->getArrayYOrigin()

The restricted getter method for the arrayYOrigin attribute.

Input parameters: none

Return value: the current value of the arrayYOrigin attribute

Side effects: none

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

arrayIdentifier

From the MAGE-OM documentation for the arrayIdentifier attribute:

An identifying string, e.g. a barcode.

$val = $array->setArrayIdentifier($val)

The restricted setter method for the arrayIdentifier attribute.

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

Return value: the current value of the arrayIdentifier attribute

Side effects: none

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

$val = $array->getArrayIdentifier()

The restricted getter method for the arrayIdentifier attribute.

Input parameters: none

Return value: the current value of the arrayIdentifier attribute

Side effects: none

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

originRelativeTo

From the MAGE-OM documentation for the originRelativeTo attribute:

What the array origin is relative to, e.g. upper left corner, fiducial, etc.

$val = $array->setOriginRelativeTo($val)

The restricted setter method for the originRelativeTo attribute.

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

Return value: the current value of the originRelativeTo attribute

Side effects: none

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

$val = $array->getOriginRelativeTo()

The restricted getter method for the originRelativeTo attribute.

Input parameters: none

Return value: the current value of the originRelativeTo attribute

Side effects: none

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

Attributes Inherited from Bio::MAGE::Identifiable

identifier

From the MAGE-OM documentation for the identifier attribute:

An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.

$val = $identifiable->setIdentifier($val)

The restricted setter method for the identifier attribute.

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

Return value: the current value of the identifier attribute

Side effects: none

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

$val = $identifiable->getIdentifier()

The restricted getter method for the identifier attribute.

Input parameters: none

Return value: the current value of the identifier attribute

Side effects: none

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

name

From the MAGE-OM documentation for the name attribute:

The potentially ambiguous common identifier.

$val = $identifiable->setName($val)

The restricted setter method for the name attribute.

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

Return value: the current value of the name attribute

Side effects: none

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

$val = $identifiable->getName()

The restricted getter method for the name attribute.

Input parameters: none

Return value: the current value of the name attribute

Side effects: none

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

ASSOCIATIONS

Associations are references to other class objects which can be shared by multiple class instances at the same time. In the Perl implementation of MAGE-OM classes, associations are implemented using three separate methods:

get*

Retrieves the current value. If the association has list cardinality, an array reference is returned.

set*

Sets the current value replacing any existing value. If the association has list cardinality, the argument must be an array reference. Unless you know what you are doing, you probably should be using the add* methods.

add*

This method exists only for associations with list cardinality. It appends a list of objects to any values that may already be stored in the association.

Bio::MAGE::Array::Array: has the following association accessor methods:

arrayGroup

From the MAGE-OM documentation for the arrayGroup association:

Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.

$val = $array->setArrayGroup($val)

The restricted setter method for the arrayGroup association.

Input parameters: the value to which the arrayGroup association will be set : an instance of type Bio::MAGE::Array::ArrayGroup.

Return value: the current value of the arrayGroup association : an instance of type Bio::MAGE::Array::ArrayGroup.

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::Array::ArrayGroup

$val = $array->getArrayGroup()

The restricted getter method for the arrayGroup association.

Input parameters: none

Return value: the current value of the arrayGroup association : an instance of type Bio::MAGE::Array::ArrayGroup.

Side effects: none

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

arrayDesign

From the MAGE-OM documentation for the arrayDesign association:

The association of a physical array with its array design.

$val = $array->setArrayDesign($val)

The restricted setter method for the arrayDesign association.

Input parameters: the value to which the arrayDesign association will be set : an instance of type Bio::MAGE::ArrayDesign::ArrayDesign.

Return value: the current value of the arrayDesign association : an instance of type Bio::MAGE::ArrayDesign::ArrayDesign.

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::ArrayDesign::ArrayDesign

$val = $array->getArrayDesign()

The restricted getter method for the arrayDesign association.

Input parameters: none

Return value: the current value of the arrayDesign association : an instance of type Bio::MAGE::ArrayDesign::ArrayDesign.

Side effects: none

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

information

From the MAGE-OM documentation for the information association:

Association between the manufactured array and the information on that manufacture.

$val = $array->setInformation($val)

The restricted setter method for the information association.

Input parameters: the value to which the information association will be set : an instance of type Bio::MAGE::Array::ArrayManufacture.

Return value: the current value of the information association : an instance of type Bio::MAGE::Array::ArrayManufacture.

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::Array::ArrayManufacture

$val = $array->getInformation()

The restricted getter method for the information association.

Input parameters: none

Return value: the current value of the information association : an instance of type Bio::MAGE::Array::ArrayManufacture.

Side effects: none

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

arrayManufactureDeviations

From the MAGE-OM documentation for the arrayManufactureDeviations association:

Association to classes to describe deviations from the ArrayDesign.

$array_ref = $array->setArrayManufactureDeviations($array_ref)

The restricted setter method for the arrayManufactureDeviations association.

Input parameters: the value to which the arrayManufactureDeviations association will be set : a reference to an array of objects of type Bio::MAGE::Array::ArrayManufactureDeviation

Return value: the current value of the arrayManufactureDeviations association : a reference to an array of objects of type Bio::MAGE::Array::ArrayManufactureDeviation

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::Array::ArrayManufactureDeviation instances

$array_ref = $array->getArrayManufactureDeviations()

The restricted getter method for the arrayManufactureDeviations association.

Input parameters: none

Return value: the current value of the arrayManufactureDeviations association : a reference to an array of objects of type Bio::MAGE::Array::ArrayManufactureDeviation

Side effects: none

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

$array->addArrayManufactureDeviations(@vals)

Because the arrayManufactureDeviations association has list cardinality, it may store more than one value. This method adds the current list of objects in the arrayManufactureDeviations association.

Input parameters: the list of values @vals to add to the arrayManufactureDeviations association. NOTE: submitting a single value is permitted.

Return value: none

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::Array::ArrayManufactureDeviation

Associations Inherited from Bio::MAGE::Describable

security

From the MAGE-OM documentation for the security association:

Information on the security for the instance of the class.

$val = $describable->setSecurity($val)

The restricted setter method for the security association.

Input parameters: the value to which the security association will be set : an instance of type Bio::MAGE::AuditAndSecurity::Security.

Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.

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::AuditAndSecurity::Security

$val = $describable->getSecurity()

The restricted getter method for the security association.

Input parameters: none

Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.

Side effects: none

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

auditTrail

From the MAGE-OM documentation for the auditTrail association:

A list of Audit instances that track changes to the instance of Describable.

$array_ref = $describable->setAuditTrail($array_ref)

The restricted setter method for the auditTrail association.

Input parameters: the value to which the auditTrail association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit

Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit

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::AuditAndSecurity::Audit instances

$array_ref = $describable->getAuditTrail()

The restricted getter method for the auditTrail association.

Input parameters: none

Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit

Side effects: none

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

$describable->addAuditTrail(@vals)

Because the auditTrail association has list cardinality, it may store more than one value. This method adds the current list of objects in the auditTrail association.

Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.

Return value: none

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::AuditAndSecurity::Audit

descriptions

From the MAGE-OM documentation for the descriptions association:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

$array_ref = $describable->setDescriptions($array_ref)

The restricted setter method for the descriptions association.

Input parameters: the value to which the descriptions association will be set : a reference to an array of objects of type Bio::MAGE::Description::Description

Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description

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::Description::Description instances

$array_ref = $describable->getDescriptions()

The restricted getter method for the descriptions association.

Input parameters: none

Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description

Side effects: none

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

$describable->addDescriptions(@vals)

Because the descriptions association has list cardinality, it may store more than one value. This method adds the current list of objects in the descriptions association.

Input parameters: the list of values @vals to add to the descriptions association. NOTE: submitting a single value is permitted.

Return value: none

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::Description::Description

Associations Inherited from Bio::MAGE::Extendable

propertySets

From the MAGE-OM documentation for the propertySets association:

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 = $extendable->setPropertySets($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 = $extendable->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

$extendable->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: none

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

BUGS

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

AUTHOR

Jason E. Stewart (www.openinformatics.com)

SEE ALSO

perl(1).