use Bio::MAGE::HigherLevelAnalysis::Node;
# creating an empty instance my $node = Bio::MAGE::HigherLevelAnalysis::Node->new();
# creating an already populated instance my $node = Bio::MAGE::HigherLevelAnalysis::Node->new(nodeValue=>$nodeValue_value, nodeContents=>$nodeContents_value, nodes=>$nodes_value);
# setting and retrieving object associations my $nodeValue_val = $node->nodeValue(); $node->nodeValue($value);
my $nodeContents_val = $node->nodeContents(); $node->nodeContents($value);
my $nodes_val = $node->nodes(); $node->nodes($value);
From the MAGE-OM documentation for the Node
class:
An individual component of a clustering. May contain other nodes.
Bio::MAGE::HigherLevelAnalysis::Node has the following super classes
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::HigherLevelAnalysis::Node->methodname()
syntax.
new()
new(%args)
new()
accepts the following optional
named-value style arguments:
Bio::MAGE::HigherLevelAnalysis::Node
).
Bio::MAGE::HigherLevelAnalysis::Node
).
Bio::MAGE::HigherLevelAnalysis::Node
).
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::HigherLevelAnalysis::Node: has the following attribute accessor methods:
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::HigherLevelAnalysis::Node: has the following association accessor methods:
nodeValue
association:
Values or measurements for this node that may be produced by the clustering algorithm. Typical are distance values for the nodes.
setNodeValue($array_ref)
Input parameters: the value to which the nodeValue association will be set : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::NodeValue
Return value: the current value of the nodeValue association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::NodeValue
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::HigherLevelAnalysis::NodeValue
instances
getNodeValue()
Input parameters: none
Return value: the current value of the nodeValue association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::NodeValue
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addNodeValue(@vals)
Input parameters: the list of values @vals
to add to the nodeValue
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::HigherLevelAnalysis::NodeValue
nodeContents
association:
The contents of the node, expressed as either a one, two or three dimensional object.
setNodeContents($array_ref)
Input parameters: the value to which the nodeContents association will be set : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::NodeContents
Return value: the current value of the nodeContents association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::NodeContents
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::HigherLevelAnalysis::NodeContents
instances
getNodeContents()
Input parameters: none
Return value: the current value of the nodeContents association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::NodeContents
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addNodeContents(@vals)
Input parameters: the list of values @vals
to add to the nodeContents
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::HigherLevelAnalysis::NodeContents
nodes
association:
Nested nodes of the BioAssayDataCluster.
setNodes($array_ref)
Input parameters: the value to which the nodes association will be set : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::Node
Return value: the current value of the nodes association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::Node
Side effects: none
Exceptions: will call croak()
if no input parameters are specified, or
if too many input parameters are specified , or if $array_ref is not a reference to an array class Bio::MAGE::HigherLevelAnalysis::Node
instances
getNodes()
Input parameters: none
Return value: the current value of the nodes association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::Node
Side effects: none
Exceptions: will call croak()
if any input parameters are specified
addNodes(@vals)
Input parameters: the list of values @vals
to add to the nodes
association. NOTE: submitting a single value is permitted.
Return value: none
Side effects: none
Exceptions: will call croak()
if no input parameters are specified
, or if any of the objects in @vals is not an instance of class Bio::MAGE::HigherLevelAnalysis::Node
Associations Inherited from Bio::MAGE::Describable
security
association:
Information on the security for the instance of the class.
setSecurity($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).