Bio::O...ProTerm(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::Ontology::InterProTerm 💖

okay bestie, gather round, because this one lives in the Bioperl ecosystem and it's literally the InterProI term interface implementation. Perl-verse girlies, this one's for you. 🫶

✨ NAME ✨

Bio::Ontology::InterProTerm — the implementation of the InterProI term interface</>, no cap.

🌸 SYNOPSIS 🌸

look, here's the vibe in code form:

  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";

that's it. that's the whole mood. 💅

🦋 DESCRIPTION 🦋

So basically this is a simple extension</> of Bio::Ontology::Term that's specially built for InterPro terms</>. It inherits the whole Term glow-up and then adds its own InterPro-specific little extras on top. iconic behaviour, honestly.

💌 FEEDBACK 💌

Mailing Lists

User feedback is, like, an integral part</> of the evolution of this and other Bioperl modules — genuinely, they mean it. 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, bestie. 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 — receipts help, always. 🎀

Reporting Bugs

Report bugs to the Bioperl bug tracking system so they can 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 _</> — iykyk, that underscore is the "backstage pass only" signal.

🎀 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. baby's first term. ✨
  • 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. blank slate energy, we love a fresh start. 🧚
  • 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. so either it slays or it screams. 😭
  • 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 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 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 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</>. they're giving "we still love you but we're not dating anymore". 🙈

🎀 secondary_ids

  • Title: secondary_ids
  • Usage: $obj->secondary_ids($newval)
  • Function: This is deprecated</>. Use get_secondary_ids() or add_secondary_id() instead. fr fr, switch it up. 💅
  • Example:
  • Returns: reference to an array of strings
  • Args: reference to an array of strings
and that's the whole page, bestie! 🫶 this one shipped as perl v5.32.1</> on 2021-08-15</>, and it's part of the User Contributed Perl Documentation</> collection — go forth and annotate your InterPro terms, you absolute main character. 👑✨
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