molstar
Version:
A comprehensive macromolecular library.
181 lines • 6.97 kB
JavaScript
/**
* Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Adapted from CIFTools.js (https://github.com/dsehnal/CIFTools.js)
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { encodeMsgPack } from '../../../common/msgpack/encode';
import { ArrayEncoder, ArrayEncoding as E, VERSION } from '../../../common/binary-cif';
import { Category } from '../encoder';
import { getIncludedFields, getCategoryInstanceData } from './util';
import { classifyIntArray, classifyFloatArray } from '../../../common/binary-cif/classifier';
var BinaryEncoder = /** @class */ (function () {
function BinaryEncoder(encoder, encodingProvider, autoClassify) {
this.autoClassify = autoClassify;
this.dataBlocks = [];
this.filter = Category.DefaultFilter;
this.formatter = Category.DefaultFormatter;
this.isBinary = true;
this.binaryEncodingProvider = void 0;
this.binaryEncodingProvider = encodingProvider;
this.data = {
encoder: encoder,
version: VERSION,
dataBlocks: this.dataBlocks
};
}
BinaryEncoder.prototype.setFilter = function (filter) {
this.filter = filter || Category.DefaultFilter;
};
BinaryEncoder.prototype.isCategoryIncluded = function (name) {
return this.filter.includeCategory(name);
};
BinaryEncoder.prototype.setFormatter = function (formatter) {
this.formatter = formatter || Category.DefaultFormatter;
};
BinaryEncoder.prototype.startDataBlock = function (header) {
this.dataBlocks.push({
header: (header || '').replace(/[ \n\t]/g, '').toUpperCase(),
categories: []
});
};
BinaryEncoder.prototype.writeCategory = function (category, context, options) {
if (!this.data) {
throw new Error('The writer contents have already been encoded, no more writing.');
}
if (!this.dataBlocks.length) {
throw new Error('No data block created.');
}
if (!(options === null || options === void 0 ? void 0 : options.ignoreFilter) && !this.filter.includeCategory(category.name))
return;
var _a = getCategoryInstanceData(category, context), instance = _a.instance, rowCount = _a.rowCount, source = _a.source;
if (!rowCount)
return;
var cat = { name: '_' + category.name, columns: [], rowCount: rowCount };
var fields = getIncludedFields(instance);
for (var _i = 0, fields_1 = fields; _i < fields_1.length; _i++) {
var f = fields_1[_i];
if (!this.filter.includeField(category.name, f.name))
continue;
var format = this.formatter.getFormat(category.name, f.name);
cat.columns.push(encodeField(category.name, f, source, rowCount, format, this.binaryEncodingProvider, this.autoClassify));
}
// no columns included.
if (!cat.columns.length)
return;
this.dataBlocks[this.dataBlocks.length - 1].categories.push(cat);
};
BinaryEncoder.prototype.encode = function () {
if (this.encodedData)
return;
this.encodedData = encodeMsgPack(this.data);
this.data = null;
this.dataBlocks = null;
};
BinaryEncoder.prototype.writeTo = function (writer) {
writer.writeBinary(this.encodedData);
};
BinaryEncoder.prototype.getData = function () {
this.encode();
return this.encodedData;
};
BinaryEncoder.prototype.getSize = function () {
return this.encodedData.length;
};
return BinaryEncoder;
}());
export { BinaryEncoder };
function getArrayCtor(field, format) {
if (format && format.typedArray)
return format.typedArray;
if (field.defaultFormat && field.defaultFormat.typedArray)
return field.defaultFormat.typedArray;
if (field.type === 0 /* Str */)
return Array;
if (field.type === 1 /* Int */)
return Int32Array;
return Float64Array;
}
function getDefaultEncoder(type) {
if (type === 0 /* Str */)
return ArrayEncoder.by(E.stringArray);
return ArrayEncoder.by(E.byteArray);
}
function tryGetEncoder(categoryName, field, format, provider) {
if (format && format.encoder) {
return format.encoder;
}
else if (field.defaultFormat && field.defaultFormat.encoder) {
return field.defaultFormat.encoder;
}
else if (provider) {
return provider.get(categoryName, field.name);
}
else {
return void 0;
}
}
function classify(type, data) {
if (type === 0 /* Str */)
return ArrayEncoder.by(E.stringArray);
if (type === 1 /* Int */)
return classifyIntArray(data);
return classifyFloatArray(data);
}
function encodeField(categoryName, field, data, totalCount, format, encoderProvider, autoClassify) {
var _a = getFieldData(field, getArrayCtor(field, format), totalCount, data), array = _a.array, allPresent = _a.allPresent, mask = _a.mask;
var encoder = tryGetEncoder(categoryName, field, format, encoderProvider);
if (!encoder) {
if (autoClassify)
encoder = classify(field.type, array);
else
encoder = getDefaultEncoder(field.type);
}
var encoded = encoder.encode(array);
var maskData = void 0;
if (!allPresent) {
var maskRLE = ArrayEncoder.by(E.runLength).and(E.byteArray).encode(mask);
if (maskRLE.data.length < mask.length) {
maskData = maskRLE;
}
else {
maskData = ArrayEncoder.by(E.byteArray).encode(mask);
}
}
return {
name: field.name,
data: encoded,
mask: maskData
};
}
function getFieldData(field, arrayCtor, totalCount, data) {
var isStr = field.type === 0 /* Str */;
var array = new arrayCtor(totalCount);
var mask = new Uint8Array(totalCount);
var valueKind = field.valueKind;
var getter = field.value;
var allPresent = true;
var offset = 0;
for (var _d = 0; _d < data.length; _d++) {
var d = data[_d].data;
var keys = data[_d].keys();
while (keys.hasNext) {
var key = keys.move();
var p = valueKind ? valueKind(key, d) : 0 /* Present */;
if (p !== 0 /* Present */) {
mask[offset] = p;
if (isStr)
array[offset] = '';
allPresent = false;
}
else {
mask[offset] = 0 /* Present */;
array[offset] = getter(key, d, offset);
}
offset++;
}
}
return { array: array, allPresent: allPresent, mask: mask };
}
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