@gmod/jbrowse
Version:
JBrowse - client-side genome browser
517 lines (436 loc) • 14.7 kB
JavaScript
//
// jDataView by Vjeux - Jan 2010
//
// A unique way to read a binary file in the browser
// http://github.com/vjeux/jDataView
// http://blog.vjeux.com/ <vjeuxx@gmail.com>
//
(function (global) {
var compatibility = {
ArrayBuffer: typeof ArrayBuffer !== 'undefined',
DataView: typeof DataView !== 'undefined' &&
('getFloat64' in DataView.prototype || // Chrome
'getFloat64' in new DataView(new ArrayBuffer(1))), // Node
// NodeJS Buffer in v0.5.5 and newer
NodeBuffer: false//typeof Buffer !== 'undefined' && 'readInt16LE' in Buffer.prototype
};
var dataTypes = {
'Int8': 1,
'Int16': 2,
'Int32': 4,
'Uint8': 1,
'Uint16': 2,
'Uint32': 4,
'Float32': 4,
'Float64': 8
};
var nodeNaming = {
'Int8': 'Int8',
'Int16': 'Int16',
'Int32': 'Int32',
'Uint8': 'UInt8',
'Uint16': 'UInt16',
'Uint32': 'UInt32',
'Float32': 'Float',
'Float64': 'Double'
};
var jDataView = function (buffer, byteOffset, byteLength, littleEndian) {
if (!(this instanceof jDataView)) {
throw new Error("jDataView constructor may not be called as a function");
}
this.buffer = buffer;
// Handle Type Errors
if (!(compatibility.NodeBuffer && buffer instanceof Buffer) &&
!(compatibility.ArrayBuffer && buffer instanceof ArrayBuffer) &&
typeof buffer !== 'string') {
throw new TypeError('jDataView buffer has an incompatible type');
}
// Check parameters and existing functionnalities
this._isArrayBuffer = compatibility.ArrayBuffer && buffer instanceof ArrayBuffer;
this._isDataView = compatibility.DataView && this._isArrayBuffer;
this._isNodeBuffer = compatibility.NodeBuffer && buffer instanceof Buffer;
// Default Values
this._littleEndian = Boolean(littleEndian);
var bufferLength = this._isArrayBuffer ? buffer.byteLength : buffer.length;
if (byteOffset === undefined) {
byteOffset = 0;
}
this.byteOffset = byteOffset;
if (byteLength === undefined) {
byteLength = bufferLength - byteOffset;
}
this.byteLength = byteLength;
if (!this._isDataView) {
// Do additional checks to simulate DataView
if (typeof byteOffset !== 'number') {
throw new TypeError('jDataView byteOffset is not a number');
}
if (typeof byteLength !== 'number') {
throw new TypeError('jDataView byteLength is not a number');
}
if (byteOffset < 0) {
throw new Error('jDataView byteOffset is negative');
}
if (byteLength < 0) {
throw new Error('jDataView byteLength is negative');
}
}
// Instanciate
if (this._isDataView) {
this._view = new DataView(buffer, byteOffset, byteLength);
this._start = 0;
}
this._start = byteOffset;
if (byteOffset + byteLength > bufferLength) {
throw new Error("jDataView (byteOffset + byteLength) value is out of bounds");
}
this._offset = 0;
// Create uniform reading methods (wrappers) for the following data types
if (this._isDataView) { // DataView: we use the direct method
for (var type in dataTypes) {
if (!dataTypes.hasOwnProperty(type)) {
continue;
}
(function(type, view){
var size = dataTypes[type];
view['get' + type] = function (byteOffset, littleEndian) {
// Handle the lack of endianness
if (littleEndian === undefined) {
littleEndian = view._littleEndian;
}
// Handle the lack of byteOffset
if (byteOffset === undefined) {
byteOffset = view._offset;
}
// Move the internal offset forward
view._offset = byteOffset + size;
return view._view['get' + type](byteOffset, littleEndian);
}
})(type, this);
}
} else if (this._isNodeBuffer && compatibility.NodeBuffer) {
for (var type in dataTypes) {
if (!dataTypes.hasOwnProperty(type)) {
continue;
}
var name;
if (type === 'Int8' || type === 'Uint8') {
name = 'read' + nodeNaming[type];
} else if (littleEndian) {
name = 'read' + nodeNaming[type] + 'LE';
} else {
name = 'read' + nodeNaming[type] + 'BE';
}
(function(type, view, name){
var size = dataTypes[type];
view['get' + type] = function (byteOffset, littleEndian) {
// Handle the lack of endianness
if (littleEndian === undefined) {
littleEndian = view._littleEndian;
}
// Handle the lack of byteOffset
if (byteOffset === undefined) {
byteOffset = view._offset;
}
// Move the internal offset forward
view._offset = byteOffset + size;
return view.buffer[name](view._start + byteOffset);
}
})(type, this, name);
}
} else {
for (var type in dataTypes) {
if (!dataTypes.hasOwnProperty(type)) {
continue;
}
(function(type, view){
var size = dataTypes[type];
view['get' + type] = function (byteOffset, littleEndian) {
// Handle the lack of endianness
if (littleEndian === undefined) {
littleEndian = view._littleEndian;
}
// Handle the lack of byteOffset
if (byteOffset === undefined) {
byteOffset = view._offset;
}
// Move the internal offset forward
view._offset = byteOffset + size;
if (view._isArrayBuffer && (view._start + byteOffset) % size === 0 && (size === 1 || littleEndian)) {
// ArrayBuffer: we use a typed array of size 1 if the alignment is good
// ArrayBuffer does not support endianess flag (for size > 1)
return new global[type + 'Array'](view.buffer, view._start + byteOffset, 1)[0];
} else {
// Error checking:
if (typeof byteOffset !== 'number') {
throw new TypeError('jDataView byteOffset is not a number');
}
if (byteOffset + size > view.byteLength) {
throw new Error('jDataView (byteOffset + size) value is out of bounds');
}
return view['_get' + type](view._start + byteOffset, littleEndian);
}
}
})(type, this);
}
}
};
if (compatibility.NodeBuffer) {
jDataView.createBuffer = function () {
return new Buffer(arguments);
}
} else if (compatibility.ArrayBuffer) {
jDataView.createBuffer = function () {
return new Uint8Array(arguments).buffer;
}
} else {
jDataView.createBuffer = function () {
return String.fromCharCode.apply(null, arguments);
}
}
jDataView.prototype = {
compatibility: compatibility,
// Helpers
_getBytes: function (length, byteOffset, littleEndian) {
var result;
// Handle the lack of endianness
if (littleEndian === undefined) {
littleEndian = this._littleEndian;
}
// Handle the lack of byteOffset
if (byteOffset === undefined) {
byteOffset = this._offset;
}
// Error Checking
if (typeof byteOffset !== 'number') {
throw new TypeError('jDataView byteOffset is not a number');
}
if (length < 0 || byteOffset + length > this.byteLength) {
throw new Error('jDataView length or (byteOffset+length) value is out of bounds');
}
byteOffset += this._start;
if (this._isArrayBuffer) {
result = new Uint8Array(this.buffer, byteOffset, length);
}
else {
result = this.buffer.slice(byteOffset, byteOffset + length);
if (!this._isNodeBuffer) {
result = Array.prototype.map.call(result, function (char) {
return char.charCodeAt(0) & 0xff;
});
}
}
if (littleEndian && length > 1) {
if (!(result instanceof Array)) {
result = Array.prototype.slice.call(result);
}
result.reverse();
}
this._offset = byteOffset - this._start + length;
return result;
},
// wrapper for external calls (do not return inner buffer directly to prevent it's modifying)
getBytes: function (length, byteOffset, littleEndian) {
var result = this._getBytes.apply(this, arguments);
if (!(result instanceof Array)) {
result = Array.prototype.slice.call(result);
}
return result;
},
getString: function (length, byteOffset) {
var value;
if (this._isNodeBuffer) {
// Handle the lack of byteOffset
if (byteOffset === undefined) {
byteOffset = this._offset;
}
// Error Checking
if (typeof byteOffset !== 'number') {
throw new TypeError('jDataView byteOffset is not a number');
}
if (length < 0 || byteOffset + length > this.byteLength) {
throw new Error('jDataView length or (byteOffset+length) value is out of bounds');
}
value = this.buffer.toString('ascii', this._start + byteOffset, this._start + byteOffset + length);
this._offset = byteOffset + length;
}
else {
value = String.fromCharCode.apply(null, this._getBytes(length, byteOffset, false));
}
return value;
},
getChar: function (byteOffset) {
return this.getString(1, byteOffset);
},
tell: function () {
return this._offset;
},
seek: function (byteOffset) {
if (typeof byteOffset !== 'number') {
throw new TypeError('jDataView byteOffset is not a number');
}
if (byteOffset < 0 || byteOffset > this.byteLength) {
throw new Error('jDataView byteOffset value is out of bounds');
}
return this._offset = byteOffset;
},
// Compatibility functions on a String Buffer
_getFloat64: function (byteOffset, littleEndian) {
var b = this._getBytes(8, byteOffset, littleEndian),
sign = 1 - (2 * (b[0] >> 7)),
exponent = ((((b[0] << 1) & 0xff) << 3) | (b[1] >> 4)) - (Math.pow(2, 10) - 1),
// Binary operators such as | and << operate on 32 bit values, using + and Math.pow(2) instead
mantissa = ((b[1] & 0x0f) * Math.pow(2, 48)) + (b[2] * Math.pow(2, 40)) + (b[3] * Math.pow(2, 32)) +
(b[4] * Math.pow(2, 24)) + (b[5] * Math.pow(2, 16)) + (b[6] * Math.pow(2, 8)) + b[7];
if (exponent === 1024) {
if (mantissa !== 0) {
return NaN;
} else {
return sign * Infinity;
}
}
if (exponent === -1023) { // Denormalized
return sign * mantissa * Math.pow(2, -1022 - 52);
}
return sign * (1 + mantissa * Math.pow(2, -52)) * Math.pow(2, exponent);
},
_getFloat32: function (byteOffset, littleEndian) {
var b = this._getBytes(4, byteOffset, littleEndian),
sign = 1 - (2 * (b[0] >> 7)),
exponent = (((b[0] << 1) & 0xff) | (b[1] >> 7)) - 127,
mantissa = ((b[1] & 0x7f) << 16) | (b[2] << 8) | b[3];
if (exponent === 128) {
if (mantissa !== 0) {
return NaN;
} else {
return sign * Infinity;
}
}
if (exponent === -127) { // Denormalized
return sign * mantissa * Math.pow(2, -126 - 23);
}
return sign * (1 + mantissa * Math.pow(2, -23)) * Math.pow(2, exponent);
},
_getInt32: function (byteOffset, littleEndian) {
var b = this._getUint32(byteOffset, littleEndian);
return b > Math.pow(2, 31) - 1 ? b - Math.pow(2, 32) : b;
},
_getUint32: function (byteOffset, littleEndian) {
var b = this._getBytes(4, byteOffset, littleEndian);
return (b[3] * Math.pow(2, 24)) + (b[2] << 16) + (b[1] << 8) + b[0];
},
_getInt16: function (byteOffset, littleEndian) {
var b = this._getUint16(byteOffset, littleEndian);
return b > Math.pow(2, 15) - 1 ? b - Math.pow(2, 16) : b;
},
_getUint16: function (byteOffset, littleEndian) {
var b = this._getBytes(2, byteOffset, littleEndian);
return (b[1] << 8) + b[0];
},
_getInt8: function (byteOffset) {
var b = this._getUint8(byteOffset);
return b > Math.pow(2, 7) - 1 ? b - Math.pow(2, 8) : b;
},
_getUint8: function (byteOffset) {
return this._getBytes(1, byteOffset)[0];
}
};
if (typeof jQuery !== 'undefined' && jQuery.fn.jquery >= "1.6.2") {
var convertResponseBodyToText = function (byteArray) {
// http://jsperf.com/vbscript-binary-download/6
var scrambledStr;
try {
scrambledStr = IEBinaryToArray_ByteStr(byteArray);
} catch (e) {
// http://stackoverflow.com/questions/1919972/how-do-i-access-xhr-responsebody-for-binary-data-from-javascript-in-ie
// http://miskun.com/javascript/internet-explorer-and-binary-files-data-access/
var IEBinaryToArray_ByteStr_Script =
"Function IEBinaryToArray_ByteStr(Binary)\r\n"+
" IEBinaryToArray_ByteStr = CStr(Binary)\r\n"+
"End Function\r\n"+
"Function IEBinaryToArray_ByteStr_Last(Binary)\r\n"+
" Dim lastIndex\r\n"+
" lastIndex = LenB(Binary)\r\n"+
" if lastIndex mod 2 Then\r\n"+
" IEBinaryToArray_ByteStr_Last = AscB( MidB( Binary, lastIndex, 1 ) )\r\n"+
" Else\r\n"+
" IEBinaryToArray_ByteStr_Last = -1\r\n"+
" End If\r\n"+
"End Function\r\n";
// http://msdn.microsoft.com/en-us/library/ms536420(v=vs.85).aspx
// proprietary IE function
window.execScript(IEBinaryToArray_ByteStr_Script, 'vbscript');
scrambledStr = IEBinaryToArray_ByteStr(byteArray);
}
var lastChr = IEBinaryToArray_ByteStr_Last(byteArray),
result = "",
i = 0,
l = scrambledStr.length % 8,
thischar;
while (i < l) {
thischar = scrambledStr.charCodeAt(i++);
result += String.fromCharCode(thischar & 0xff, thischar >> 8);
}
l = scrambledStr.length
while (i < l) {
result += String.fromCharCode(
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8,
(thischar = scrambledStr.charCodeAt(i++), thischar & 0xff), thischar >> 8);
}
if (lastChr > -1) {
result += String.fromCharCode(lastChr);
}
return result;
};
jQuery.ajaxSetup({
converters: {
'* dataview': function(data) {
return new jDataView(data);
}
},
accepts: {
dataview: "text/plain; charset=x-user-defined"
},
responseHandler: {
dataview: function (responses, options, xhr) {
// Array Buffer Firefox
if ('mozResponseArrayBuffer' in xhr) {
responses.text = xhr.mozResponseArrayBuffer;
}
// Array Buffer Chrome
else if ('responseType' in xhr && xhr.responseType === 'arraybuffer' && xhr.response) {
responses.text = xhr.response;
}
// Internet Explorer (Byte array accessible through VBScript -- convert to text)
else if ('responseBody' in xhr) {
responses.text = convertResponseBodyToText(xhr.responseBody);
}
// Older Browsers
else {
responses.text = xhr.responseText;
}
}
}
});
jQuery.ajaxPrefilter('dataview', function(options, originalOptions, jqXHR) {
// trying to set the responseType on IE 6 causes an error
if (jQuery.support.ajaxResponseType) {
if (!options.hasOwnProperty('xhrFields')) {
options.xhrFields = {};
}
options.xhrFields.responseType = 'arraybuffer';
}
options.mimeType = 'text/plain; charset=x-user-defined';
});
}
global.jDataView = (global.module || {}).exports = jDataView;
if (typeof module !== 'undefined') {
module.exports = jDataView;
}
})(window);