molstar 3.3.1 → 3.4.0

package/lib/mol-io/common/io-buffer.d.ts

@@ -0,0 +1,206 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted and converted to TypeScript from https://github.com/image-js/iobuffer
+ * MIT License, Copyright (c) 2015 Michaël Zasso
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { TypedArray } from '../../mol-util/type-helpers';
+export interface IOBufferParameters {
+    offset?: number;
+}
+/**
+ * Class for writing and reading binary data
+ */
+export declare class IOBuffer {
+    private _lastWrittenByte;
+    private _mark;
+    private _marks;
+    private _data;
+    offset: number;
+    littleEndian: boolean;
+    buffer: ArrayBuffer;
+    length: number;
+    byteLength: number;
+    byteOffset: number;
+    /**
+     * If it's a number, it will initialize the buffer with the number as
+     * the buffer's length. If it's undefined, it will initialize the buffer
+     * with a default length of 8 Kb. If its an ArrayBuffer, a TypedArray,
+     * it will create a view over the underlying ArrayBuffer.
+     */
+    constructor(data: number | ArrayBuffer | TypedArray, params?: IOBufferParameters);
+    /**
+     * Checks if the memory allocated to the buffer is sufficient to store more bytes after the offset
+     * @param byteLength The needed memory in bytes
+     */
+    available(byteLength?: number): boolean;
+    /**
+     * Check if little-endian mode is used for reading and writing multi-byte values
+     * Returns true if little-endian mode is used, false otherwise
+     */
+    isLittleEndian(): boolean;
+    /**
+     * Set little-endian mode for reading and writing multi-byte values
+     */
+    setLittleEndian(): this;
+    /**
+     * Check if big-endian mode is used for reading and writing multi-byte values
+     * Returns true if big-endian mode is used, false otherwise
+     */
+    isBigEndian(): boolean;
+    /**
+     * Switches to big-endian mode for reading and writing multi-byte values
+     */
+    setBigEndian(): this;
+    /**
+     * Move the pointer n bytes forward
+     */
+    skip(n: number): this;
+    /**
+     * Move the pointer to the given offset
+     */
+    seek(offset: number): this;
+    /**
+     * Store the current pointer offset.
+     */
+    mark(): this;
+    /**
+     * Move the pointer back to the last pointer offset set by mark
+     */
+    reset(): this;
+    /**
+     * Push the current pointer offset to the mark stack
+     */
+    pushMark(): this;
+    /**
+     * Pop the last pointer offset from the mark stack, and set the current pointer offset to the popped value
+     */
+    popMark(): this;
+    /**
+     * Move the pointer offset back to 0
+     */
+    rewind(): this;
+    /**
+     * Make sure the buffer has sufficient memory to write a given byteLength at the current pointer offset
+     * If the buffer's memory is insufficient, this method will create a new buffer (a copy) with a length
+     * that is twice (byteLength + current offset)
+     */
+    ensureAvailable(byteLength: number): this;
+    /**
+     * Read a byte and return false if the byte's value is 0, or true otherwise
+     * Moves pointer forward
+     */
+    readBoolean(): boolean;
+    /**
+     * Read a signed 8-bit integer and move pointer forward
+     */
+    readInt8(): number;
+    /**
+     * Read an unsigned 8-bit integer and move pointer forward
+     */
+    readUint8(): number;
+    /**
+     * Alias for {@link IOBuffer#readUint8}
+     */
+    readByte(): number;
+    /**
+     * Read n bytes and move pointer forward.
+     */
+    readBytes(n: number): Uint8Array;
+    /**
+     * Read a 16-bit signed integer and move pointer forward
+     */
+    readInt16(): number;
+    /**
+     * Read a 16-bit unsigned integer and move pointer forward
+     */
+    readUint16(): number;
+    /**
+     * Read a 32-bit signed integer and move pointer forward
+     */
+    readInt32(): number;
+    /**
+     * Read a 32-bit unsigned integer and move pointer forward
+     */
+    readUint32(): number;
+    /**
+     * Read a 32-bit floating number and move pointer forward
+     */
+    readFloat32(): number;
+    /**
+     * Read a 64-bit floating number and move pointer forward
+     */
+    readFloat64(): number;
+    /**
+     * Read 1-byte ascii character and move pointer forward
+     */
+    readChar(): string;
+    /**
+     * Read n 1-byte ascii characters and move pointer forward
+     */
+    readChars(n?: number): string;
+    /**
+     * Write 0xff if the passed value is truthy, 0x00 otherwise
+     */
+    writeBoolean(value?: boolean): this;
+    /**
+     * Write value as an 8-bit signed integer
+     */
+    writeInt8(value: number): this;
+    /**
+     * Write value as a 8-bit unsigned integer
+     */
+    writeUint8(value: number): this;
+    /**
+     * An alias for IOBuffer#writeUint8
+     */
+    writeByte(value: number): this;
+    /**
+     * Write bytes
+     */
+    writeBytes(bytes: number[] | Uint8Array): this;
+    /**
+     * Write value as an 16-bit signed integer
+     */
+    writeInt16(value: number): this;
+    /**
+     * Write value as a 16-bit unsigned integer
+     */
+    writeUint16(value: number): this;
+    /**
+     * Write a 32-bit signed integer at the current pointer offset
+     */
+    writeInt32(value: number): this;
+    /**
+     * Write a 32-bit unsigned integer at the current pointer offset
+     */
+    writeUint32(value: number): this;
+    /**
+     * Write a 32-bit floating number at the current pointer offset
+     */
+    writeFloat32(value: number): this;
+    /**
+     * Write a 64-bit floating number at the current pointer offset
+     */
+    writeFloat64(value: number): this;
+    /**
+     * Write the charCode of the passed string's first character to the current pointer offset
+     */
+    writeChar(str: string): this;
+    /**
+     * Write the charCodes of the passed string's characters to the current pointer offset
+     */
+    writeChars(str: string): this;
+    /**
+     * Export a Uint8Array view of the internal buffer.
+     * The view starts at the byte offset and its length
+     * is calculated to stop at the last written byte or the original length.
+     */
+    toArray(): Uint8Array;
+    /**
+     * Update the last written byte offset
+     */
+    private _updateLastWrittenByte;
+}

package/lib/mol-io/common/io-buffer.js

@@ -0,0 +1,405 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted and converted to TypeScript from https://github.com/image-js/iobuffer
+ * MIT License, Copyright (c) 2015 Michaël Zasso
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+var defaultByteLength = 1024 * 8;
+var charArray = [];
+/**
+ * Class for writing and reading binary data
+ */
+var IOBuffer = /** @class */ (function () {
+    /**
+     * If it's a number, it will initialize the buffer with the number as
+     * the buffer's length. If it's undefined, it will initialize the buffer
+     * with a default length of 8 Kb. If its an ArrayBuffer, a TypedArray,
+     * it will create a view over the underlying ArrayBuffer.
+     */
+    function IOBuffer(data, params) {
+        if (params === void 0) { params = {}; }
+        this._mark = 0;
+        this._marks = [];
+        this.offset = 0; // The current offset of the buffer's pointer
+        this.littleEndian = true;
+        var dataIsGiven = false;
+        if (data === undefined) {
+            data = defaultByteLength;
+        }
+        if (typeof data === 'number') {
+            data = new ArrayBuffer(data);
+        }
+        else {
+            dataIsGiven = true;
+        }
+        var offset = params.offset ? params.offset >>> 0 : 0;
+        var byteLength = data.byteLength - offset;
+        var dvOffset = offset;
+        if (!(data instanceof ArrayBuffer)) {
+            if (data.byteLength !== data.buffer.byteLength) {
+                dvOffset = data.byteOffset + offset;
+            }
+            data = data.buffer;
+        }
+        if (dataIsGiven) {
+            this._lastWrittenByte = byteLength;
+        }
+        else {
+            this._lastWrittenByte = 0;
+        }
+        this.buffer = data;
+        this.length = byteLength;
+        this.byteLength = byteLength;
+        this.byteOffset = dvOffset;
+        this._data = new DataView(this.buffer, dvOffset, byteLength);
+    }
+    /**
+     * Checks if the memory allocated to the buffer is sufficient to store more bytes after the offset
+     * @param byteLength The needed memory in bytes
+     */
+    IOBuffer.prototype.available = function (byteLength) {
+        if (byteLength === void 0) { byteLength = 1; }
+        return (this.offset + byteLength) <= this.length;
+    };
+    /**
+     * Check if little-endian mode is used for reading and writing multi-byte values
+     * Returns true if little-endian mode is used, false otherwise
+     */
+    IOBuffer.prototype.isLittleEndian = function () {
+        return this.littleEndian;
+    };
+    /**
+     * Set little-endian mode for reading and writing multi-byte values
+     */
+    IOBuffer.prototype.setLittleEndian = function () {
+        this.littleEndian = true;
+        return this;
+    };
+    /**
+     * Check if big-endian mode is used for reading and writing multi-byte values
+     * Returns true if big-endian mode is used, false otherwise
+     */
+    IOBuffer.prototype.isBigEndian = function () {
+        return !this.littleEndian;
+    };
+    /**
+     * Switches to big-endian mode for reading and writing multi-byte values
+     */
+    IOBuffer.prototype.setBigEndian = function () {
+        this.littleEndian = false;
+        return this;
+    };
+    /**
+     * Move the pointer n bytes forward
+     */
+    IOBuffer.prototype.skip = function (n) {
+        if (n === undefined)
+            n = 1;
+        this.offset += n;
+        return this;
+    };
+    /**
+     * Move the pointer to the given offset
+     */
+    IOBuffer.prototype.seek = function (offset) {
+        this.offset = offset;
+        return this;
+    };
+    /**
+     * Store the current pointer offset.
+     */
+    IOBuffer.prototype.mark = function () {
+        this._mark = this.offset;
+        return this;
+    };
+    /**
+     * Move the pointer back to the last pointer offset set by mark
+     */
+    IOBuffer.prototype.reset = function () {
+        this.offset = this._mark;
+        return this;
+    };
+    /**
+     * Push the current pointer offset to the mark stack
+     */
+    IOBuffer.prototype.pushMark = function () {
+        this._marks.push(this.offset);
+        return this;
+    };
+    /**
+     * Pop the last pointer offset from the mark stack, and set the current pointer offset to the popped value
+     */
+    IOBuffer.prototype.popMark = function () {
+        var offset = this._marks.pop();
+        if (offset === undefined)
+            throw new Error('Mark stack empty');
+        this.seek(offset);
+        return this;
+    };
+    /**
+     * Move the pointer offset back to 0
+     */
+    IOBuffer.prototype.rewind = function () {
+        this.offset = 0;
+        return this;
+    };
+    /**
+     * Make sure the buffer has sufficient memory to write a given byteLength at the current pointer offset
+     * If the buffer's memory is insufficient, this method will create a new buffer (a copy) with a length
+     * that is twice (byteLength + current offset)
+     */
+    IOBuffer.prototype.ensureAvailable = function (byteLength) {
+        if (byteLength === undefined)
+            byteLength = 1;
+        if (!this.available(byteLength)) {
+            var lengthNeeded = this.offset + byteLength;
+            var newLength = lengthNeeded * 2;
+            var newArray = new Uint8Array(newLength);
+            newArray.set(new Uint8Array(this.buffer));
+            this.buffer = newArray.buffer;
+            this.length = this.byteLength = newLength;
+            this._data = new DataView(this.buffer);
+        }
+        return this;
+    };
+    /**
+     * Read a byte and return false if the byte's value is 0, or true otherwise
+     * Moves pointer forward
+     */
+    IOBuffer.prototype.readBoolean = function () {
+        return this.readUint8() !== 0;
+    };
+    /**
+     * Read a signed 8-bit integer and move pointer forward
+     */
+    IOBuffer.prototype.readInt8 = function () {
+        return this._data.getInt8(this.offset++);
+    };
+    /**
+     * Read an unsigned 8-bit integer and move pointer forward
+     */
+    IOBuffer.prototype.readUint8 = function () {
+        return this._data.getUint8(this.offset++);
+    };
+    /**
+     * Alias for {@link IOBuffer#readUint8}
+     */
+    IOBuffer.prototype.readByte = function () {
+        return this.readUint8();
+    };
+    /**
+     * Read n bytes and move pointer forward.
+     */
+    IOBuffer.prototype.readBytes = function (n) {
+        if (n === undefined)
+            n = 1;
+        var bytes = new Uint8Array(n);
+        for (var i = 0; i < n; i++) {
+            bytes[i] = this.readByte();
+        }
+        return bytes;
+    };
+    /**
+     * Read a 16-bit signed integer and move pointer forward
+     */
+    IOBuffer.prototype.readInt16 = function () {
+        var value = this._data.getInt16(this.offset, this.littleEndian);
+        this.offset += 2;
+        return value;
+    };
+    /**
+     * Read a 16-bit unsigned integer and move pointer forward
+     */
+    IOBuffer.prototype.readUint16 = function () {
+        var value = this._data.getUint16(this.offset, this.littleEndian);
+        this.offset += 2;
+        return value;
+    };
+    /**
+     * Read a 32-bit signed integer and move pointer forward
+     */
+    IOBuffer.prototype.readInt32 = function () {
+        var value = this._data.getInt32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    };
+    /**
+     * Read a 32-bit unsigned integer and move pointer forward
+     */
+    IOBuffer.prototype.readUint32 = function () {
+        var value = this._data.getUint32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    };
+    /**
+     * Read a 32-bit floating number and move pointer forward
+     */
+    IOBuffer.prototype.readFloat32 = function () {
+        var value = this._data.getFloat32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    };
+    /**
+     * Read a 64-bit floating number and move pointer forward
+     */
+    IOBuffer.prototype.readFloat64 = function () {
+        var value = this._data.getFloat64(this.offset, this.littleEndian);
+        this.offset += 8;
+        return value;
+    };
+    /**
+     * Read 1-byte ascii character and move pointer forward
+     */
+    IOBuffer.prototype.readChar = function () {
+        return String.fromCharCode(this.readInt8());
+    };
+    /**
+     * Read n 1-byte ascii characters and move pointer forward
+     */
+    IOBuffer.prototype.readChars = function (n) {
+        if (n === void 0) { n = 1; }
+        charArray.length = n;
+        for (var i = 0; i < n; i++) {
+            charArray[i] = this.readChar();
+        }
+        return charArray.join('');
+    };
+    /**
+     * Write 0xff if the passed value is truthy, 0x00 otherwise
+     */
+    IOBuffer.prototype.writeBoolean = function (value) {
+        if (value === void 0) { value = false; }
+        this.writeUint8(value ? 0xff : 0x00);
+        return this;
+    };
+    /**
+     * Write value as an 8-bit signed integer
+     */
+    IOBuffer.prototype.writeInt8 = function (value) {
+        this.ensureAvailable(1);
+        this._data.setInt8(this.offset++, value);
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write value as a 8-bit unsigned integer
+     */
+    IOBuffer.prototype.writeUint8 = function (value) {
+        this.ensureAvailable(1);
+        this._data.setUint8(this.offset++, value);
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * An alias for IOBuffer#writeUint8
+     */
+    IOBuffer.prototype.writeByte = function (value) {
+        return this.writeUint8(value);
+    };
+    /**
+     * Write bytes
+     */
+    IOBuffer.prototype.writeBytes = function (bytes) {
+        this.ensureAvailable(bytes.length);
+        for (var i = 0; i < bytes.length; i++) {
+            this._data.setUint8(this.offset++, bytes[i]);
+        }
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write value as an 16-bit signed integer
+     */
+    IOBuffer.prototype.writeInt16 = function (value) {
+        this.ensureAvailable(2);
+        this._data.setInt16(this.offset, value, this.littleEndian);
+        this.offset += 2;
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write value as a 16-bit unsigned integer
+     */
+    IOBuffer.prototype.writeUint16 = function (value) {
+        this.ensureAvailable(2);
+        this._data.setUint16(this.offset, value, this.littleEndian);
+        this.offset += 2;
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write a 32-bit signed integer at the current pointer offset
+     */
+    IOBuffer.prototype.writeInt32 = function (value) {
+        this.ensureAvailable(4);
+        this._data.setInt32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write a 32-bit unsigned integer at the current pointer offset
+     */
+    IOBuffer.prototype.writeUint32 = function (value) {
+        this.ensureAvailable(4);
+        this._data.setUint32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write a 32-bit floating number at the current pointer offset
+     */
+    IOBuffer.prototype.writeFloat32 = function (value) {
+        this.ensureAvailable(4);
+        this._data.setFloat32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write a 64-bit floating number at the current pointer offset
+     */
+    IOBuffer.prototype.writeFloat64 = function (value) {
+        this.ensureAvailable(8);
+        this._data.setFloat64(this.offset, value, this.littleEndian);
+        this.offset += 8;
+        this._updateLastWrittenByte();
+        return this;
+    };
+    /**
+     * Write the charCode of the passed string's first character to the current pointer offset
+     */
+    IOBuffer.prototype.writeChar = function (str) {
+        return this.writeUint8(str.charCodeAt(0));
+    };
+    /**
+     * Write the charCodes of the passed string's characters to the current pointer offset
+     */
+    IOBuffer.prototype.writeChars = function (str) {
+        for (var i = 0; i < str.length; i++) {
+            this.writeUint8(str.charCodeAt(i));
+        }
+        return this;
+    };
+    /**
+     * Export a Uint8Array view of the internal buffer.
+     * The view starts at the byte offset and its length
+     * is calculated to stop at the last written byte or the original length.
+     */
+    IOBuffer.prototype.toArray = function () {
+        return new Uint8Array(this.buffer, this.byteOffset, this._lastWrittenByte);
+    };
+    /**
+     * Update the last written byte offset
+     */
+    IOBuffer.prototype._updateLastWrittenByte = function () {
+        if (this.offset > this._lastWrittenByte) {
+            this._lastWrittenByte = this.offset;
+        }
+    };
+    return IOBuffer;
+}());
+export { IOBuffer };

package/lib/mol-io/common/netcdf/reader.d.ts

@@ -0,0 +1,78 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from https://github.com/cheminfo-js/netcdfjs
+ * MIT License, Copyright (c) 2016 cheminfo
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { IOBuffer } from '../io-buffer';
+export interface NetCDFRecordDimension {
+    length: number;
+    id?: number;
+    name?: string;
+    recordStep?: number;
+}
+export interface NetCDFVariable {
+    name: string;
+    dimensions: any[];
+    attributes: any[];
+    type: string;
+    size: number;
+    offset: number;
+    record: boolean;
+}
+export interface NetCDFHeader {
+    recordDimension: NetCDFRecordDimension;
+    version: number;
+    dimensions: {
+        name: string;
+        size: number;
+    }[];
+    globalAttributes: {
+        name: string;
+        type: string;
+        value: string | number;
+    }[];
+    variables: NetCDFVariable[];
+}
+export interface NetCDFDimension {
+    name: string;
+    size: number;
+}
+/**
+ * Reads a NetCDF v3.x file
+ * https://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html
+ */
+export declare class NetcdfReader {
+    header: Partial<NetCDFHeader>;
+    buffer: IOBuffer;
+    constructor(data: ArrayBuffer);
+    /**
+     * Version for the NetCDF format
+     */
+    get version(): "classic format" | "64-bit offset format";
+    get recordDimension(): NetCDFRecordDimension | undefined;
+    get dimensions(): {
+        name: string;
+        size: number;
+    }[] | undefined;
+    get globalAttributes(): {
+        name: string;
+        type: string;
+        value: string | number;
+    }[] | undefined;
+    get variables(): NetCDFVariable[] | undefined;
+    /**
+     * Checks if a variable is available
+     * @param {string|object} variableName - Name of the variable to check
+     * @return {Boolean} - Variable existence
+     */
+    hasDataVariable(variableName: string): boolean | undefined;
+    /**
+     * Retrieves the data for a given variable
+     * @param {string|object} variableName - Name of the variable to search or variable object
+     * @return {Array} - List with the variable values
+     */
+    getDataVariable(variableName: string | NetCDFVariable): any[];
+}