@gmod/jbrowse
Version:
JBrowse - client-side genome browser
317 lines (285 loc) • 9.42 kB
JavaScript
define( [],
function() {
/**
* @class JBrowse.Model.ArrayRepr
* @constructor
*
* @description
*
* Class for operating on indexed array representations of objects.
*
* For example, if we have a lot of objects with similar attrbutes, 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.
*/
function ArrayRepr (classes) {
this.classes = classes;
this.fields = [];
for (var cl = 0; cl < classes.length; cl++) {
this.fields[cl] = {};
for (var f = 0; f < classes[cl].attributes.length; f++) {
this.fields[cl][classes[cl].attributes[f]] = f + 1;
}
if (classes[cl].proto === undefined)
classes[cl].proto = {};
if (classes[cl].isArrayAttr === undefined)
classes[cl].isArrayAttr = {};
}
}
/**
* @private
*/
ArrayRepr.prototype.attrIndices = function(attr) {
return this.classes.map(
function(x) {
return (x.attributes.indexOf(attr)+1) || (x.attributes.indexOf(attr.toLowerCase())+1) || undefined;
}
);
};
ArrayRepr.prototype.get = function(obj, attr) {
if (attr in this.fields[obj[0]]) {
return obj[this.fields[obj[0]][attr]];
}
else {
// try lowercase
var lcattr = attr.toLowerCase();
if( lcattr in this.fields[obj[0]]) {
return obj[this.fields[obj[0]][lcattr]];
}
else {
var adhocIndex = this.classes[obj[0]].attributes.length + 1;
if ((adhocIndex >= obj.length) || (!(attr in obj[adhocIndex]))) {
if (attr in this.classes[obj[0]].proto)
return this.classes[obj[0]].proto[attr];
return undefined;
}
return obj[adhocIndex][attr];
}
}
};
ArrayRepr.prototype.set = function(obj, attr, val) {
if (attr in this.fields[obj[0]]) {
obj[this.fields[obj[0]][attr]] = val;
} else {
// try lowercase
var lcattr = attr.toLowerCase();
if( lcattr in this.fields[obj[0]]) {
obj[this.fields[obj[0]][lcattr]] = val;
}
else {
var adhocIndex = this.classes[obj[0]].attributes.length + 1;
if (adhocIndex >= obj.length)
obj[adhocIndex] = {};
obj[adhocIndex][attr] = val;
}
}
};
ArrayRepr.prototype.makeSetter = function(attr) {
var self = this;
return function(obj, val) { self.set(obj, attr, val); };
};
ArrayRepr.prototype.makeGetter = function(attr) {
var self = this;
return function(obj) { return self.get(obj, attr); };
};
ArrayRepr.prototype.makeFastSetter = function(attr) {
// can be used only if attr is guaranteed to be in
// the "classes" array for this object
var indices = this.attrIndices(attr);
return function(obj, val) {
if (indices[obj[0]] !== undefined)
obj[indices[obj[0]]] = val;
};
};
ArrayRepr.prototype.makeFastGetter = function(attr) {
// can be used only if attr is guaranteed to be in
// the "classes" array for this object
var indices = this.attrIndices(attr);
return function(obj) {
if (indices[obj[0]] !== undefined)
return obj[indices[obj[0]]];
else
return undefined;
};
};
ArrayRepr.prototype.construct = function(self, obj, klass) {
var result = new Array(self.classes[klass].length);
for (var attr in obj) {
this.set(result, attr, obj[attr]);
}
return result;
};
/**
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') );
*/
ArrayRepr.prototype.accessors = function () {
return this._accessors = this._accessors || this._makeAccessors();
};
/**
* @private
*/
ArrayRepr.prototype._makeAccessors = function() {
var that = this,
indices = {},
tags,
accessors = {
get: function(field) {
var f = this.get.field_accessors[field.toLowerCase()];
if( f )
return f.call(this);
else
return undefined;
},
set: function(field,val) {
var f = this.set.field_accessors[field];
if( f )
return f.call(this,val);
else
return undefined;
},
tags: function() {
return tags[ this[0] ] || [];
}
};
accessors.get.field_accessors = {};
accessors.set.field_accessors = {};
// make a data structure as: { attr_name: [offset,offset,offset], }
// that will be convenient for finding the location of the attr
// for a given class like: indexForAttr{attrname}[classnum]
dojo.forEach( this.classes, function(cdef,classnum) {
dojo.forEach( cdef.attributes || [], function(attrname,offset) {
indices[attrname] = indices[attrname] || [];
indices[attrname][classnum] = offset + 1;
attrname = attrname.toLowerCase();
indices[attrname] = indices[attrname] || [];
indices[attrname][classnum] = offset + 1;
});
});
// lowercase all the class attributes
tags = dojo.map( this.classes, function(c) {
return c.attributes;
});
// use that to make precalculated get and set accessors for each field
for( var attrname in indices ) {
if( ! indices.hasOwnProperty(attrname) ) continue;
// get
accessors.get.field_accessors[ attrname ] = (function() {
var attr_indices = indices[attrname];
return !attr_indices ? function() { return undefined; } : function() {
return this[ attr_indices[ this[0] ] ];
};
})();
// set
accessors.set.field_accessors[ attrname ] = (function() {
var attr_indices = indices[attrname];
return !attr_indices ? function() { return undefined; } : function(v) {
return ( this[ attr_indices[ this[0] ] ] = v );
};
})();
}
return accessors;
};
return ArrayRepr;
});
/*
Copyright (c) 2007-2010 The Evolutionary Software Foundation
Created by Mitchell Skinner <mitch_skinner@berkeley.edu>
This package and its accompanying libraries are free software; you can
redistribute it and/or modify it under the terms of the LGPL (either
version 2.1, or at your option, any later version) or the Artistic
License 2.0. Refer to LICENSE for the full license text.
*/