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Man Pages


Manual Reference Pages  -  BIO::ONTOLOGY::INTERPROTERM (3)

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NAME

Bio::Ontology::InterProTerm - Implementation of InterProI term interface

CONTENTS

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

    Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.



  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists



    Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

    Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:



  https://github.com/bioperl/bioperl-live/issues



AUTHOR - Peter Dimitrov

Email dimitrov@gnf.org

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



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