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

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

💖 Bio::OntologyIO::Handlers::InterProHandler 💖

okay bestie, gather round, because today we're reading the manual for Bio::OntologyIO::Handlers::InterProHandler(3pm), which is the XML handler class for InterProParser. she's a Perl module, she's user-contributed, and she is literally here to vibe with your InterPro XML files. no cap. 🦋

✨ NAME ✨

Bio::OntologyIO::Handlers::InterProHandler — the XML handler class for InterProParser. that's it, that's the whole name. iconic. 💅

🌸 SYNOPSIS 🌸

# do not use directly - used and instantiated by InterProParser

so like… do not touch her directly, bestie. she gets used and instantiated by InterProParser. she's the behind-the-scenes main character, the backstage queen. periodt. 👑

🌈 DESCRIPTION 🌈

she handles the xml events that InterProParser generates when it's parsing InterPro XML files. that's her whole job. she catches the events, she does the thing. lowkey obsessed with how clean that division of labor is. 🎀

💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is, like, an integral part of the evolution of this module and every other Bioperl module. so send your comments and suggestions — preferably to the Bioperl mailing list — because your participation is much appreciated. fr fr. 🫶

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

🆘 Support

okay so if you have a usage question or a support issue, please, please, direct it to the mailing list:

bioperl-l@bioperl.org

and not to the module maintainer directly. why? because there are lots of experienced, responsive experts on there who will look at your problem and quickly address it. ✨ and if you can, include a thorough description of the problem with code and data examples. give them the whole story, bestie, not just the vibes. 😭

🐛 Reporting Bugs

found a bug? report it to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web at:

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

go forth and file, queen. 🐞

👑 AUTHOR — Peter Dimitrov 👑

Email dimitrov@gnf.org

🌟 CONTRIBUTORS 🌟

Juguang Xiao, juguang@tll.org.sg

🧚 APPENDIX 🧚

the rest of this documentation details each of the object methods. internal methods are usually preceded with a _. iykyk. 🤫

🛠️ new

  • Title: new
  • Usage: $h = Bio::OntologyIO::Handlers::InterProHandler->new;
  • Function: Initializes global variables
  • Example:
  • Returns: an InterProHandler object
  • Args:

🛠️ ontology_engine

  • Title: ontology_engine
  • Usage: $obj->ontology_engine($newval)
  • Function: Get/set the ontology engine. Can be initialized only once.
  • Example:
  • Returns: value of ontology_engine (a scalar)
  • Args: new value (a scalar, optional)

🛠️ ontology

  • Title: ontology
  • Usage:
  • Function: Get the ontology to add the InterPro terms to.

The value is determined automatically once ontology_engine has been set and if it hasn't been set before.

  • Example:
  • Returns: A L<Bio::Ontology::OntologyI> implementing object.
  • Args: On set, a L<Bio::Ontology::OntologyI> implementing object.

🛠️ term_factory

  • Title: term_factory
  • Usage: $obj->term_factory($newval)
  • Function: Get/set the ontology term object factory
  • Example:
  • Returns: value of term_factory (a Bio::Factory::ObjectFactory instance)
  • Args: on set, new value (a Bio::Factory::ObjectFactory instance or undef, optional)

🛠️ _cite_skip

  • Title: _cite_skip
  • Usage: $obj->_cite_skip($newval)
  • Function:
  • Example:
  • Returns: value of _cite_skip (a scalar)
  • Args: new value (a scalar, optional)

🛠️ _hash

  • Title: _hash
  • Usage: $obj->_hash($newval)
  • Function:
  • Example:
  • Returns: value of _hash (a scalar)
  • Args: new value (a scalar, optional)

🛠️ _stack

  • Title: _stack
  • Usage: $obj->_stack($newval)
  • Function:
  • Example:
  • Returns: value of _stack (a scalar)
  • Args: new value (a scalar, optional)

🛠️ _top

  • Title: _top
  • Usage:
  • Function:
  • Example:
  • Returns:
  • Args:

🛠️ _term

  • Title: _term
  • Usage: $obj->_term($newval)
  • Function: Get/set method for the term currently processed.
  • Example:
  • Returns: value of term (a scalar)
  • Args: new value (a scalar, optional)

🛠️ _clear_term

  • Title: _clear_term
  • Usage:
  • Function: Removes the current term from the handler
  • Example:
  • Returns:
  • Args:

🛠️ _names

  • Title: _names
  • Usage: $obj->_names($newval)
  • Function:
  • Example:
  • Returns: value of _names (a scalar)
  • Args: new value (a scalar, optional)

🛠️ _create_relationship

  • Title: _create_relationship
  • Usage:
  • Function: Helper function. Adds relationships to one of the relationship stores.
  • Example:
  • Returns:
  • Args:

🛠️ start_element

  • Title: start_element
  • Usage:
  • Function: This is a method that is derived from XML::SAX::Base and has to be overridden for processing start of xml element events. Used internally only.
  • Example:
  • Returns:
  • Args:

🛠️ _char_storage

  • Title: _char_storage
  • Usage: $obj->_char_storage($newval)
  • Function:
  • Example:
  • Returns: value of _char_storage (a scalar)
  • Args: new value (a scalar, optional)

🛠️ characters

  • Title: characters
  • Usage:
  • Function: This is a method that is derived from XML::SAX::Base and has to be overridden for processing xml characters events. Used internally only.
  • Example:
  • Returns:
  • Args:

🛠️ end_element

  • Title: end_element
  • Usage:
  • Function: This is a method that is derived from XML::SAX::Base and has to be overridden for processing end of xml element events. Used internally only.
  • Example:
  • Returns:
  • Args:

🛠️ secondary_accessions_map

  • Title: secondary_accessions_map
  • Usage: $obj->secondary_accessions_map($newval)
  • Function:
  • Example: $map = $interpro_handler->secondary_accessions_map();
  • Returns: Reference to a hash that maps InterPro identifier to an array reference of secondary accessions following the InterPro xml schema.
  • Args: Empty hash reference

🛠️ _increment_record_count

  • Title: _increment_record_count
  • Usage:
  • Function:
  • Example:
  • Returns:
  • Args:

🛠️ _increment_processed_count

  • Title: _increment_processed_count
  • Usage:
  • Function:
  • Example:
  • Returns:
  • Args:

and that's the whole manual, bestie. every last method, every empty Function field, every single <rainbow>L<Bio::Ontology::OntologyI></rainbow> reference, preserved with love. 💖

this little beauty is perl v5.32.1, dated 2021-08-15, and it lives under the Bio::O...andler(3pm) name (short and mysterious, like a baddie with a past 😌). slay, stay hydrated, and go parse some XML. mwah. 💅✨

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