Bio::MAGE::BioSequence::BioSequence - Class for the MAGE-OM API
use Bio::MAGE::BioSequence::BioSequence # creating an empty instance my $biosequence = Bio::MAGE::BioSequence::BioSequence->new(); # creating an instance with existing data my $biosequence = Bio::MAGE::BioSequence::BioSequence->new( identifier=>$identifier_val, isApproximateLength=>$isapproximatelength_val, length=>$length_val, sequence=>$sequence_val, name=>$name_val, isCircular=>$iscircular_val, sequenceDatabases=>\@databaseentry_list, auditTrail=>\@audit_list, polymerType=>$ontologyentry_ref, species=>$ontologyentry_ref, propertySets=>\@namevaluetype_list, ontologyEntries=>\@ontologyentry_list, descriptions=>\@description_list, seqFeatures=>\@seqfeature_list, security=>$security_ref, type=>$ontologyentry_ref, ); # 'identifier' attribute my $identifier_val = $biosequence->identifier(); # getter $biosequence->identifier($value); # setter # 'isApproximateLength' attribute my $isApproximateLength_val = $biosequence->isApproximateLength(); # getter $biosequence->isApproximateLength($value); # setter # 'length' attribute my $length_val = $biosequence->length(); # getter $biosequence->length($value); # setter # 'sequence' attribute my $sequence_val = $biosequence->sequence(); # getter $biosequence->sequence($value); # setter # 'name' attribute my $name_val = $biosequence->name(); # getter $biosequence->name($value); # setter # 'isCircular' attribute my $isCircular_val = $biosequence->isCircular(); # getter $biosequence->isCircular($value); # setter # 'sequenceDatabases' association my $databaseentry_array_ref = $biosequence->sequenceDatabases(); # getter $biosequence->sequenceDatabases(\@databaseentry_list); # setter # 'auditTrail' association my $audit_array_ref = $biosequence->auditTrail(); # getter $biosequence->auditTrail(\@audit_list); # setter # 'polymerType' association my $ontologyentry_ref = $biosequence->polymerType(); # getter $biosequence->polymerType($ontologyentry_ref); # setter # 'species' association my $ontologyentry_ref = $biosequence->species(); # getter $biosequence->species($ontologyentry_ref); # setter # 'propertySets' association my $namevaluetype_array_ref = $biosequence->propertySets(); # getter $biosequence->propertySets(\@namevaluetype_list); # setter # 'ontologyEntries' association my $ontologyentry_array_ref = $biosequence->ontologyEntries(); # getter $biosequence->ontologyEntries(\@ontologyentry_list); # setter # 'descriptions' association my $description_array_ref = $biosequence->descriptions(); # getter $biosequence->descriptions(\@description_list); # setter # 'seqFeatures' association my $seqfeature_array_ref = $biosequence->seqFeatures(); # getter $biosequence->seqFeatures(\@seqfeature_list); # setter # 'security' association my $security_ref = $biosequence->security(); # getter $biosequence->security($security_ref); # setter # 'type' association my $ontologyentry_ref = $biosequence->type(); # getter $biosequence->type($ontologyentry_ref); # setter
From the MAGE-OM documentation for the BioSequence class:
BioSequence
A BioSequence is a representation of a DNA, RNA, or protein sequence. It can be represented by a Clone, Gene, or the sequence.
Bio::MAGE::BioSequence::BioSequence has the following superclasses:
Bio::MAGE::Identifiable
The following methods can all be called without first having an instance of the class via the Bio::MAGE::BioSequence::BioSequence->methodname() syntax.
The object constructor new() accepts the following optional named-value style arguments:
new()
identifier
Sets the value of the identifier attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
isApproximateLength
Sets the value of the isApproximateLength attribute
length
Sets the value of the length attribute
sequence
Sets the value of the sequence attribute
name
Sets the value of the name attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
isCircular
Sets the value of the isCircular attribute
sequenceDatabases
Sets the value of the sequenceDatabases association
The value must be of type: array of Bio::MAGE::Description::DatabaseEntry.
Bio::MAGE::Description::DatabaseEntry
auditTrail
Sets the value of the auditTrail association (this association was inherited from class Bio::MAGE::Describable).
Bio::MAGE::Describable
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.
Bio::MAGE::AuditAndSecurity::Audit
propertySets
Sets the value of the propertySets association (this association was inherited from class Bio::MAGE::Extendable).
Bio::MAGE::Extendable
The value must be of type: array of Bio::MAGE::NameValueType.
Bio::MAGE::NameValueType
species
Sets the value of the species association
The value must be of type: instance of Bio::MAGE::Description::OntologyEntry.
Bio::MAGE::Description::OntologyEntry
polymerType
Sets the value of the polymerType association
ontologyEntries
Sets the value of the ontologyEntries association
The value must be of type: array of Bio::MAGE::Description::OntologyEntry.
seqFeatures
Sets the value of the seqFeatures association
The value must be of type: array of Bio::MAGE::BioSequence::SeqFeature.
Bio::MAGE::BioSequence::SeqFeature
descriptions
Sets the value of the descriptions association (this association was inherited from class Bio::MAGE::Describable).
The value must be of type: array of Bio::MAGE::Description::Description.
Bio::MAGE::Description::Description
security
Sets the value of the security association (this association was inherited from class Bio::MAGE::Describable).
The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.
Bio::MAGE::AuditAndSecurity::Security
type
Sets the value of the type association
The new() method is the class constructor.
Parameters: if given a list of name/value parameters the corresponding slots, attributes, or associations will have their initial values set by the constructor.
Return value: It returns a reference to an object of the class.
Side effects: It invokes the initialize() method if it is defined by the class.
initialize()
The get_slot_names() method is used to retrieve the name of all slots defined in a given class.
get_slot_names()
NOTE: the list of names does not include attribute or association names.
Return value: A list of the names of all slots defined for this class.
Side effects: none
returns the list of attribute data members for this class.
returns the list of association data members for this class.
returns the list of superclasses for this class.
returns the list of subclasses for this class.
Returns the full class name for this class.
Returns the base package name (i.e. no 'namespace::') of the package that contains this class.
returns the association meta-information in a hash where the keys are the association names and the values are Association objects that provide the meta-information for the association.
Association
When invoked with an existing object reference and not a class name, the new() method acts as a copy constructor - with the new object's initial values set to be those of the existing object.
Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.
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.
set_slots()
Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define.
croak()
The get_slots() method is used to get the values of a number of slots at the same time.
get_slots()
Return value: a list of instance objects
The set_slot() method sets the slot $name to the value $val
set_slot()
$name
$val
Return value: the new value of the slot, i.e. $val
The get_slot() method is used to get the values of a number of slots at the same time.
get_slot()
Return value: a single slot value, or undef if the slot has not been initialized.
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::BioSequence::BioSequence has the following attribute accessor methods:
Bio::MAGE::BioSequence::BioSequence
Methods for the identifier attribute.
From the MAGE-OM documentation:
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.
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
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified
The restricted getter method for the identifier attribute.
Input parameters: none
Exceptions: will call croak() if any input parameters are specified
Methods for the isApproximateLength attribute.
If length not positively known will be true
The restricted setter method for the isApproximateLength attribute.
Input parameters: the value to which the isApproximateLength attribute will be set
Return value: the current value of the isApproximateLength attribute
The restricted getter method for the isApproximateLength attribute.
Methods for the length attribute.
The number of residues in the biosequence.
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
The restricted getter method for the length attribute.
Methods for the sequence attribute.
The actual components of the sequence, for instance, for DNA a string consisting of A,T,C and G.
The attribute is optional and instead of specified here, can be found through the DatabaseEntry.
The restricted setter method for the sequence attribute.
Input parameters: the value to which the sequence attribute will be set
Return value: the current value of the sequence attribute
The restricted getter method for the sequence attribute.
Methods for the name attribute.
The potentially ambiguous common identifier.
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
The restricted getter method for the name attribute.
Methods for the isCircular attribute.
Indicates if the BioSequence is circular in nature.
The restricted setter method for the isCircular attribute.
Input parameters: the value to which the isCircular attribute will be set
Return value: the current value of the isCircular attribute
The restricted getter method for the isCircular attribute.
Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association:
There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1
There may be one item in the association, i.e. this is an optional data field.
1..N
There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
0..N
There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.
Bio::MAGE::BioSequence::BioSequence has the following association accessor methods:
Methods for the sequenceDatabases association.
References an entry in a species database, like GenBank, UniGene, etc.
The restricted setter method for the sequenceDatabases association.
Input parameters: the value to which the sequenceDatabases association will be set : a reference to an array of objects of type Bio::MAGE::Description::DatabaseEntry
Return value: the current value of the sequenceDatabases association : a reference to an array of objects of type Bio::MAGE::Description::DatabaseEntry
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::DatabaseEntry instances
$array_ref
The restricted getter method for the sequenceDatabases association.
Because the sequenceDatabases association has list cardinality, it may store more than one value. This method adds the current list of objects in the sequenceDatabases association.
Input parameters: the list of values @vals to add to the sequenceDatabases association. NOTE: submitting a single value is permitted.
@vals
Return value: the number of items stored in the slot after adding @vals
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::DatabaseEntry
Methods for the auditTrail association.
A list of Audit instances that track changes to the instance of Describable.
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
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
The restricted getter method for the auditTrail association.
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.
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
Methods 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.
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
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
The restricted getter method for the propertySets association.
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.
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
Methods for the species association.
The organism from which this sequence was obtained.
The restricted setter method for the species association.
Input parameters: the value to which the species association will be set : one of the accepted enumerated values.
Return value: the current value of the species association : one of the accepted enumerated values.
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
The restricted getter method for the species association.
Return value: the current value of the species association : an instance of type Bio::MAGE::Description::OntologyEntry.
Methods for the polymerType association.
A choice of protein, RNA, or DNA.
The restricted setter method for the polymerType association.
Input parameters: the value to which the polymerType association will be set : one of the accepted enumerated values.
Return value: the current value of the polymerType association : one of the accepted enumerated values.
The restricted getter method for the polymerType association.
Return value: the current value of the polymerType association : an instance of type Bio::MAGE::Description::OntologyEntry.
Methods for the ontologyEntries association.
Ontology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.
The restricted setter method for the ontologyEntries association.
Input parameters: the value to which the ontologyEntries association will be set : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
Return value: the current value of the ontologyEntries association : a reference to an array of objects of type Bio::MAGE::Description::OntologyEntry
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
The restricted getter method for the ontologyEntries association.
Because the ontologyEntries association has list cardinality, it may store more than one value. This method adds the current list of objects in the ontologyEntries association.
Input parameters: the list of values @vals to add to the ontologyEntries association. NOTE: submitting a single value is permitted.
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
Methods for the seqFeatures association.
Association to annotations for subsequences. Corresponds to the GenBank Frame Table.
The restricted setter method for the seqFeatures association.
Input parameters: the value to which the seqFeatures association will be set : a reference to an array of objects of type Bio::MAGE::BioSequence::SeqFeature
Return value: the current value of the seqFeatures association : a reference to an array of objects of type Bio::MAGE::BioSequence::SeqFeature
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::BioSequence::SeqFeature instances
The restricted getter method for the seqFeatures association.
Because the seqFeatures association has list cardinality, it may store more than one value. This method adds the current list of objects in the seqFeatures association.
Input parameters: the list of values @vals to add to the seqFeatures association. NOTE: submitting a single value is permitted.
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::BioSequence::SeqFeature
Methods for the descriptions association.
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
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
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
The restricted getter method for the descriptions association.
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.
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
Methods for the security association.
Information on the security for the instance of the class.
The restricted setter method for the security association.
Input parameters: the value to which the security association will be set : one of the accepted enumerated values.
Return value: the current value of the security association : one of the accepted enumerated values.
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
The restricted getter method for the security association.
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
Methods for the type association.
The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.
The restricted setter method for the type association.
Input parameters: the value to which the type association will be set : one of the accepted enumerated values.
Return value: the current value of the type association : one of the accepted enumerated values.
The restricted getter method for the type association.
Return value: the current value of the type association : an instance of type Bio::MAGE::Description::OntologyEntry.
sub initialize {
my $self = shift; return 1;
}
In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations.
slots
attributes
associations
This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes - use only if you understand the inner workings of the API. Most often slots are used by generic methods such as those in the XML writing and reading classes.
slot
Slots are implemented using unified getter/setter methods:
Retrieves the current value of the slot.
Store $new_var in the slot - the return value is also $new_var.
Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods.
The terms attribute and association indicate data members of the class that were specified directly from the UML model.
attribute
association
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
Retrieves the current value.
NOTE: For associations, if the association has list cardinality, an array reference is returned.
DATA CHECKING: Ensure that no argument is provided.
Sets the current value, replacing any existing value.
NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.
DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.
NOTE: Only present in associations with list cardinality.
Appends a list of objects to any values that may already be stored in the association.
DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.
The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:
Bio::MAGE::Base
See elsewhere in this page for a detailed description of these methods.
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
Jason E. Stewart (jasons 'at' cpan 'dot' org)
perl(1).
5 POD Errors
The following errors were encountered while parsing the POD:
'=item' outside of any '=over'
You forgot a '=back' before '=head2'
Expected '=item 2'
Expected '=item 3'
Expected '=item 4'
To install Bio::MAGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MAGE
CPAN shell
perl -MCPAN -e shell install Bio::MAGE
For more information on module installation, please visit the detailed CPAN module installation guide.