molstar 3.0.0 → 3.0.1

package/lib/commonjs/servers/volume/server/query/data-model.d.ts

@@ -1,91 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import * as DataFormat from '../../common/data-format';
-import * as Coords from '../algebra/coordinate';
-import * as Box from '../algebra/box';
-import { Writer } from '../../../../mol-io/writer/writer';
-import { SpacegroupCell } from '../../../../mol-math/geometry';
-import { FileHandle } from '../../../../mol-io/common/file-handle';
-import { TypedArrayValueArray } from '../../../../mol-io/common/typed-array';
-export interface Sampling {
-    index: number;
-    rate: number;
-    byteOffset: number;
-    dataDomain: Coords.GridDomain<'Data'>;
-    blockDomain: Coords.GridDomain<'Block'>;
-}
-export interface DataContext {
-    file: FileHandle;
-    header: DataFormat.Header;
-    spacegroup: SpacegroupCell;
-    dataBox: Box.Fractional;
-    sampling: Sampling[];
-}
-export interface BlockData {
-    sampleCount: number[];
-    values: TypedArrayValueArray;
-}
-export declare type QueryOutputStream = Writer & {
-    end: () => void;
-};
-export declare namespace QueryParamsBox {
-    type Cartesian = {
-        kind: 'Cartesian';
-        a: Coords.Cartesian;
-        b: Coords.Cartesian;
-    };
-    type Fractional = {
-        kind: 'Fractional';
-        a: Coords.Fractional;
-        b: Coords.Fractional;
-    };
-    type Cell = {
-        kind: 'Cell';
-    };
-}
-export declare type QueryParamsBox = QueryParamsBox.Cartesian | QueryParamsBox.Fractional | QueryParamsBox.Cell;
-export interface QueryParams {
-    sourceFilename: string;
-    sourceId: string;
-    asBinary: boolean;
-    box: QueryParamsBox;
-    detail: number;
-    forcedSamplingLevel?: number;
-}
-export declare type QueryBlock = {
-    coord: Coords.Grid<'Block'>;
-    offsets: Coords.Fractional[];
-};
-export interface QuerySamplingInfo {
-    sampling: Sampling;
-    fractionalBox: Box.Fractional;
-    gridDomain: Coords.GridDomain<'Query'>;
-    blocks: QueryBlock[];
-}
-export declare type QueryContext = QueryContext.Error | QueryContext.Empty | QueryContext.Data;
-export declare namespace QueryContext {
-    type Base = {
-        guid: string;
-        params: QueryParams;
-    };
-    export type Error = {
-        kind: 'Error';
-        message: string;
-    } & Base;
-    export type Empty = {
-        kind: 'Empty';
-        data: DataContext;
-    } & Base;
-    export type Data = {
-        kind: 'Data';
-        data: DataContext;
-        samplingInfo: QuerySamplingInfo;
-        values: TypedArrayValueArray[];
-    } & Base;
-    export {};
-}

package/lib/commonjs/servers/volume/server/query/data-model.js

@@ -1,10 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-//# sourceMappingURL=data-model.js.map

package/lib/commonjs/servers/volume/server/query/encode.d.ts

@@ -1,9 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import * as Data from './data-model';
-export declare function encode(query: Data.QueryContext, output: Data.QueryOutputStream): void;

package/lib/commonjs/servers/volume/server/query/encode.js

@@ -1,162 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.encode = void 0;
-var cif_1 = require("../../../../mol-io/writer/cif");
-var version_1 = require("../version");
-var binary_cif_1 = require("../../../../mol-io/common/binary-cif");
-var typed_array_1 = require("../../../../mol-io/common/typed-array");
-function encode(query, output) {
-    var w = cif_1.CifWriter.createEncoder({ binary: query.params.asBinary, encoderName: "VolumeServer ".concat(version_1.VOLUME_SERVER_VERSION) });
-    write(w, query);
-    w.encode();
-    w.writeTo(output);
-}
-exports.encode = encode;
-function string(name, str, isSpecified) {
-    if (isSpecified) {
-        return cif_1.CifWriter.Field.str(name, function (i, d) { return str(d); }, { valueKind: function (i, d) { return isSpecified(d) ? 0 /* Present */ : 1 /* NotPresent */; } });
-    }
-    return cif_1.CifWriter.Field.str(name, function (i, d) { return str(d); });
-}
-function int32(name, value) {
-    return cif_1.CifWriter.Field.int(name, function (i, d) { return value(d); });
-}
-function float64(name, value, digitCount) {
-    if (digitCount === void 0) { digitCount = 6; }
-    return cif_1.CifWriter.Field.float(name, function (i, d) { return value(d); }, { digitCount: digitCount, typedArray: Float64Array });
-}
-var _volume_data_3d_info_fields = [
-    string('name', function (ctx) { return ctx.header.channels[ctx.channelIndex]; }),
-    int32('axis_order[0]', function (ctx) { return ctx.header.axisOrder[0]; }),
-    int32('axis_order[1]', function (ctx) { return ctx.header.axisOrder[1]; }),
-    int32('axis_order[2]', function (ctx) { return ctx.header.axisOrder[2]; }),
-    float64('origin[0]', function (ctx) { return ctx.grid.origin[0]; }),
-    float64('origin[1]', function (ctx) { return ctx.grid.origin[1]; }),
-    float64('origin[2]', function (ctx) { return ctx.grid.origin[2]; }),
-    float64('dimensions[0]', function (ctx) { return ctx.grid.dimensions[0]; }),
-    float64('dimensions[1]', function (ctx) { return ctx.grid.dimensions[1]; }),
-    float64('dimensions[2]', function (ctx) { return ctx.grid.dimensions[2]; }),
-    int32('sample_rate', function (ctx) { return ctx.sampleRate; }),
-    int32('sample_count[0]', function (ctx) { return ctx.grid.sampleCount[0]; }),
-    int32('sample_count[1]', function (ctx) { return ctx.grid.sampleCount[1]; }),
-    int32('sample_count[2]', function (ctx) { return ctx.grid.sampleCount[2]; }),
-    int32('spacegroup_number', function (ctx) { return ctx.header.spacegroup.number; }),
-    float64('spacegroup_cell_size[0]', function (ctx) { return ctx.header.spacegroup.size[0]; }, 3),
-    float64('spacegroup_cell_size[1]', function (ctx) { return ctx.header.spacegroup.size[1]; }, 3),
-    float64('spacegroup_cell_size[2]', function (ctx) { return ctx.header.spacegroup.size[2]; }, 3),
-    float64('spacegroup_cell_angles[0]', function (ctx) { return ctx.header.spacegroup.angles[0]; }, 3),
-    float64('spacegroup_cell_angles[1]', function (ctx) { return ctx.header.spacegroup.angles[1]; }, 3),
-    float64('spacegroup_cell_angles[2]', function (ctx) { return ctx.header.spacegroup.angles[2]; }, 3),
-    float64('mean_source', function (ctx) { return ctx.globalValuesInfo.mean; }),
-    float64('mean_sampled', function (ctx) { return ctx.sampledValuesInfo.mean; }),
-    float64('sigma_source', function (ctx) { return ctx.globalValuesInfo.sigma; }),
-    float64('sigma_sampled', function (ctx) { return ctx.sampledValuesInfo.sigma; }),
-    float64('min_source', function (ctx) { return ctx.globalValuesInfo.min; }),
-    float64('min_sampled', function (ctx) { return ctx.sampledValuesInfo.min; }),
-    float64('max_source', function (ctx) { return ctx.globalValuesInfo.max; }),
-    float64('max_sampled', function (ctx) { return ctx.sampledValuesInfo.max; })
-];
-var _volume_data_3d_info = {
-    name: 'volume_data_3d_info',
-    instance: function (result) {
-        var ctx = {
-            header: result.query.data.header,
-            channelIndex: result.channelIndex,
-            grid: result.query.samplingInfo.gridDomain,
-            sampleRate: result.query.samplingInfo.sampling.rate,
-            globalValuesInfo: result.query.data.header.sampling[0].valuesInfo[result.channelIndex],
-            sampledValuesInfo: result.query.data.header.sampling[result.query.samplingInfo.sampling.index].valuesInfo[result.channelIndex]
-        };
-        return { fields: _volume_data_3d_info_fields, source: [{ data: ctx, rowCount: 1 }] };
-    }
-};
-function _volume_data_3d_number(i, ctx) {
-    return ctx[i];
-}
-var _volume_data_3d = {
-    name: 'volume_data_3d',
-    instance: function (ctx) {
-        var data = ctx.query.values[ctx.channelIndex];
-        var E = binary_cif_1.ArrayEncoding;
-        var encoder;
-        var typedArray;
-        if (ctx.query.data.header.valueType === typed_array_1.TypedArrayValueType.Float32 || ctx.query.data.header.valueType === typed_array_1.TypedArrayValueType.Int16) {
-            var min = void 0, max = void 0;
-            min = data[0], max = data[0];
-            for (var i = 0, n = data.length; i < n; i++) {
-                var v = data[i];
-                if (v < min)
-                    min = v;
-                else if (v > max)
-                    max = v;
-            }
-            typedArray = Float32Array;
-            // encode into 255 steps and store each value in 1 byte.
-            encoder = E.by(E.intervalQuantizaiton(min, max, 255, Uint8Array)).and(E.byteArray);
-        }
-        else {
-            typedArray = Int8Array;
-            // just encode the bytes
-            encoder = E.by(E.byteArray);
-        }
-        var fields = [cif_1.CifWriter.Field.float('values', _volume_data_3d_number, { encoder: encoder, typedArray: typedArray, digitCount: 6 })];
-        return cif_1.CifWriter.categoryInstance(fields, { data: data, rowCount: data.length });
-    }
-};
-function pickQueryBoxDimension(ctx, e, d) {
-    var box = ctx.params.box;
-    switch (box.kind) {
-        case 'Cartesian':
-        case 'Fractional':
-            return "".concat(Math.round(1000000 * box[e][d]) / 1000000);
-        default: return '';
-    }
-}
-function queryBoxDimension(e, d) {
-    return string("query_box_".concat(e, "[").concat(d, "]"), function (ctx) { return pickQueryBoxDimension(ctx, e, d); }, function (ctx) { return ctx.params.box.kind !== 'Cell'; });
-}
-var _density_server_result_fields = [
-    string('server_version', function (ctx) { return version_1.VOLUME_SERVER_VERSION; }),
-    string('datetime_utc', function (ctx) { return new Date().toISOString().replace(/T/, ' ').replace(/\..+/, ''); }),
-    string('guid', function (ctx) { return ctx.guid; }),
-    string('is_empty', function (ctx) { return ctx.kind === 'Empty' || ctx.kind === 'Error' ? 'yes' : 'no'; }),
-    string('has_error', function (ctx) { return ctx.kind === 'Error' ? 'yes' : 'no'; }),
-    string('error', function (ctx) { return ctx.kind === 'Error' ? ctx.message : ''; }, function (ctx) { return ctx.kind === 'Error'; }),
-    string('query_source_id', function (ctx) { return ctx.params.sourceId; }),
-    string('query_type', function (ctx) { return 'box'; }),
-    string('query_box_type', function (ctx) { return ctx.params.box.kind.toLowerCase(); }),
-    queryBoxDimension('a', 0),
-    queryBoxDimension('a', 1),
-    queryBoxDimension('a', 2),
-    queryBoxDimension('b', 0),
-    queryBoxDimension('b', 1),
-    queryBoxDimension('b', 2)
-];
-var _density_server_result = {
-    name: 'density_server_result',
-    instance: function (ctx) { return cif_1.CifWriter.categoryInstance(_density_server_result_fields, { data: ctx, rowCount: 1 }); }
-};
-function write(encoder, query) {
-    encoder.startDataBlock('SERVER');
-    encoder.writeCategory(_density_server_result, query);
-    switch (query.kind) {
-        case 'Data':
-    }
-    if (query.kind === 'Data') {
-        var header = query.data.header;
-        for (var i = 0; i < header.channels.length; i++) {
-            encoder.startDataBlock(header.channels[i]);
-            var ctx = { query: query, channelIndex: i };
-            encoder.writeCategory(_volume_data_3d_info, ctx);
-            encoder.writeCategory(_volume_data_3d, ctx);
-        }
-    }
-}
-//# sourceMappingURL=encode.js.map

package/lib/commonjs/servers/volume/server/query/execute.d.ts

@@ -1,9 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import * as Data from './data-model';
-export declare function execute(params: Data.QueryParams, outputProvider: () => Data.QueryOutputStream): Promise<boolean>;

package/lib/commonjs/servers/volume/server/query/execute.js

@@ -1,254 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.execute = void 0;
-var tslib_1 = require("tslib");
-var DataFormat = (0, tslib_1.__importStar)(require("../../common/data-format"));
-var File = (0, tslib_1.__importStar)(require("../../common/file"));
-var Coords = (0, tslib_1.__importStar)(require("../algebra/coordinate"));
-var Box = (0, tslib_1.__importStar)(require("../algebra/box"));
-var console_logger_1 = require("../../../../mol-util/console-logger");
-var state_1 = require("../state");
-var identify_1 = require("./identify");
-var compose_1 = require("./compose");
-var encode_1 = require("./encode");
-var geometry_1 = require("../../../../mol-math/geometry");
-var linear_algebra_1 = require("../../../../mol-math/linear-algebra");
-var mol_util_1 = require("../../../../mol-util");
-var typed_array_1 = require("../../../../mol-io/common/typed-array");
-var config_1 = require("../../config");
-var file_handle_1 = require("../../../common/file-handle");
-function execute(params, outputProvider) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var start, guid, sourceFile, _a, e_1;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    start = getTime();
-                    state_1.State.pendingQueries++;
-                    guid = mol_util_1.UUID.create22();
-                    params.detail = Math.min(Math.max(0, params.detail | 0), config_1.LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1);
-                    console_logger_1.ConsoleLogger.logId(guid, 'Info', "id=".concat(params.sourceId, ",encoding=").concat(params.asBinary ? 'binary' : 'text', ",detail=").concat(params.detail, ",").concat(queryBoxToString(params.box)));
-                    _b.label = 1;
-                case 1:
-                    _b.trys.push([1, 4, 5, 6]);
-                    _a = file_handle_1.fileHandleFromDescriptor;
-                    return [4 /*yield*/, File.openRead(params.sourceFilename)];
-                case 2:
-                    sourceFile = _a.apply(void 0, [_b.sent(), params.sourceFilename]);
-                    return [4 /*yield*/, _execute(sourceFile, params, guid, outputProvider)];
-                case 3:
-                    _b.sent();
-                    return [2 /*return*/, true];
-                case 4:
-                    e_1 = _b.sent();
-                    console_logger_1.ConsoleLogger.errorId(guid, e_1);
-                    return [2 /*return*/, false];
-                case 5:
-                    if (sourceFile)
-                        sourceFile.close();
-                    console_logger_1.ConsoleLogger.logId(guid, 'Time', "".concat(Math.round(getTime() - start), "ms"));
-                    state_1.State.pendingQueries--;
-                    return [7 /*endfinally*/];
-                case 6: return [2 /*return*/];
-            }
-        });
-    });
-}
-exports.execute = execute;
-function getTime() {
-    var t = process.hrtime();
-    return t[0] * 1000 + t[1] / 1000000;
-}
-function blockDomain(domain, blockSize) {
-    var delta = Coords.fractional(blockSize * domain.delta[0], blockSize * domain.delta[1], blockSize * domain.delta[2]);
-    return Coords.domain('Block', {
-        origin: domain.origin,
-        dimensions: domain.dimensions,
-        delta: delta,
-        sampleCount: Coords.sampleCounts(domain.dimensions, delta)
-    });
-}
-function createSampling(header, index, dataOffset) {
-    var sampling = header.sampling[index];
-    var dataDomain = Coords.domain('Data', {
-        origin: Coords.fractional(header.origin[0], header.origin[1], header.origin[2]),
-        dimensions: Coords.fractional(header.dimensions[0], header.dimensions[1], header.dimensions[2]),
-        delta: Coords.fractional(header.dimensions[0] / sampling.sampleCount[0], header.dimensions[1] / sampling.sampleCount[1], header.dimensions[2] / sampling.sampleCount[2]),
-        sampleCount: sampling.sampleCount
-    });
-    return {
-        index: index,
-        rate: sampling.rate,
-        byteOffset: sampling.byteOffset + dataOffset,
-        dataDomain: dataDomain,
-        blockDomain: blockDomain(dataDomain, header.blockSize)
-    };
-}
-function createDataContext(file) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var _a, header, dataOffset, origin, dimensions;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0: return [4 /*yield*/, DataFormat.readHeader(file)];
-                case 1:
-                    _a = _b.sent(), header = _a.header, dataOffset = _a.dataOffset;
-                    origin = Coords.fractional(header.origin[0], header.origin[1], header.origin[2]);
-                    dimensions = Coords.fractional(header.dimensions[0], header.dimensions[1], header.dimensions[2]);
-                    return [2 /*return*/, {
-                            file: file,
-                            header: header,
-                            spacegroup: geometry_1.SpacegroupCell.create(header.spacegroup.number, linear_algebra_1.Vec3.ofArray(header.spacegroup.size), linear_algebra_1.Vec3.scale(linear_algebra_1.Vec3.zero(), linear_algebra_1.Vec3.ofArray(header.spacegroup.angles), Math.PI / 180)),
-                            dataBox: { a: origin, b: Coords.add(origin, dimensions) },
-                            sampling: header.sampling.map(function (s, i) { return createSampling(header, i, dataOffset); })
-                        }];
-            }
-        });
-    });
-}
-function createQuerySampling(data, sampling, queryBox) {
-    var fractionalBox = Box.gridToFractional(Box.expandGridBox(Box.fractionalToGrid(queryBox, sampling.dataDomain), 1));
-    var blocks = (0, identify_1.findUniqueBlocks)(data, sampling, fractionalBox);
-    var ret = {
-        sampling: sampling,
-        fractionalBox: fractionalBox,
-        gridDomain: Box.fractionalToDomain(fractionalBox, 'Query', sampling.dataDomain.delta),
-        blocks: blocks
-    };
-    return ret;
-}
-function pickSampling(data, queryBox, forcedLevel, precision) {
-    if (forcedLevel > 0) {
-        return createQuerySampling(data, data.sampling[Math.min(data.sampling.length, forcedLevel) - 1], queryBox);
-    }
-    var sizeLimit = config_1.LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[precision] || (2 * 1024 * 1024);
-    for (var _i = 0, _a = data.sampling; _i < _a.length; _i++) {
-        var s = _a[_i];
-        var gridBox = Box.fractionalToGrid(queryBox, s.dataDomain);
-        var approxSize = Box.volume(gridBox);
-        if (approxSize <= sizeLimit) {
-            var sampling = createQuerySampling(data, s, queryBox);
-            if (sampling.blocks.length <= config_1.LimitsConfig.maxRequestBlockCount) {
-                return sampling;
-            }
-        }
-    }
-    return createQuerySampling(data, data.sampling[data.sampling.length - 1], queryBox);
-}
-function emptyQueryContext(data, params, guid) {
-    return { kind: 'Empty', guid: guid, params: params, data: data };
-}
-function getQueryBox(data, queryBox) {
-    switch (queryBox.kind) {
-        case 'Cartesian': return Box.fractionalBoxReorderAxes(Box.cartesianToFractional(queryBox, data.spacegroup), data.header.axisOrder);
-        case 'Fractional': return Box.fractionalBoxReorderAxes(queryBox, data.header.axisOrder);
-        default: return data.dataBox;
-    }
-}
-function allocateValues(domain, numChannels, valueType) {
-    var values = [];
-    for (var i = 0; i < numChannels; i++) {
-        values[values.length] = (0, typed_array_1.createTypedArray)(valueType, domain.sampleVolume);
-    }
-    return values;
-}
-function createQueryContext(data, params, guid) {
-    var inputQueryBox = getQueryBox(data, params.box);
-    var queryBox;
-    if (!data.header.spacegroup.isPeriodic) {
-        if (!Box.areIntersecting(data.dataBox, inputQueryBox)) {
-            return emptyQueryContext(data, params, guid);
-        }
-        queryBox = Box.intersect(data.dataBox, inputQueryBox);
-    }
-    else {
-        queryBox = inputQueryBox;
-    }
-    var dimensions = Box.dimensions(queryBox);
-    if (dimensions.some(function (d) { return isNaN(d); })) {
-        throw new Error('The query box is not defined.');
-    }
-    if (dimensions[0] * dimensions[1] * dimensions[2] > config_1.LimitsConfig.maxFractionalBoxVolume) {
-        throw new Error('The query box volume is too big.');
-    }
-    var samplingInfo = pickSampling(data, queryBox, params.forcedSamplingLevel !== void 0 ? params.forcedSamplingLevel : 0, params.detail);
-    if (samplingInfo.blocks.length === 0)
-        return emptyQueryContext(data, params, guid);
-    return {
-        kind: 'Data',
-        guid: guid,
-        data: data,
-        params: params,
-        samplingInfo: samplingInfo,
-        values: allocateValues(samplingInfo.gridDomain, data.header.channels.length, data.header.valueType)
-    };
-}
-function _execute(file, params, guid, outputProvider) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var output, data, query, e_2, query;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    output = void 0;
-                    _a.label = 1;
-                case 1:
-                    _a.trys.push([1, 5, 6, 7]);
-                    return [4 /*yield*/, createDataContext(file)];
-                case 2:
-                    data = _a.sent();
-                    query = createQueryContext(data, params, guid);
-                    if (!(query.kind === 'Data')) return [3 /*break*/, 4];
-                    // Step 3b: Compose the result data
-                    return [4 /*yield*/, (0, compose_1.compose)(query)];
-                case 3:
-                    // Step 3b: Compose the result data
-                    _a.sent();
-                    _a.label = 4;
-                case 4:
-                    // Step 4: Encode the result
-                    output = outputProvider();
-                    (0, encode_1.encode)(query, output);
-                    output.end();
-                    return [3 /*break*/, 7];
-                case 5:
-                    e_2 = _a.sent();
-                    query = { kind: 'Error', guid: guid, params: params, message: "".concat(e_2) };
-                    try {
-                        if (!output)
-                            output = outputProvider();
-                        (0, encode_1.encode)(query, output);
-                    }
-                    catch (f) {
-                        throw f;
-                    }
-                    throw e_2;
-                case 6:
-                    if (output)
-                        output.end();
-                    return [7 /*endfinally*/];
-                case 7: return [2 /*return*/];
-            }
-        });
-    });
-}
-function roundCoord(c) {
-    return Math.round(100000 * c) / 100000;
-}
-function queryBoxToString(queryBox) {
-    switch (queryBox.kind) {
-        case 'Cartesian':
-        case 'Fractional':
-            var a = queryBox.a, b = queryBox.b;
-            var r = roundCoord;
-            return "box-type=".concat(queryBox.kind, ",box-a=(").concat(r(a[0]), ",").concat(r(a[1]), ",").concat(r(a[2]), "),box-b=(").concat(r(b[0]), ",").concat(r(b[1]), ",").concat(r(b[2]), ")");
-        default:
-            return "box-type=".concat(queryBox.kind);
-    }
-}
-//# sourceMappingURL=execute.js.map

package/lib/commonjs/servers/volume/server/query/identify.d.ts

@@ -1,11 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import * as Box from '../algebra/box';
-import * as Data from './data-model';
-/** Find a list of unique blocks+offsets that overlap with the query region. */
-export declare function findUniqueBlocks(data: Data.DataContext, sampling: Data.Sampling, queryBox: Box.Fractional): Data.QueryBlock[];

package/lib/commonjs/servers/volume/server/query/identify.js

@@ -1,112 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.findUniqueBlocks = void 0;
-var tslib_1 = require("tslib");
-var Coords = (0, tslib_1.__importStar)(require("../algebra/coordinate"));
-var Box = (0, tslib_1.__importStar)(require("../algebra/box"));
-// import { FastMap } from '../utils/collections'
-/** Find a list of unique blocks+offsets that overlap with the query region. */
-function findUniqueBlocks(data, sampling, queryBox) {
-    var translations = data.header.spacegroup.isPeriodic
-        // find all query box translations that overlap with the unit cell.
-        ? findDataOverlapTranslationList(queryBox, sampling.dataDomain)
-        // no translations
-        : [Coords.fractional(0, 0, 0)];
-    var blocks = new Map();
-    for (var _i = 0, translations_1 = translations; _i < translations_1.length; _i++) {
-        var t = translations_1[_i];
-        findUniqueBlocksOffset(data, sampling, queryBox, t, blocks);
-    }
-    var blockList = [];
-    blocks.forEach(function (b) { this.push(b); }, blockList);
-    // sort the data so that the first coodinate changes the fastest
-    // this is because that's how the data is laid out in the underlaying
-    // data format and reading the data 'in order' makes it faster.
-    blockList.sort(function (a, b) {
-        var x = a.coord, y = b.coord;
-        for (var i = 2; i >= 0; i--) {
-            if (x[i] !== y[i])
-                return x[i] - y[i];
-        }
-        return 0;
-    });
-    return blockList;
-}
-exports.findUniqueBlocks = findUniqueBlocks;
-/**
- * Find the integer interval [x, y] so that for all k \in [x, y]
- * [a + k, b + k] intersects with (u, v)
- */
-function overlapMultiplierRange(a, b, u, v) {
-    var x = Math.ceil(u - b) | 0, y = Math.floor(v - a) | 0;
-    if (Coords.round(b + x) <= Coords.round(u))
-        x++;
-    if (Coords.round(a + y) >= Coords.round(v))
-        y--;
-    if (x > y)
-        return void 0;
-    return [x, y];
-}
-/**
- * Finds that list of "unit" offsets (in fractional space) so that
- * shift(box, offset) has non-empty interaction with the region
- * described in the give domain.
- */
-function findDataOverlapTranslationList(box, domain) {
-    var ranges = [];
-    var translations = [];
-    var origin = domain.origin, dimensions = domain.dimensions;
-    for (var i = 0; i < 3; i++) {
-        var range = overlapMultiplierRange(box.a[i], box.b[i], origin[i], origin[i] + dimensions[i]);
-        if (!range)
-            return translations;
-        ranges[i] = range;
-    }
-    var u = ranges[0], v = ranges[1], w = ranges[2];
-    for (var k = w[0]; k <= w[1]; k++) {
-        for (var j = v[0]; j <= v[1]; j++) {
-            for (var i = u[0]; i <= u[1]; i++) {
-                translations.push(Coords.fractional(i, j, k));
-            }
-        }
-    }
-    return translations;
-}
-function addUniqueBlock(blocks, coord, offset) {
-    var hash = Coords.linearGridIndex(coord);
-    if (blocks.has(hash)) {
-        var entry = blocks.get(hash);
-        entry.offsets.push(offset);
-    }
-    else {
-        blocks.set(hash, { coord: coord, offsets: [offset] });
-    }
-}
-function findUniqueBlocksOffset(data, sampling, queryBox, offset, blocks) {
-    var shifted = Box.shift(queryBox, offset);
-    var intersection = Box.intersect(shifted, data.dataBox);
-    // Intersection can be empty in the case of "aperiodic spacegroups"
-    if (!intersection)
-        return;
-    var blockDomain = sampling.blockDomain;
-    // this gets the "3d range" of block indices that contain data that overlaps
-    // with the query region.
-    //
-    // Clamping the data makes sure we avoid silly rounding errors (hopefully :))
-    var _a = Box.clampGridToSamples(Box.fractionalToGrid(intersection, blockDomain)), min = _a.a, max = _a.b;
-    for (var i = min[0]; i < max[0]; i++) {
-        for (var j = min[1]; j < max[1]; j++) {
-            for (var k = min[2]; k < max[2]; k++) {
-                addUniqueBlock(blocks, Coords.grid(blockDomain, i, j, k), offset);
-            }
-        }
-    }
-}
-//# sourceMappingURL=identify.js.map

package/lib/commonjs/servers/volume/server/state.d.ts

@@ -1,12 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Taken/adapted from DensityServer (https://github.com/dsehnal/DensityServer)
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-export declare const State: {
-    pendingQueries: number;
-    shutdownOnZeroPending: boolean;
-    querySerial: number;
-};