Website:WormBase::API

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NOTE: This document is likely out of date. Consult WormBase::Model.pm for the most up-to-date documentation.

The following AceDB model elements are handled generically in the reimplementation. This maximizes code reuse and makes model and template writing easier and faster.

Common elements are provided by WormBase::Model, superclass for all WormBase::Model::* classes. Should you come across any of these elements when converting a model, you can use them automatically without writing a line of code.

Usage: To use any of the common elements:

  • your Model class should inherit from WormBase::Model.
  • you should specify the name of the AceDB model element in lowercase in the configuration file


Element/Tag Notes Returns
Name Scalar. Name of the object as text.
References Array reference of Paper objects drawn from the Reference tag of an object. Got it?
Remark To be grammatically correct, the accessor to Remark tags in AceDB is actually "remarks" Array reference of remarks as text.
Species Species as an Ace::Object.


Model Helpers

Element/Tag Notes Returns
ID2species convert a protein ID into its corresponding species Scalar string corresponding to the species.
genetic_position
interpolated_position
best_blastp_matches


Todo

Evidence (to be handled by View)

Phenotype


API Data Structure

Each method of each API class will return a hashref with the following generic structure:

{   description => 'a short human readable description, no more than 5000 words',
    data           => 'a string, arrayref, or hashref, as needed and described',
}

Examples

find some examples