biojs-io-fasta
Version:
Parses FASTA files
2,093 lines • 58.1 kB
JavaScript
require=(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);throw new Error("Cannot find module '"+o+"'")}var f=n[o]={exports:{}};t[o][0].call(f.exports,function(e){var n=t[o][1][e];return s(n?n:e)},f,f.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s})({1:[function(require,module,exports){
// Generated by CoffeeScript 1.9.0
module.exports = function(out) {
var i, key, _i, _j, _len, _ref, _ref1;
out = out || {};
for (i = _i = 0, _ref = arguments.length; 0 <= _ref ? _i < _ref : _i > _ref; i = 0 <= _ref ? ++_i : --_i) {
if (!arguments[i]) {
continue;
}
_ref1 = arguments[i];
for (_j = 0, _len = _ref1.length; _j < _len; _j++) {
key = _ref1[_j];
if (arguments[i].hasOwnProperty(key)) {
out[key] = arguments[i][key];
}
}
}
return out;
};
},{}],2:[function(require,module,exports){
// Generated by CoffeeScript 1.9.0
var Fasta, extend, st;
st = require("msa-seqtools");
extend = require("./extend");
module.exports = Fasta = {
getMeta: st.getMeta,
extend: function(metaParser) {
var customFasta;
customFasta = extend(Fasta);
Fasta.getMeta = metaParser;
return customFasta;
},
parse: function(text) {
var currentSeq, getMeta, id, label, line, obj, seqs, _i, _len;
seqs = [];
if (!text || text.length === 0) {
return [];
}
if (Object.prototype.toString.call(text) !== '[object Array]') {
text = text.split("\n");
}
getMeta = Fasta.getMeta;
for (_i = 0, _len = text.length; _i < _len; _i++) {
line = text[_i];
if (line[0] === ">" || line[0] === ";") {
label = line.slice(1);
obj = getMeta(label);
label = obj.name;
id = obj.id || seqs.length;
currentSeq = new st.model("", obj.name, id);
currentSeq.ids = obj.ids || {};
currentSeq.details = obj.details || {};
seqs.push(currentSeq);
} else {
currentSeq.seq += line;
}
}
return seqs;
},
write: function(seqs, access) {
var seq, text, _i, _len;
text = "";
for (_i = 0, _len = seqs.length; _i < _len; _i++) {
seq = seqs[_i];
if (access != null) {
seq = access(seq);
}
text += ">" + seq.name + "\n";
text += (st.splitNChars(seq.seq, 80)).join("\n");
text += "\n";
}
return text;
}
};
},{"./extend":1,"msa-seqtools":15}],"bRhrlU":[function(require,module,exports){
// Generated by CoffeeScript 1.9.0
var Fasta, GenericReader;
GenericReader = require("biojs-io-parser");
Fasta = require("./fasta");
module.exports = Fasta;
GenericReader.mixin(Fasta);
},{"./fasta":2,"biojs-io-parser":5}],"biojs-io-fasta":[function(require,module,exports){
module.exports=require('bRhrlU');
},{}],5:[function(require,module,exports){
var GenericReader;
var xhr = require('request');
var vow = require('vow');
module.exports = GenericReader = (function() {
function GenericReader() {}
// returns a promise if callback is undefined
GenericReader.read = function(url, callback) {
var onret;
onret = (function(_this) {
return function(err, response, text) {
return GenericReader._onRetrieval(err, text, callback, _this);
};
})(this);
if(typeof callback === "undefined"){
var prom = vow.defer();
callback = function(err, res){
if(err){
prom.reject(err);
}else{
prom.resolve(res);
}
};
xhr(url, onret);
return prom.promise();
}else{
return xhr(url, onret);
}
};
GenericReader._onRetrieval = function(err, text, callback, _this) {
var rText;
if(typeof err !== "undefined"){
rText = _this.parse(text);
}
return callback.call(_this, err, rText);
};
// provide a convenient shortcut to inherit
GenericReader.extend = function(obj, statics){
return extend(GenericReader, obj, statics);
};
// Mixin utility
GenericReader.mixin = function(proto) {
var exports = ['read'];
if(typeof proto !== "object"){
proto = proto.prototype;
}
exports.forEach(function(name) {
proto[name] = GenericReader[name];
}, this);
return proto;
};
return GenericReader;
})();
},{"request":7,"vow":6}],6:[function(require,module,exports){
(function (process){
/**
* @module vow
* @author Filatov Dmitry <dfilatov@yandex-team.ru>
* @version 0.4.8
* @license
* Dual licensed under the MIT and GPL licenses:
* * http://www.opensource.org/licenses/mit-license.php
* * http://www.gnu.org/licenses/gpl.html
*/
(function(global) {
var undef,
nextTick = (function() {
var fns = [],
enqueueFn = function(fn) {
return fns.push(fn) === 1;
},
callFns = function() {
var fnsToCall = fns, i = 0, len = fns.length;
fns = [];
while(i < len) {
fnsToCall[i++]();
}
};
if(typeof setImmediate === 'function') { // ie10, nodejs >= 0.10
return function(fn) {
enqueueFn(fn) && setImmediate(callFns);
};
}
if(typeof process === 'object' && process.nextTick) { // nodejs < 0.10
return function(fn) {
enqueueFn(fn) && process.nextTick(callFns);
};
}
if(global.postMessage) { // modern browsers
var isPostMessageAsync = true;
if(global.attachEvent) {
var checkAsync = function() {
isPostMessageAsync = false;
};
global.attachEvent('onmessage', checkAsync);
global.postMessage('__checkAsync', '*');
global.detachEvent('onmessage', checkAsync);
}
if(isPostMessageAsync) {
var msg = '__promise' + +new Date,
onMessage = function(e) {
if(e.data === msg) {
e.stopPropagation && e.stopPropagation();
callFns();
}
};
global.addEventListener?
global.addEventListener('message', onMessage, true) :
global.attachEvent('onmessage', onMessage);
return function(fn) {
enqueueFn(fn) && global.postMessage(msg, '*');
};
}
}
var doc = global.document;
if('onreadystatechange' in doc.createElement('script')) { // ie6-ie8
var createScript = function() {
var script = doc.createElement('script');
script.onreadystatechange = function() {
script.parentNode.removeChild(script);
script = script.onreadystatechange = null;
callFns();
};
(doc.documentElement || doc.body).appendChild(script);
};
return function(fn) {
enqueueFn(fn) && createScript();
};
}
return function(fn) { // old browsers
enqueueFn(fn) && setTimeout(callFns, 0);
};
})(),
throwException = function(e) {
nextTick(function() {
throw e;
});
},
isFunction = function(obj) {
return typeof obj === 'function';
},
isObject = function(obj) {
return obj !== null && typeof obj === 'object';
},
toStr = Object.prototype.toString,
isArray = Array.isArray || function(obj) {
return toStr.call(obj) === '[object Array]';
},
getArrayKeys = function(arr) {
var res = [],
i = 0, len = arr.length;
while(i < len) {
res.push(i++);
}
return res;
},
getObjectKeys = Object.keys || function(obj) {
var res = [];
for(var i in obj) {
obj.hasOwnProperty(i) && res.push(i);
}
return res;
},
defineCustomErrorType = function(name) {
var res = function(message) {
this.name = name;
this.message = message;
};
res.prototype = new Error();
return res;
},
wrapOnFulfilled = function(onFulfilled, idx) {
return function(val) {
onFulfilled.call(this, val, idx);
};
};
/**
* @class Deferred
* @exports vow:Deferred
* @description
* The `Deferred` class is used to encapsulate newly-created promise object along with functions that resolve, reject or notify it.
*/
/**
* @constructor
* @description
* You can use `vow.defer()` instead of using this constructor.
*
* `new vow.Deferred()` gives the same result as `vow.defer()`.
*/
var Deferred = function() {
this._promise = new Promise();
};
Deferred.prototype = /** @lends Deferred.prototype */{
/**
* Returns corresponding promise.
*
* @returns {vow:Promise}
*/
promise : function() {
return this._promise;
},
/**
* Resolves corresponding promise with given `value`.
*
* @param {*} value
*
* @example
* ```js
* var defer = vow.defer(),
* promise = defer.promise();
*
* promise.then(function(value) {
* // value is "'success'" here
* });
*
* defer.resolve('success');
* ```
*/
resolve : function(value) {
this._promise.isResolved() || this._promise._resolve(value);
},
/**
* Rejects corresponding promise with given `reason`.
*
* @param {*} reason
*
* @example
* ```js
* var defer = vow.defer(),
* promise = defer.promise();
*
* promise.fail(function(reason) {
* // reason is "'something is wrong'" here
* });
*
* defer.reject('something is wrong');
* ```
*/
reject : function(reason) {
if(this._promise.isResolved()) {
return;
}
if(vow.isPromise(reason)) {
reason = reason.then(function(val) {
var defer = vow.defer();
defer.reject(val);
return defer.promise();
});
this._promise._resolve(reason);
}
else {
this._promise._reject(reason);
}
},
/**
* Notifies corresponding promise with given `value`.
*
* @param {*} value
*
* @example
* ```js
* var defer = vow.defer(),
* promise = defer.promise();
*
* promise.progress(function(value) {
* // value is "'20%'", "'40%'" here
* });
*
* defer.notify('20%');
* defer.notify('40%');
* ```
*/
notify : function(value) {
this._promise.isResolved() || this._promise._notify(value);
}
};
var PROMISE_STATUS = {
PENDING : 0,
RESOLVED : 1,
FULFILLED : 2,
REJECTED : 3
};
/**
* @class Promise
* @exports vow:Promise
* @description
* The `Promise` class is used when you want to give to the caller something to subscribe to,
* but not the ability to resolve or reject the deferred.
*/
/**
* @constructor
* @param {Function} resolver See https://github.com/domenic/promises-unwrapping/blob/master/README.md#the-promise-constructor for details.
* @description
* You should use this constructor directly only if you are going to use `vow` as DOM Promises implementation.
* In other case you should use `vow.defer()` and `defer.promise()` methods.
* @example
* ```js
* function fetchJSON(url) {
* return new vow.Promise(function(resolve, reject, notify) {
* var xhr = new XMLHttpRequest();
* xhr.open('GET', url);
* xhr.responseType = 'json';
* xhr.send();
* xhr.onload = function() {
* if(xhr.response) {
* resolve(xhr.response);
* }
* else {
* reject(new TypeError());
* }
* };
* });
* }
* ```
*/
var Promise = function(resolver) {
this._value = undef;
this._status = PROMISE_STATUS.PENDING;
this._fulfilledCallbacks = [];
this._rejectedCallbacks = [];
this._progressCallbacks = [];
if(resolver) { // NOTE: see https://github.com/domenic/promises-unwrapping/blob/master/README.md
var _this = this,
resolverFnLen = resolver.length;
resolver(
function(val) {
_this.isResolved() || _this._resolve(val);
},
resolverFnLen > 1?
function(reason) {
_this.isResolved() || _this._reject(reason);
} :
undef,
resolverFnLen > 2?
function(val) {
_this.isResolved() || _this._notify(val);
} :
undef);
}
};
Promise.prototype = /** @lends Promise.prototype */ {
/**
* Returns value of fulfilled promise or reason in case of rejection.
*
* @returns {*}
*/
valueOf : function() {
return this._value;
},
/**
* Returns `true` if promise is resolved.
*
* @returns {Boolean}
*/
isResolved : function() {
return this._status !== PROMISE_STATUS.PENDING;
},
/**
* Returns `true` if promise is fulfilled.
*
* @returns {Boolean}
*/
isFulfilled : function() {
return this._status === PROMISE_STATUS.FULFILLED;
},
/**
* Returns `true` if promise is rejected.
*
* @returns {Boolean}
*/
isRejected : function() {
return this._status === PROMISE_STATUS.REJECTED;
},
/**
* Adds reactions to promise.
*
* @param {Function} [onFulfilled] Callback that will to be invoked with the value after promise has been fulfilled
* @param {Function} [onRejected] Callback that will to be invoked with the reason after promise has been rejected
* @param {Function} [onProgress] Callback that will to be invoked with the value after promise has been notified
* @param {Object} [ctx] Context of callbacks execution
* @returns {vow:Promise} A new promise, see https://github.com/promises-aplus/promises-spec for details
*/
then : function(onFulfilled, onRejected, onProgress, ctx) {
var defer = new Deferred();
this._addCallbacks(defer, onFulfilled, onRejected, onProgress, ctx);
return defer.promise();
},
/**
* Adds rejection reaction only. It is shortcut for `promise.then(undefined, onRejected)`.
*
* @param {Function} onRejected Callback to be called with the value after promise has been rejected
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
'catch' : function(onRejected, ctx) {
return this.then(undef, onRejected, ctx);
},
/**
* Adds rejection reaction only. It is shortcut for `promise.then(null, onRejected)`. It's alias for `catch`.
*
* @param {Function} onRejected Callback to be called with the value after promise has been rejected
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
fail : function(onRejected, ctx) {
return this.then(undef, onRejected, ctx);
},
/**
* Adds resolving reaction (to fulfillment and rejection both).
*
* @param {Function} onResolved Callback that to be called with the value after promise has been rejected
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
always : function(onResolved, ctx) {
var _this = this,
cb = function() {
return onResolved.call(this, _this);
};
return this.then(cb, cb, ctx);
},
/**
* Adds progress reaction.
*
* @param {Function} onProgress Callback to be called with the value when promise has been notified
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
progress : function(onProgress, ctx) {
return this.then(undef, undef, onProgress, ctx);
},
/**
* Like `promise.then`, but "spreads" the array into a variadic value handler.
* It is useful with `vow.all` and `vow.allResolved` methods.
*
* @param {Function} [onFulfilled] Callback that will to be invoked with the value after promise has been fulfilled
* @param {Function} [onRejected] Callback that will to be invoked with the reason after promise has been rejected
* @param {Object} [ctx] Context of callbacks execution
* @returns {vow:Promise}
*
* @example
* ```js
* var defer1 = vow.defer(),
* defer2 = vow.defer();
*
* vow.all([defer1.promise(), defer2.promise()]).spread(function(arg1, arg2) {
* // arg1 is "1", arg2 is "'two'" here
* });
*
* defer1.resolve(1);
* defer2.resolve('two');
* ```
*/
spread : function(onFulfilled, onRejected, ctx) {
return this.then(
function(val) {
return onFulfilled.apply(this, val);
},
onRejected,
ctx);
},
/**
* Like `then`, but terminates a chain of promises.
* If the promise has been rejected, throws it as an exception in a future turn of the event loop.
*
* @param {Function} [onFulfilled] Callback that will to be invoked with the value after promise has been fulfilled
* @param {Function} [onRejected] Callback that will to be invoked with the reason after promise has been rejected
* @param {Function} [onProgress] Callback that will to be invoked with the value after promise has been notified
* @param {Object} [ctx] Context of callbacks execution
*
* @example
* ```js
* var defer = vow.defer();
* defer.reject(Error('Internal error'));
* defer.promise().done(); // exception to be thrown
* ```
*/
done : function(onFulfilled, onRejected, onProgress, ctx) {
this
.then(onFulfilled, onRejected, onProgress, ctx)
.fail(throwException);
},
/**
* Returns a new promise that will be fulfilled in `delay` milliseconds if the promise is fulfilled,
* or immediately rejected if promise is rejected.
*
* @param {Number} delay
* @returns {vow:Promise}
*/
delay : function(delay) {
var timer,
promise = this.then(function(val) {
var defer = new Deferred();
timer = setTimeout(
function() {
defer.resolve(val);
},
delay);
return defer.promise();
});
promise.always(function() {
clearTimeout(timer);
});
return promise;
},
/**
* Returns a new promise that will be rejected in `timeout` milliseconds
* if the promise is not resolved beforehand.
*
* @param {Number} timeout
* @returns {vow:Promise}
*
* @example
* ```js
* var defer = vow.defer(),
* promiseWithTimeout1 = defer.promise().timeout(50),
* promiseWithTimeout2 = defer.promise().timeout(200);
*
* setTimeout(
* function() {
* defer.resolve('ok');
* },
* 100);
*
* promiseWithTimeout1.fail(function(reason) {
* // promiseWithTimeout to be rejected in 50ms
* });
*
* promiseWithTimeout2.then(function(value) {
* // promiseWithTimeout to be fulfilled with "'ok'" value
* });
* ```
*/
timeout : function(timeout) {
var defer = new Deferred(),
timer = setTimeout(
function() {
defer.reject(new vow.TimedOutError('timed out'));
},
timeout);
this.then(
function(val) {
defer.resolve(val);
},
function(reason) {
defer.reject(reason);
});
defer.promise().always(function() {
clearTimeout(timer);
});
return defer.promise();
},
_vow : true,
_resolve : function(val) {
if(this._status > PROMISE_STATUS.RESOLVED) {
return;
}
if(val === this) {
this._reject(TypeError('Can\'t resolve promise with itself'));
return;
}
this._status = PROMISE_STATUS.RESOLVED;
if(val && !!val._vow) { // shortpath for vow.Promise
val.isFulfilled()?
this._fulfill(val.valueOf()) :
val.isRejected()?
this._reject(val.valueOf()) :
val.then(
this._fulfill,
this._reject,
this._notify,
this);
return;
}
if(isObject(val) || isFunction(val)) {
var then;
try {
then = val.then;
}
catch(e) {
this._reject(e);
return;
}
if(isFunction(then)) {
var _this = this,
isResolved = false;
try {
then.call(
val,
function(val) {
if(isResolved) {
return;
}
isResolved = true;
_this._resolve(val);
},
function(err) {
if(isResolved) {
return;
}
isResolved = true;
_this._reject(err);
},
function(val) {
_this._notify(val);
});
}
catch(e) {
isResolved || this._reject(e);
}
return;
}
}
this._fulfill(val);
},
_fulfill : function(val) {
if(this._status > PROMISE_STATUS.RESOLVED) {
return;
}
this._status = PROMISE_STATUS.FULFILLED;
this._value = val;
this._callCallbacks(this._fulfilledCallbacks, val);
this._fulfilledCallbacks = this._rejectedCallbacks = this._progressCallbacks = undef;
},
_reject : function(reason) {
if(this._status > PROMISE_STATUS.RESOLVED) {
return;
}
this._status = PROMISE_STATUS.REJECTED;
this._value = reason;
this._callCallbacks(this._rejectedCallbacks, reason);
this._fulfilledCallbacks = this._rejectedCallbacks = this._progressCallbacks = undef;
},
_notify : function(val) {
this._callCallbacks(this._progressCallbacks, val);
},
_addCallbacks : function(defer, onFulfilled, onRejected, onProgress, ctx) {
if(onRejected && !isFunction(onRejected)) {
ctx = onRejected;
onRejected = undef;
}
else if(onProgress && !isFunction(onProgress)) {
ctx = onProgress;
onProgress = undef;
}
var cb;
if(!this.isRejected()) {
cb = { defer : defer, fn : isFunction(onFulfilled)? onFulfilled : undef, ctx : ctx };
this.isFulfilled()?
this._callCallbacks([cb], this._value) :
this._fulfilledCallbacks.push(cb);
}
if(!this.isFulfilled()) {
cb = { defer : defer, fn : onRejected, ctx : ctx };
this.isRejected()?
this._callCallbacks([cb], this._value) :
this._rejectedCallbacks.push(cb);
}
if(this._status <= PROMISE_STATUS.RESOLVED) {
this._progressCallbacks.push({ defer : defer, fn : onProgress, ctx : ctx });
}
},
_callCallbacks : function(callbacks, arg) {
var len = callbacks.length;
if(!len) {
return;
}
var isResolved = this.isResolved(),
isFulfilled = this.isFulfilled();
nextTick(function() {
var i = 0, cb, defer, fn;
while(i < len) {
cb = callbacks[i++];
defer = cb.defer;
fn = cb.fn;
if(fn) {
var ctx = cb.ctx,
res;
try {
res = ctx? fn.call(ctx, arg) : fn(arg);
}
catch(e) {
defer.reject(e);
continue;
}
isResolved?
defer.resolve(res) :
defer.notify(res);
}
else {
isResolved?
isFulfilled?
defer.resolve(arg) :
defer.reject(arg) :
defer.notify(arg);
}
}
});
}
};
/** @lends Promise */
var staticMethods = {
/**
* Coerces given `value` to a promise, or returns the `value` if it's already a promise.
*
* @param {*} value
* @returns {vow:Promise}
*/
cast : function(value) {
return vow.cast(value);
},
/**
* Returns a promise to be fulfilled only after all the items in `iterable` are fulfilled,
* or to be rejected when any of the `iterable` is rejected.
*
* @param {Array|Object} iterable
* @returns {vow:Promise}
*/
all : function(iterable) {
return vow.all(iterable);
},
/**
* Returns a promise to be fulfilled only when any of the items in `iterable` are fulfilled,
* or to be rejected when the first item is rejected.
*
* @param {Array} iterable
* @returns {vow:Promise}
*/
race : function(iterable) {
return vow.anyResolved(iterable);
},
/**
* Returns a promise that has already been resolved with the given `value`.
* If `value` is a promise, returned promise will be adopted with the state of given promise.
*
* @param {*} value
* @returns {vow:Promise}
*/
resolve : function(value) {
return vow.resolve(value);
},
/**
* Returns a promise that has already been rejected with the given `reason`.
*
* @param {*} reason
* @returns {vow:Promise}
*/
reject : function(reason) {
return vow.reject(reason);
}
};
for(var prop in staticMethods) {
staticMethods.hasOwnProperty(prop) &&
(Promise[prop] = staticMethods[prop]);
}
var vow = /** @exports vow */ {
Deferred : Deferred,
Promise : Promise,
/**
* Creates a new deferred. This method is a factory method for `vow:Deferred` class.
* It's equivalent to `new vow.Deferred()`.
*
* @returns {vow:Deferred}
*/
defer : function() {
return new Deferred();
},
/**
* Static equivalent to `promise.then`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Function} [onFulfilled] Callback that will to be invoked with the value after promise has been fulfilled
* @param {Function} [onRejected] Callback that will to be invoked with the reason after promise has been rejected
* @param {Function} [onProgress] Callback that will to be invoked with the value after promise has been notified
* @param {Object} [ctx] Context of callbacks execution
* @returns {vow:Promise}
*/
when : function(value, onFulfilled, onRejected, onProgress, ctx) {
return vow.cast(value).then(onFulfilled, onRejected, onProgress, ctx);
},
/**
* Static equivalent to `promise.fail`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Function} onRejected Callback that will to be invoked with the reason after promise has been rejected
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
fail : function(value, onRejected, ctx) {
return vow.when(value, undef, onRejected, ctx);
},
/**
* Static equivalent to `promise.always`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Function} onResolved Callback that will to be invoked with the reason after promise has been resolved
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
always : function(value, onResolved, ctx) {
return vow.when(value).always(onResolved, ctx);
},
/**
* Static equivalent to `promise.progress`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Function} onProgress Callback that will to be invoked with the reason after promise has been notified
* @param {Object} [ctx] Context of callback execution
* @returns {vow:Promise}
*/
progress : function(value, onProgress, ctx) {
return vow.when(value).progress(onProgress, ctx);
},
/**
* Static equivalent to `promise.spread`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Function} [onFulfilled] Callback that will to be invoked with the value after promise has been fulfilled
* @param {Function} [onRejected] Callback that will to be invoked with the reason after promise has been rejected
* @param {Object} [ctx] Context of callbacks execution
* @returns {vow:Promise}
*/
spread : function(value, onFulfilled, onRejected, ctx) {
return vow.when(value).spread(onFulfilled, onRejected, ctx);
},
/**
* Static equivalent to `promise.done`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Function} [onFulfilled] Callback that will to be invoked with the value after promise has been fulfilled
* @param {Function} [onRejected] Callback that will to be invoked with the reason after promise has been rejected
* @param {Function} [onProgress] Callback that will to be invoked with the value after promise has been notified
* @param {Object} [ctx] Context of callbacks execution
*/
done : function(value, onFulfilled, onRejected, onProgress, ctx) {
vow.when(value).done(onFulfilled, onRejected, onProgress, ctx);
},
/**
* Checks whether the given `value` is a promise-like object
*
* @param {*} value
* @returns {Boolean}
*
* @example
* ```js
* vow.isPromise('something'); // returns false
* vow.isPromise(vow.defer().promise()); // returns true
* vow.isPromise({ then : function() { }); // returns true
* ```
*/
isPromise : function(value) {
return isObject(value) && isFunction(value.then);
},
/**
* Coerces given `value` to a promise, or returns the `value` if it's already a promise.
*
* @param {*} value
* @returns {vow:Promise}
*/
cast : function(value) {
return vow.isPromise(value)?
value :
vow.resolve(value);
},
/**
* Static equivalent to `promise.valueOf`.
* If given `value` is not an instance of `vow.Promise`, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @returns {*}
*/
valueOf : function(value) {
return value && isFunction(value.valueOf)? value.valueOf() : value;
},
/**
* Static equivalent to `promise.isFulfilled`.
* If given `value` is not an instance of `vow.Promise`, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @returns {Boolean}
*/
isFulfilled : function(value) {
return value && isFunction(value.isFulfilled)? value.isFulfilled() : true;
},
/**
* Static equivalent to `promise.isRejected`.
* If given `value` is not an instance of `vow.Promise`, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @returns {Boolean}
*/
isRejected : function(value) {
return value && isFunction(value.isRejected)? value.isRejected() : false;
},
/**
* Static equivalent to `promise.isResolved`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @returns {Boolean}
*/
isResolved : function(value) {
return value && isFunction(value.isResolved)? value.isResolved() : true;
},
/**
* Returns a promise that has already been resolved with the given `value`.
* If `value` is a promise, returned promise will be adopted with the state of given promise.
*
* @param {*} value
* @returns {vow:Promise}
*/
resolve : function(value) {
var res = vow.defer();
res.resolve(value);
return res.promise();
},
/**
* Returns a promise that has already been fulfilled with the given `value`.
* If `value` is a promise, returned promise will be fulfilled with fulfill/rejection value of given promise.
*
* @param {*} value
* @returns {vow:Promise}
*/
fulfill : function(value) {
var defer = vow.defer(),
promise = defer.promise();
defer.resolve(value);
return promise.isFulfilled()?
promise :
promise.then(null, function(reason) {
return reason;
});
},
/**
* Returns a promise that has already been rejected with the given `reason`.
* If `reason` is a promise, returned promise will be rejected with fulfill/rejection value of given promise.
*
* @param {*} reason
* @returns {vow:Promise}
*/
reject : function(reason) {
var defer = vow.defer();
defer.reject(reason);
return defer.promise();
},
/**
* Invokes a given function `fn` with arguments `args`
*
* @param {Function} fn
* @param {...*} [args]
* @returns {vow:Promise}
*
* @example
* ```js
* var promise1 = vow.invoke(function(value) {
* return value;
* }, 'ok'),
* promise2 = vow.invoke(function() {
* throw Error();
* });
*
* promise1.isFulfilled(); // true
* promise1.valueOf(); // 'ok'
* promise2.isRejected(); // true
* promise2.valueOf(); // instance of Error
* ```
*/
invoke : function(fn, args) {
var len = Math.max(arguments.length - 1, 0),
callArgs;
if(len) { // optimization for V8
callArgs = Array(len);
var i = 0;
while(i < len) {
callArgs[i++] = arguments[i];
}
}
try {
return vow.resolve(callArgs?
fn.apply(global, callArgs) :
fn.call(global));
}
catch(e) {
return vow.reject(e);
}
},
/**
* Returns a promise to be fulfilled only after all the items in `iterable` are fulfilled,
* or to be rejected when any of the `iterable` is rejected.
*
* @param {Array|Object} iterable
* @returns {vow:Promise}
*
* @example
* with array:
* ```js
* var defer1 = vow.defer(),
* defer2 = vow.defer();
*
* vow.all([defer1.promise(), defer2.promise(), 3])
* .then(function(value) {
* // value is "[1, 2, 3]" here
* });
*
* defer1.resolve(1);
* defer2.resolve(2);
* ```
*
* @example
* with object:
* ```js
* var defer1 = vow.defer(),
* defer2 = vow.defer();
*
* vow.all({ p1 : defer1.promise(), p2 : defer2.promise(), p3 : 3 })
* .then(function(value) {
* // value is "{ p1 : 1, p2 : 2, p3 : 3 }" here
* });
*
* defer1.resolve(1);
* defer2.resolve(2);
* ```
*/
all : function(iterable) {
var defer = new Deferred(),
isPromisesArray = isArray(iterable),
keys = isPromisesArray?
getArrayKeys(iterable) :
getObjectKeys(iterable),
len = keys.length,
res = isPromisesArray? [] : {};
if(!len) {
defer.resolve(res);
return defer.promise();
}
var i = len;
vow._forEach(
iterable,
function(value, idx) {
res[keys[idx]] = value;
if(!--i) {
defer.resolve(res);
}
},
defer.reject,
defer.notify,
defer,
keys);
return defer.promise();
},
/**
* Returns a promise to be fulfilled only after all the items in `iterable` are resolved.
*
* @param {Array|Object} iterable
* @returns {vow:Promise}
*
* @example
* ```js
* var defer1 = vow.defer(),
* defer2 = vow.defer();
*
* vow.allResolved([defer1.promise(), defer2.promise()]).spread(function(promise1, promise2) {
* promise1.isRejected(); // returns true
* promise1.valueOf(); // returns "'error'"
* promise2.isFulfilled(); // returns true
* promise2.valueOf(); // returns "'ok'"
* });
*
* defer1.reject('error');
* defer2.resolve('ok');
* ```
*/
allResolved : function(iterable) {
var defer = new Deferred(),
isPromisesArray = isArray(iterable),
keys = isPromisesArray?
getArrayKeys(iterable) :
getObjectKeys(iterable),
i = keys.length,
res = isPromisesArray? [] : {};
if(!i) {
defer.resolve(res);
return defer.promise();
}
var onResolved = function() {
--i || defer.resolve(iterable);
};
vow._forEach(
iterable,
onResolved,
onResolved,
defer.notify,
defer,
keys);
return defer.promise();
},
allPatiently : function(iterable) {
return vow.allResolved(iterable).then(function() {
var isPromisesArray = isArray(iterable),
keys = isPromisesArray?
getArrayKeys(iterable) :
getObjectKeys(iterable),
rejectedPromises, fulfilledPromises,
len = keys.length, i = 0, key, promise;
if(!len) {
return isPromisesArray? [] : {};
}
while(i < len) {
key = keys[i++];
promise = iterable[key];
if(vow.isRejected(promise)) {
rejectedPromises || (rejectedPromises = isPromisesArray? [] : {});
isPromisesArray?
rejectedPromises.push(promise.valueOf()) :
rejectedPromises[key] = promise.valueOf();
}
else if(!rejectedPromises) {
(fulfilledPromises || (fulfilledPromises = isPromisesArray? [] : {}))[key] = vow.valueOf(promise);
}
}
if(rejectedPromises) {
throw rejectedPromises;
}
return fulfilledPromises;
});
},
/**
* Returns a promise to be fulfilled only when any of the items in `iterable` is fulfilled,
* or to be rejected when all the items are rejected (with the reason of the first rejected item).
*
* @param {Array} iterable
* @returns {vow:Promise}
*/
any : function(iterable) {
var defer = new Deferred(),
len = iterable.length;
if(!len) {
defer.reject(Error());
return defer.promise();
}
var i = 0, reason;
vow._forEach(
iterable,
defer.resolve,
function(e) {
i || (reason = e);
++i === len && defer.reject(reason);
},
defer.notify,
defer);
return defer.promise();
},
/**
* Returns a promise to be fulfilled only when any of the items in `iterable` is fulfilled,
* or to be rejected when the first item is rejected.
*
* @param {Array} iterable
* @returns {vow:Promise}
*/
anyResolved : function(iterable) {
var defer = new Deferred(),
len = iterable.length;
if(!len) {
defer.reject(Error());
return defer.promise();
}
vow._forEach(
iterable,
defer.resolve,
defer.reject,
defer.notify,
defer);
return defer.promise();
},
/**
* Static equivalent to `promise.delay`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Number} delay
* @returns {vow:Promise}
*/
delay : function(value, delay) {
return vow.resolve(value).delay(delay);
},
/**
* Static equivalent to `promise.timeout`.
* If given `value` is not a promise, then `value` is equivalent to fulfilled promise.
*
* @param {*} value
* @param {Number} timeout
* @returns {vow:Promise}
*/
timeout : function(value, timeout) {
return vow.resolve(value).timeout(timeout);
},
_forEach : function(promises, onFulfilled, onRejected, onProgress, ctx, keys) {
var len = keys? keys.length : promises.length,
i = 0;
while(i < len) {
vow.when(
promises[keys? keys[i] : i],
wrapOnFulfilled(onFulfilled, i),
onRejected,
onProgress,
ctx);
++i;
}
},
TimedOutError : defineCustomErrorType('TimedOut')
};
var defineAsGlobal = true;
if(typeof module === 'object' && typeof module.exports === 'object') {
module.exports = vow;
defineAsGlobal = false;
}
if(typeof modules === 'object' && isFunction(modules.define)) {
modules.define('vow', function(provide) {
provide(vow);
});
defineAsGlobal = false;
}
if(typeof define === 'function') {
define(function(require, exports, module) {
module.exports = vow;
});
defineAsGlobal = false;
}
defineAsGlobal && (global.vow = vow);
})(this);
}).call(this,require("FWaASH"))
},{"FWaASH":14}],7:[function(require,module,exports){
"use strict";
var window = require("global/window")
var once = require("once")
var parseHeaders = require("parse-headers")
var XHR = window.XMLHttpRequest || noop
var XDR = "withCredentials" in (new XHR()) ? XHR : window.XDomainRequest
module.exports = createXHR
function createXHR(options, callback) {
function readystatechange() {
if (xhr.readyState === 4) {
loadFunc()
}
}
function getBody() {
// Chrome with requestType=blob throws errors arround when even testing access to responseText
var body = undefined
if (xhr.response) {
body = xhr.response
} else if (xhr.responseType === "text" || !xhr.responseType) {
body = xhr.responseText || xhr.responseXML
}
if (isJson) {
try {
body = JSON.parse(body)
} catch (e) {}
}
return body
}
var failureResponse = {
body: undefined,
headers: {},
statusCode: 0,
method: method,
url: uri,
rawRequest: xhr
}
function errorFunc(evt) {
clearTimeout(timeoutTimer)
if(!(evt instanceof Error)){
evt = new Error("" + (evt || "unknown") )
}
evt.statusCode = 0
callback(evt, failureResponse)
}
// will load the data & process the response in a special response object
function loadFunc() {
clearTimeout(timeoutTimer)
var status = (xhr.status === 1223 ? 204 : xhr.status)
var response = failureResponse
var err = null
if (status !== 0){
response = {
body: getBody(),
statusCode: status,
method: method,
headers: {},
url: uri,
rawRequest: xhr
}
if(xhr.getAllResponseHeaders){ //remember xhr can in fact be XDR for CORS in IE
response.headers = parseHeaders(xhr.getAllResponseHeaders())
}
} else {
err = new Error("Internal XMLHttpRequest Error")
}
callback(err, response, response.body)
}
if (typeof options === "string") {
options = { uri: options }
}
options = options || {}
if(typeof callback === "undefined"){
throw new Error("callback argument missing")
}
callback = once(callback)
var xhr = options.xhr || null
if (!xhr) {
if (options.cors || options.useXDR) {
xhr = new XDR()
}else{
xhr = new XHR()
}
}
var key
var uri = xhr.url = options.uri || options.url
var method = xhr.method = options.method || "GET"
var body = options.body || options.data
var headers = xhr.headers = options.headers || {}
var sync = !!options.sync
var isJson = false
var timeoutTimer
if ("json" in options) {
isJson = true
headers["Accept"] || (headers["Accept"] = "application/json") //Don't override existing accept header declared by user
if (method !== "GET" && method !== "HEAD") {
headers["Content-Type"] = "application/json"
body = JSON.stringify(options.json)
}
}
xhr.onreadystatechange = readystatechange
xhr.onload = loadFunc
xhr.onerror = errorFunc
// IE9 must have onprogress be set to a unique function.
xhr.onprogress = function () {
// IE must die
}
xhr.ontimeout = errorFunc
xhr.open(method, uri, !sync)
//has to be after open
xhr.withCredentials = !!options.withCredentials
// Cannot set timeout with sync request
// not setting timeout on the xhr object, because of old webkits etc. not handling that correctly
// both npm's request and jquery 1.x use this kind of timeout, so this is being consistent
if (!sync && options.timeout > 0 ) {
timeoutTimer = setTimeout(function(){
xhr.abort("timeout");
}, options.timeout+2 );
}
if (xhr.setRequestHeader) {
for(key in headers){
if(headers.hasOwnProperty(key)){
xhr.setRequestHeader(key, headers[key])
}
}
} else if (options.headers) {
throw new Error("Headers cannot be set on an XDomainRequest object")
}
if ("responseType" in options) {
xhr.responseType = options.responseType
}
if ("beforeSend" in options &&
typeof options.beforeSend === "function"
) {
options.beforeSend(xhr)
}
xhr.send(body)
return xhr
}
function noop() {}
},{"global/window":8,"once":9,"parse-headers":13}],8:[function(require,module,exports){
(function (global){
if (typeof window !== "undefined") {
module.exports = window;
} else if (typeof global !== "undefined") {
module.exports = global;
} else if (typeof self !== "undefined"){
module.exports = self;
} else {
module.exports = {};
}
}).call(this,typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {})
},{}],9:[function(require,module,exports){
module.exports = once
once.proto = once(function () {
Object.defineProperty(Function.prototype, 'once', {
value: function () {
return once(this)
},
configurable: true
})
})
function once (fn) {
var called = false
return function () {
if (called) return
called = true
return fn.apply(this, arguments)
}
}
},{}],10:[function(require,module,exports){
var isFunction = require('is-function')
module.exports = forEach
var toString = Object.prototype.toString
var hasOwnProperty = Object.prototype.hasOwnProperty
function forEach(list, iterator, context) {
if (!isFunction(iterator)) {
throw new TypeError('iterator must be a function')
}
if (arguments.length < 3) {
context = this
}
if (toString.call(list) === '[object Array]')
forEachArray(list, iterator, context)
else if (typeof list === 'string')
forEachString(list, iterator, context)
else
forEachObject(list, iterator, context)
}
function forEachArray(array, iterator, context) {
for (var i = 0, len = array.length; i < len; i++) {
if (hasOwnProperty.call(array, i)) {
iterator.call(context, array[i], i, array)
}
}
}
function forEachString(string, iterator, context) {
for (var i = 0, len = string.length; i < len; i++) {
// no such thing as a sparse string.
iterator.call(context, string.charAt(i), i, string)
}
}
function forEachObject(object, iterator, context) {
for (var k in object) {
if (hasOwnProperty.call(object, k)) {
iterator.call(context, object[k], k, object)
}
}
}
},{"is-function":11}],11:[function(require,module,exports){
module.exports = isFunction
var toString = Object.prototype.toString
function isFunction (fn) {
var string = toString.call(fn)
return string === '[object Function]' ||
(typeof fn === 'function' && string !== '[object RegExp]') ||
(typeof window !== 'undefined' &&
// IE8 and below
(fn === window.setTimeout ||
fn === window.alert ||
fn === window.confirm ||
fn === window.prompt))
};
},{}],12:[function(require,module,exports){
exports = module.exports = trim;
function trim(str){
return str.replace(/^\s*|\s*$/g, '');
}
exports.left = function(str){
return str.replace(/^\s*/, '');
};
exports.right = function(str){
return str.replace(/\s*$/, '');
};
},{}],13:[function(require,module,exports){
var trim = require('trim')
, forEach = require('for-each')
, isArray = function(arg) {
return Object.prototype.toString.call(arg) === '[object Array]';
}
module.exports = function (headers) {
if (!headers)
return {}
var result = {}
forEach(
trim(headers).split('\n')
, function (row) {
var index = row.indexOf(':')
, key = trim(row.slice(0, index)).toLowerCase()
, value = trim(row.slice(index + 1))
if (typeof(result[key]) === 'undefined') {
result[key] = value
} else if (isArray(result[key])) {
result[key].push(value)
} else {
result[key] = [ result[key], value ]
}
}
)
return result
}
},{"for-each":10,"trim":12}],14:[function(require,module,exports){
// shim for using process in browser
var process = module.exports = {};
process.nextTick = (function () {
var canSetImmediate = typeof window !== 'undefined'
&& window.setImmediate;
var canPost = typeof window !== 'undefined'
&& window.postMessage && window.addEventListener
;
if (canSetImmediate) {
return function (f) { return window.setImmediate(f) };
}
if (canPost) {
var queue = [];
window.addEventListener('message', function (ev) {
var source = ev.source;
if ((source === window || source === null) && ev.data === 'process-tick') {
ev.stopPropagation();
if (queue.length > 0) {
var fn = queue.shift();
fn();
}
}
}, true);
return function nextTick(fn) {
queue.push(fn);
window.postMessage('process-tick', '*');
};
}
return function nextTick(fn) {
setTimeout(fn, 0);
};
})();
process.title = 'browser';
process.browser = true;
process.env = {};
process.argv = [];
function noop() {}
process.on = noop;
process.addListener = noop;
process.once = noop;
process.off = noop;
process.removeListener = noop;
process.removeAllListeners = noop;
process.emit = noop;
process.binding = function (name) {
throw new Error('process.binding is not supported');
}
// TODO(shtylman)
process.cwd = function () { return '/' };
process.chdir = function (dir) {
throw new Error('process.chdir is not supported');
};
},{}],15:[function(require,module,exports){
/*
* msa-seqtools
* https://github.com/greenify/msa-seqtools
*
* Copyright (c) 2014 greenify
* Licensed under the MIT license.
*/
var st = {};
module.exports = st;
/****
* Seems to be lots of different ways to format FASTA headers.
*
* Generally there's an ID and a DESCRIPTION
* >ID DESCRIPTION
*
* >(parts|of|ID) (DESCRIPTION with optional key=values)
*
* This is complicated by the fact that the "values" in the description can have spaces
* e.g. OS=Arabidopsis thaliana GN=CCD8
*
****
*/
// extract IDs and push them to the meta dict
st.getMeta = function(label) {
var full_id = false, full_desc = false;
var name, ids = {}, details = {}, description;
// console.log( "getMeta.label: ", label );
var label_parts = label.split(" ");
if ( label_parts.length >= 1 ) {
full_id = label_parts.shift(); // everything up to the first white space
full_desc = label_parts.join(" "); // everything else
}
else {
full_id = label;
}
// console.log( "full_id", full_id );
// console.log( "full_desc", full_desc );
if ( full_id ) {
var id_parts = full_id.split('|');
// the last item is the accession
name = id_parts.pop();
details.en = name;
// everything else should be pairs: db|id
while ( id_parts.length != 0 ) {
var db = id_parts.shift();
var id = id_parts.shift();
ids[ db ] = id;
}
}
else {
name = full_id;
}
if ( full_desc ) {
var kv_parts = full_desc.split('=');
if ( kv_parts.length > 1 ) {
var current_key, next_key;
var kv;
var kv_idx_max = kv_parts.length - 1;
var kv_idx = 0;
kv_parts.forEach( function( value_and_maybe_next_key ) {
value_and_maybe_next_key = value_and_maybe_next_key.trim();
var value_parts = value_and_maybe_next_key.split(" ");
var value;
if ( value_parts.length > 1 ) {
next_key = value_parts.pop();
value = value_parts.join(' ');
}
else {
value = value_and_maybe_next_key;
}
if ( current_key ) {
var key = current_key.toLowerCase();
details[ key ] = value;
//console.log( "details[" + key + "] = " + value );
}
else {
description = value;
//console.log( "description=" + value );
}
current_key = next_key;
});
}
else {
description = kv_parts.shift();
}
}
var meta = {
name: name,
ids: ids,
details: details,
};
if ( description ) {
meta.desc = description
}
// console.log( "meta", meta );
return meta;
};
var findSepInArr = function(arr, sep) {
for (var i = 0; i < arr.lenght; i++) {
if (arr[i].indexOf(i)) {
return i;
}
}
return arr.length - 1;
};
var strToDict = function(str, sep, toJoin) {
toJoin = toJoin || {};
var entries = str.split(sep);
toJoin[entries[0].toLowerCase()] = entries[1];
return toJoin;
};
var identDB = {
"sp": {
link: "http://www.uniprot.org/%s",
name: "Uniprot"
},
"tr": {
link: "http://www.uniprot.org/%s",
name: "Trembl"
},
"gb": {
link: "http://www.ncbi.nlm.nih.gov/nuccore/%s",
name: "Genbank"
},
"pdb": {
link: "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s",
name: "PDB"
}
};
st.buildLinks = function(meta) {
var links = {};
meta = meta || {};
Object.keys(meta).forEach(function(id) {
if (id in identDB) {
var entry = identDB[id];
var link = entry.link.replace("%s", meta[id]);
links[entry.name] = link;
}
});
return links;
};
// search for a text
st.contains = function(text, search) {
return ''.indexOf.call(text, search, 0) !== -1;
};
// split after e.g. 80 chars
st.splitNChars = function(txt, num) {
var i, _ref;
num = num || 80;
var result = [];
for (i = 0, _ref = txt.length - 1; i <= _ref; i += num) {
result.push(txt.substr(i, num));
}
return result;
};
st.reverse = function(seq) {
return seq.split('').reverse().join('');
}
st.complement = function(seq) {
var newSeq = seq + "";
var replacements = [
// cg
[/g/g, "0"],
[/c/g, "1"],
[/0/g, "c"],
[/1/g, "g"],
// CG
[/G/g, "0"],
[/C/g, "1"],
[/0/g, "C"],
[/1/g, "G"],
// at
[/a/g, "0"],
[/t/g, "1"],
[/0/g, "t"],
[/1/g, "a"],
// AT
[/A/g, "0"],
[/T/g, "1"],
[/0/g, "T"],
[/1/g, "A"],
];
for(var rep in replacements){
newSeq = newSeq.replace(replacements[rep][0], replacements[rep][1]);
}
return newSeq;
}
st.reverseComplement = function(seq){
return st.reverse(st.complement(seq));
}
st.model = function Seq(seq, name, id) {
this.seq = seq;
this.name = name;
this.id = id;
this.ids = {};
};
},{}]},{},[])