SYNOPSIS
my $term = Bio::Ontology::InterProTerm->new(
-interpro_id => "IPR000001",
-name => "Kringle",
-definition => "Kringles are autonomous structural domains ...",
-ontology => "Domain"
);
print $term->interpro_id(), "\n";
print $term->name(), "\n";
print $term->definition(), "\n";
print $term->is_obsolete(), "\n";
print $term->ontology->name(), "\n";
DESCRIPTION
This is a simple extension of Bio::Ontology::Term for InterPro terms.FEEDBACK
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Reporting Bugs
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https://github.com/bioperl/bioperl-live/issues
AUTHOR - Peter Dimitrov
Email [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new
Usage : $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000002",
-name => "Cdc20/Fizzy",
-definition => "The Cdc20/Fizzy region is almost always ...",
-ontology => "Domain"
);
Function: Creates a new Bio::Ontology::InterProTerm.
Example :
Returns : A new Bio::Ontology::InterProTerm object.
Args :
-interpro_id => the InterPro ID of the term. Has the form IPRdddddd, where dddddd is a zero-padded six digit number
-name => the name of this InterPro term [scalar]
-definition => the definition/abstract of this InterPro term [scalar]
-ontology => ontology of InterPro terms [Bio::Ontology::OntologyI]
-comment => a comment [scalar]
init
Title : init Usage : $term->init(); Function: Initializes this InterProTerm to all "" and empty lists. Example : Returns : Args :
_check_interpro_id
Title : _check_interpro_id Usage : Function: Performs simple check in order to validate that its argument has the form IPRdddddd, where dddddd is a zero-padded six digit number. Example : Returns : Returns its argument if valid, otherwise throws exception. Args : String
interpro_id
Title : interpro_id Usage : $obj->interpro_id($newval) Function: Set/get for the interpro_id of this InterProTerm Example : Returns : value of interpro_id (a scalar) Args : new value (a scalar, optional)
short_name
Title : short_name Usage : $obj->short_name($newval) Function: Set/get for the short name of this InterProTerm. Example : Returns : value of short_name (a scalar) Args : new value (a scalar, optional)
protein_count
Title : protein_count Usage : $obj->protein_count($newval) Function: Set/get for the protein count of this InterProTerm. Example : Returns : value of protein_count (a scalar) Args : new value (a scalar, optional)
get_references
Title : get_references Usage : Function: Get the references for this InterPro term. Example : Returns : An array of L<Bio::Annotation::Reference> objects Args :
add_reference
Title : add_reference Usage : Function: Add one or more references to this InterPro term. Example : Returns : Args : One or more L<Bio::Annotation::Reference> objects.
remove_references
Title : remove_references
Usage :
Function: Remove all references for this InterPro term.
Example :
Returns : The list of previous references as an array of
L<Bio::Annotation::Reference> objects.
Args :
get_members
Title : get_members Usage : @arr = get_members() Function: Get the list of member(s) for this object. Example : Returns : An array of Bio::Annotation::DBLink objects Args :
add_member
Title : add_member Usage : Function: Add one or more member(s) to this object. Example : Returns : Args : One or more Bio::Annotation::DBLink objects.
remove_members
Title : remove_members
Usage :
Function: Remove all members for this class.
Example :
Returns : The list of previous members as an array of
Bio::Annotation::DBLink objects.
Args :
get_examples
Title : get_examples
Usage : @arr = get_examples()
Function: Get the list of example(s) for this object.
This is an element of the InterPro xml schema.
Example :
Returns : An array of Bio::Annotation::DBLink objects
Args :
add_example
Title : add_example
Usage :
Function: Add one or more example(s) to this object.
This is an element of the InterPro xml schema.
Example :
Returns :
Args : One or more Bio::Annotation::DBLink objects.
remove_examples
Title : remove_examples
Usage :
Function: Remove all examples for this class.
This is an element of the InterPro xml schema.
Example :
Returns : The list of previous examples as an array of
Bio::Annotation::DBLink objects.
Args :
get_external_documents
Title : get_external_documents
Usage : @arr = get_external_documents()
Function: Get the list of external_document(s) for this object.
This is an element of the InterPro xml schema.
Example :
Returns : An array of Bio::Annotation::DBLink objects
Args :
add_external_document
Title : add_external_document
Usage :
Function: Add one or more external_document(s) to this object.
This is an element of the InterPro xml schema.
Example :
Returns :
Args : One or more Bio::Annotation::DBLink objects.
remove_external_documents
Title : remove_external_documents
Usage :
Function: Remove all external_documents for this class.
This is an element of the InterPro xml schema.
Example :
Returns : The list of previous external_documents as an array of
Bio::Annotation::DBLink objects.
Args :
class_list
Title : class_list Usage : $obj->class_list($newval) Function: Set/get for class list element of the InterPro xml schema Example : Returns : reference to an array of Bio::Annotation::DBLink objects Args : reference to an array of Bio::Annotation::DBLink objects
to_string
Title : to_string() Usage : print $term->to_string(); Function: to_string method for InterPro terms. Returns : A string representation of this InterPro term. Args :
Deprecated methods
These are here for backwards compatibility.secondary_ids
Title : secondary_ids
Usage : $obj->secondary_ids($newval)
Function: This is deprecated. Use get_secondary_ids() or
add_secondary_id() instead.
Example :
Returns : reference to an array of strings
Args : reference to an array of strings