@gmod/nclist/dist/array_representation.d.ts

Read features from JBrowse 1 format nested containment list JSON

/**
 * @class ArrayRepr
 *
 * Class for operating on indexed array representations of objects.
 *
 * For example, if we have a lot of objects with similar attributes, e.g.:
 *
 * <pre class="code">
 *     [
 *         {start: 1, end: 2, strand: -1},
 *         {start: 5, end: 6, strand: 1},
 *         ...
 *     ]
 * </pre>
 *
 * @description
 * we can represent them more compactly (e.g., in JSON) something like this:
 *
 * <pre class="code">
 *     class = ["start", "end", "strand"]
 *     [
 *         [1, 2, -1],
 *         [5, 6, 1],
 *         ...
 *     ]
 * </pre>
 *
 * If we want to represent a few different kinds of objects in our big list,
 * we can have multiple "class" arrays, and tag each object to identify
 * which "class" array describes it.
 *
 * For example, if we have a lot of instances of a few types of objects,
 * like this:
 *
 * <pre class="code">
 *     [
 *         {start: 1, end: 2, strand: 1, id: 1},
 *         {start: 5, end: 6, strand: 1, id: 2},
 *         ...
 *         {start: 10, end: 20, chunk: 1},
 *         {start: 30, end: 40, chunk: 2},
 *         ...
 *     ]
 * </pre>
 *
 * We could use the first array position to indicate the "class" for the
 * object, like this:
 *
 * <pre class="code">
 *     classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]]
 *     [
 *         [0, 1, 2, 1, 1],
 *         [0, 5, 6, 1, 2],
 *         ...
 *         [1, 10, 20, 1],
 *         [1, 30, 40, 1]
 *     ]
 * </pre>
 *
 * Also, if we occasionally want to add an ad-hoc attribute, we could just
 * stick an optional dictionary onto the end:
 *
 * <pre class="code">
 *     classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]]
 *     [
 *         [0, 1, 2, 1, 1],
 *         [0, 5, 6, 1, 2, {foo: 1}]
 *     ]
 * </pre>
 *
 * Given that individual objects are being represented by arrays, generic
 * code needs some way to differentiate arrays that are meant to be objects
 * from arrays that are actually meant to be arrays.
 * So for each class, we include a dict with <attribute name>: true mappings
 * for each attribute that is meant to be an array.
 *
 * Also, in cases where some attribute values are the same for all objects
 * in a particular set, it may be convenient to define a "prototype"
 * with default values for all objects in the set
 *
 * In the end, we get something like this:
 *
 * <pre class="code">
 *     classes=[
 *         {'attributes': ['Start', 'End', 'Subfeatures'],
 *          'proto': {'Chrom': 'chr1'},
 *          'isArrayAttr': {Subfeatures: true}}
 *         ]
 * </pre>
 *
 * That's what this class facilitates.
 */
declare class ArrayRepr {
    constructor(classes: any);
    /**
     * @private
     */
    attrIndices(attr: any): any;
    get(obj: any, attr: any): any;
    makeSetter(attr: any): (obj: any, val: any) => void;
    makeGetter(attr: any): (obj: any) => any;
    makeFastGetter(attr: any): (obj: any) => any;
    /**
     * Returns fast pre-compiled getter and setter functions for use with
     * Arrays that use this representation.
     * When the returned <code>get</code> and <code>set</code> functions are
     * added as methods to an Array that contains data in this
     * representation, they provide fast access by name to the data.
     *
     * @returns {Object} <code>{ get: function() {...}, set: function(val) {...} }</code>
     *
     * @example
     * var accessors = attrs.accessors();
     * var feature = get_feature_from_someplace();
     * feature.get = accessors.get;
     * // print out the feature start and end
     * console.log( feature.get('start') + ',' + feature.get('end') );
     */
    accessors(): any;
    /**
     * @private
     */
    _makeAccessors(): {
        get(field: any): any;
        set(field: any, val: any): any;
        tags(): any;
    };
}
export default ArrayRepr;