molstar
Version:
A comprehensive macromolecular library.
376 lines • 15.5 kB
JavaScript
;
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
* ported from https://github.com/photopea/UZIP.js/blob/master/UZIP.js
* MIT License, Copyright (c) 2018 Photopea
*
* - added `ungzip`
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.zip = exports.Zip = exports.deflate = exports.ungzip = exports.inflate = exports.inflateRaw = exports.unzip = void 0;
var tslib_1 = require("tslib");
var bin_1 = require("./bin");
var checksum_1 = require("./checksum");
var inflate_1 = require("./inflate");
var deflate_1 = require("./deflate");
var mol_task_1 = require("../../mol-task");
function unzip(runtime, buf, onlyNames) {
if (onlyNames === void 0) { onlyNames = false; }
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var out, data, eocd, o, cnu, coffs, i, csize, usize, nl, el, cl, roff;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
out = Object.create(null);
data = new Uint8Array(buf);
eocd = data.length - 4;
while ((0, bin_1.readUint)(data, eocd) !== 0x06054b50)
eocd--;
o = eocd;
o += 4; // sign = 0x06054b50
o += 4; // disks = 0;
cnu = (0, bin_1.readUshort)(data, o);
o += 2;
// const cnt = readUshort(data, o);
o += 2;
// const csize = readUint(data, o);
o += 4;
coffs = (0, bin_1.readUint)(data, o);
o += 4;
o = coffs;
i = 0;
_a.label = 1;
case 1:
if (!(i < cnu)) return [3 /*break*/, 4];
// const sign = readUint(data, o);
o += 4;
o += 4; // versions;
o += 4; // flag + compr
o += 4; // time
// const crc32 = readUint(data, o);
o += 4;
csize = (0, bin_1.readUint)(data, o);
o += 4;
usize = (0, bin_1.readUint)(data, o);
o += 4;
nl = (0, bin_1.readUshort)(data, o);
el = (0, bin_1.readUshort)(data, o + 2);
cl = (0, bin_1.readUshort)(data, o + 4);
o += 6; // name, extra, comment
o += 8; // disk, attribs
roff = (0, bin_1.readUint)(data, o);
o += 4;
o += nl + el + cl;
return [4 /*yield*/, _readLocal(runtime, data, roff, out, csize, usize, onlyNames)];
case 2:
_a.sent();
_a.label = 3;
case 3:
i++;
return [3 /*break*/, 1];
case 4:
// console.log(out);
return [2 /*return*/, out];
}
});
});
}
exports.unzip = unzip;
function _readLocal(runtime, data, o, out, csize, usize, onlyNames) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var cmpr, nlen, elen, name, file, buf;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
// const sign = readUint(data, o);
o += 4;
// const ver = readUshort(data, o);
o += 2;
// const gpflg = readUshort(data, o);
o += 2;
cmpr = (0, bin_1.readUshort)(data, o);
o += 2;
// const time = readUint(data, o);
o += 4;
// const crc32 = readUint(data, o);
o += 4;
// var csize = rUi(data, o); o+=4;
// var usize = rUi(data, o); o+=4;
o += 8;
nlen = (0, bin_1.readUshort)(data, o);
o += 2;
elen = (0, bin_1.readUshort)(data, o);
o += 2;
name = (0, bin_1.readUTF8)(data, o, nlen);
o += nlen; // console.log(name);
o += elen;
if (onlyNames) {
out[name] = { size: usize, csize: csize };
return [2 /*return*/];
}
file = new Uint8Array(data.buffer, o);
if (!(cmpr === 0)) return [3 /*break*/, 1];
out[name] = new Uint8Array(file.buffer.slice(o, o + csize));
return [3 /*break*/, 4];
case 1:
if (!(cmpr === 8)) return [3 /*break*/, 3];
buf = new Uint8Array(usize);
return [4 /*yield*/, inflateRaw(runtime, file, buf)];
case 2:
_a.sent();
out[name] = buf;
return [3 /*break*/, 4];
case 3: throw new Error("unknown compression method: " + cmpr);
case 4: return [2 /*return*/];
}
});
});
}
function inflateRaw(runtime, file, buf) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
return (0, tslib_1.__generator)(this, function (_a) {
return [2 /*return*/, (0, inflate_1._inflate)(runtime, file, buf)];
});
});
}
exports.inflateRaw = inflateRaw;
function inflate(runtime, file, buf) {
// const CMF = file[0]
// const FLG = file[1]
// const CM = (CMF&15)
// const CINFO = (CMF>>>4);
// console.log(CM, CINFO,CMF,FLG);
return inflateRaw(runtime, new Uint8Array(file.buffer, file.byteOffset + 2, file.length - 6), buf);
}
exports.inflate = inflate;
// https://tools.ietf.org/html/rfc1952
function ungzip(runtime, file, buf) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var flg, o, xlen, zero, zero, crc32, isize, blocks, inflated, crcValue;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
flg = file[3];
o = 10;
if (flg & 4) { // FEXTRA
xlen = (0, bin_1.readUshort)(file, o);
// console.log('FEXTRA', xlen)
o += xlen;
}
if (flg & 8) { // FNAME
zero = o;
while (file[zero] !== 0)
++zero;
// const name = readUTF8(file, o, zero - o)
// console.log('FNAME', name, zero - o)
o = zero + 1;
}
if (flg & 16) { // FCOMMENT
zero = o;
while (file[zero] !== 0)
++zero;
// const comment = readUTF8(file, o, zero - o)
// console.log('FCOMMENT', comment)
o = zero + 1;
}
if (flg & 1) { // FHCRC
// const hcrc = readUshort(file, o)
// console.log('FHCRC', hcrc)
o += 2;
}
crc32 = (0, bin_1.toInt32)((0, bin_1.readUint)(file, file.length - 8));
isize = (0, bin_1.readUint)(file, file.length - 4);
if (buf === undefined)
buf = new Uint8Array(isize);
blocks = new Uint8Array(file.buffer, file.byteOffset + o, file.length - o - 8);
return [4 /*yield*/, inflateRaw(runtime, blocks, buf)];
case 1:
inflated = _a.sent();
crcValue = (0, checksum_1.crc)(inflated, 0, inflated.length);
if (crc32 !== crcValue) {
console.error("ungzip: checksums don't match");
}
return [2 /*return*/, inflated];
}
});
});
}
exports.ungzip = ungzip;
function deflate(runtime, data, opts /* , buf, off*/) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var off, buf, crcValue;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
if (opts === undefined)
opts = { level: 6 };
off = 0;
buf = new Uint8Array(50 + Math.floor(data.length * 1.1));
buf[off] = 120;
buf[off + 1] = 156;
off += 2;
return [4 /*yield*/, (0, deflate_1._deflateRaw)(runtime, data, buf, off, opts.level)];
case 1:
off = _a.sent();
crcValue = (0, checksum_1.adler)(data, 0, data.length);
buf[off + 0] = ((crcValue >>> 24) & 255);
buf[off + 1] = ((crcValue >>> 16) & 255);
buf[off + 2] = ((crcValue >>> 8) & 255);
buf[off + 3] = ((crcValue >>> 0) & 255);
return [2 /*return*/, new Uint8Array(buf.buffer, 0, off + 4)];
}
});
});
}
exports.deflate = deflate;
function deflateRaw(runtime, data, opts) {
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var buf, off;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
if (opts === undefined)
opts = { level: 6 };
buf = new Uint8Array(50 + Math.floor(data.length * 1.1));
return [4 /*yield*/, (0, deflate_1._deflateRaw)(runtime, data, buf, 0, opts.level)];
case 1:
off = _a.sent();
return [2 /*return*/, new Uint8Array(buf.buffer, 0, off)];
}
});
});
}
function Zip(obj, noCmpr) {
if (noCmpr === void 0) { noCmpr = false; }
return mol_task_1.Task.create('Zip', function (ctx) { return zip(ctx, obj, noCmpr); });
}
exports.Zip = Zip;
function zip(runtime, obj, noCmpr) {
if (noCmpr === void 0) { noCmpr = false; }
return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
var tot, zpd, _a, _b, _i, p, cpr, buf, crcValue, _c, _d, _e, p, data, o, fof, p, file, i, ioff, p, file, csize;
var _f;
return (0, tslib_1.__generator)(this, function (_g) {
switch (_g.label) {
case 0:
tot = 0;
zpd = {};
_a = [];
for (_b in obj)
_a.push(_b);
_i = 0;
_g.label = 1;
case 1:
if (!(_i < _a.length)) return [3 /*break*/, 6];
p = _a[_i];
cpr = !_noNeed(p) && !noCmpr, buf = obj[p];
crcValue = (0, checksum_1.crc)(buf, 0, buf.length);
_c = zpd;
_d = p;
_f = {
cpr: cpr,
usize: buf.length,
crc: crcValue
};
if (!cpr) return [3 /*break*/, 3];
return [4 /*yield*/, deflateRaw(runtime, buf)];
case 2:
_e = _g.sent();
return [3 /*break*/, 4];
case 3:
_e = buf;
_g.label = 4;
case 4:
_c[_d] = (_f.file = (_e),
_f);
_g.label = 5;
case 5:
_i++;
return [3 /*break*/, 1];
case 6:
for (p in zpd)
tot += zpd[p].file.length + 30 + 46 + 2 * (0, bin_1.sizeUTF8)(p);
tot += 22;
data = new Uint8Array(tot);
o = 0;
fof = [];
for (p in zpd) {
file = zpd[p];
fof.push(o);
o = _writeHeader(data, o, p, file, 0);
}
i = 0;
ioff = o;
for (p in zpd) {
file = zpd[p];
fof.push(o);
o = _writeHeader(data, o, p, file, 1, fof[i++]);
}
csize = o - ioff;
(0, bin_1.writeUint)(data, o, 0x06054b50);
o += 4;
o += 4; // disks
(0, bin_1.writeUshort)(data, o, i);
o += 2;
(0, bin_1.writeUshort)(data, o, i);
o += 2; // number of c d records
(0, bin_1.writeUint)(data, o, csize);
o += 4;
(0, bin_1.writeUint)(data, o, ioff);
o += 4;
o += 2;
return [2 /*return*/, data.buffer];
}
});
});
}
exports.zip = zip;
// no need to compress .PNG, .ZIP, .JPEG ....
function _noNeed(fn) {
var ext = fn.split('.').pop().toLowerCase();
return 'png,jpg,jpeg,zip'.indexOf(ext) !== -1;
}
function _writeHeader(data, o, p, obj, t, roff) {
if (roff === void 0) { roff = 0; }
var file = obj.file;
(0, bin_1.writeUint)(data, o, t === 0 ? 0x04034b50 : 0x02014b50);
o += 4; // sign
if (t === 1)
o += 2; // ver made by
(0, bin_1.writeUshort)(data, o, 20);
o += 2; // ver
(0, bin_1.writeUshort)(data, o, 0);
o += 2; // gflip
(0, bin_1.writeUshort)(data, o, obj.cpr ? 8 : 0);
o += 2; // cmpr
(0, bin_1.writeUint)(data, o, 0);
o += 4; // time
(0, bin_1.writeUint)(data, o, obj.crc);
o += 4; // crc32
(0, bin_1.writeUint)(data, o, file.length);
o += 4; // csize
(0, bin_1.writeUint)(data, o, obj.usize);
o += 4; // usize
(0, bin_1.writeUshort)(data, o, (0, bin_1.sizeUTF8)(p));
o += 2; // nlen
(0, bin_1.writeUshort)(data, o, 0);
o += 2; // elen
if (t === 1) {
o += 2; // comment length
o += 2; // disk number
o += 6; // attributes
(0, bin_1.writeUint)(data, o, roff);
o += 4; // usize
}
var nlen = (0, bin_1.writeUTF8)(data, o, p);
o += nlen;
if (t === 0) {
data.set(file, o);
o += file.length;
}
return o;
}
//# sourceMappingURL=zip.js.map