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move ArrayRepr JS into its own js file
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@rbuels
rbuels committed Feb 6, 2012
1 parent afbd3cf commit 3a659fe
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1 change: 1 addition & 0 deletions index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
when the JS gets minified (see the minification rule in the Makefile) -->
<script type="text/javascript" src="js/Browser.js"></script>
<script type="text/javascript" src="js/Util.js"></script>
<script type="text/javascript" src="js/ArrayRepr.js"></script>
<script type="text/javascript" src="js/NCList.js"></script>
<script type="text/javascript" src="js/LazyPatricia.js"></script>
<script type="text/javascript" src="js/LazyArray.js"></script>
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184 changes: 184 additions & 0 deletions js/ArrayRepr.js
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@@ -0,0 +1,184 @@
/*
class for operating on indexed representations of objects
For example, if we have a lot of objects with similar attributes, e.g.:
[
{start: 1, end: 2, strand: -1},
{start: 5, end: 6, strand: 1},
...
]
we can represent them more compactly (e.g., in JSON) something like this:
class = ["start", "end", "strand"]
[
[1, 2, -1],
[5, 6, 1],
...
]
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:
[
{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},
...
]
We could use the first array position to indicate the "class" for the
object, like this:
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]
]
Also, if we occasionally want to add an ad-hoc attribute, we could just
stick an optional dictionary onto the end:
classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]]
[
[0, 1, 2, 1, 1],
[0, 5, 6, 1, 2, {foo: 1}]
]
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:
classes=[
{'attributes': ['Start', 'End', 'Subfeatures'],
'proto': {'Chrom': 'chr1'},
'isArrayAttr': {Subfeatures: true}}
]
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 = {};
}
}

ArrayRepr.prototype.attrIndices = function(attr) {
return this.classes.map(
function(x) {
var i = x.attributes.indexOf(attr);
return i >= 0 ? i + 1 : undefined;
}
);
};

ArrayRepr.prototype.get = function(obj, attr) {
if (attr in this.fields[obj[0]]) {
return obj[this.fields[obj[0]][attr]];
} 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.fastGet = function(obj, attr) {
// can be used only if attr is guaranteed to be in
// the "classes" array for this object
return obj[self.fields[obj[0]][attr]];
};

ArrayRepr.prototype.set = function(obj, attr, val) {
if (attr in this.fields[obj[0]]) {
obj[this.fields[obj[0]][attr]] = val;
} else {
var adhocIndex = self.classes[obj[0]].length + 1;
if (adhocIndex >= obj.length)
obj[adhocIndex] = {};
obj[adhocIndex][attr] = val;
}
};

ArrayRepr.prototype.fastSet = function(obj, attr, val) {
// can be used only if attr is guaranteed to be in
// the "classes" array for this object
obj[this.fields[obj[0]][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;
};

/*
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.
*/
173 changes: 0 additions & 173 deletions js/Util.js
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Original file line number Diff line number Diff line change
Expand Up @@ -298,179 +298,6 @@ Finisher.prototype.finish = function() {
};


/*
class for operating on indexed representations of objects
For example, if we have a lot of objects with similar attributes, e.g.:
[
{start: 1, end: 2, strand: -1},
{start: 5, end: 6, strand: 1},
...
]
we can represent them more compactly (e.g., in JSON) something like this:
class = ["start", "end", "strand"]
[
[1, 2, -1],
[5, 6, 1],
...
]
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:
[
{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},
...
]
We could use the first array position to indicate the "class" for the
object, like this:
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]
]
Also, if we occasionally want to add an ad-hoc attribute, we could just
stick an optional dictionary onto the end:
classes = [["start", "end", "strand", "id"], ["start", "end", "chunk"]]
[
[0, 1, 2, 1, 1],
[0, 5, 6, 1, 2, {foo: 1}]
]
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:
classes=[
{'attributes': ['Start', 'End', 'Subfeatures'],
'proto': {'Chrom': 'chr1'},
'isArrayAttr': {Subfeatures: true}}
]
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 = {};
}
}

ArrayRepr.prototype.attrIndices = function(attr) {
return this.classes.map(
function(x) {
var i = x.attributes.indexOf(attr);
return i >= 0 ? i + 1 : undefined;
}
);
};

ArrayRepr.prototype.get = function(obj, attr) {
if (attr in this.fields[obj[0]]) {
return obj[this.fields[obj[0]][attr]];
} 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.fastGet = function(obj, attr) {
// can be used only if attr is guaranteed to be in
// the "classes" array for this object
return obj[self.fields[obj[0]][attr]];
};

ArrayRepr.prototype.set = function(obj, attr, val) {
if (attr in this.fields[obj[0]]) {
obj[this.fields[obj[0]][attr]] = val;
} else {
var adhocIndex = self.classes[obj[0]].length + 1;
if (adhocIndex >= obj.length)
obj[adhocIndex] = {};
obj[adhocIndex][attr] = val;
}
};

ArrayRepr.prototype.fastSet = function(obj, attr, val) {
// can be used only if attr is guaranteed to be in
// the "classes" array for this object
obj[this.fields[obj[0]][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;
};

/*
Copyright (c) 2007-2010 The Evolutionary Software Foundation
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