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

Bio::MAGE::Array::ArrayGroup

SYNOPSIS

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

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

    # creating an already populated instance
  my $arraygroup = Bio::MAGE::Array::ArrayGroup->new(width=>$width_value,
                        numArrays=>$numArrays_value,
                        arraySpacingY=>$arraySpacingY_value,
                        length=>$length_value,
                        orientationMarkPosition=>$orientationMarkPosition_value,
                        arraySpacingX=>$arraySpacingX_value,
                        barcode=>$barcode_value,
                        orientationMark=>$orientationMark_value,
                        arrays=>$arrays_value,
                        distanceUnit=>$distanceUnit_value,
                        substrateType=>$substrateType_value,
                        fiducials=>$fiducials_value);

    # setting and retrieving object attributes
  my $width_val = $arraygroup->width();
  $arraygroup->width($value);

  my $numArrays_val = $arraygroup->numArrays();
  $arraygroup->numArrays($value);

  my $arraySpacingY_val = $arraygroup->arraySpacingY();
  $arraygroup->arraySpacingY($value);

  my $length_val = $arraygroup->length();
  $arraygroup->length($value);

  my $orientationMarkPosition_val = $arraygroup->orientationMarkPosition();
  $arraygroup->orientationMarkPosition($value);

  my $arraySpacingX_val = $arraygroup->arraySpacingX();
  $arraygroup->arraySpacingX($value);

  my $barcode_val = $arraygroup->barcode();
  $arraygroup->barcode($value);

  my $orientationMark_val = $arraygroup->orientationMark();
  $arraygroup->orientationMark($value);

    # setting and retrieving object associations
  my $arrays_val = $arraygroup->arrays();
  $arraygroup->arrays($value);

  my $distanceUnit_val = $arraygroup->distanceUnit();
  $arraygroup->distanceUnit($value);

  my $substrateType_val = $arraygroup->substrateType();
  $arraygroup->substrateType($value);

  my $fiducials_val = $arraygroup->fiducials();
  $arraygroup->fiducials($value);

DESCRIPTION

From the MAGE-OM documentation for the ArrayGroup class:

An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays.

The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes.

INHERITANCE

Bio::MAGE::Array::ArrayGroup 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::ArrayGroup->methodname() syntax.

new()

new(%args)

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

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

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

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

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

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

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

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

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

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

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

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

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

• 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::ArrayGroup.

$package_name = package()

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

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

width

From the MAGE-OM documentation for the width attribute:

The width of the platform

$val = $arraygroup->setWidth($val)

The restricted setter method for the width attribute.

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

Return value: the current value of the width attribute

Side effects: none

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

$val = $arraygroup->getWidth()

The restricted getter method for the width attribute.

Input parameters: none

Return value: the current value of the width attribute

Side effects: none

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

numArrays

From the MAGE-OM documentation for the numArrays attribute:

This attribute defines the number of arrays on a chip or a slide.

$val = $arraygroup->setNumArrays($val)

The restricted setter method for the numArrays attribute.

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

Return value: the current value of the numArrays attribute

Side effects: none

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

$val = $arraygroup->getNumArrays()

The restricted getter method for the numArrays attribute.

Input parameters: none

Return value: the current value of the numArrays attribute

Side effects: none

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

arraySpacingY

From the MAGE-OM documentation for the arraySpacingY attribute:

If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

$val = $arraygroup->setArraySpacingY($val)

The restricted setter method for the arraySpacingY attribute.

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

Return value: the current value of the arraySpacingY attribute

Side effects: none

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

$val = $arraygroup->getArraySpacingY()

The restricted getter method for the arraySpacingY attribute.

Input parameters: none

Return value: the current value of the arraySpacingY attribute

Side effects: none

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

length

From the MAGE-OM documentation for the length attribute:

The length of the platform.

$val = $arraygroup->setLength($val)

The restricted setter method for the length attribute.

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

Return value: the current value of the length attribute

Side effects: none

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

$val = $arraygroup->getLength()

The restricted getter method for the length attribute.

Input parameters: none

Return value: the current value of the length attribute

Side effects: none

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

orientationMarkPosition

From the MAGE-OM documentation for the orientationMarkPosition attribute:

One of top, bottom, left or right.

$val = $arraygroup->setOrientationMarkPosition($val)

The restricted setter method for the orientationMarkPosition attribute.

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

Return value: the current value of the orientationMarkPosition attribute

Side effects: none

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

$val = $arraygroup->getOrientationMarkPosition()

The restricted getter method for the orientationMarkPosition attribute.

Input parameters: none

Return value: the current value of the orientationMarkPosition attribute

Side effects: none

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

arraySpacingX

From the MAGE-OM documentation for the arraySpacingX attribute:

If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

$val = $arraygroup->setArraySpacingX($val)

The restricted setter method for the arraySpacingX attribute.

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

Return value: the current value of the arraySpacingX attribute

Side effects: none

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

$val = $arraygroup->getArraySpacingX()

The restricted getter method for the arraySpacingX attribute.

Input parameters: none

Return value: the current value of the arraySpacingX attribute

Side effects: none

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

barcode

From the MAGE-OM documentation for the barcode attribute:

Identifier for the ArrayGroup.

$val = $arraygroup->setBarcode($val)

The restricted setter method for the barcode attribute.

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

Return value: the current value of the barcode attribute

Side effects: none

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

$val = $arraygroup->getBarcode()

The restricted getter method for the barcode attribute.

Input parameters: none

Return value: the current value of the barcode attribute

Side effects: none

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

orientationMark

From the MAGE-OM documentation for the orientationMark attribute:

For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.

$val = $arraygroup->setOrientationMark($val)

The restricted setter method for the orientationMark attribute.

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

Return value: the current value of the orientationMark attribute

Side effects: none

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

$val = $arraygroup->getOrientationMark()

The restricted getter method for the orientationMark attribute.

Input parameters: none

Return value: the current value of the orientationMark 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::ArrayGroup: has the following association accessor methods:

arrays

From the MAGE-OM documentation for the arrays 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.

$array_ref = $arraygroup->setArrays($array_ref)

The restricted setter method for the arrays association.

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

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

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::Array instances

$array_ref = $arraygroup->getArrays()

The restricted getter method for the arrays association.

Input parameters: none

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

Side effects: none

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

$arraygroup->addArrays(@vals)

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

Input parameters: the list of values @vals to add to the arrays 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::Array

distanceUnit

From the MAGE-OM documentation for the distanceUnit association:

The unit of the measurement attributes.

$val = $arraygroup->setDistanceUnit($val)

The restricted setter method for the distanceUnit association.

Input parameters: the value to which the distanceUnit association will be set : an instance of type Bio::MAGE::Measurement::DistanceUnit.

Return value: the current value of the distanceUnit association : an instance of type Bio::MAGE::Measurement::DistanceUnit.

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::Measurement::DistanceUnit

$val = $arraygroup->getDistanceUnit()

The restricted getter method for the distanceUnit association.

Input parameters: none

Return value: the current value of the distanceUnit association : an instance of type Bio::MAGE::Measurement::DistanceUnit.

Side effects: none

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

substrateType

From the MAGE-OM documentation for the substrateType association:

Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.

$val = $arraygroup->setSubstrateType($val)

The restricted setter method for the substrateType association.

Input parameters: the value to which the substrateType association will be set : an instance of type Bio::MAGE::Description::OntologyEntry.

Return value: the current value of the substrateType association : an instance of type Bio::MAGE::Description::OntologyEntry.

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::Description::OntologyEntry

$val = $arraygroup->getSubstrateType()

The restricted getter method for the substrateType association.

Input parameters: none

Return value: the current value of the substrateType association : an instance of type Bio::MAGE::Description::OntologyEntry.

Side effects: none

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

fiducials

From the MAGE-OM documentation for the fiducials association:

Association to the marks on the Array for alignment for the scanner.

$array_ref = $arraygroup->setFiducials($array_ref)

The restricted setter method for the fiducials association.

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

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

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::Fiducial instances

$array_ref = $arraygroup->getFiducials()

The restricted getter method for the fiducials association.

Input parameters: none

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

Side effects: none

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

$arraygroup->addFiducials(@vals)

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

Input parameters: the list of values @vals to add to the fiducials 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::Fiducial

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).