Bring up to date with master

src/core/operations/AESEncrypt.mjs

@@ -65,8 +65,8 @@ class AESEncrypt extends Operation {
      * @throws {OperationError} if invalid key length
      */
     run(input, args) {
-        const key = Utils.convertToByteArray(args[0].string, args[0].option),
-            iv = Utils.convertToByteArray(args[1].string, args[1].option),
+        const key = Utils.convertToByteString(args[0].string, args[0].option),
+            iv = Utils.convertToByteString(args[1].string, args[1].option),
             mode = args[2],
             inputType = args[3],
             outputType = args[4];

src/core/operations/BLAKE2b.mjs

@@ -0,0 +1,79 @@
+/**
+ * @author h345983745
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import blakejs from "blakejs";
+import OperationError from "../errors/OperationError";
+import Utils from "../Utils";
+import { toBase64 } from "../lib/Base64";
+
+/**
+ * BLAKE2b operation
+ */
+class BLAKE2b extends Operation {
+
+    /**
+     * BLAKE2b constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "BLAKE2b";
+        this.module = "Hashing";
+        this.description = `Performs BLAKE2b hashing on the input.  
+        <br><br> BLAKE2b is a flavour of the BLAKE cryptographic hash function that is optimized for 64-bit platforms and produces digests of any size between 1 and 64 bytes.
+        <br><br> Supports the use of an optional key.`;
+        this.infoURL = "https://wikipedia.org/wiki/BLAKE_(hash_function)#BLAKE2b_algorithm";
+        this.inputType = "ArrayBuffer";
+        this.outputType = "string";
+        this.args = [
+            {
+                "name": "Size",
+                "type": "option",
+                "value": ["512", "384", "256", "160", "128"]
+            }, {
+                "name": "Output Encoding",
+                "type": "option",
+                "value": ["Hex", "Base64", "Raw"]
+            }, {
+                "name": "Key",
+                "type": "toggleString",
+                "value": "",
+                "toggleValues": ["UTF8", "Decimal", "Base64", "Hex", "Latin1"]
+            }
+        ];
+    }
+
+    /**
+     * @param {ArrayBuffer} input
+     * @param {Object[]} args
+     * @returns {string} The input having been hashed with BLAKE2b in the encoding format speicifed.
+     */
+    run(input, args) {
+        const [outSize, outFormat] = args;
+        let key = Utils.convertToByteArray(args[2].string || "", args[2].option);
+        if (key.length === 0) {
+            key = null;
+        } else if (key.length > 64) {
+            throw new OperationError(["Key cannot be greater than 64 bytes", "It is currently " + key.length + " bytes."].join("\n"));
+        }
+
+        input = new Uint8Array(input);
+        switch (outFormat) {
+            case "Hex":
+                return blakejs.blake2bHex(input, key, outSize / 8);
+            case "Base64":
+                return toBase64(blakejs.blake2b(input, key, outSize / 8));
+            case "Raw":
+                return Utils.arrayBufferToStr(blakejs.blake2b(input, key, outSize / 8).buffer);
+            default:
+                return new OperationError("Unsupported Output Type");
+        }
+    }
+
+}
+
+export default BLAKE2b;

src/core/operations/BLAKE2s.mjs

@@ -0,0 +1,80 @@
+/**
+ * @author h345983745
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import blakejs from "blakejs";
+import OperationError from "../errors/OperationError";
+import Utils from "../Utils";
+import { toBase64 } from "../lib/Base64";
+
+/**
+ * BLAKE2s Operation
+ */
+class BLAKE2s extends Operation {
+
+    /**
+     * BLAKE2s constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "BLAKE2s";
+        this.module = "Hashing";
+        this.description = `Performs BLAKE2s hashing on the input.  
+        <br><br>BLAKE2s is a flavour of the BLAKE cryptographic hash function that is optimized for 8- to 32-bit platforms and produces digests of any size between 1 and 32 bytes.
+        <br><br>Supports the use of an optional key.`;
+        this.infoURL = "https://wikipedia.org/wiki/BLAKE_(hash_function)#BLAKE2";
+        this.inputType = "ArrayBuffer";
+        this.outputType = "string";
+        this.args = [
+            {
+                "name": "Size",
+                "type": "option",
+                "value": ["256", "160", "128"]
+            }, {
+                "name": "Output Encoding",
+                "type": "option",
+                "value": ["Hex", "Base64", "Raw"]
+            },
+            {
+                "name": "Key",
+                "type": "toggleString",
+                "value": "",
+                "toggleValues": ["UTF8", "Decimal", "Base64", "Hex", "Latin1"]
+            }
+        ];
+    }
+
+    /**
+     * @param {ArrayBuffer} input
+     * @param {Object[]} args
+     * @returns {string} The input having been hashed with BLAKE2s in the encoding format speicifed.
+     */
+    run(input, args) {
+        const [outSize, outFormat] = args;
+        let key = Utils.convertToByteArray(args[2].string || "", args[2].option);
+        if (key.length === 0) {
+            key = null;
+        } else if (key.length > 32) {
+            throw new OperationError(["Key cannot be greater than 32 bytes", "It is currently " + key.length + " bytes."].join("\n"));
+        }
+
+        input = new Uint8Array(input);
+        switch (outFormat) {
+            case "Hex":
+                return blakejs.blake2sHex(input, key, outSize / 8);
+            case "Base64":
+                return toBase64(blakejs.blake2s(input, key, outSize / 8));
+            case "Raw":
+                return Utils.arrayBufferToStr(blakejs.blake2s(input, key, outSize / 8).buffer);
+            default:
+                return new OperationError("Unsupported Output Type");
+        }
+    }
+
+}
+
+export default BLAKE2s;

src/core/operations/Bombe.mjs

@@ -0,0 +1,175 @@
+/**
+ * Emulation of the Bombe machine.
+ *
+ * @author s2224834
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import {BombeMachine} from "../lib/Bombe";
+import {ROTORS, ROTORS_FOURTH, REFLECTORS, Reflector} from "../lib/Enigma";
+
+/**
+ * Bombe operation
+ */
+class Bombe extends Operation {
+    /**
+     * Bombe constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Bombe";
+        this.module = "Default";
+        this.description = "Emulation of the Bombe machine used at Bletchley Park to attack Enigma, based on work by Polish and British cryptanalysts.<br><br>To run this you need to have a 'crib', which is some known plaintext for a chunk of the target ciphertext, and know the rotors used. (See the 'Bombe (multiple runs)' operation if you don't know the rotors.) The machine will suggest possible configurations of the Enigma. Each suggestion has the rotor start positions (left to right) and known plugboard pairs.<br><br>Choosing a crib: First, note that Enigma cannot encrypt a letter to itself, which allows you to rule out some positions for possible cribs. Secondly, the Bombe does not simulate the Enigma's middle rotor stepping. The longer your crib, the more likely a step happened within it, which will prevent the attack working. However, other than that, longer cribs are generally better. The attack produces a 'menu' which maps ciphertext letters to plaintext, and the goal is to produce 'loops': for example, with ciphertext ABC and crib CAB, we have the mappings A&lt;-&gt;C, B&lt;-&gt;A, and C&lt;-&gt;B, which produces a loop A-B-C-A. The more loops, the better the crib. The operation will output this: if your menu has too few loops or is too short, a large number of incorrect outputs will usually be produced. Try a different crib. If the menu seems good but the right answer isn't produced, your crib may be wrong, or you may have overlapped the middle rotor stepping - try a different crib.<br><br>Output is not sufficient to fully decrypt the data. You will have to recover the rest of the plugboard settings by inspection. And the ring position is not taken into account: this affects when the middle rotor steps. If your output is correct for a bit, and then goes wrong, adjust the ring and start position on the right-hand rotor together until the output improves. If necessary, repeat for the middle rotor.<br><br>By default this operation runs the checking machine, a manual process to verify the quality of Bombe stops, on each stop, discarding stops which fail. If you want to see how many times the hardware actually stops for a given input, disable the checking machine.<br><br>More detailed descriptions of the Enigma, Typex and Bombe operations <a href='https://github.com/gchq/CyberChef/wiki/Enigma,-the-Bombe,-and-Typex'>can be found here</a>.";
+        this.infoURL = "https://wikipedia.org/wiki/Bombe";
+        this.inputType = "string";
+        this.outputType = "JSON";
+        this.presentType = "html";
+        this.args = [
+            {
+                name: "Model",
+                type: "argSelector",
+                value: [
+                    {
+                        name: "3-rotor",
+                        off: [1]
+                    },
+                    {
+                        name: "4-rotor",
+                        on: [1]
+                    }
+                ]
+            },
+            {
+                name: "Left-most (4th) rotor",
+                type: "editableOption",
+                value: ROTORS_FOURTH,
+                defaultIndex: 0
+            },
+            {
+                name: "Left-hand rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 0
+            },
+            {
+                name: "Middle rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 1
+            },
+            {
+                name: "Right-hand rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 2
+            },
+            {
+                name: "Reflector",
+                type: "editableOption",
+                value: REFLECTORS
+            },
+            {
+                name: "Crib",
+                type: "string",
+                value: ""
+            },
+            {
+                name: "Crib offset",
+                type: "number",
+                value: 0
+            },
+            {
+                name: "Use checking machine",
+                type: "boolean",
+                value: true
+            }
+        ];
+    }
+
+    /**
+     * Format and send a status update message.
+     * @param {number} nLoops - Number of loops in the menu
+     * @param {number} nStops - How many stops so far
+     * @param {number} progress - Progress (as a float in the range 0..1)
+     */
+    updateStatus(nLoops, nStops, progress) {
+        const msg = `Bombe run with ${nLoops} loop${nLoops === 1 ? "" : "s"} in menu (2+ desirable): ${nStops} stops, ${Math.floor(100 * progress)}% done`;
+        self.sendStatusMessage(msg);
+    }
+
+    /**
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {string}
+     */
+    run(input, args) {
+        const model = args[0];
+        const reflectorstr = args[5];
+        let crib = args[6];
+        const offset = args[7];
+        const check = args[8];
+        const rotors = [];
+        for (let i=0; i<4; i++) {
+            if (i === 0 && model === "3-rotor") {
+                // No fourth rotor
+                continue;
+            }
+            let rstr = args[i + 1];
+            // The Bombe doesn't take stepping into account so we'll just ignore it here
+            if (rstr.includes("<")) {
+                rstr = rstr.split("<", 2)[0];
+            }
+            rotors.push(rstr);
+        }
+        // Rotors are handled in reverse
+        rotors.reverse();
+        if (crib.length === 0) {
+            throw new OperationError("Crib cannot be empty");
+        }
+        if (offset < 0) {
+            throw new OperationError("Offset cannot be negative");
+        }
+        // For symmetry with the Enigma op, for the input we'll just remove all invalid characters
+        input = input.replace(/[^A-Za-z]/g, "").toUpperCase();
+        crib = crib.replace(/[^A-Za-z]/g, "").toUpperCase();
+        const ciphertext = input.slice(offset);
+        const reflector = new Reflector(reflectorstr);
+        let update;
+        if (ENVIRONMENT_IS_WORKER()) {
+            update = this.updateStatus;
+        } else {
+            update = undefined;
+        }
+        const bombe = new BombeMachine(rotors, reflector, ciphertext, crib, check, update);
+        const result = bombe.run();
+        return {
+            nLoops: bombe.nLoops,
+            result: result
+        };
+    }
+
+
+    /**
+     * Displays the Bombe results in an HTML table
+     *
+     * @param {Object} output
+     * @param {number} output.nLoops
+     * @param {Array[]} output.result
+     * @returns {html}
+     */
+    present(output) {
+        let html = `Bombe run on menu with ${output.nLoops} loop${output.nLoops === 1 ? "" : "s"} (2+ desirable). Note: Rotor positions are listed left to right and start at the beginning of the crib, and ignore stepping and the ring setting. Some plugboard settings are determined. A decryption preview starting at the beginning of the crib and ignoring stepping is also provided.\n\n`;
+        html += "<table class='table table-hover table-sm table-bordered table-nonfluid'><tr><th>Rotor stops</th>  <th>Partial plugboard</th>  <th>Decryption preview</th></tr>\n";
+        for (const [setting, stecker, decrypt] of output.result) {
+            html += `<tr><td>${setting}</td>  <td>${stecker}</td>  <td>${decrypt}</td></tr>\n`;
+        }
+        html += "</table>";
+        return html;
+    }
+}
+
+export default Bombe;

src/core/operations/Bzip2Compress.mjs

@@ -0,0 +1,72 @@
+/**
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import Bzip2 from "libbzip2-wasm";
+
+/**
+ * Bzip2 Compress operation
+ */
+class Bzip2Compress extends Operation {
+
+    /**
+     * Bzip2Compress constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Bzip2 Compress";
+        this.module = "Compression";
+        this.description = "Bzip2 is a compression library developed by Julian Seward (of GHC fame) that uses the Burrows-Wheeler algorithm. It only supports compressing single files and its compression is slow, however is more effective than Deflate (.gz & .zip).";
+        this.infoURL = "https://wikipedia.org/wiki/Bzip2";
+        this.inputType = "ArrayBuffer";
+        this.outputType = "ArrayBuffer";
+        this.args = [
+            {
+                name: "Block size (100s of kb)",
+                type: "number",
+                value: 9,
+                min: 1,
+                max: 9
+            },
+            {
+                name: "Work factor",
+                type: "number",
+                value: 30
+            }
+        ];
+    }
+
+    /**
+     * @param {ArrayBuffer} input
+     * @param {Object[]} args
+     * @returns {File}
+     */
+    run(input, args) {
+        const [blockSize, workFactor] = args;
+        if (input.byteLength <= 0) {
+            throw new OperationError("Please provide an input.");
+        }
+        if (ENVIRONMENT_IS_WORKER()) self.sendStatusMessage("Loading Bzip2...");
+        return new Promise((resolve, reject) => {
+            Bzip2().then(bzip2 => {
+                if (ENVIRONMENT_IS_WORKER()) self.sendStatusMessage("Compressing data...");
+                const inpArray = new Uint8Array(input);
+                const bzip2cc = bzip2.compressBZ2(inpArray, blockSize, workFactor);
+                if (bzip2cc.error !== 0) {
+                    reject(new OperationError(bzip2cc.error_msg));
+                } else {
+                    const output = bzip2cc.output;
+                    resolve(output.buffer.slice(output.byteOffset, output.byteLength + output.byteOffset));
+                }
+            });
+        });
+    }
+
+}
+
+export default Bzip2Compress;

src/core/operations/Bzip2Decompress.mjs

@@ -1,12 +1,12 @@
 /**
- * @author n1474335 [n1474335@gmail.com]
- * @copyright Crown Copyright 2016
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
  * @license Apache-2.0
  */
 
 import Operation from "../Operation";
-import bzip2 from "../vendor/bzip2";
 import OperationError from "../errors/OperationError";
+import Bzip2 from "libbzip2-wasm";
 
 /**
  * Bzip2 Decompress operation
@@ -23,9 +23,15 @@ class Bzip2Decompress extends Operation {
         this.module = "Compression";
         this.description = "Decompresses data using the Bzip2 algorithm.";
         this.infoURL = "https://wikipedia.org/wiki/Bzip2";
-        this.inputType = "byteArray";
-        this.outputType = "string";
-        this.args = [];
+        this.inputType = "ArrayBuffer";
+        this.outputType = "ArrayBuffer";
+        this.args = [
+            {
+                name: "Use low-memory, slower decompression algorithm",
+                type: "boolean",
+                value: false
+            }
+        ];
         this.patterns = [
             {
                 "match": "^\\x42\\x5a\\x68",
@@ -41,14 +47,24 @@ class Bzip2Decompress extends Operation {
      * @returns {string}
      */
     run(input, args) {
-        const compressed = new Uint8Array(input);
-
-        try {
-            const bzip2Reader = bzip2.array(compressed);
-            return bzip2.simple(bzip2Reader);
-        } catch (err) {
-            throw new OperationError(err);
+        const [small] = args;
+        if (input.byteLength <= 0) {
+            throw new OperationError("Please provide an input.");
         }
+        if (ENVIRONMENT_IS_WORKER()) self.sendStatusMessage("Loading Bzip2...");
+        return new Promise((resolve, reject) => {
+            Bzip2().then(bzip2 => {
+                if (ENVIRONMENT_IS_WORKER()) self.sendStatusMessage("Decompressing data...");
+                const inpArray = new Uint8Array(input);
+                const bzip2cc = bzip2.decompressBZ2(inpArray, small ? 1 : 0);
+                if (bzip2cc.error !== 0) {
+                    reject(new OperationError(bzip2cc.error_msg));
+                } else {
+                    const output = bzip2cc.output;
+                    resolve(output.buffer.slice(output.byteOffset, output.byteLength + output.byteOffset));
+                }
+            });
+        });
     }
 
 }

src/core/operations/Enigma.mjs

@@ -0,0 +1,214 @@
+/**
+ * Emulation of the Enigma machine.
+ *
+ * @author s2224834
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import {ROTORS, LETTERS, ROTORS_FOURTH, REFLECTORS, Rotor, Reflector, Plugboard, EnigmaMachine} from "../lib/Enigma";
+
+/**
+ * Enigma operation
+ */
+class Enigma extends Operation {
+    /**
+     * Enigma constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Enigma";
+        this.module = "Default";
+        this.description = "Encipher/decipher with the WW2 Enigma machine.<br><br>Enigma was used by the German military, among others, around the WW2 era as a portable cipher machine to protect sensitive military, diplomatic and commercial communications.<br><br>The standard set of German military rotors and reflectors are provided. To configure the plugboard, enter a string of connected pairs of letters, e.g. <code>AB CD EF</code> connects A to B, C to D, and E to F. This is also used to create your own reflectors. To create your own rotor, enter the letters that the rotor maps A to Z to, in order, optionally followed by <code>&lt;</code> then a list of stepping points.<br>This is deliberately fairly permissive with rotor placements etc compared to a real Enigma (on which, for example, a four-rotor Enigma uses only the thin reflectors and the beta or gamma rotor in the 4th slot).<br><br>More detailed descriptions of the Enigma, Typex and Bombe operations <a href='https://github.com/gchq/CyberChef/wiki/Enigma,-the-Bombe,-and-Typex'>can be found here</a>.";
+        this.infoURL = "https://wikipedia.org/wiki/Enigma_machine";
+        this.inputType = "string";
+        this.outputType = "string";
+        this.args = [
+            {
+                name: "Model",
+                type: "argSelector",
+                value: [
+                    {
+                        name: "3-rotor",
+                        off: [1, 2, 3]
+                    },
+                    {
+                        name: "4-rotor",
+                        on: [1, 2, 3]
+                    }
+                ]
+            },
+            {
+                name: "Left-most (4th) rotor",
+                type: "editableOption",
+                value: ROTORS_FOURTH,
+                defaultIndex: 0
+            },
+            {
+                name: "Left-most rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Left-most rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Left-hand rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 0
+            },
+            {
+                name: "Left-hand rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Left-hand rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Middle rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 1
+            },
+            {
+                name: "Middle rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Middle rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Right-hand rotor",
+                type: "editableOption",
+                value: ROTORS,
+                // Default config is the rotors I-III *left to right*
+                defaultIndex: 2
+            },
+            {
+                name: "Right-hand rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Right-hand rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Reflector",
+                type: "editableOption",
+                value: REFLECTORS
+            },
+            {
+                name: "Plugboard",
+                type: "string",
+                value: ""
+            },
+            {
+                name: "Strict output",
+                hint: "Remove non-alphabet letters and group output",
+                type: "boolean",
+                value: true
+            },
+        ];
+    }
+
+    /**
+     * Helper - for ease of use rotors are specified as a single string; this
+     * method breaks the spec string into wiring and steps parts.
+     *
+     * @param {string} rotor - Rotor specification string.
+     * @param {number} i - For error messages, the number of this rotor.
+     * @returns {string[]}
+     */
+    parseRotorStr(rotor, i) {
+        if (rotor === "") {
+            throw new OperationError(`Rotor ${i} must be provided.`);
+        }
+        if (!rotor.includes("<")) {
+            return [rotor, ""];
+        }
+        return rotor.split("<", 2);
+    }
+
+    /**
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {string}
+     */
+    run(input, args) {
+        const model = args[0];
+        const reflectorstr = args[13];
+        const plugboardstr = args[14];
+        const removeOther = args[15];
+        const rotors = [];
+        for (let i=0; i<4; i++) {
+            if (i === 0 && model === "3-rotor") {
+                // Skip the 4th rotor settings
+                continue;
+            }
+            const [rotorwiring, rotorsteps] = this.parseRotorStr(args[i*3 + 1], 1);
+            rotors.push(new Rotor(rotorwiring, rotorsteps, args[i*3 + 2], args[i*3 + 3]));
+        }
+        // Rotors are handled in reverse
+        rotors.reverse();
+        const reflector = new Reflector(reflectorstr);
+        const plugboard = new Plugboard(plugboardstr);
+        if (removeOther) {
+            input = input.replace(/[^A-Za-z]/g, "");
+        }
+        const enigma = new EnigmaMachine(rotors, reflector, plugboard);
+        let result = enigma.crypt(input);
+        if (removeOther) {
+            // Five character cipher groups is traditional
+            result = result.replace(/([A-Z]{5})(?!$)/g, "$1 ");
+        }
+        return result;
+    }
+
+    /**
+     * Highlight Enigma
+     * This is only possible if we're passing through non-alphabet characters.
+     *
+     * @param {Object[]} pos
+     * @param {number} pos[].start
+     * @param {number} pos[].end
+     * @param {Object[]} args
+     * @returns {Object[]} pos
+     */
+    highlight(pos, args) {
+        if (args[13] === false) {
+            return pos;
+        }
+    }
+
+    /**
+     * Highlight Enigma in reverse
+     *
+     * @param {Object[]} pos
+     * @param {number} pos[].start
+     * @param {number} pos[].end
+     * @param {Object[]} args
+     * @returns {Object[]} pos
+     */
+    highlightReverse(pos, args) {
+        if (args[13] === false) {
+            return pos;
+        }
+    }
+
+}
+
+export default Enigma;

src/core/operations/Entropy.mjs

@@ -4,8 +4,13 @@
  * @license Apache-2.0
  */
 
+import * as d3temp from "d3";
+import * as nodomtemp from "nodom";
+
 import Operation from "../Operation";
-import Utils from "../Utils";
+
+const d3 = d3temp.default ? d3temp.default : d3temp;
+const nodom = nodomtemp.default ? nodomtemp.default: nodomtemp;
 
 /**
  * Entropy operation
@@ -19,30 +24,45 @@ class Entropy extends Operation {
         super();
 
         this.name = "Entropy";
-        this.module = "Default";
+        this.module = "Charts";
         this.description = "Shannon Entropy, in the context of information theory, is a measure of the rate at which information is produced by a source of data. It can be used, in a broad sense, to detect whether data is likely to be structured or unstructured. 8 is the maximum, representing highly unstructured, 'random' data. English language text usually falls somewhere between 3.5 and 5. Properly encrypted or compressed data should have an entropy of over 7.5.";
         this.infoURL = "https://wikipedia.org/wiki/Entropy_(information_theory)";
-        this.inputType = "byteArray";
-        this.outputType = "number";
+        this.inputType = "ArrayBuffer";
+        this.outputType = "json";
         this.presentType = "html";
-        this.args = [];
+        this.args = [
+            {
+                "name": "Visualisation",
+                "type": "option",
+                "value": ["Shannon scale", "Histogram (Bar)", "Histogram (Line)", "Curve", "Image"]
+            }
+        ];
     }
 
     /**
-     * @param {byteArray} input
-     * @param {Object[]} args
+     * Calculates the frequency of bytes in the input.
+     *
+     * @param {Uint8Array} input
      * @returns {number}
      */
-    run(input, args) {
+    calculateShannonEntropy(input) {
         const prob = [],
-            uniques = input.unique(),
-            str = Utils.byteArrayToChars(input);
-        let i;
+            occurrences = new Array(256).fill(0);
 
-        for (i = 0; i < uniques.length; i++) {
-            prob.push(str.count(Utils.chr(uniques[i])) / input.length);
+        // Count occurrences of each byte in the input
+        let i;
+        for (i = 0; i < input.length; i++) {
+            occurrences[input[i]]++;
         }
 
+        // Store probability list
+        for (i = 0; i < occurrences.length; i++) {
+            if (occurrences[i] > 0) {
+                prob.push(occurrences[i] / input.length);
+            }
+        }
+
+        // Calculate Shannon entropy
         let entropy = 0,
             p;
 
@@ -54,44 +74,357 @@ class Entropy extends Operation {
         return -entropy;
     }
 
+    /**
+     * Calculates the scanning entropy of the input
+     *
+     * @param {Uint8Array} inputBytes
+     * @returns {Object}
+     */
+    calculateScanningEntropy(inputBytes) {
+        const entropyData = [];
+        const binWidth = inputBytes.length < 256 ? 8 : 256;
+
+        for (let bytePos = 0; bytePos < inputBytes.length; bytePos += binWidth) {
+            const block = inputBytes.slice(bytePos, bytePos+binWidth);
+            entropyData.push(this.calculateShannonEntropy(block));
+        }
+
+        return { entropyData, binWidth };
+    }
+
+    /**
+     * Calculates the frequency of bytes in the input.
+     *
+     * @param {object} svg
+     * @param {function} xScale
+     * @param {function} yScale
+     * @param {integer} svgHeight
+     * @param {integer} svgWidth
+     * @param {object} margins
+     * @param {string} xTitle
+     * @param {string} yTitle
+     */
+    createAxes(svg, xScale, yScale, svgHeight, svgWidth, margins, title, xTitle, yTitle) {
+        // Axes
+        const yAxis = d3.axisLeft()
+            .scale(yScale);
+
+        const xAxis = d3.axisBottom()
+            .scale(xScale);
+
+        svg.append("g")
+            .attr("transform", `translate(0, ${svgHeight - margins.bottom})`)
+            .call(xAxis);
+
+        svg.append("g")
+            .attr("transform", `translate(${margins.left},0)`)
+            .call(yAxis);
+
+        // Axes labels
+        svg.append("text")
+            .attr("transform", "rotate(-90)")
+            .attr("y", 0 - margins.left)
+            .attr("x", 0 - (svgHeight / 2))
+            .attr("dy", "1em")
+            .style("text-anchor", "middle")
+            .text(yTitle);
+
+        svg.append("text")
+            .attr("transform", `translate(${svgWidth / 2}, ${svgHeight - margins.bottom + 40})`)
+            .style("text-anchor", "middle")
+            .text(xTitle);
+
+        // Add title
+        svg.append("text")
+            .attr("transform", `translate(${svgWidth / 2}, ${margins.top - 10})`)
+            .style("text-anchor", "middle")
+            .text(title);
+    }
+
+    /**
+     * Calculates the frequency of bytes in the input.
+     *
+     * @param {Uint8Array} inputBytes
+     * @returns {number[]}
+     */
+    calculateByteFrequency(inputBytes) {
+        const freq = new Array(256).fill(0);
+        if (inputBytes.length === 0) return freq;
+
+        // Count occurrences of each byte in the input
+        let i;
+        for (i = 0; i < inputBytes.length; i++) {
+            freq[inputBytes[i]]++;
+        }
+
+        for (i = 0; i < freq.length; i++) {
+            freq[i] = freq[i] / inputBytes.length;
+        }
+
+        return freq;
+    }
+
+    /**
+     * Calculates the frequency of bytes in the input.
+     *
+     * @param {number[]} byteFrequency
+     * @returns {HTML}
+     */
+    createByteFrequencyLineHistogram(byteFrequency) {
+        const margins = { top: 30, right: 20, bottom: 50, left: 30 };
+
+        const svgWidth = 500,
+            svgHeight = 500;
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${svgWidth} ${svgHeight}`);
+
+        const yScale = d3.scaleLinear()
+            .domain([0, d3.max(byteFrequency, d => d)])
+            .range([svgHeight - margins.bottom, margins.top]);
+
+        const xScale = d3.scaleLinear()
+            .domain([0, byteFrequency.length - 1])
+            .range([margins.left, svgWidth - margins.right]);
+
+        const line = d3.line()
+            .x((_, i) => xScale(i))
+            .y(d => yScale(d))
+            .curve(d3.curveMonotoneX);
+
+        svg.append("path")
+            .datum(byteFrequency)
+            .attr("fill", "none")
+            .attr("stroke", "steelblue")
+            .attr("d", line);
+
+        this.createAxes(svg, xScale, yScale, svgHeight, svgWidth, margins, "", "Byte", "Byte Frequency");
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+    /**
+     * Creates a byte frequency histogram
+     *
+     * @param {number[]} byteFrequency
+     * @returns {HTML}
+     */
+    createByteFrequencyBarHistogram(byteFrequency) {
+        const margins = { top: 30, right: 20, bottom: 50, left: 30 };
+
+        const svgWidth = 500,
+            svgHeight = 500,
+            binWidth = 1;
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${svgWidth} ${svgHeight}`);
+
+        const yExtent = d3.extent(byteFrequency, d => d);
+        const yScale = d3.scaleLinear()
+            .domain(yExtent)
+            .range([svgHeight - margins.bottom, margins.top]);
+
+        const xScale = d3.scaleLinear()
+            .domain([0, byteFrequency.length - 1])
+            .range([margins.left - binWidth, svgWidth - margins.right]);
+
+        svg.selectAll("rect")
+            .data(byteFrequency)
+            .enter().append("rect")
+            .attr("x", (_, i) => xScale(i) + binWidth)
+            .attr("y", dataPoint => yScale(dataPoint))
+            .attr("width", binWidth)
+            .attr("height", dataPoint => yScale(yExtent[0]) - yScale(dataPoint))
+            .attr("fill", "blue");
+
+        this.createAxes(svg, xScale, yScale, svgHeight, svgWidth, margins, "", "Byte", "Byte Frequency");
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+    /**
+     * Creates a byte frequency histogram
+     *
+     * @param {number[]} entropyData
+     * @returns {HTML}
+     */
+    createEntropyCurve(entropyData) {
+        const margins = { top: 30, right: 20, bottom: 50, left: 30 };
+
+        const svgWidth = 500,
+            svgHeight = 500;
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${svgWidth} ${svgHeight}`);
+
+        const yScale = d3.scaleLinear()
+            .domain([0, d3.max(entropyData, d => d)])
+            .range([svgHeight - margins.bottom, margins.top]);
+
+        const xScale = d3.scaleLinear()
+            .domain([0, entropyData.length])
+            .range([margins.left, svgWidth - margins.right]);
+
+        const line = d3.line()
+            .x((_, i) => xScale(i))
+            .y(d => yScale(d))
+            .curve(d3.curveMonotoneX);
+
+        if (entropyData.length > 0) {
+            svg.append("path")
+                .datum(entropyData)
+                .attr("d", line);
+
+            svg.selectAll("path").attr("fill", "none").attr("stroke", "steelblue");
+        }
+
+        this.createAxes(svg, xScale, yScale, svgHeight, svgWidth, margins, "Scanning Entropy", "Block", "Entropy");
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+    /**
+     * Creates an image representation of the entropy
+     *
+     * @param {number[]} entropyData
+     * @returns {HTML}
+     */
+    createEntropyImage(entropyData) {
+        const svgHeight = 100,
+            svgWidth = 100,
+            cellSize = 1,
+            nodes = [];
+
+        for (let i = 0; i < entropyData.length; i++) {
+            nodes.push({
+                x: i % svgWidth,
+                y: Math.floor(i / svgWidth),
+                entropy: entropyData[i]
+            });
+        }
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${svgWidth} ${svgHeight}`);
+
+        const greyScale = d3.scaleLinear()
+            .domain([0, d3.max(entropyData, d => d)])
+            .range(["#000000", "#FFFFFF"])
+            .interpolate(d3.interpolateRgb);
+
+        svg
+            .selectAll("rect")
+            .data(nodes)
+            .enter().append("rect")
+            .attr("x", d => d.x * cellSize)
+            .attr("y", d => d.y * cellSize)
+            .attr("width", cellSize)
+            .attr("height", cellSize)
+            .style("fill", d => greyScale(d.entropy));
+
+        return svg._groups[0][0].outerHTML;
+    }
+
     /**
      * Displays the entropy as a scale bar for web apps.
      *
      * @param {number} entropy
-     * @returns {html}
+     * @returns {HTML}
      */
-    present(entropy) {
+    createShannonEntropyVisualization(entropy) {
         return `Shannon entropy: ${entropy}
-<br><canvas id='chart-area'></canvas><br>
-- 0 represents no randomness (i.e. all the bytes in the data have the same value) whereas 8, the maximum, represents a completely random string.
-- Standard English text usually falls somewhere between 3.5 and 5.
-- Properly encrypted or compressed data of a reasonable length should have an entropy of over 7.5.
+        <br><canvas id='chart-area'></canvas><br>
+        - 0 represents no randomness (i.e. all the bytes in the data have the same value) whereas 8, the maximum, represents a completely random string.
+        - Standard English text usually falls somewhere between 3.5 and 5.
+        - Properly encrypted or compressed data of a reasonable length should have an entropy of over 7.5.
 
-The following results show the entropy of chunks of the input data. Chunks with particularly high entropy could suggest encrypted or compressed sections.
+        The following results show the entropy of chunks of the input data. Chunks with particularly high entropy could suggest encrypted or compressed sections.
 
-<br><script>
-    var canvas = document.getElementById("chart-area"),
-        parentRect = canvas.parentNode.getBoundingClientRect(),
-        entropy = ${entropy},
-        height = parentRect.height * 0.25;
+        <br><script>
+            var canvas = document.getElementById("chart-area"),
+                parentRect = canvas.parentNode.getBoundingClientRect(),
+                entropy = ${entropy},
+                height = parentRect.height * 0.25;
 
-    canvas.width = parentRect.width * 0.95;
-    canvas.height = height > 150 ? 150 : height;
+            canvas.width = parentRect.width * 0.95;
+            canvas.height = height > 150 ? 150 : height;
 
-    CanvasComponents.drawScaleBar(canvas, entropy, 8, [
-        {
-            label: "English text",
-            min: 3.5,
-            max: 5
-        },{
-            label: "Encrypted/compressed",
-            min: 7.5,
-            max: 8
-        }
-    ]);
-</script>`;
+            CanvasComponents.drawScaleBar(canvas, entropy, 8, [
+                {
+                    label: "English text",
+                    min: 3.5,
+                    max: 5
+                },{
+                    label: "Encrypted/compressed",
+                    min: 7.5,
+                    max: 8
+                }
+            ]);
+        </script>`;
     }
 
+    /**
+     * @param {ArrayBuffer} input
+     * @param {Object[]} args
+     * @returns {json}
+     */
+    run(input, args) {
+        const visualizationType = args[0];
+        input = new Uint8Array(input);
+
+        switch (visualizationType) {
+            case "Histogram (Bar)":
+            case "Histogram (Line)":
+                return this.calculateByteFrequency(input);
+            case "Curve":
+            case "Image":
+                return this.calculateScanningEntropy(input).entropyData;
+            case "Shannon scale":
+            default:
+                return this.calculateShannonEntropy(input);
+        }
+    }
+
+    /**
+     * Displays the entropy in a visualisation for web apps.
+     *
+     * @param {json} entropyData
+     * @param {Object[]} args
+     * @returns {html}
+     */
+    present(entropyData, args) {
+        const visualizationType = args[0];
+
+        switch (visualizationType) {
+            case "Histogram (Bar)":
+                return this.createByteFrequencyBarHistogram(entropyData);
+            case "Histogram (Line)":
+                return this.createByteFrequencyLineHistogram(entropyData);
+            case "Curve":
+                return this.createEntropyCurve(entropyData);
+            case "Image":
+                return this.createEntropyImage(entropyData);
+            case "Shannon scale":
+            default:
+                return this.createShannonEntropyVisualization(entropyData);
+        }
+    }
 }
 
 export default Entropy;

src/core/operations/ExtractFiles.mjs

@@ -23,7 +23,7 @@ class ExtractFiles extends Operation {
 
         this.name = "Extract Files";
         this.module = "Default";
-        this.description = "TODO";
+        this.description = "Performs file carving to attempt to extract files from the input.<br><br>This operation is currently capable of carving out the following formats:<ul><li>JPG</li><li>EXE</li><li>ZIP</li><li>PDF</li><li>PNG</li><li>BMP</li><li>FLV</li><li>RTF</li><li>DOCX, PPTX, XLSX</li><li>EPUB</li><li>GZIP</li><li>ZLIB</li><li>ELF, BIN, AXF, O, PRX, SO</li></ul>";
         this.infoURL = "https://forensicswiki.org/wiki/File_Carving";
         this.inputType = "ArrayBuffer";
         this.outputType = "List<File>";

src/core/operations/GenerateAllHashes.mjs

@@ -28,6 +28,8 @@ import Fletcher64Checksum from "./Fletcher64Checksum";
 import Adler32Checksum from "./Adler32Checksum";
 import CRC16Checksum from "./CRC16Checksum";
 import CRC32Checksum from "./CRC32Checksum";
+import BLAKE2b from "./BLAKE2b";
+import BLAKE2s from "./BLAKE2s";
 
 /**
  * Generate all hashes operation
@@ -86,6 +88,14 @@ class GenerateAllHashes extends Operation {
                 "\nWhirlpool-0: " + (new Whirlpool()).run(arrayBuffer, ["Whirlpool-0"]) +
                 "\nWhirlpool-T: " + (new Whirlpool()).run(arrayBuffer, ["Whirlpool-T"]) +
                 "\nWhirlpool:   " + (new Whirlpool()).run(arrayBuffer, ["Whirlpool"]) +
+                "\nBLAKE2b-128: " + (new BLAKE2b).run(arrayBuffer, ["128", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2b-160: " + (new BLAKE2b).run(arrayBuffer, ["160", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2b-256: " + (new BLAKE2b).run(arrayBuffer, ["256", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2b-384: " + (new BLAKE2b).run(arrayBuffer, ["384", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2b-512: " + (new BLAKE2b).run(arrayBuffer, ["512", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2s-128: " + (new BLAKE2s).run(arrayBuffer, ["128", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2s-160: " + (new BLAKE2s).run(arrayBuffer, ["160", "Hex", {string: "", option: "UTF8"}]) +
+                "\nBLAKE2s-256: " + (new BLAKE2s).run(arrayBuffer, ["256", "Hex", {string: "", option: "UTF8"}]) +
                 "\nSSDEEP:      " + (new SSDEEP()).run(str) +
                 "\nCTPH:        " + (new CTPH()).run(str) +
                 "\n\nChecksums:" +

src/core/operations/HTMLToText.mjs

@@ -0,0 +1,41 @@
+/**
+ * @author tlwr [toby@toby.codes]
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+
+/**
+ * HTML To Text operation
+ */
+class HTMLToText extends Operation {
+
+    /**
+     * HTMLToText constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "HTML To Text";
+        this.module = "Default";
+        this.description = "Converts an HTML output from an operation to a readable string instead of being rendered in the DOM.";
+        this.infoURL = "";
+        this.inputType = "html";
+        this.outputType = "string";
+        this.args = [];
+    }
+
+    /**
+     * @param {html} input
+     * @param {Object[]} args
+     * @returns {string}
+     */
+    run(input, args) {
+        return input;
+    }
+
+}
+
+export default HTMLToText;

src/core/operations/HeatmapChart.mjs

@@ -0,0 +1,266 @@
+/**
+ * @author tlwr [toby@toby.codes]
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import * as d3temp from "d3";
+import * as nodomtemp from "nodom";
+import { getScatterValues, RECORD_DELIMITER_OPTIONS, COLOURS, FIELD_DELIMITER_OPTIONS } from "../lib/Charts";
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import Utils from "../Utils";
+
+const d3 = d3temp.default ? d3temp.default : d3temp;
+const nodom = nodomtemp.default ? nodomtemp.default: nodomtemp;
+
+/**
+ * Heatmap chart operation
+ */
+class HeatmapChart extends Operation {
+
+    /**
+     * HeatmapChart constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Heatmap chart";
+        this.module = "Charts";
+        this.description = "A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors.";
+        this.infoURL = "https://wikipedia.org/wiki/Heat_map";
+        this.inputType = "string";
+        this.outputType = "html";
+        this.args = [
+            {
+                name: "Record delimiter",
+                type: "option",
+                value: RECORD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Field delimiter",
+                type: "option",
+                value: FIELD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Number of vertical bins",
+                type: "number",
+                value: 25,
+            },
+            {
+                name: "Number of horizontal bins",
+                type: "number",
+                value: 25,
+            },
+            {
+                name: "Use column headers as labels",
+                type: "boolean",
+                value: true,
+            },
+            {
+                name: "X label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Y label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Draw bin edges",
+                type: "boolean",
+                value: false,
+            },
+            {
+                name: "Min colour value",
+                type: "string",
+                value: COLOURS.min,
+            },
+            {
+                name: "Max colour value",
+                type: "string",
+                value: COLOURS.max,
+            },
+        ];
+    }
+
+    /**
+     * Heatmap chart operation.
+     *
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {html}
+     */
+    run(input, args) {
+        const recordDelimiter = Utils.charRep(args[0]),
+            fieldDelimiter = Utils.charRep(args[1]),
+            vBins = args[2],
+            hBins = args[3],
+            columnHeadingsAreIncluded = args[4],
+            drawEdges = args[7],
+            minColour = args[8],
+            maxColour = args[9],
+            dimension = 500;
+        if (vBins <= 0) throw new OperationError("Number of vertical bins must be greater than 0");
+        if (hBins <= 0) throw new OperationError("Number of horizontal bins must be greater than 0");
+
+        let xLabel = args[5],
+            yLabel = args[6];
+        const { headings, values } = getScatterValues(
+            input,
+            recordDelimiter,
+            fieldDelimiter,
+            columnHeadingsAreIncluded
+        );
+
+        if (headings) {
+            xLabel = headings.x;
+            yLabel = headings.y;
+        }
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${dimension} ${dimension}`);
+
+        const margin = {
+                top: 10,
+                right: 0,
+                bottom: 40,
+                left: 30,
+            },
+            width = dimension - margin.left - margin.right,
+            height = dimension - margin.top - margin.bottom,
+            binWidth = width / hBins,
+            binHeight = height/ vBins,
+            marginedSpace = svg.append("g")
+                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+        const bins = this.getHeatmapPacking(values, vBins, hBins),
+            maxCount = Math.max(...bins.map(row => {
+                const lengths = row.map(cell => cell.length);
+                return Math.max(...lengths);
+            }));
+
+        const xExtent = d3.extent(values, d => d[0]),
+            yExtent = d3.extent(values, d => d[1]);
+
+        const xAxis = d3.scaleLinear()
+            .domain(xExtent)
+            .range([0, width]);
+        const yAxis = d3.scaleLinear()
+            .domain(yExtent)
+            .range([height, 0]);
+
+        const colour = d3.scaleSequential(d3.interpolateLab(minColour, maxColour))
+            .domain([0, maxCount]);
+
+        marginedSpace.append("clipPath")
+            .attr("id", "clip")
+            .append("rect")
+            .attr("width", width)
+            .attr("height", height);
+
+        marginedSpace.append("g")
+            .attr("class", "bins")
+            .attr("clip-path", "url(#clip)")
+            .selectAll("g")
+            .data(bins)
+            .enter()
+            .append("g")
+            .selectAll("rect")
+            .data(d => d)
+            .enter()
+            .append("rect")
+            .attr("x", (d) => binWidth * d.x)
+            .attr("y", (d) => (height - binHeight * (d.y + 1)))
+            .attr("width", binWidth)
+            .attr("height", binHeight)
+            .attr("fill", (d) => colour(d.length))
+            .attr("stroke", drawEdges ? "rgba(0, 0, 0, 0.5)" : "none")
+            .attr("stroke-width", drawEdges ? "0.5" : "none")
+            .append("title")
+            .text(d => {
+                const count = d.length,
+                    perc = 100.0 * d.length / values.length,
+                    tooltip = `Count: ${count}\n
+                               Percentage: ${perc.toFixed(2)}%\n
+                    `.replace(/\s{2,}/g, "\n");
+                return tooltip;
+            });
+
+        marginedSpace.append("g")
+            .attr("class", "axis axis--y")
+            .call(d3.axisLeft(yAxis).tickSizeOuter(-width));
+
+        svg.append("text")
+            .attr("transform", "rotate(-90)")
+            .attr("y", -margin.left)
+            .attr("x", -(height / 2))
+            .attr("dy", "1em")
+            .style("text-anchor", "middle")
+            .text(yLabel);
+
+        marginedSpace.append("g")
+            .attr("class", "axis axis--x")
+            .attr("transform", "translate(0," + height + ")")
+            .call(d3.axisBottom(xAxis).tickSizeOuter(-height));
+
+        svg.append("text")
+            .attr("x", width / 2)
+            .attr("y", dimension)
+            .style("text-anchor", "middle")
+            .text(xLabel);
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+    /**
+     * Packs a list of x, y coordinates into a number of bins for use in a heatmap.
+     *
+     * @param {Object[]} points
+     * @param {number} number of vertical bins
+     * @param {number} number of horizontal bins
+     * @returns {Object[]} a list of bins (each bin is an Array) with x y coordinates, filled with the points
+     */
+    getHeatmapPacking(values, vBins, hBins) {
+        const xBounds = d3.extent(values, d => d[0]),
+            yBounds = d3.extent(values, d => d[1]),
+            bins = [];
+
+        if (xBounds[0] === xBounds[1]) throw "Cannot pack points. There is no difference between the minimum and maximum X coordinate.";
+        if (yBounds[0] === yBounds[1]) throw "Cannot pack points. There is no difference between the minimum and maximum Y coordinate.";
+
+        for (let y = 0; y < vBins; y++) {
+            bins.push([]);
+            for (let x = 0; x < hBins; x++) {
+                const item = [];
+                item.y = y;
+                item.x = x;
+
+                bins[y].push(item);
+            } // x
+        } // y
+
+        const epsilon = 0.000000001; // This is to clamp values that are exactly the maximum;
+
+        values.forEach(v => {
+            const fractionOfY = (v[1] - yBounds[0]) / ((yBounds[1] + epsilon) - yBounds[0]),
+                fractionOfX = (v[0] - xBounds[0]) / ((xBounds[1] + epsilon) - xBounds[0]),
+                y = Math.floor(vBins * fractionOfY),
+                x = Math.floor(hBins * fractionOfX);
+
+            bins[y][x].push({x: v[0], y: v[1]});
+        });
+
+        return bins;
+    }
+
+}
+
+export default HeatmapChart;

src/core/operations/HexDensityChart.mjs

@@ -0,0 +1,296 @@
+/**
+ * @author tlwr [toby@toby.codes]
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import * as d3temp from "d3";
+import * as d3hexbintemp from "d3-hexbin";
+import * as nodomtemp from "nodom";
+import { getScatterValues, RECORD_DELIMITER_OPTIONS, COLOURS, FIELD_DELIMITER_OPTIONS } from "../lib/Charts";
+
+import Operation from "../Operation";
+import Utils from "../Utils";
+
+const d3 = d3temp.default ? d3temp.default : d3temp;
+const d3hexbin = d3hexbintemp.default ? d3hexbintemp.default : d3hexbintemp;
+const nodom = nodomtemp.default ? nodomtemp.default: nodomtemp;
+
+
+/**
+ * Hex Density chart operation
+ */
+class HexDensityChart extends Operation {
+
+    /**
+     * HexDensityChart constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Hex Density chart";
+        this.module = "Charts";
+        this.description = "Hex density charts are used in a similar way to scatter charts, however rather than rendering tens of thousands of points, it groups the points into a few hundred hexagons to show the distribution.";
+        this.inputType = "string";
+        this.outputType = "html";
+        this.args = [
+            {
+                name: "Record delimiter",
+                type: "option",
+                value: RECORD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Field delimiter",
+                type: "option",
+                value: FIELD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Pack radius",
+                type: "number",
+                value: 25,
+            },
+            {
+                name: "Draw radius",
+                type: "number",
+                value: 15,
+            },
+            {
+                name: "Use column headers as labels",
+                type: "boolean",
+                value: true,
+            },
+            {
+                name: "X label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Y label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Draw hexagon edges",
+                type: "boolean",
+                value: false,
+            },
+            {
+                name: "Min colour value",
+                type: "string",
+                value: COLOURS.min,
+            },
+            {
+                name: "Max colour value",
+                type: "string",
+                value: COLOURS.max,
+            },
+            {
+                name: "Draw empty hexagons within data boundaries",
+                type: "boolean",
+                value: false,
+            }
+        ];
+    }
+
+
+    /**
+     * Hex Bin chart operation.
+     *
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {html}
+     */
+    run(input, args) {
+        const recordDelimiter = Utils.charRep(args[0]),
+            fieldDelimiter = Utils.charRep(args[1]),
+            packRadius = args[2],
+            drawRadius = args[3],
+            columnHeadingsAreIncluded = args[4],
+            drawEdges = args[7],
+            minColour = args[8],
+            maxColour = args[9],
+            drawEmptyHexagons = args[10],
+            dimension = 500;
+
+        let xLabel = args[5],
+            yLabel = args[6];
+        const { headings, values } = getScatterValues(
+            input,
+            recordDelimiter,
+            fieldDelimiter,
+            columnHeadingsAreIncluded
+        );
+
+        if (headings) {
+            xLabel = headings.x;
+            yLabel = headings.y;
+        }
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${dimension} ${dimension}`);
+
+        const margin = {
+                top: 10,
+                right: 0,
+                bottom: 40,
+                left: 30,
+            },
+            width = dimension - margin.left - margin.right,
+            height = dimension - margin.top - margin.bottom,
+            marginedSpace = svg.append("g")
+                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+        const hexbin = d3hexbin.hexbin()
+            .radius(packRadius)
+            .extent([0, 0], [width, height]);
+
+        const hexPoints = hexbin(values),
+            maxCount = Math.max(...hexPoints.map(b => b.length));
+
+        const xExtent = d3.extent(hexPoints, d => d.x),
+            yExtent = d3.extent(hexPoints, d => d.y);
+        xExtent[0] -= 2 * packRadius;
+        xExtent[1] += 3 * packRadius;
+        yExtent[0] -= 2 * packRadius;
+        yExtent[1] += 2 * packRadius;
+
+        const xAxis = d3.scaleLinear()
+            .domain(xExtent)
+            .range([0, width]);
+        const yAxis = d3.scaleLinear()
+            .domain(yExtent)
+            .range([height, 0]);
+
+        const colour = d3.scaleSequential(d3.interpolateLab(minColour, maxColour))
+            .domain([0, maxCount]);
+
+        marginedSpace.append("clipPath")
+            .attr("id", "clip")
+            .append("rect")
+            .attr("width", width)
+            .attr("height", height);
+
+        if (drawEmptyHexagons) {
+            marginedSpace.append("g")
+                .attr("class", "empty-hexagon")
+                .selectAll("path")
+                .data(this.getEmptyHexagons(hexPoints, packRadius))
+                .enter()
+                .append("path")
+                .attr("d", d => {
+                    return `M${xAxis(d.x)},${yAxis(d.y)} ${hexbin.hexagon(drawRadius)}`;
+                })
+                .attr("fill", (d) => colour(0))
+                .attr("stroke", drawEdges ? "black" : "none")
+                .attr("stroke-width", drawEdges ? "0.5" : "none")
+                .append("title")
+                .text(d => {
+                    const count = 0,
+                        perc = 0,
+                        tooltip = `Count: ${count}\n
+                                Percentage: ${perc.toFixed(2)}%\n
+                                Center: ${d.x.toFixed(2)}, ${d.y.toFixed(2)}\n
+                        `.replace(/\s{2,}/g, "\n");
+                    return tooltip;
+                });
+        }
+
+        marginedSpace.append("g")
+            .attr("class", "hexagon")
+            .attr("clip-path", "url(#clip)")
+            .selectAll("path")
+            .data(hexPoints)
+            .enter()
+            .append("path")
+            .attr("d", d => {
+                return `M${xAxis(d.x)},${yAxis(d.y)} ${hexbin.hexagon(drawRadius)}`;
+            })
+            .attr("fill", (d) => colour(d.length))
+            .attr("stroke", drawEdges ? "black" : "none")
+            .attr("stroke-width", drawEdges ? "0.5" : "none")
+            .append("title")
+            .text(d => {
+                const count = d.length,
+                    perc = 100.0 * d.length / values.length,
+                    CX = d.x,
+                    CY = d.y,
+                    xMin = Math.min(...d.map(d => d[0])),
+                    xMax = Math.max(...d.map(d => d[0])),
+                    yMin = Math.min(...d.map(d => d[1])),
+                    yMax = Math.max(...d.map(d => d[1])),
+                    tooltip = `Count: ${count}\n
+                               Percentage: ${perc.toFixed(2)}%\n
+                               Center: ${CX.toFixed(2)}, ${CY.toFixed(2)}\n
+                               Min X: ${xMin.toFixed(2)}\n
+                               Max X: ${xMax.toFixed(2)}\n
+                               Min Y: ${yMin.toFixed(2)}\n
+                               Max Y: ${yMax.toFixed(2)}
+                    `.replace(/\s{2,}/g, "\n");
+                return tooltip;
+            });
+
+        marginedSpace.append("g")
+            .attr("class", "axis axis--y")
+            .call(d3.axisLeft(yAxis).tickSizeOuter(-width));
+
+        svg.append("text")
+            .attr("transform", "rotate(-90)")
+            .attr("y", -margin.left)
+            .attr("x", -(height / 2))
+            .attr("dy", "1em")
+            .style("text-anchor", "middle")
+            .text(yLabel);
+
+        marginedSpace.append("g")
+            .attr("class", "axis axis--x")
+            .attr("transform", "translate(0," + height + ")")
+            .call(d3.axisBottom(xAxis).tickSizeOuter(-height));
+
+        svg.append("text")
+            .attr("x", width / 2)
+            .attr("y", dimension)
+            .style("text-anchor", "middle")
+            .text(xLabel);
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+
+    /**
+     * Hex Bin chart operation.
+     *
+     * @param {Object[]} - centres
+     * @param {number} - radius
+     * @returns {Object[]}
+     */
+    getEmptyHexagons(centres, radius) {
+        const emptyCentres = [],
+            boundingRect = [d3.extent(centres, d => d.x), d3.extent(centres, d => d.y)],
+            hexagonCenterToEdge = Math.cos(2 * Math.PI / 12) * radius,
+            hexagonEdgeLength = Math.sin(2 * Math.PI / 12) * radius;
+        let indent = false;
+
+        for (let y = boundingRect[1][0]; y <= boundingRect[1][1] + radius; y += hexagonEdgeLength + radius) {
+            for (let x = boundingRect[0][0]; x <= boundingRect[0][1] + radius; x += 2 * hexagonCenterToEdge) {
+                let cx = x;
+                const cy = y;
+
+                if (indent && x >= boundingRect[0][1]) break;
+                if (indent) cx += hexagonCenterToEdge;
+
+                emptyCentres.push({x: cx, y: cy});
+            }
+            indent = !indent;
+        }
+
+        return emptyCentres;
+    }
+
+}
+
+export default HexDensityChart;

src/core/operations/IndexOfCoincidence.mjs

@@ -0,0 +1,107 @@
+/**
+ * @author George O [georgeomnet+cyberchef@gmail.com]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import Utils from "../Utils";
+
+/**
+ * Index of Coincidence operation
+ */
+class IndexOfCoincidence extends Operation {
+
+    /**
+     * IndexOfCoincidence constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Index of Coincidence";
+        this.module = "Default";
+        this.description = "Index of Coincidence (IC) is the probability of two randomly selected characters being the same. This can be used to determine whether text is readable or random, with English text having an IC of around 0.066. IC can therefore be a sound method to automate frequency analysis.";
+        this.infoURL = "https://wikipedia.org/wiki/Index_of_coincidence";
+        this.inputType = "string";
+        this.outputType = "number";
+        this.presentType = "html";
+        this.args = [];
+    }
+
+    /**
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {number}
+     */
+    run(input, args) {
+        const text = input.toLowerCase().replace(/[^a-z]/g, ""),
+            frequencies = new Array(26).fill(0),
+            alphabet = Utils.expandAlphRange("a-z");
+        let coincidence = 0.00,
+            density = 0.00,
+            result = 0.00,
+            i;
+
+        for (i=0; i < alphabet.length; i++) {
+            frequencies[i] = text.count(alphabet[i]);
+        }
+
+        for (i=0; i < frequencies.length; i++) {
+            coincidence += frequencies[i] * (frequencies[i] - 1);
+        }
+
+        density = frequencies.sum();
+
+        // Ensure that we don't divide by 0
+        if (density < 2) density = 2;
+
+        result = coincidence / (density * (density - 1));
+
+        return result;
+    }
+
+    /**
+     * Displays the IC as a scale bar for web apps.
+     *
+     * @param {number} ic
+     * @returns {html}
+     */
+    present(ic) {
+        return `Index of Coincidence: ${ic}
+Normalized: ${ic * 26}
+<br><canvas id='chart-area'></canvas><br>
+- 0 represents complete randomness (all characters are unique), whereas 1 represents no randomness (all characters are identical).
+- English text generally has an IC of between 0.67 to 0.78.
+- 'Random' text is determined by the probability that each letter occurs the same number of times as another.
+
+The graph shows the IC of the input data. A low IC generally means that the text is random, compressed or encrypted.
+
+<script type='application/javascript'>
+  var canvas = document.getElementById("chart-area"),
+      parentRect = canvas.parentNode.getBoundingClientRect(),
+      ic = ${ic};
+
+  canvas.width = parentRect.width * 0.95;
+  canvas.height = parentRect.height * 0.25;
+
+  ic = ic > 0.25 ? 0.25 : ic;
+
+  CanvasComponents.drawScaleBar(canvas, ic, 0.25, [
+    {
+      label: "English text",
+      min: 0.05,
+      max: 0.08
+    },
+    {
+      label: "> 0.25",
+      min: 0.24,
+      max: 0.25
+    }
+  ]);
+</script>
+     `;
+    }
+
+}
+
+export default IndexOfCoincidence;

src/core/operations/JSONToCSV.mjs

@@ -51,6 +51,10 @@ class JSONToCSV extends Operation {
         this.rowDelim = rowDelim;
         const self = this;
 
+        if (!(input instanceof Array)) {
+            input = [input];
+        }
+
         try {
             // If the JSON is an array of arrays, this is easy
             if (input[0] instanceof Array) {
@@ -89,6 +93,8 @@ class JSONToCSV extends Operation {
      * @returns {string}
      */
     escapeCellContents(data) {
+        if (typeof data === "number") data = data.toString();
+
         // Double quotes should be doubled up
         data = data.replace(/"/g, '""');
 

src/core/operations/JavaScriptParser.mjs

@@ -21,7 +21,7 @@ class JavaScriptParser extends Operation {
         this.name = "JavaScript Parser";
         this.module = "Code";
         this.description = "Returns an Abstract Syntax Tree for valid JavaScript code.";
-        this.infoURL = "https://en.wikipedia.org/wiki/Abstract_syntax_tree";
+        this.infoURL = "https://wikipedia.org/wiki/Abstract_syntax_tree";
         this.inputType = "string";
         this.outputType = "string";
         this.args = [

src/core/operations/MultipleBombe.mjs

@@ -0,0 +1,305 @@
+/**
+ * Emulation of the Bombe machine.
+ * This version carries out multiple Bombe runs to handle unknown rotor configurations.
+ *
+ * @author s2224834
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import {BombeMachine} from "../lib/Bombe";
+import {ROTORS, ROTORS_FOURTH, REFLECTORS, Reflector} from "../lib/Enigma";
+
+/**
+ * Convenience method for flattening the preset ROTORS object into a newline-separated string.
+ * @param {Object[]} - Preset rotors object
+ * @param {number} s - Start index
+ * @param {number} n - End index
+ * @returns {string}
+ */
+function rotorsFormat(rotors, s, n) {
+    const res = [];
+    for (const i of rotors.slice(s, n)) {
+        res.push(i.value);
+    }
+    return res.join("\n");
+}
+
+/**
+ * Combinatorics choose function
+ * @param {number} n
+ * @param {number} k
+ * @returns number
+ */
+function choose(n, k) {
+    let res = 1;
+    for (let i=1; i<=k; i++) {
+        res *= (n + 1 - i) / i;
+    }
+    return res;
+}
+
+/**
+ * Bombe operation
+ */
+class MultipleBombe extends Operation {
+    /**
+     * Bombe constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Multiple Bombe";
+        this.module = "Default";
+        this.description = "Emulation of the Bombe machine used to attack Enigma. This version carries out multiple Bombe runs to handle unknown rotor configurations.<br><br>You should test your menu on the single Bombe operation before running it here. See the description of the Bombe operation for instructions on choosing a crib.<br><br>More detailed descriptions of the Enigma, Typex and Bombe operations <a href='https://github.com/gchq/CyberChef/wiki/Enigma,-the-Bombe,-and-Typex'>can be found here</a>.";
+        this.infoURL = "https://wikipedia.org/wiki/Bombe";
+        this.inputType = "string";
+        this.outputType = "JSON";
+        this.presentType = "html";
+        this.args = [
+            {
+                "name": "Standard Enigmas",
+                "type": "populateMultiOption",
+                "value": [
+                    {
+                        name: "German Service Enigma (First - 3 rotor)",
+                        value: [
+                            rotorsFormat(ROTORS, 0, 5),
+                            "",
+                            rotorsFormat(REFLECTORS, 0, 1)
+                        ]
+                    },
+                    {
+                        name: "German Service Enigma (Second - 3 rotor)",
+                        value: [
+                            rotorsFormat(ROTORS, 0, 8),
+                            "",
+                            rotorsFormat(REFLECTORS, 0, 2)
+                        ]
+                    },
+                    {
+                        name: "German Service Enigma (Third - 4 rotor)",
+                        value: [
+                            rotorsFormat(ROTORS, 0, 8),
+                            rotorsFormat(ROTORS_FOURTH, 1, 2),
+                            rotorsFormat(REFLECTORS, 2, 3)
+                        ]
+                    },
+                    {
+                        name: "German Service Enigma (Fourth - 4 rotor)",
+                        value: [
+                            rotorsFormat(ROTORS, 0, 8),
+                            rotorsFormat(ROTORS_FOURTH, 1, 3),
+                            rotorsFormat(REFLECTORS, 2, 4)
+                        ]
+                    },
+                    {
+                        name: "User defined",
+                        value: ["", "", ""]
+                    },
+                ],
+                "target": [1, 2, 3]
+            },
+            {
+                name: "Main rotors",
+                type: "text",
+                value: ""
+            },
+            {
+                name: "4th rotor",
+                type: "text",
+                value: ""
+            },
+            {
+                name: "Reflectors",
+                type: "text",
+                value: ""
+            },
+            {
+                name: "Crib",
+                type: "string",
+                value: ""
+            },
+            {
+                name: "Crib offset",
+                type: "number",
+                value: 0
+            },
+            {
+                name: "Use checking machine",
+                type: "boolean",
+                value: true
+            }
+        ];
+    }
+
+    /**
+     * Format and send a status update message.
+     * @param {number} nLoops - Number of loops in the menu
+     * @param {number} nStops - How many stops so far
+     * @param {number} progress - Progress (as a float in the range 0..1)
+     */
+    updateStatus(nLoops, nStops, progress, start) {
+        const elapsed = new Date().getTime() - start;
+        const remaining = (elapsed / progress) * (1 - progress) / 1000;
+        const hours = Math.floor(remaining / 3600);
+        const minutes = `0${Math.floor((remaining % 3600) / 60)}`.slice(-2);
+        const seconds = `0${Math.floor(remaining % 60)}`.slice(-2);
+        const msg = `Bombe run with ${nLoops} loop${nLoops === 1 ? "" : "s"} in menu (2+ desirable): ${nStops} stops, ${Math.floor(100 * progress)}% done, ${hours}:${minutes}:${seconds} remaining`;
+        self.sendStatusMessage(msg);
+    }
+
+    /**
+     * Early rotor description string validation.
+     * Drops stepping information.
+     * @param {string} rstr - The rotor description string
+     * @returns {string} - Rotor description with stepping stripped, if any
+     */
+    validateRotor(rstr) {
+        // The Bombe doesn't take stepping into account so we'll just ignore it here
+        if (rstr.includes("<")) {
+            rstr = rstr.split("<", 2)[0];
+        }
+        // Duplicate the validation of the rotor strings here, otherwise you might get an error
+        // thrown halfway into a big Bombe run
+        if (!/^[A-Z]{26}$/.test(rstr)) {
+            throw new OperationError("Rotor wiring must be 26 unique uppercase letters");
+        }
+        if (new Set(rstr).size !== 26) {
+            throw new OperationError("Rotor wiring must be 26 unique uppercase letters");
+        }
+        return rstr;
+    }
+
+    /**
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {string}
+     */
+    run(input, args) {
+        const mainRotorsStr = args[1];
+        const fourthRotorsStr = args[2];
+        const reflectorsStr = args[3];
+        let crib = args[4];
+        const offset = args[5];
+        const check = args[6];
+        const rotors = [];
+        const fourthRotors = [];
+        const reflectors = [];
+        for (let rstr of mainRotorsStr.split("\n")) {
+            rstr = this.validateRotor(rstr);
+            rotors.push(rstr);
+        }
+        if (rotors.length < 3) {
+            throw new OperationError("A minimum of three rotors must be supplied");
+        }
+        if (fourthRotorsStr !== "") {
+            for (let rstr of fourthRotorsStr.split("\n")) {
+                rstr = this.validateRotor(rstr);
+                fourthRotors.push(rstr);
+            }
+        }
+        if (fourthRotors.length === 0) {
+            fourthRotors.push("");
+        }
+        for (const rstr of reflectorsStr.split("\n")) {
+            const reflector = new Reflector(rstr);
+            reflectors.push(reflector);
+        }
+        if (reflectors.length === 0) {
+            throw new OperationError("A minimum of one reflector must be supplied");
+        }
+        if (crib.length === 0) {
+            throw new OperationError("Crib cannot be empty");
+        }
+        if (offset < 0) {
+            throw new OperationError("Offset cannot be negative");
+        }
+        // For symmetry with the Enigma op, for the input we'll just remove all invalid characters
+        input = input.replace(/[^A-Za-z]/g, "").toUpperCase();
+        crib = crib.replace(/[^A-Za-z]/g, "").toUpperCase();
+        const ciphertext = input.slice(offset);
+        let update;
+        if (ENVIRONMENT_IS_WORKER()) {
+            update = this.updateStatus;
+        } else {
+            update = undefined;
+        }
+        let bombe = undefined;
+        const output = {bombeRuns: []};
+        // I could use a proper combinatorics algorithm here... but it would be more code to
+        // write one, and we don't seem to have one in our existing libraries, so massively nested
+        // for loop it is
+        const totalRuns = choose(rotors.length, 3) * 6 * fourthRotors.length * reflectors.length;
+        let nRuns = 0;
+        let nStops = 0;
+        const start = new Date().getTime();
+        for (const rotor1 of rotors) {
+            for (const rotor2 of rotors) {
+                if (rotor2 === rotor1) {
+                    continue;
+                }
+                for (const rotor3 of rotors) {
+                    if (rotor3 === rotor2 || rotor3 === rotor1) {
+                        continue;
+                    }
+                    for (const rotor4 of fourthRotors) {
+                        for (const reflector of reflectors) {
+                            nRuns++;
+                            const runRotors = [rotor1, rotor2, rotor3];
+                            if (rotor4 !== "") {
+                                runRotors.push(rotor4);
+                            }
+                            if (bombe === undefined) {
+                                bombe = new BombeMachine(runRotors, reflector, ciphertext, crib, check);
+                                output.nLoops = bombe.nLoops;
+                            } else {
+                                bombe.changeRotors(runRotors, reflector);
+                            }
+                            const result = bombe.run();
+                            nStops += result.length;
+                            if (update !== undefined) {
+                                update(bombe.nLoops, nStops, nRuns / totalRuns, start);
+                            }
+                            if (result.length > 0) {
+                                output.bombeRuns.push({
+                                    rotors: runRotors,
+                                    reflector: reflector.pairs,
+                                    result: result
+                                });
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        return output;
+    }
+
+
+    /**
+     * Displays the MultiBombe results in an HTML table
+     *
+     * @param {Object} output
+     * @param {number} output.nLoops
+     * @param {Array[]} output.result
+     * @returns {html}
+     */
+    present(output) {
+        let html = `Bombe run on menu with ${output.nLoops} loop${output.nLoops === 1 ? "" : "s"} (2+ desirable). Note: Rotors and rotor positions are listed left to right, ignore stepping and the ring setting, and positions start at the beginning of the crib. Some plugboard settings are determined. A decryption preview starting at the beginning of the crib and ignoring stepping is also provided.\n`;
+
+        for (const run of output.bombeRuns) {
+            html += `\nRotors: ${run.rotors.slice().reverse().join(", ")}\nReflector: ${run.reflector}\n`;
+            html += "<table class='table table-hover table-sm table-bordered table-nonfluid'><tr><th>Rotor stops</th>  <th>Partial plugboard</th>  <th>Decryption preview</th></tr>\n";
+            for (const [setting, stecker, decrypt] of run.result) {
+                html += `<tr><td>${setting}</td>  <td>${stecker}</td>  <td>${decrypt}</td></tr>\n`;
+            }
+            html += "</table>\n";
+        }
+        return html;
+    }
+}
+
+export default MultipleBombe;

src/core/operations/PEMToHex.mjs

@@ -21,7 +21,7 @@ class PEMToHex extends Operation {
         this.name = "PEM to Hex";
         this.module = "PublicKey";
         this.description = "Converts PEM (Privacy Enhanced Mail) format to a hexadecimal DER (Distinguished Encoding Rules) string.";
-        this.infoURL = "https://en.wikipedia.org/wiki/X.690#DER_encoding";
+        this.infoURL = "https://wikipedia.org/wiki/X.690#DER_encoding";
         this.inputType = "string";
         this.outputType = "string";
         this.args = [];

src/core/operations/ProtobufDecode.mjs

@@ -0,0 +1,46 @@
+/**
+ * @author GCHQ Contributor [3]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import Protobuf from "../lib/Protobuf";
+
+/**
+ * Protobuf Decode operation
+ */
+class ProtobufDecode extends Operation {
+
+    /**
+     * ProtobufDecode constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Protobuf Decode";
+        this.module = "Default";
+        this.description = "Decodes any Protobuf encoded data to a JSON representation of the data using the field number as the field key.";
+        this.infoURL = "https://wikipedia.org/wiki/Protocol_Buffers";
+        this.inputType = "byteArray";
+        this.outputType = "JSON";
+        this.args = [];
+    }
+
+    /**
+     * @param {byteArray} input
+     * @param {Object[]} args
+     * @returns {JSON}
+     */
+    run(input, args) {
+        try {
+            return Protobuf.decode(input);
+        } catch (err) {
+            throw new OperationError(err);
+        }
+    }
+
+}
+
+export default ProtobufDecode;

src/core/operations/RegularExpression.mjs

@@ -230,6 +230,7 @@ function regexHighlight (input, regex, displayTotal) {
         title = "",
         hl = 1,
         total = 0;
+    const captureGroups = [];
 
     output = input.replace(regex, (match, ...args) => {
         args.pop(); // Throw away full string
@@ -247,9 +248,15 @@ function regexHighlight (input, regex, displayTotal) {
         // Switch highlight
         hl = hl === 1 ? 2 : 1;
 
-        total++;
+        // Store highlighted match and replace with a placeholder
+        captureGroups.push(`<span class='hl${hl}' title='${title}'>${Utils.escapeHtml(match)}</span>`);
+        return `[cc_capture_group_${total++}]`;
+    });
 
-        return `<span class='hl${hl}' title='${title}'>${Utils.escapeHtml(match)}</span>`;
+    // Safely escape all remaining text, then replace placeholders
+    output = Utils.escapeHtml(output);
+    output = output.replace(/\[cc_capture_group_(\d+)\]/g, (_, i) => {
+        return captureGroups[i];
     });
 
     if (displayTotal)

src/core/operations/ScatterChart.mjs

@@ -0,0 +1,199 @@
+/**
+ * @author tlwr [toby@toby.codes]
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import * as d3temp from "d3";
+import * as nodomtemp from "nodom";
+import { getScatterValues, getScatterValuesWithColour, RECORD_DELIMITER_OPTIONS, COLOURS, FIELD_DELIMITER_OPTIONS } from "../lib/Charts";
+
+import Operation from "../Operation";
+import Utils from "../Utils";
+
+const d3 = d3temp.default ? d3temp.default : d3temp;
+const nodom = nodomtemp.default ? nodomtemp.default: nodomtemp;
+
+/**
+ * Scatter chart operation
+ */
+class ScatterChart extends Operation {
+
+    /**
+     * ScatterChart constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Scatter chart";
+        this.module = "Charts";
+        this.description = "Plots two-variable data as single points on a graph.";
+        this.infoURL = "https://wikipedia.org/wiki/Scatter_plot";
+        this.inputType = "string";
+        this.outputType = "html";
+        this.args = [
+            {
+                name: "Record delimiter",
+                type: "option",
+                value: RECORD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Field delimiter",
+                type: "option",
+                value: FIELD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Use column headers as labels",
+                type: "boolean",
+                value: true,
+            },
+            {
+                name: "X label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Y label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Colour",
+                type: "string",
+                value: COLOURS.max,
+            },
+            {
+                name: "Point radius",
+                type: "number",
+                value: 10,
+            },
+            {
+                name: "Use colour from third column",
+                type: "boolean",
+                value: false,
+            }
+        ];
+    }
+
+    /**
+     * Scatter chart operation.
+     *
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {html}
+     */
+    run(input, args) {
+        const recordDelimiter = Utils.charRep(args[0]),
+            fieldDelimiter = Utils.charRep(args[1]),
+            columnHeadingsAreIncluded = args[2],
+            fillColour = args[5],
+            radius = args[6],
+            colourInInput = args[7],
+            dimension = 500;
+
+        let xLabel = args[3],
+            yLabel = args[4];
+
+        const dataFunction = colourInInput ? getScatterValuesWithColour : getScatterValues;
+        const { headings, values } = dataFunction(
+            input,
+            recordDelimiter,
+            fieldDelimiter,
+            columnHeadingsAreIncluded
+        );
+
+        if (headings) {
+            xLabel = headings.x;
+            yLabel = headings.y;
+        }
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${dimension} ${dimension}`);
+
+        const margin = {
+                top: 10,
+                right: 0,
+                bottom: 40,
+                left: 30,
+            },
+            width = dimension - margin.left - margin.right,
+            height = dimension - margin.top - margin.bottom,
+            marginedSpace = svg.append("g")
+                .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+
+        const xExtent = d3.extent(values, d => d[0]),
+            xDelta = xExtent[1] - xExtent[0],
+            yExtent = d3.extent(values, d => d[1]),
+            yDelta = yExtent[1] - yExtent[0],
+            xAxis = d3.scaleLinear()
+                .domain([xExtent[0] - (0.1 * xDelta), xExtent[1] + (0.1 * xDelta)])
+                .range([0, width]),
+            yAxis = d3.scaleLinear()
+                .domain([yExtent[0] - (0.1 * yDelta), yExtent[1] + (0.1 * yDelta)])
+                .range([height, 0]);
+
+        marginedSpace.append("clipPath")
+            .attr("id", "clip")
+            .append("rect")
+            .attr("width", width)
+            .attr("height", height);
+
+        marginedSpace.append("g")
+            .attr("class", "points")
+            .attr("clip-path", "url(#clip)")
+            .selectAll("circle")
+            .data(values)
+            .enter()
+            .append("circle")
+            .attr("cx", (d) => xAxis(d[0]))
+            .attr("cy", (d) => yAxis(d[1]))
+            .attr("r", d => radius)
+            .attr("fill", d => {
+                return colourInInput ? d[2] : fillColour;
+            })
+            .attr("stroke", "rgba(0, 0, 0, 0.5)")
+            .attr("stroke-width", "0.5")
+            .append("title")
+            .text(d => {
+                const x = d[0],
+                    y = d[1],
+                    tooltip = `X: ${x}\n
+                               Y: ${y}\n
+                    `.replace(/\s{2,}/g, "\n");
+                return tooltip;
+            });
+
+        marginedSpace.append("g")
+            .attr("class", "axis axis--y")
+            .call(d3.axisLeft(yAxis).tickSizeOuter(-width));
+
+        svg.append("text")
+            .attr("transform", "rotate(-90)")
+            .attr("y", -margin.left)
+            .attr("x", -(height / 2))
+            .attr("dy", "1em")
+            .style("text-anchor", "middle")
+            .text(yLabel);
+
+        marginedSpace.append("g")
+            .attr("class", "axis axis--x")
+            .attr("transform", "translate(0," + height + ")")
+            .call(d3.axisBottom(xAxis).tickSizeOuter(-height));
+
+        svg.append("text")
+            .attr("x", width / 2)
+            .attr("y", dimension)
+            .style("text-anchor", "middle")
+            .text(xLabel);
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+}
+
+export default ScatterChart;

src/core/operations/SeriesChart.mjs

@@ -0,0 +1,227 @@
+/**
+ * @author tlwr [toby@toby.codes]
+ * @author Matt C [me@mitt.dev]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import * as d3temp from "d3";
+import * as nodomtemp from "nodom";
+import { getSeriesValues, RECORD_DELIMITER_OPTIONS, FIELD_DELIMITER_OPTIONS } from "../lib/Charts";
+
+import Operation from "../Operation";
+import Utils from "../Utils";
+
+const d3 = d3temp.default ? d3temp.default : d3temp;
+const nodom = nodomtemp.default ? nodomtemp.default: nodomtemp;
+
+/**
+ * Series chart operation
+ */
+class SeriesChart extends Operation {
+
+    /**
+     * SeriesChart constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Series chart";
+        this.module = "Charts";
+        this.description = "A time series graph is a line graph of repeated measurements taken over regular time intervals.";
+        this.inputType = "string";
+        this.outputType = "html";
+        this.args = [
+            {
+                name: "Record delimiter",
+                type: "option",
+                value: RECORD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "Field delimiter",
+                type: "option",
+                value: FIELD_DELIMITER_OPTIONS,
+            },
+            {
+                name: "X label",
+                type: "string",
+                value: "",
+            },
+            {
+                name: "Point radius",
+                type: "number",
+                value: 1,
+            },
+            {
+                name: "Series colours",
+                type: "string",
+                value: "mediumseagreen, dodgerblue, tomato",
+            },
+        ];
+    }
+
+    /**
+     * Series chart operation.
+     *
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {html}
+     */
+    run(input, args) {
+        const recordDelimiter = Utils.charRep(args[0]),
+            fieldDelimiter = Utils.charRep(args[1]),
+            xLabel = args[2],
+            pipRadius = args[3],
+            seriesColours = args[4].split(","),
+            svgWidth = 500,
+            interSeriesPadding = 20,
+            xAxisHeight = 50,
+            seriesLabelWidth = 50,
+            seriesHeight = 100,
+            seriesWidth = svgWidth - seriesLabelWidth - interSeriesPadding;
+
+        const { xValues, series } = getSeriesValues(input, recordDelimiter, fieldDelimiter),
+            allSeriesHeight = Object.keys(series).length * (interSeriesPadding + seriesHeight),
+            svgHeight = allSeriesHeight + xAxisHeight + interSeriesPadding;
+
+        const document = new nodom.Document();
+        let svg = document.createElement("svg");
+        svg = d3.select(svg)
+            .attr("width", "100%")
+            .attr("height", "100%")
+            .attr("viewBox", `0 0 ${svgWidth} ${svgHeight}`);
+
+        const xAxis = d3.scalePoint()
+            .domain(xValues)
+            .range([0, seriesWidth]);
+
+        svg.append("g")
+            .attr("class", "axis axis--x")
+            .attr("transform", `translate(${seriesLabelWidth}, ${xAxisHeight})`)
+            .call(
+                d3.axisTop(xAxis).tickValues(xValues.filter((x, i) => {
+                    return [0, Math.round(xValues.length / 2), xValues.length -1].indexOf(i) >= 0;
+                }))
+            );
+
+        svg.append("text")
+            .attr("x", svgWidth / 2)
+            .attr("y", xAxisHeight / 2)
+            .style("text-anchor", "middle")
+            .text(xLabel);
+
+        const tooltipText = {},
+            tooltipAreaWidth = seriesWidth / xValues.length;
+
+        xValues.forEach(x => {
+            const tooltip = [];
+
+            series.forEach(serie => {
+                const y = serie.data[x];
+                if (typeof y === "undefined") return;
+
+                tooltip.push(`${serie.name}: ${y}`);
+            });
+
+            tooltipText[x] = tooltip.join("\n");
+        });
+
+        const chartArea = svg.append("g")
+            .attr("transform", `translate(${seriesLabelWidth}, ${xAxisHeight})`);
+
+        chartArea
+            .append("g")
+            .selectAll("rect")
+            .data(xValues)
+            .enter()
+            .append("rect")
+            .attr("x", x => {
+                return xAxis(x) - (tooltipAreaWidth / 2);
+            })
+            .attr("y", 0)
+            .attr("width", tooltipAreaWidth)
+            .attr("height", allSeriesHeight)
+            .attr("stroke", "none")
+            .attr("fill", "transparent")
+            .append("title")
+            .text(x => {
+                return `${x}\n
+                    --\n
+                    ${tooltipText[x]}\n
+                `.replace(/\s{2,}/g, "\n");
+            });
+
+        const yAxesArea = svg.append("g")
+            .attr("transform", `translate(0, ${xAxisHeight})`);
+
+        series.forEach((serie, seriesIndex) => {
+            const yExtent = d3.extent(Object.values(serie.data)),
+                yAxis = d3.scaleLinear()
+                    .domain(yExtent)
+                    .range([seriesHeight, 0]);
+
+            const seriesGroup = chartArea
+                .append("g")
+                .attr("transform", `translate(0, ${seriesHeight * seriesIndex + interSeriesPadding * (seriesIndex + 1)})`);
+
+            let path = "";
+            xValues.forEach((x, xIndex) => {
+                let nextX = xValues[xIndex + 1],
+                    y = serie.data[x],
+                    nextY= serie.data[nextX];
+
+                if (typeof y === "undefined" || typeof nextY === "undefined") return;
+
+                x = xAxis(x); nextX = xAxis(nextX);
+                y = yAxis(y); nextY = yAxis(nextY);
+
+                path += `M ${x} ${y} L ${nextX} ${nextY} z `;
+            });
+
+            seriesGroup
+                .append("path")
+                .attr("d", path)
+                .attr("fill", "none")
+                .attr("stroke", seriesColours[seriesIndex % seriesColours.length])
+                .attr("stroke-width", "1");
+
+            xValues.forEach(x => {
+                const y = serie.data[x];
+                if (typeof y === "undefined") return;
+
+                seriesGroup
+                    .append("circle")
+                    .attr("cx", xAxis(x))
+                    .attr("cy", yAxis(y))
+                    .attr("r", pipRadius)
+                    .attr("fill", seriesColours[seriesIndex % seriesColours.length])
+                    .append("title")
+                    .text(d => {
+                        return `${x}\n
+                            --\n
+                            ${tooltipText[x]}\n
+                        `.replace(/\s{2,}/g, "\n");
+                    });
+            });
+
+            yAxesArea
+                .append("g")
+                .attr("transform", `translate(${seriesLabelWidth - interSeriesPadding}, ${seriesHeight * seriesIndex + interSeriesPadding * (seriesIndex + 1)})`)
+                .attr("class", "axis axis--y")
+                .call(d3.axisLeft(yAxis).ticks(5));
+
+            yAxesArea
+                .append("g")
+                .attr("transform", `translate(0, ${seriesHeight / 2 + seriesHeight * seriesIndex + interSeriesPadding * (seriesIndex + 1)})`)
+                .append("text")
+                .style("text-anchor", "middle")
+                .attr("transform", "rotate(-90)")
+                .text(serie.name);
+        });
+
+        return svg._groups[0][0].outerHTML;
+    }
+
+}
+
+export default SeriesChart;

src/core/operations/TextEncodingBruteForce.mjs

@@ -79,7 +79,7 @@ class TextEncodingBruteForce extends Operation {
         let table = "<table class='table table-hover table-sm table-bordered table-nonfluid'><tr><th>Encoding</th><th>Value</th></tr>";
 
         for (const enc in encodings) {
-            const value = Utils.printable(encodings[enc], true);
+            const value = Utils.escapeHtml(Utils.printable(encodings[enc], true));
             table += `<tr><td>${enc}</td><td>${value}</td></tr>`;
         }
 

src/core/operations/Typex.mjs

@@ -0,0 +1,250 @@
+/**
+ * Emulation of the Typex machine.
+ *
+ * @author s2224834
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import {LETTERS, Reflector} from "../lib/Enigma";
+import {ROTORS, REFLECTORS, TypexMachine, Plugboard, Rotor} from "../lib/Typex";
+
+/**
+ * Typex operation
+ */
+class Typex extends Operation {
+    /**
+     * Typex constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "Typex";
+        this.module = "Default";
+        this.description = "Encipher/decipher with the WW2 Typex machine.<br><br>Typex was originally built by the British Royal Air Force prior to WW2, and is based on the Enigma machine with some improvements made, including using five rotors with more stepping points and interchangeable wiring cores. It was used across the British and Commonewealth militaries. A number of later variants were produced; here we simulate a WW2 era Mark 22 Typex with plugboards for the reflector and input. Typex rotors were changed regularly and none are public: a random example set are provided.<br><br>To configure the reflector plugboard, enter a string of connected pairs of letters in the reflector box, e.g. <code>AB CD EF</code> connects A to B, C to D, and E to F (you'll need to connect every letter). There is also an input plugboard: unlike Enigma's plugboard, it's not restricted to pairs, so it's entered like a rotor (without stepping). To create your own rotor, enter the letters that the rotor maps A to Z to, in order, optionally followed by <code>&lt;</code> then a list of stepping points.<br><br>More detailed descriptions of the Enigma, Typex and Bombe operations <a href='https://github.com/gchq/CyberChef/wiki/Enigma,-the-Bombe,-and-Typex'>can be found here</a>.";
+        this.infoURL = "https://wikipedia.org/wiki/Typex";
+        this.inputType = "string";
+        this.outputType = "string";
+        this.args = [
+            {
+                name: "1st (left-hand) rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 0
+            },
+            {
+                name: "1st rotor reversed",
+                type: "boolean",
+                value: false
+            },
+            {
+                name: "1st rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "1st rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "2nd rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 1
+            },
+            {
+                name: "2nd rotor reversed",
+                type: "boolean",
+                value: false
+            },
+            {
+                name: "2nd rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "2nd rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "3rd (middle) rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 2
+            },
+            {
+                name: "3rd rotor reversed",
+                type: "boolean",
+                value: false
+            },
+            {
+                name: "3rd rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "3rd rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "4th (static) rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 3
+            },
+            {
+                name: "4th rotor reversed",
+                type: "boolean",
+                value: false
+            },
+            {
+                name: "4th rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "4th rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "5th (right-hand, static) rotor",
+                type: "editableOption",
+                value: ROTORS,
+                defaultIndex: 4
+            },
+            {
+                name: "5th rotor reversed",
+                type: "boolean",
+                value: false
+            },
+            {
+                name: "5th rotor ring setting",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "5th rotor initial value",
+                type: "option",
+                value: LETTERS
+            },
+            {
+                name: "Reflector",
+                type: "editableOption",
+                value: REFLECTORS
+            },
+            {
+                name: "Plugboard",
+                type: "string",
+                value: ""
+            },
+            {
+                name: "Typex keyboard emulation",
+                type: "option",
+                value: ["None", "Encrypt", "Decrypt"]
+            },
+            {
+                name: "Strict output",
+                hint: "Remove non-alphabet letters and group output",
+                type: "boolean",
+                value: true
+            },
+        ];
+    }
+
+    /**
+     * Helper - for ease of use rotors are specified as a single string; this
+     * method breaks the spec string into wiring and steps parts.
+     *
+     * @param {string} rotor - Rotor specification string.
+     * @param {number} i - For error messages, the number of this rotor.
+     * @returns {string[]}
+     */
+    parseRotorStr(rotor, i) {
+        if (rotor === "") {
+            throw new OperationError(`Rotor ${i} must be provided.`);
+        }
+        if (!rotor.includes("<")) {
+            return [rotor, ""];
+        }
+        return rotor.split("<", 2);
+    }
+
+    /**
+     * @param {string} input
+     * @param {Object[]} args
+     * @returns {string}
+     */
+    run(input, args) {
+        const reflectorstr = args[20];
+        const plugboardstr = args[21];
+        const typexKeyboard = args[22];
+        const removeOther = args[23];
+        const rotors = [];
+        for (let i=0; i<5; i++) {
+            const [rotorwiring, rotorsteps] = this.parseRotorStr(args[i*4]);
+            rotors.push(new Rotor(rotorwiring, rotorsteps, args[i*4 + 1], args[i*4+2], args[i*4+3]));
+        }
+        // Rotors are handled in reverse
+        rotors.reverse();
+        const reflector = new Reflector(reflectorstr);
+        let plugboardstrMod = plugboardstr;
+        if (plugboardstrMod === "") {
+            plugboardstrMod = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
+        }
+        const plugboard = new Plugboard(plugboardstrMod);
+        if (removeOther) {
+            if (typexKeyboard === "Encrypt") {
+                input = input.replace(/[^A-Za-z0-9 /%£()',.-]/g, "");
+            } else {
+                input = input.replace(/[^A-Za-z]/g, "");
+            }
+        }
+        const typex = new TypexMachine(rotors, reflector, plugboard, typexKeyboard);
+        let result = typex.crypt(input);
+        if (removeOther && typexKeyboard !== "Decrypt") {
+            // Five character cipher groups is traditional
+            result = result.replace(/([A-Z]{5})(?!$)/g, "$1 ");
+        }
+        return result;
+    }
+
+    /**
+     * Highlight Typex
+     * This is only possible if we're passing through non-alphabet characters.
+     *
+     * @param {Object[]} pos
+     * @param {number} pos[].start
+     * @param {number} pos[].end
+     * @param {Object[]} args
+     * @returns {Object[]} pos
+     */
+    highlight(pos, args) {
+        if (args[18] === false) {
+            return pos;
+        }
+    }
+
+    /**
+     * Highlight Typex in reverse
+     *
+     * @param {Object[]} pos
+     * @param {number} pos[].start
+     * @param {number} pos[].end
+     * @param {Object[]} args
+     * @returns {Object[]} pos
+     */
+    highlightReverse(pos, args) {
+        if (args[18] === false) {
+            return pos;
+        }
+    }
+
+}
+
+export default Typex;

src/core/operations/UnescapeString.mjs

@@ -20,7 +20,7 @@ class UnescapeString extends Operation {
 
         this.name = "Unescape string";
         this.module = "Default";
-        this.description = "Unescapes characters in a string that have been escaped. For example, <code>Don\\'t stop me now</code> becomes <code>Don't stop me now</code>.<br><br>Supports the following escape sequences:<ul><li><code>\\n</code> (Line feed/newline)</li><li><code>\\r</code> (Carriage return)</li><li><code>\\t</code> (Horizontal tab)</li><li><code>\\b</code> (Backspace)</li><li><code>\\f</code> (Form feed)</li><li><code>\\xnn</code> (Hex, where n is 0-f)</li><li><code>\\\\</code> (Backslash)</li><li><code>\\'</code> (Single quote)</li><li><code>\\&quot;</code> (Double quote)</li><li><code>\\unnnn</code> (Unicode character)</li><li><code>\\u{nnnnnn}</code> (Unicode code point)</li></ul>";
+        this.description = "Unescapes characters in a string that have been escaped. For example, <code>Don\\'t stop me now</code> becomes <code>Don't stop me now</code>.<br><br>Supports the following escape sequences:<ul><li><code>\\n</code> (Line feed/newline)</li><li><code>\\r</code> (Carriage return)</li><li><code>\\t</code> (Horizontal tab)</li><li><code>\\b</code> (Backspace)</li><li><code>\\f</code> (Form feed)</li><li><code>\\nnn</code> (Octal, where n is 0-7)</li><li><code>\\xnn</code> (Hex, where n is 0-f)</li><li><code>\\\\</code> (Backslash)</li><li><code>\\'</code> (Single quote)</li><li><code>\\&quot;</code> (Double quote)</li><li><code>\\unnnn</code> (Unicode character)</li><li><code>\\u{nnnnnn}</code> (Unicode code point)</li></ul>";
         this.infoURL = "https://wikipedia.org/wiki/Escape_sequence";
         this.inputType = "string";
         this.outputType = "string";

src/core/operations/VarIntDecode.mjs

@@ -0,0 +1,46 @@
+/**
+ * @author GCHQ Contributor [3]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import Protobuf from "../lib/Protobuf";
+
+/**
+ * VarInt Decode operation
+ */
+class VarIntDecode extends Operation {
+
+    /**
+     * VarIntDecode constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "VarInt Decode";
+        this.module = "Default";
+        this.description = "Decodes a VarInt encoded integer. VarInt is an efficient way of encoding variable length integers and is commonly used with Protobuf.";
+        this.infoURL = "https://developers.google.com/protocol-buffers/docs/encoding#varints";
+        this.inputType = "byteArray";
+        this.outputType = "number";
+        this.args = [];
+    }
+
+    /**
+     * @param {byteArray} input
+     * @param {Object[]} args
+     * @returns {number}
+     */
+    run(input, args) {
+        try {
+            return Protobuf.varIntDecode(input);
+        } catch (err) {
+            throw new OperationError(err);
+        }
+    }
+
+}
+
+export default VarIntDecode;

src/core/operations/VarIntEncode.mjs

@@ -0,0 +1,46 @@
+/**
+ * @author GCHQ Contributor [3]
+ * @copyright Crown Copyright 2019
+ * @license Apache-2.0
+ */
+
+import Operation from "../Operation";
+import OperationError from "../errors/OperationError";
+import Protobuf from "../lib/Protobuf";
+
+/**
+ * VarInt Encode operation
+ */
+class VarIntEncode extends Operation {
+
+    /**
+     * VarIntEncode constructor
+     */
+    constructor() {
+        super();
+
+        this.name = "VarInt Encode";
+        this.module = "Default";
+        this.description = "Encodes a Vn integer as a VarInt. VarInt is an efficient way of encoding variable length integers and is commonly used with Protobuf.";
+        this.infoURL = "https://developers.google.com/protocol-buffers/docs/encoding#varints";
+        this.inputType = "number";
+        this.outputType = "byteArray";
+        this.args = [];
+    }
+
+    /**
+     * @param {number} input
+     * @param {Object[]} args
+     * @returns {byteArray}
+     */
+    run(input, args) {
+        try {
+            return Protobuf.varIntEncode(input);
+        } catch (err) {
+            throw new OperationError(err);
+        }
+    }
+
+}
+
+export default VarIntEncode;