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<html lang="en" style="font-size:16px"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width,initial-scale=1"><meta name="Author" content="David Koes & 3Dmoljs Contributors"><meta name="Description" content="A modern, object-oriented JavaScript library for visualizing molecular data"><title>Source: parsers/cifutils/decoder.ts</title><!--[if lt IE 9]>
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* Copyright (c) 2017-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* From CIFTools.js
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Encoding, EncodedData } from './encoding';
const IsNativeEndianLittle = new Uint16Array(new Uint8Array([0x12, 0x34]).buffer)[0] === 0x3412;
function flipByteOrder(data: Uint8Array, bytes: number) {
const buffer = new ArrayBuffer(data.length);
const ret = new Uint8Array(buffer);
for (let i = 0, n = data.length; i < n; i += bytes) {
for (let j = 0; j < bytes; j++) {
ret[i + bytes - j - 1] = data[i + j];
}
}
return buffer;
}
/**
* Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/
* by Alexander Rose <alexander.rose@weirdbyte.de>, MIT License, Copyright (c) 2016
*/
export function decode(data: EncodedData): any[] {
let current: any = data.data;
for (let i = data.encoding.length - 1; i >= 0; i--) {
current = decodeStep(current, data.encoding[i]);
}
return current as any[];
}
function decodeStep(data: any, encoding: Encoding): any {
switch (encoding.kind) {
case 'ByteArray': {
switch (encoding.type) {
case Encoding.IntDataType.Uint8: return data;
case Encoding.IntDataType.Int8: return int8(data);
case Encoding.IntDataType.Int16: return int16(data);
case Encoding.IntDataType.Uint16: return uint16(data);
case Encoding.IntDataType.Int32: return int32(data);
case Encoding.IntDataType.Uint32: return uint32(data);
case Encoding.FloatDataType.Float32: return float32(data);
case Encoding.FloatDataType.Float64: return float64(data);
default: throw new Error('unreachable');
}
}
case 'FixedPoint': return fixedPoint(data, encoding);
case 'IntervalQuantization': return intervalQuantization(data, encoding);
case 'RunLength': return runLength(data, encoding);
case 'Delta': return delta(data, encoding);
case 'IntegerPacking': return integerPacking(data, encoding);
case 'StringArray': return stringArray(data, encoding);
}
}
function getIntArray(type: Encoding.IntDataType, size: number) {
switch (type) {
case Encoding.IntDataType.Int8: return new Int8Array(size);
case Encoding.IntDataType.Int16: return new Int16Array(size);
case Encoding.IntDataType.Int32: return new Int32Array(size);
case Encoding.IntDataType.Uint8: return new Uint8Array(size);
case Encoding.IntDataType.Uint16: return new Uint16Array(size);
case Encoding.IntDataType.Uint32: return new Uint32Array(size);
default: return new Int32Array(size);
}
}
function getFloatArray(type: Encoding.FloatDataType, size: number) {
switch (type) {
case Encoding.FloatDataType.Float32: return new Float32Array(size);
case Encoding.FloatDataType.Float64: return new Float64Array(size);
default: return new Float64Array(size);
}
}
function int8(data: Uint8Array) { return new Int8Array(data.buffer, data.byteOffset); }
function view<T>(data: Uint8Array, byteSize: number, c: new (buffer: ArrayBuffer) => T) {
if (data.byteOffset != 0 || data.byteLength != data.buffer.byteLength) { //dkoes - extract from larger buffer if needed
data = new Uint8Array(data);
}
if (IsNativeEndianLittle) return new c(data.buffer as ArrayBuffer);
return new c(flipByteOrder(data, byteSize));
}
function int16(data: Uint8Array) { return view(data, 2, Int16Array); }
function uint16(data: Uint8Array) { return view(data, 2, Uint16Array); }
function int32(data: Uint8Array) { return view(data, 4, Int32Array); }
function uint32(data: Uint8Array) { return view(data, 4, Uint32Array); }
function float32(data: Uint8Array) { return view(data, 4, Float32Array); }
function float64(data: Uint8Array) { return view(data, 8, Float64Array); }
function fixedPoint(data: Int32Array, encoding: Encoding.FixedPoint) {
const n = data.length;
const output = getFloatArray(encoding.srcType, n);
const f = 1 / encoding.factor;
for (let i = 0; i < n; i++) {
output[i] = f * data[i];
}
return output;
}
function intervalQuantization(data: Int32Array, encoding: Encoding.IntervalQuantization) {
const n = data.length;
const output = getFloatArray(encoding.srcType, n);
const delta = (encoding.max - encoding.min) / (encoding.numSteps - 1);
const min = encoding.min;
for (let i = 0; i < n; i++) {
output[i] = min + delta * data[i];
}
return output;
}
function runLength(data: Int32Array, encoding: Encoding.RunLength) {
const output = getIntArray(encoding.srcType, encoding.srcSize);
let dataOffset = 0;
for (let i = 0, il = data.length; i < il; i += 2) {
const value = data[i]; // value to be repeated
const length = data[i + 1]; // number of repeats
for (let j = 0; j < length; ++j) {
output[dataOffset++] = value;
}
}
return output;
}
function delta(data: (Int8Array | Int16Array | Int32Array), encoding: Encoding.Delta) {
const n = data.length;
const output = getIntArray(encoding.srcType, n);
if (!n) return data;
output[0] = data[0] + (encoding.origin | 0);
for (let i = 1; i < n; ++i) {
output[i] = data[i] + output[i - 1];
}
return output;
}
function integerPackingSigned(data: (Int8Array | Int16Array), encoding: Encoding.IntegerPacking) {
const upperLimit = encoding.byteCount === 1 ? 0x7F : 0x7FFF;
const lowerLimit = -upperLimit - 1;
const n = data.length;
const output = new Int32Array(encoding.srcSize);
let i = 0;
let j = 0;
while (i < n) {
let value = 0, t = data[i];
while (t === upperLimit || t === lowerLimit) {
value += t;
i++;
t = data[i];
}
value += t;
output[j] = value;
i++;
j++;
}
return output;
}
function integerPackingUnsigned(data: (Uint8Array | Uint16Array), encoding: Encoding.IntegerPacking) {
const upperLimit = encoding.byteCount === 1 ? 0xFF : 0xFFFF;
const n = data.length;
const output = new Int32Array(encoding.srcSize);
let i = 0;
let j = 0;
while (i < n) {
let value = 0, t = data[i];
while (t === upperLimit) {
value += t;
i++;
t = data[i];
}
value += t;
output[j] = value;
i++;
j++;
}
return output;
}
function integerPacking(data: (Int8Array | Int16Array | Uint8Array | Uint16Array), encoding: Encoding.IntegerPacking) {
if (data.length === encoding.srcSize) return data;
return encoding.isUnsigned ? integerPackingUnsigned(data as any, encoding) : integerPackingSigned(data as any, encoding);
}
function stringArray(data: Uint8Array, encoding: Encoding.StringArray) {
const offsets = decode({ encoding: encoding.offsetEncoding, data: encoding.offsets });
const indices = decode({ encoding: encoding.dataEncoding, data });
const str = encoding.stringData;
const strings = new Array(offsets.length);
strings[0] = '';
for (let i = 1, _i = offsets.length; i < _i; i++) {
strings[i] = str.substring(offsets[i - 1], offsets[i]);
}
let offset = 0;
const result = new Array(indices.length);
for (let i = 0, _i = indices.length; i < _i; i++) {
result[offset++] = strings[indices[i] + 1];
}
return result;
}</code></pre></article></section><footer class="footer" id="PeOAagUepe"><div class="wrapper">3Dmol.js © 2019-2024 | <a href="https://pitt.edu/" target="_blank">University of Pittsburgh</a> | <a href="https://github.com/3dmol/3Dmol.js/blob/master/LICENSE" target="_blank">License</a></div></footer></div></div></div><div class="search-container" id="PkfLWpAbet" style="display:none"><div class="wrapper" id="iCxFxjkHbP"><button class="icon-button search-close-button" id="VjLlGakifb" aria-label="close search"><svg><use xlink:href="#close-icon"></use></svg></button><div class="search-box-c"><svg><use xlink:href="#search-icon"></use></svg> <input type="text" id="vpcKVYIppa" class="search-input" placeholder="Search..." autofocus></div><div class="search-result-c" id="fWwVHRuDuN"><span class="search-result-c-text">Type anything to view search result</span></div></div></div><div class="mobile-menu-icon-container"><button class="icon-button" id="mobile-menu" data-isopen="false" 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