use Bio::MAGE::ArrayDesign::FeatureGroup;
# creating an empty instance my $featuregroup = Bio::MAGE::ArrayDesign::FeatureGroup->new();
# creating an already populated instance my $featuregroup = Bio::MAGE::ArrayDesign::FeatureGroup->new(featureLength=>$featureLength_value, featureWidth=>$featureWidth_value, featureHeight=>$featureHeight_value, featureShape=>$featureShape_value, features=>$features_value, distanceUnit=>$distanceUnit_value, technologyType=>$technologyType_value);
# setting and retrieving object attributes my $featureLength_val = $featuregroup->featureLength(); $featuregroup->featureLength($value);
my $featureWidth_val = $featuregroup->featureWidth(); $featuregroup->featureWidth($value);
my $featureHeight_val = $featuregroup->featureHeight(); $featuregroup->featureHeight($value);
# setting and retrieving object associations my $featureShape_val = $featuregroup->featureShape(); $featuregroup->featureShape($value);
my $features_val = $featuregroup->features(); $featuregroup->features($value);
my $distanceUnit_val = $featuregroup->distanceUnit(); $featuregroup->distanceUnit($value);
my $technologyType_val = $featuregroup->technologyType(); $featuregroup->technologyType($value);
From the MAGE-OM documentation for the FeatureGroup
class:
A collection of like features.
Bio::MAGE::ArrayDesign::FeatureGroup has the following super classes
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::ArrayDesign::FeatureGroup->methodname()
syntax.
new()
new(%args)
new()
accepts the following optional
named-value style arguments:
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::FeatureGroup
).
Bio::MAGE::ArrayDesign::DesignElementGroup
).
Bio::MAGE::ArrayDesign::DesignElementGroup
).
Bio::MAGE::Identifiable
).
Bio::MAGE::Identifiable
).
Bio::MAGE::Describable
).
Bio::MAGE::Describable
).
Bio::MAGE::Describable
).
Bio::MAGE::Extendable
).
set_slots(%parameters)
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.
get_slots(@name_list)
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
set_slot($name,$val)
set_slot()
method sets the slot $name
to the value $val
Return value: the new value of the slot, i.e. $val
Side effects: none
get_slot($name)
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
get_slot_names()
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
class_name()
package()
subclasses()
superclasses()
attribute_methods()
association_methods()
associations()
Bio::MAGE::Association
objects that provide the meta-information for the association.
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::ArrayDesign::FeatureGroup: has the following attribute accessor methods:
featureLength
attribute:
The length of the feature.
setFeatureLength($val)
Input parameters: the value to which the featureLength attribute will be set
Return value: the current value of the featureLength attribute
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified
getFeatureLength()
Input parameters: none
Return value: the current value of the featureLength attribute
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
featureWidth
attribute:
The width of the feature.
setFeatureWidth($val)
Input parameters: the value to which the featureWidth attribute will be set
Return value: the current value of the featureWidth attribute
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified
getFeatureWidth()
Input parameters: none
Return value: the current value of the featureWidth attribute
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
featureHeight
attribute:
The height of the feature.
setFeatureHeight($val)
Input parameters: the value to which the featureHeight attribute will be set
Return value: the current value of the featureHeight attribute
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified
getFeatureHeight()
Input parameters: none
Return value: the current value of the featureHeight attribute
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
Attributes Inherited from Bio::MAGE::Identifiable
identifier
attribute:
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
setIdentifier($val)
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
getIdentifier()
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
attribute:
The potentially ambiguous common identifier.
setName($val)
Input parameters: the value to which the name attribute will be set
Return value: the current value of the name attribute
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified
getName()
Input parameters: none
Return value: the current value of the name attribute
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
Associations are references to other class objects which can be shared by multiple class instances at the same time. In the Perl implementation of MAGE-OM classes, associations are implemented using three separate methods:
Bio::MAGE::ArrayDesign::FeatureGroup: has the following association accessor methods:
featureShape
association:
The expected shape of the feature on the array: circular, oval, square, etc.
setFeatureShape($val)
Input parameters: the value to which the featureShape association will be set : an instance of type Bio::MAGE::Description::OntologyEntry
.
Return value: the current value of the featureShape 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 $val is not an instance of class Bio::MAGE::Description::OntologyEntry
getFeatureShape()
Input parameters: none
Return value: the current value of the featureShape association : an instance of type Bio::MAGE::Description::OntologyEntry
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
features
association:
The features that belong to this group.
setFeatures($array_ref)
Input parameters: the value to which the features association will be set : a reference to an array of objects of type Bio::MAGE::DesignElement::Feature
Return value: the current value of the features association : a reference to an array of objects of type Bio::MAGE::DesignElement::Feature
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::DesignElement::Feature
instances
getFeatures()
Input parameters: none
Return value: the current value of the features association : a reference to an array of objects of type Bio::MAGE::DesignElement::Feature
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addFeatures(@vals)
Input parameters: the list of values @vals
to add to the features
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::DesignElement::Feature
distanceUnit
association:
The unit for the feature measures.
setDistanceUnit($val)
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 $val is not an instance of class Bio::MAGE::Measurement::DistanceUnit
getDistanceUnit()
Input parameters: none
Return value: the current value of the distanceUnit association : an instance of type Bio::MAGE::Measurement::DistanceUnit
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
technologyType
association:
The technology type of this design. By specifying a technology type, higher level analysis can use appropriate algorithms to compare the results from multiple arrays. The technology type may be spotted cDNA or in situ photolithography.
setTechnologyType($val)
Input parameters: the value to which the technologyType association will be set : an instance of type Bio::MAGE::Description::OntologyEntry
.
Return value: the current value of the technologyType 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 $val is not an instance of class Bio::MAGE::Description::OntologyEntry
getTechnologyType()
Input parameters: none
Return value: the current value of the technologyType association : an instance of type Bio::MAGE::Description::OntologyEntry
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
Associations Inherited from Bio::MAGE::ArrayDesign::DesignElementGroup
species
association:
The organism from which the biosequences of this group are from.
setSpecies($val)
Input parameters: the value to which the species association will be set : an instance of type Bio::MAGE::Description::OntologyEntry
.
Return value: the current value of the species 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 $val is not an instance of class Bio::MAGE::Description::OntologyEntry
getSpecies()
Input parameters: none
Return value: the current value of the species association : an instance of type Bio::MAGE::Description::OntologyEntry
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
types
association:
The specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo.
setTypes($array_ref)
Input parameters: the value to which the types association will be set : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
Return value: the current value of the types association : a reference to an array of objects 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 $array_ref is not a reference to an array class Bio::MAGE::Description::OntologyEntry
instances
getTypes()
Input parameters: none
Return value: the current value of the types association : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addTypes(@vals)
Input parameters: the list of values @vals
to add to the types
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::OntologyEntry
Associations Inherited from Bio::MAGE::Describable
security
association:
Information on the security for the instance of the class.
setSecurity($val)
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 $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security
getSecurity()
Input parameters: none
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security
.
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
auditTrail
association:
A list of Audit instances that track changes to the instance of Describable.
setAuditTrail($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit
instances
getAuditTrail()
Input parameters: none
Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addAuditTrail(@vals)
Input parameters: the list of values @vals
to add to the auditTrail
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit
descriptions
association:
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
setDescriptions($array_ref)
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 $array_ref is not a reference to an array class Bio::MAGE::Description::Description
instances
getDescriptions()
Input parameters: none
Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addDescriptions(@vals)
Input parameters: the list of values @vals
to add to the descriptions
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description
Associations Inherited from Bio::MAGE::Extendable
propertySets
association:
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
setPropertySets($array_ref)
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
getPropertySets()
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
addPropertySets(@vals)
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
Please send bug reports to mged-mage@lists.sf.net
Jason E. Stewart (www.openinformatics.com)
perl(1).