Update the README.

.drone.yaml

@@ -5,6 +5,42 @@ name: default
 steps:
   - name: test
     image: clojure:temurin-11-lein-2.10.0-alpine
+    volumes:
+      - name: package_cache
+        path: /root/.m2/
     commands:
       - lein test
 
+  - name: build
+    image: clojure:temurin-11-lein-2.10.0-alpine
+    volumes:
+      - name: package_cache
+        path: /root/.m2/
+    commands:
+      - lein uberjar
+    when:
+      event: tag
+
+  - name: gitea_release
+    image: plugins/gitea-release
+    settings:
+      api_key:
+        from_secret: API_KEY
+      base_url:
+        from_secret: BASE_URL
+      files:
+        - target/uberjar/*.jar
+      checksum:
+        - md5
+        - sha1
+        - sha256
+        - sha512
+        - adler32
+        - crc32
+    when:
+      event: tag
+
+volumes:
+  - name: package_cache
+    temp: {}
+

.gitlab-ci.yml

@@ -0,0 +1,10 @@
+image: clojure:temurin-11-lein-2.10.0-alpine
+
+stages:
+  - test
+
+unit tests:
+  stage: test
+  script:
+    - lein test
+

CHANGELOG.md

@@ -0,0 +1,362 @@
+# Change Log
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.9.15] - 2023-11-26
+
+### Changed
+- Update the CHANGELOG.
+- Update the version.
+- Update the README.
+
+## [0.9.14] - 2023-11-26
+
+### Added
+- Add analyzer for the simple substitution cipher.
+- Add the analyzer options and their actions for the simple substiotution.
+
+## [0.9.13] - 2023-11-26
+
+### Fixed
+- Fix the test name.
+
+## [0.9.12] - 2023-11-20
+
+### Changed
+- Update the CHANGELOG.
+- Update the version.
+- Update the README.
+
+## [0.9.11] - 2023-11-14
+
+### Added
+- Add the function that return all key combinations for a possible key vector.
+
+### Changed
+- Rename the function from get-possible-keys to get-all-combinations-for-blocks.
+
+## [0.9.10] - 2023-11-13
+
+### Added
+- Add a function to get all permutations for a block.
+
+## [0.9.9] - 2023-11-12
+
+### Added
+- Add a function to convert a count map to a reversed map.
+- Add a function to get the ordered sequence that can form a key.
+
+## [0.9.8] - 2023-11-11
+
+### Added
+- Add functions to get possible keys.
+
+## [0.9.7] - 2023-11-03
+
+### Added
+- Add the default frequency factory.
+
+## [0.9.6] - 2023-11-01
+
+### Added
+- Add int-string? to check if a string is a number.
+- Add key? to check if a string is a gamma key.
+- Add key validation for Caesar and Gamma ciphers.
+
+### Changed
+- Rename unsigned-int? to unsigned-int-string?
+
+## [0.9.5] - 2023-10-31
+## [0.9.5] - 2023-10-31
+
+### Added
+- Add the option for the gamma cipher.
+
+## [0.9.4] - 2023-10-31
+
+### Fixed
+- Fix the key parsing in the gamma actions.
+
+## [0.9.3] - 2023-10-31
+
+### Added
+- Add the action of encryption for the gamma cipher.
+- Add the action of decryption for the gamma cipher.
+
+## [0.9.2] - 2023-10-29
+
+### Added
+- Add a function to encrypt a message with the gamma cipher.
+- Add a function to decrypt a message with the gamma cipher.
+
+## [0.9.1] - 2023-10-28
+
+### Changed
+- Refactor the simple substitute to use the decrypt-by-table function. 
+
+## [0.9.0] - 2023-10-27
+
+### Added
+- Add the gamma generator.
+- Add the functions to encrypt and decrypt with the gamma cipher.
+
+## [0.8.5] - 2023-10-25
+
+### Added
+- Add the main for the cli module.
+
+## [0.8.4] - 2023-10-24
+
+### Changed
+- Update the simple substitution cipher to split the decrypt-message.
+
+## [0.8.3] - 2023-10-24
+
+### Added
+- Add functions to make a frequency map.
+
+## [0.8.2] - 2023-10-23
+
+### Added
+- Add a function to invert the table in a decoded json.
+- Add the parser to parse the string as an integer if it's needed.
+- Add the simple substitution cipher.
+
+## [0.8.1] - 2023-10-22
+
+### Added
+- Add a generator for the sorted substitution table.
+- Add the parsers to parse keys.
+
+### Changed
+- Update the simple substitution cipher to split the functions.
+
+## [0.8.0] - 2023-10-21
+
+### Added
+- Add the simple substitution cipher.
+
+## [0.7.2] - 2023-10-21
+
+### Changed
+- Update the CHANGELOG.
+- Update the version.
+- Update the README.
+- Update the CI/CD configuration to publish the artifacts to the release.
+- Update the diffs in the CHANGELOG.
+
+## [0.7.1] - 2023-10-20
+
+### Removed
+- Remove the test for FrequencyAnalyzer.
+- Remove the option for FrequencyAnalyzer.
+
+## [0.7.0] - 2023-10-20
+
+### Changed
+- Refactor to move actions to separated files.
+
+## [0.6.3] - 2023-10-14
+
+### Added
+- Add the IsNonsense interface for FrequencyAnalyzer.
+
+### Changed
+- Update the frequency analyzer.
+
+## [0.6.2] - 2023-10-14
+
+### Added
+- Add the analyzer options and their actions.
+- Add the available ciphers and analyzer for the help.
+- Add validations to check if a cipher or an analyzer is available.
+
+### Changed
+- Refactor to move options to a separated file.
+
+## [0.6.1] - 2023-10-13
+
+### Added
+- Add the function to make a frequency string from a map.
+
+### Fixed
+- Fix the bug that the default language symbols override the symbols.
+
+### Changed
+- Update the FrequencyAnalyzer to use the frequency string instead.
+
+## [0.6.0] - 2023-10-12
+
+### Fixed
+- Fix the typo "frequences" to frequencies.
+
+### Changed
+- Refactor the project structure.
+
+## [0.5.5] - 2023-10-09
+
+### Added
+- Add the Gitlab CI/CD configuration.
+
+## [0.5.4] - 2023-10-05
+
+### Added
+- Add the java source path.
+- Add the Caesar decrypted interface for Java.
+- Add a frequency analyzer as a stub.
+- Add the clojure wrapper for the frequency analizer and its test.
+
+## [0.5.3] - 2023-10-05
+
+### Added
+- Add the CHANGELOG.
+
+## [0.5.2] - 2023-10-02
+
+### Fixed
+- Fix checking for file existence only when the options are set.
+- Fix writing to a file only when the option is set.
+
+## [0.5.1] - 2023-09-28
+
+### Added
+- Add the output option to save into a file.
+- Add the file errors to prevent using an invalid file path.
+
+## [0.5.0] - 2023-09-22
+
+### Changed
+- Update symbol defaults, factories to have only lower alphabets.
+- Update the Caesar to be case-insensitive and skip unknown symbols.
+- Update Caesar Analyzers to be case-insensitive and testable.
+
+## [0.4.3] - 2023-09-21
+
+### Added
+- Add the language option for symbols.
+
+### Changed
+- Update the CLI to have separated actions and an option initializer.
+
+## [0.4.2] - 2023-09-18
+
+### Added
+- Add tests for the cipher-analyzers module.
+
+### Changed
+- Rename the cipher_analyzer module to cipher-analyzers.
+
+## [0.4.1] - 2023-09-17
+
+### Added
+- Add symbol factories for punctuation, space, defaults symbols.
+- Add the action-type to distinguish the actions.
+- Add the symbol option and its default.
+- Add the cracking option.
+
+### Changed
+- Rename the language_analyzer module to language-analyzer.
+- Update the nonsense for the is-nonsense? test.
+- Rename the symbol_frequences module to symbol-frequences.
+
+## [0.4.0] - 2023-09-15
+
+### Added
+- Add Chi-squared Statistic function to analyze texts.
+- Add the caesar-analyzers to get the plaintext from a ciphertext.
+
+## [0.3.5] - 2023-09-14
+
+### Added
+- Add the frequences of symbols as defaults.
+
+## [0.3.4] - 2023-09-13
+
+### Added
+- Add a simple language analyzers.
+
+## [0.3.3] - 2023-09-12
+
+### Added
+- Add an option to read a message from a file.
+
+## [0.3.2] - 2023-09-11
+
+### Added
+- Add the CI/CD configuration.
+
+## [0.3.1] - 2023-09-11
+
+### Added
+- Add factories for symbols.
+- Add tests for factories.
+
+## [0.3.0] - 2023-09-10
+
+### Added
+- Add a simple cli interface.
+
+## [0.2.0] - 2023-09-09
+
+### Added
+- Add a implementation of Caesar cipher.
+
+## [0.1.0] - 2023-09-09
+
+### Added
+- Project initialization.
+
+[Unreleased]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.15...main?from_project_id=50218541&straight=false
+[0.9.15]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.14...0.0.9.15?from_project_id=50218541&straight=false
+[0.9.14]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.13...0.0.9.14?from_project_id=50218541&straight=false
+[0.9.13]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.12...0.0.9.13?from_project_id=50218541&straight=false
+[0.9.12]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.11...0.0.9.12?from_project_id=50218541&straight=false
+[0.9.11]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.10...0.0.9.11?from_project_id=50218541&straight=false
+[0.9.10]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.9...0.9.10?from_project_id=50218541&straight=false
+[0.9.9]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.8...0.9.9?from_project_id=50218541&straight=false
+[0.9.8]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.7...0.9.8?from_project_id=50218541&straight=false
+[0.9.7]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.6...0.9.7?from_project_id=50218541&straight=false
+[0.9.6]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.5...0.9.6?from_project_id=50218541&straight=false
+[0.9.5]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.4...0.9.5?from_project_id=50218541&straight=false
+[0.9.4]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.3...0.9.4?from_project_id=50218541&straight=false
+[0.9.3]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.2...0.9.3?from_project_id=50218541&straight=false
+[0.9.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.1...0.9.2?from_project_id=50218541&straight=false
+[0.9.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.9.0...0.9.1?from_project_id=50218541&straight=false
+[0.9.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.8.5...0.9.0?from_project_id=50218541&straight=false
+[0.8.5]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.8.4...0.8.5?from_project_id=50218541&straight=false
+[0.8.4]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.8.3...0.8.4?from_project_id=50218541&straight=false
+[0.8.3]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.8.2...0.8.3?from_project_id=50218541&straight=false
+[0.8.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.8.1...0.8.2?from_project_id=50218541&straight=false
+[0.8.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.8.0...0.8.1?from_project_id=50218541&straight=false
+[0.8.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.7.2...0.8.0?from_project_id=50218541&straight=false
+[0.7.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.7.1...0.7.2?from_project_id=50218541&straight=false
+[0.7.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.7.0...0.7.1?from_project_id=50218541&straight=false
+[0.7.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.6.3...0.7.0?from_project_id=50218541&straight=false
+[0.6.3]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.6.2...0.6.3?from_project_id=50218541&straight=false
+[0.6.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.6.1...0.6.2?from_project_id=50218541&straight=false
+[0.6.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.6.0...0.6.1?from_project_id=50218541&straight=false
+[0.6.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.5.5...0.6.0?from_project_id=50218541&straight=false
+[0.5.5]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.5.4...0.5.5?from_project_id=50218541&straight=false
+[0.5.4]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.5.3...0.5.4?from_project_id=50218541&straight=false
+[0.5.3]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.5.2...0.5.3?from_project_id=50218541&straight=false
+[0.5.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.5.1...0.5.2?from_project_id=50218541&straight=false
+[0.5.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.5.0...0.5.1?from_project_id=50218541&straight=false
+[0.5.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.4.3...0.5.0?from_project_id=50218541&straight=false
+[0.4.3]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.4.2...0.4.3?from_project_id=50218541&straight=false
+[0.4.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.4.1...0.4.2?from_project_id=50218541&straight=false
+[0.4.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.4.0...0.4.1?from_project_id=50218541&straight=false
+[0.4.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.3.5...0.4.0?from_project_id=50218541&straight=false
+[0.3.5]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.3.4...0.3.5?from_project_id=50218541&straight=false
+[0.3.4]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.3.3...0.3.4?from_project_id=50218541&straight=false
+[0.3.3]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.3.2...0.3.3?from_project_id=50218541&straight=false
+[0.3.2]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.3.1...0.3.2?from_project_id=50218541&straight=false
+[0.3.1]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.3.0...0.3.1?from_project_id=50218541&straight=false
+[0.3.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.2.0...0.3.0?from_project_id=50218541&straight=false
+[0.2.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/compare/0.1.0...0.2.0?from_project_id=50218541&straight=false
+[0.1.0]: https://gitlab.com/KKlochko/cipher-analytical-machine/-/commit/a7a715b94276fc8f46fb6a44139636d27b551599
+

README.md

@@ -11,10 +11,12 @@ Download from https://gitlab.com/KKlochko/cipher-analytical-machine.
 You need install java, before run the application.
 Run the application with a command:
 
-    $ java -jar cipher-analytical-machine-0.1.0-standalone.jar [args]
+    $ java -jar cipher-analytical-machine-VERSION-standalone.jar [args]
+    $ java -jar cipher-analytical-machine-0.9.15-standalone.jar [args]
 
 ## License
 
 Copyright © 2023 Kostiantyn Klochko
 
 Under the GNU Lesser General Public License v3.0 or later.
+

project.clj

@@ -1,4 +1,4 @@
-(defproject cipher-analytical-machine "0.1.0-SNAPSHOT"
+(defproject cipher-analytical-machine "0.9.15"
   :description "A program helps to learn how ciphers works."
   :url "https://gitlab.com/KKlochko/cipher-analytical-machine"
   :license {:name "LGPL"
@@ -6,8 +6,11 @@
   :dependencies [[org.clojure/clojure "1.11.1"]
                  [org.clojure/tools.cli "1.0.219"]
                  [org.apache.tika/tika-core "1.28.5"]
-                 [org.apache.tika/tika-langdetect "1.28.5"]]
+                 [org.apache.tika/tika-langdetect "1.28.5"]
+                 [cheshire "5.12.0"]
+                 [org.clojure/math.combinatorics "0.2.0"]]
   :main ^:skip-aot cipher-analytical-machine.core
+  :java-source-paths ["src/main/java"]
   :target-path "target/%s"
   :profiles {:uberjar {:aot :all
                        :jvm-opts ["-Dclojure.compiler.direct-linking=true"]}})

src/cipher_analytical_machine/analyzers/analyzers.clj

@@ -0,0 +1,67 @@
+(ns cipher-analytical-machine.analyzers.analyzers
+  (:require [clojure.string :as cs])
+  (:gen-class))
+
+(defn count-characters
+  "Count the letters and return map."
+  [text]
+  (reduce
+   (fn [acc val]
+     (assoc acc val
+            (inc (get acc val 0))))
+   {} text))
+
+(defn reverse-count-characters
+  "Convert a map of pairs to a map where the characters grouped by the count and a count is the key."
+  [count-map]
+  (reduce
+   (fn [acc [symbol count]]
+     (->> (conj (get acc count []) symbol)
+          (into [])
+          (assoc acc count)))
+   {} count-map))
+
+(defn chi-squared-letter-statistic
+  "To calculate the frequency distribution of a letter."
+  [letter-count letter-frequence length-text]
+  (let [letter-frequence (* length-text letter-frequence)]
+    (/ (Math/pow
+        (- letter-count letter-frequence) 2)
+       letter-frequence)))
+
+(defn chi-squared-statistic
+  "To calculate the frequency distribution of a language. More detail about the algorithm here: http://practicalcryptography.com/cryptanalysis/text-characterisation/chi-squared-statistic/"
+  [text letter-frequencies]
+  (let [length-text (count text)
+        letter-counts (count-characters (cs/lower-case text))]
+    ;letter-counts
+    (reduce
+     (fn [acc [char count]]
+       (+ acc
+          (if (contains? letter-frequencies char)
+            (chi-squared-letter-statistic count
+                                          (get letter-frequencies char)
+                                          length-text)
+            0)))
+            0
+            letter-counts)))
+
+(defn sort-map-by-count
+  "Return a list of pairs from a map of pairs where a pair is a character and its count. The order is descending."
+  [count-map]
+  (->> count-map
+       (reduce (fn [acc [char count]] (conj acc [char count])) [])
+       (sort-by #(- (second %)))))
+
+(defn table-to-string
+  "Return the string from a frequency table."
+  [table]
+  (->> (map first table)
+       (apply str)))
+
+(defn symbol-frequency-table
+  "Return a table where pairs is a symbol from a cipher text and its value which is a symbol from frequency table."
+  [cipher-table frequency-table]
+  (zipmap (table-to-string (sort-map-by-count cipher-table))
+          (table-to-string (sort-map-by-count frequency-table))))
+

src/cipher_analytical_machine/analyzers/caesar.clj

@@ -0,0 +1,64 @@
+(ns cipher-analytical-machine.analyzers.caesar
+  (:require [cipher-analytical-machine.ciphers.caesar :as caesar]
+            [clojure.string :as cs]
+            [cipher-analytical-machine.analyzers.language :as language]
+            [cipher-analytical-machine.analyzers.analyzers :as ca])
+  (:import [cipher_analytical_machine.ciphers.caesar Decrypted]
+           [cipher_analytical_machine.analyzers.caesar IsNonsense]
+           [cipher_analytical_machine.analyzers.caesar FrequencyAnalyzer])
+  (:gen-class))
+
+(defn get-all-texts
+  "Return a list of pairs which have a key and a second posible plaintext."
+  [ciphertext symbols]
+  (let [keys (range (count symbols))]
+    (reduce
+     (fn [acc key]
+       (conj acc [key (caesar/decrypt-message ciphertext key symbols)]))
+     '() keys)))
+
+(defn get-all-scores
+  "For pairs (key, plaintext) finds scores and return list of pairs [key, score]."
+  [letter-frequencies pairs]
+  (map (fn [[key text]]
+         [key (ca/chi-squared-statistic text letter-frequencies)])
+       pairs))
+
+(defn get-min-score-pair
+  "For pairs (key, plaintext) finds scores and return list of pairs [key, score]."
+  [pairs]
+  (reduce
+   (fn [[key value] [new-key new-value]]
+     (if (> value new-value) [new-key new-value]
+         [key value]))
+   [0 Double/MAX_VALUE]
+   pairs))
+
+(defn get-key
+  "To find the key with frequencies of letters."
+  [ciphertext symbols letter-frequencies]
+  (->> (get-all-texts ciphertext symbols)
+       (get-all-scores letter-frequencies)
+       (get-min-score-pair)
+       (first)))
+
+(defn get-plaintext
+  "Return the plaintext from a ciphertext. The function is case-insensitive."
+  [ciphertext symbols letter-frequencies]
+  (let [ciphertext (cs/lower-case ciphertext)]
+    (caesar/decrypt-message ciphertext
+                            (get-key ciphertext symbols letter-frequencies)
+                            symbols)))
+
+(defn frequency-analizer-get-plaintext
+  "Return the plaintext from a ciphertext using simple analizer. The function is case-insensitive."
+  [ciphertext symbols letter-frequencies-string language-code]
+  (let [decrypt (reify Decrypted
+                  (decrypt [this message key symbols]
+                    (caesar/decrypt-message message key symbols)))
+        is-nonsense (reify IsNonsense
+                  (isNonsense [this message]
+                    (language/is-nonsense? message language-code)))]
+    (-> (new FrequencyAnalyzer ciphertext symbols letter-frequencies-string decrypt is-nonsense)
+        .crack)))
+

src/cipher_analytical_machine/analyzers/language.clj

@@ -1,4 +1,4 @@
-(ns cipher-analytical-machine.language-analyzer
+(ns cipher-analytical-machine.analyzers.language
   (:import [org.apache.tika.language LanguageIdentifier])
   (:gen-class))
 

src/cipher_analytical_machine/analyzers/simple_substitution.clj

@@ -0,0 +1,78 @@
+(ns cipher-analytical-machine.analyzers.simple-substitution
+  (:require [clojure.string :as cs]
+            [clojure.math.combinatorics :as comb]
+            [cipher-analytical-machine.symbols.frequencies :as frequencies]
+            [cipher-analytical-machine.ciphers.simple-substitution :as ss]
+            [cipher-analytical-machine.analyzers.analyzers :as analyzers]
+            [cipher-analytical-machine.analyzers.analyzers :as ca]
+            [cipher-analytical-machine.analyzers.caesar :as caesar])
+  (:gen-class))
+
+(defn get-possible-key-vector
+  "Convert a possible key map to a vector of possible keys. For example, if you have a map: {\\a [\\a \\b \\c] \\b [\\b \\c] \\c [\\a \\c]}, then the vector is [[\\a \\b \\c] [\\b \\c] [\\a \\c]]."
+  [possible-key-map symbols]
+  (reduce
+   (fn [acc el]
+     (conj acc (get possible-key-map el)))
+   [] symbols))
+
+(defn get-possible-key-vector-from-reversed-count-map
+  "Convert a reversed count map to a vector. Example, from {2 [\\a \\b] 1 [\\d] 3 [\\e]} to [[\\e] [\\a \\b] [\\d]])."
+  [reversed-count-map]
+  (->>  reversed-count-map
+        (into [])
+        (sort-by #(- (first %)))
+        (map second)
+        (into [])))
+
+(defn get-all-permutation-for-block
+  "Return a vector for all possible blocks that can be made from a vector of symbols."
+  [symbols]
+  (->> (comb/permutations symbols)
+       (map cs/join)
+       (into [])))
+
+(defn get-all-combinations-for-blocks
+  "Return the all combination of blocks in a possible key vector. For example, if you have a map: {\\a [\\a \"bf\" \\c] \\b [\"bf\" \\c] \\c [\\a \\c]}, then the vector is [[\\a \"bf\" \\c] [\"bf\" \\c] [\\a \\c]] and keys (\"abfa\" \"abfc\" ...)."
+  [possible-key-vector]
+  (->> (apply comb/cartesian-product possible-key-vector)
+       (map cs/join)))
+
+(defn get-possible-key-combinations
+  "Return possible keys for a possible key vector. For example, if you have a map: {\\a [\\a \\b \\c] \\e [\\f \\g] \\c [\\a \\c]}, then the keys are (\"abcefg\" \"abcegf\" ...)."
+  [possible-key-vector]
+  (->> (map get-all-permutation-for-block possible-key-vector)
+       (get-all-combinations-for-blocks)))
+
+(defn get-possible-keys
+  "Return keys for a cipher text. A key is a map {\\a \\e, ...} to decrypt a text."
+  [cipher-text frequency-table]
+  (let [freq-symbol-str (frequencies/map-to-string frequency-table) ; "etaoinsrhldcumfpgwybvkxjqz"
+        char-map (-> (analyzers/count-characters cipher-text)
+                     (analyzers/reverse-count-characters))]
+    (map (fn [comb] (zipmap comb freq-symbol-str))
+         (-> (get-possible-key-vector-from-reversed-count-map char-map)
+             (get-possible-key-combinations)))))
+
+
+(defn get-plain-data
+  "Return the plain data (score, text, key) from a ciphertext (a string of character). The function is case-insensitive."
+  [cipher-text letter-frequencies]
+  (let [cipher-text (cs/lower-case cipher-text)
+        keys (get-possible-keys cipher-text letter-frequencies)]
+    (->> (map (fn [key] [(ss/decrypt-message-by-symbol-table key cipher-text) key]) keys)
+         (map (fn [[text key]] [(ca/chi-squared-statistic text letter-frequencies) text key]))
+         )))
+
+(defn get-plaintext-and-key
+  "Return the possible plaintext from a ciphertext that encoded with numbers. The function is case-insensitive."
+  [cipher-text letter-frequencies]
+  (let [maybe-key   (->> (frequencies/map-to-string letter-frequencies)
+                         (ss/generate-sorted-substitution-table))
+        cipher-text (->> (cs/split cipher-text #",")
+                         (map #(Integer/parseInt %))
+                         (ss/decrypt-message-by-symbol-table maybe-key))]
+
+    (->> (get-plain-data cipher-text letter-frequencies)
+         (map (fn [el] (drop 1 el)) ))))
+

src/cipher_analytical_machine/caesar_analyzers.clj

@@ -1,48 +0,0 @@
-(ns cipher-analytical-machine.caesar-analyzers
-  (:require [cipher-analytical-machine.caesar :as caesar]
-            [clojure.string :as cs]
-            [cipher-analytical-machine.cipher-analyzers :as ca])
-  (:gen-class))
-
-(defn get-all-texts
-  "Return a list of pairs which have a key and a second posible plaintext."
-  [ciphertext symbols]
-  (let [keys (range (count symbols))]
-    (reduce
-     (fn [acc key]
-       (conj acc [key (caesar/decrypt-message ciphertext key symbols)]))
-     '() keys)))
-
-(defn get-all-scores
-  "For pairs (key, plaintext) finds scores and return list of pairs [key, score]."
-  [letter-frequences pairs]
-  (map (fn [[key text]]
-         [key (ca/chi-squared-statistic text letter-frequences)])
-       pairs))
-
-(defn get-min-score-pair
-  "For pairs (key, plaintext) finds scores and return list of pairs [key, score]."
-  [pairs]
-  (reduce
-   (fn [[key value] [new-key new-value]]
-     (if (> value new-value) [new-key new-value]
-         [key value]))
-   [0 Double/MAX_VALUE]
-   pairs))
-
-(defn get-key
-  "To find the key with frequencies of letters."
-  [ciphertext symbols letter-frequences]
-  (->> (get-all-texts ciphertext symbols)
-       (get-all-scores letter-frequences)
-       (get-min-score-pair)
-       (first)))
-
-(defn get-plaintext
-  "Return the plaintext from a ciphertext. The function is case-insensitive."
-  [ciphertext symbols letter-frequences]
-  (let [ciphertext (cs/lower-case ciphertext)]
-    (caesar/decrypt-message ciphertext
-                            (get-key ciphertext symbols letter-frequences)
-                            symbols)))
-

src/cipher_analytical_machine/cipher_analyzers.clj

@@ -1,38 +0,0 @@
-(ns cipher-analytical-machine.cipher-analyzers
-  (:require [clojure.string :as cs])
-  (:gen-class))
-
-(defn count-characters
-  "Count the letters and return map."
-  [text]
-  (reduce
-   (fn [acc val]
-     (assoc acc val
-            (inc (get acc val 0))))
-   {} text))
-
-(defn chi-squared-letter-statistic
-  "To calculate the frequency distribution of a letter."
-  [letter-count letter-frequence length-text]
-  (let [letter-frequence (* length-text letter-frequence)]
-    (/ (Math/pow
-        (- letter-count letter-frequence) 2)
-       letter-frequence)))
-
-(defn chi-squared-statistic
-  "To calculate the frequency distribution of a language. More detail about the algorithm here: http://practicalcryptography.com/cryptanalysis/text-characterisation/chi-squared-statistic/"
-  [text letter-frequences]
-  (let [length-text (count text)
-        letter-counts (count-characters (cs/lower-case text))]
-    ;letter-counts
-    (reduce
-     (fn [acc [char count]]
-       (+ acc
-          (if (contains? letter-frequences char)
-            (chi-squared-letter-statistic count
-                                          (get letter-frequences char)
-                                          length-text)
-            0)))
-            0
-            letter-counts)))
-

src/cipher_analytical_machine/ciphers/caesar.clj

@@ -1,4 +1,4 @@
-(ns cipher-analytical-machine.caesar
+(ns cipher-analytical-machine.ciphers.caesar
   (:require [clojure.string :as cs])
   (:gen-class))
 

src/cipher_analytical_machine/ciphers/gamma.clj

@@ -0,0 +1,78 @@
+(ns cipher-analytical-machine.ciphers.gamma
+  (:require
+   [clojure.set :as set]
+   [clojure.string :as cs]
+   [cipher-analytical-machine.ciphers.simple-substitution :as ss])
+  (:gen-class))
+
+(defn add-mod
+  [f s module]
+  (-> (+ f s)
+      (mod module)))
+
+(defn generate-seq
+  "Generate a lazy sequence for a key (a b c)."
+  [a b c module]
+  ((fn build-seq [a b c]
+     (lazy-seq (cons a (build-seq b c (add-mod a c module))))) a b c))
+
+(defn generate-gamma-seq
+  "Generate the gamma seq from a sequence."
+  [acc seq module]
+  (if (= (second seq) nil) acc
+    (generate-gamma-seq
+     (conj acc (add-mod (first seq) (second seq) module))
+     (rest seq)
+     module)))
+
+(defn generate-gamma
+  "Generate the gamma from a key (a b c)."
+  [a b c module size]
+  (generate-gamma-seq []
+                      (->> (generate-seq a b c module)
+                           (take (inc size)))
+                      module))
+
+(defn encrypt-array
+  "Encrypt an array using the gamma cipher. The function is case-insensitive. The key is an array of three elements [a b c]. The array contains integer in range [0, module)."
+  [key module array]
+  (let [size (count array)
+        gamma (->> (apply conj [key module size])
+                   (apply generate-gamma))]
+    (->> gamma
+         (map vector array)
+         (map (fn [[a g]] (add-mod a g module))))))
+
+(defn encrypt-message
+  "Encrypt a message using the gamma cipher. The function is case-insensitive. The key is an array of three elements [a b c]. The array contains integer in range [0, module)."
+  [key symbols message]
+  (let [module (count symbols)
+        table (ss/generate-sorted-substitution-table symbols)]
+    (->> message
+         (ss/decrypt-by-table (set/map-invert table))
+         (encrypt-array key module)
+         (ss/decrypt-by-table table)
+         (cs/join))))
+
+(defn decrypt-array
+  "Decrypt an array using the gamma cipher. The function is case-insensitive. The key is an array of three elements [a b c]. The array contains integer in range [0, module)."
+  [key module array]
+  (let [size (count array)
+        gamma (->> (apply conj [key module size])
+                   (apply generate-gamma))]
+    (->> gamma
+         (map -)
+         (map vector array)
+         (map (fn [[a g]] (add-mod a g module))))))
+
+(defn decrypt-message
+  "Decrypt a message using the gamma cipher. The function is case-insensitive. The key is an array of three elements [a b c]. The array contains integer in range [0, module)."
+  [key symbols message]
+  (let [module (count symbols)
+        table (ss/generate-sorted-substitution-table symbols)]
+    (->> message
+         (ss/decrypt-by-table (set/map-invert table))
+         (decrypt-array key module)
+         (ss/decrypt-by-table table)
+         (cs/join))))
+

src/cipher_analytical_machine/ciphers/simple_substitution.clj

@@ -0,0 +1,74 @@
+(ns cipher-analytical-machine.ciphers.simple-substitution
+  (:require [clojure.string :as cs]
+            [cipher-analytical-machine.ciphers.caesar :as caesar])
+  (:gen-class))
+
+(defn shuffled-numbers
+  "Generate the shuffled order for integer list."
+  [size]
+  (-> size
+      (take (range))
+      (shuffle)))
+
+(defn generate-substitution-table
+  "Generate the map (char, int) for the substittion."
+  [symbols]
+  (->> (count symbols)
+       (shuffled-numbers)
+       (zipmap symbols)))
+
+(defn generate-sorted-substitution-table
+  "Generate the map (char, int) for the substittion. BUT a value is the index of a symbol (from 0)."
+  [symbols]
+  (-> (count symbols)
+      (take (range))
+      (zipmap symbols)))
+
+(defn find-value-in-table
+  "It uses the substitution table to find the value of a char or a number."
+  [char substitution-table]
+  (get substitution-table char))
+
+(defn decrypt-by-table
+  "Decrypt a message by the substitution-table"
+  [substitution-table message]
+  (map (fn [char] (find-value-in-table char substitution-table)) message))
+
+(defn encrypt-message
+  "Encrypt a message using the simple substitution cipher. The function is case-insensitive. If a symbol isn't in the symbols list, then it will be removed."
+  [message substitution-table]
+  (->> message
+       (decrypt-by-table substitution-table)
+       (remove nil?)
+       (cs/join \,)))
+
+(defn encrypt-message-with-caesar
+  "Encrypt a message using the simple substitution cipher and the Caesar cipher. The function is case-insensitive. If a symbol isn't in the symbols list, then it will be removed."
+  [message key substitution-table symbols]
+  (-> message
+      (caesar/encrypt-message key symbols)
+      (encrypt-message substitution-table)))
+
+(defn decrypt-message-by-symbol-table
+  "Decrypt a message using the simple substitution cipher. The function is case-insensitive. The substitution-table must be (symbols, symbols)."
+  [substitution-table message]
+  (->> message
+       (decrypt-by-table substitution-table)
+       (remove nil?)
+       (cs/join)))
+
+(defn decrypt-message
+  "Decrypt a message using the simple substitution cipher. The function is case-insensitive. The substitution-table must be (int, symbols)."
+  [message substitution-table]
+  (let [message (cs/split message #",")]
+    (->> message
+         (map #(Integer/parseInt %))
+         (decrypt-message-by-symbol-table substitution-table))))
+
+(defn decrypt-message-with-caesar
+  "Decrypt a message using the simple substitution cipher and the Caesar cipher. The function is case-insensitive."
+  [message key substitution-table symbols]
+  (-> message
+      (decrypt-message substitution-table)
+      (caesar/decrypt-message key symbols)))
+

src/cipher_analytical_machine/cli/actions/cracking.clj

@@ -0,0 +1,45 @@
+(ns cipher-analytical-machine.cli.actions.cracking
+  (:require
+   [cipher-analytical-machine.analyzers.caesar :as caesar-analyzers]
+   [cipher-analytical-machine.analyzers.simple-substitution :as ss-analyzers]
+   [cipher-analytical-machine.symbols.frequencies :as symbol-frequencies])
+  (:gen-class))
+
+(defn cracking-caesar
+  [options arguments]
+  (let [analyzer (:analyzer options)
+        message (:message options)
+        symbols (:symbols options)
+        frequencies (-> (get options :language "en")
+                        (symbol-frequencies/default-frequency-factory))]
+    (cond
+      (= analyzer "Chi^2")
+      (caesar-analyzers/get-plaintext message symbols frequencies)
+
+      :else
+      (caesar-analyzers/get-plaintext message symbols frequencies))))
+
+(defn cracking-simple-substitution-with-caesar
+  [options arguments]
+  (let [analyzer (:analyzer options)
+        message (:message options)
+        symbols (:symbols options)
+        frequencies (-> (get options :language "en")
+                        (symbol-frequencies/default-frequency-factory))]
+    (cond
+      (= analyzer "Chi^2")
+      (ss-analyzers/get-plaintext-and-key message frequencies)
+
+      :else
+      (ss-analyzers/get-plaintext-and-key message frequencies))))
+
+(defn cracking-actions
+  [options arguments action-type]
+  (let [cipher (:cipher options)]
+    (cond
+      (= cipher "Caesar")
+      (cracking-caesar options arguments)
+
+      (= cipher "Simple substitution and Caesar")
+      (cracking-simple-substitution-with-caesar options arguments))))
+

src/cipher_analytical_machine/cli/actions/cryptography.clj

@@ -0,0 +1,69 @@
+(ns cipher-analytical-machine.cli.actions.cryptography
+  (:require
+   [clojure.string :as cs]
+   [cipher-analytical-machine.ciphers.caesar :as caesar]
+   [cipher-analytical-machine.ciphers.simple-substitution :as ss]
+   [cipher-analytical-machine.ciphers.gamma :as gamma]
+   [cipher-analytical-machine.parsers.parsers :as ps]
+   [cipher-analytical-machine.parsers.simple-substitution :as pss])
+  (:gen-class))
+
+(defn caesar-actions
+  [options arguments action-type]
+  (let [message (:message options)
+        key (Integer/parseInt (:key options))
+        symbols (:symbols options)]
+    (cond
+      (= action-type :encrypt)
+      (caesar/encrypt-message message key symbols)
+
+      (= action-type :decrypt)
+      (caesar/decrypt-message message key symbols))))
+
+(defn simple-substitution-with-caesar-actions
+  [options arguments action-type]
+  (let [message (:message options)
+        key (:key options)
+        symbols (:symbols options)]
+    (cond
+      (= action-type :encrypt)
+      (let [data (pss/generate-table-or-decode-json key symbols)
+            key (ps/parse-unsigned-int (get data "key"))
+            substitution-table (get data "table")]
+        (println (pss/encode-key-and-substitution-table-to-json key substitution-table))
+        (ss/encrypt-message-with-caesar message key substitution-table symbols))
+
+      (= action-type :decrypt)
+      (let [data (-> (pss/decode-key-and-substitution-table-from-json key)
+                     (pss/invert-table-in-map))
+            key (get data "key")
+            substitution-table (get data "table")]
+        (ss/decrypt-message-with-caesar message key substitution-table symbols)))))
+
+(defn gamma-actions
+  [options arguments action-type]
+  (let [message (:message options)
+        key (->> (cs/split (:key options) #",")
+                 (map #(Integer/parseInt %))
+                 (into []))
+        symbols (:symbols options)]
+    (cond
+      (= action-type :encrypt)
+      (gamma/encrypt-message key symbols message)
+
+      (= action-type :decrypt)
+      (gamma/decrypt-message key symbols message))))
+
+(defn cryptography-actions
+  [options arguments action-type]
+  (let [cipher (:cipher options)]
+    (cond
+      (= cipher "Caesar")
+      (caesar-actions options arguments action-type)
+
+      (= cipher "Simple substitution and Caesar")
+      (simple-substitution-with-caesar-actions options arguments action-type)
+
+      (= cipher "Gamma")
+      (gamma-actions options arguments action-type))))
+

src/cipher_analytical_machine/cli/cli.clj

@@ -1,35 +1,16 @@
-(ns cipher-analytical-machine.cli
+(ns cipher-analytical-machine.cli.cli
   (:require
-   [cipher-analytical-machine.file :as file]
-   [cipher-analytical-machine.caesar :as caesar]
-   [cipher-analytical-machine.caesar-analyzers :as caesar-analyzers]
-   [cipher-analytical-machine.symbol-factories :as sf]
-   [cipher-analytical-machine.symbol-frequences :as symbol-frequences]
+   [cipher-analytical-machine.parsers.parsers :as ps]
+   [cipher-analytical-machine.parsers.gamma :as gamma-ps]
+   [cipher-analytical-machine.cli.file :as file]
+   [cipher-analytical-machine.symbols.factories :as sf]
+   [cipher-analytical-machine.cli.options :as options]
    [clojure.string :as cs]
+   [cipher-analytical-machine.cli.actions.cryptography :as cryptography]
+   [cipher-analytical-machine.cli.actions.cracking :as cracking]
    [clojure.tools.cli :refer [parse-opts]])
   (:gen-class))
 
-(def cipher-options
-  #{"Caesar"})
-
-(def language-options
-  #{"en", "uk"})
-
-(def cli-options
-  [["-m" "--message MESSAGE" "The message will be encrypted or decrypted."]
-   ["-M" "--message-file MESSAGE-FILE" "The file contains the message that will be encrypted or decrypted."]
-   ["-k" "--key KEY" "The key will be used to encrypt or decrypt."]
-   ["-c" "--cipher CIPHER" "The cipher will be used to encrypt or decrypt a message."
-    :default "Caesar"]
-   ["-e" "--encrypt" "Encrypt the message."]
-   ["-d" "--decrypt" "Decrypt the message."]
-   ["-s" "--symbols" "The string will be used as a set of symbols for a cipher."
-    :default (sf/default-symbol-factory "en")]
-   ["-l" "--language CODE" "The string will be used to set a default symbols for a cipher."
-    :validate [#(contains? language-options %) "Must be a code from the list: en, uk!!!"]]
-   ["-C" "--cracking" "Cracking the encrypted message."]
-   ["-h" "--help"]])
-
 (defn usage [options-summary]
   (->> ["This is cipher-analytical-machine. It can help you to learn how ciphers works."
         ""
@@ -37,6 +18,12 @@
         ""
         "Options:"
         options-summary
+        ""
+        "Available values"
+        ""
+        (options/get-available-cipher-options-as-string)
+        ""
+        (options/get-available-analyzers-options-as-string)
         ""]
        (cs/join \newline)))
 
@@ -54,7 +41,7 @@
   should exit (with an error message, and optional ok status), or a map
   indicating the action the program should take and the options provided."
   [args]
-  (let [{:keys [options arguments errors summary]} (parse-opts args cli-options)]
+  (let [{:keys [options arguments errors summary]} (parse-opts args options/cli-options)]
     (cond
       (:help options)
       {:exit-message (usage summary) :ok? true}
@@ -68,12 +55,39 @@
       (map-has-keys? options [:message, :message-file])
       {:exit-message (error-msg ["You can't use message and message-file options at the same time!!!"])}
 
+      (and (contains? options :message-file)
+           (file/is-file-not-exists? (:message-file options)))
+      {:exit-message (error-msg ["Please, check the path to the message file!!!"])}
+
+      (and (contains? options :output-file)
+           (file/is-file-exists? (:output-file options)))
+      {:exit-message (error-msg ["Please, choose another file!!! Overwriting was prevented!!!"])}
+
+      (false? (contains? options/cipher-options (:cipher options)))
+      {:exit-message (error-msg ["Please, choose an available cipher!!!\n"
+                                 (options/get-available-cipher-options-as-string)])}
+
+      (and (map-has-keys? options [:cipher, :cracking, :analyzer])
+           (false? (contains?
+             (get options/analyzers-options (:cipher options)) (:analyzer options))))
+      {:exit-message (error-msg ["Please, choose an available analyzer!!!\n"
+                                 (options/get-available-analyzers-options-as-string)])}
+
       (and (map-has-keys? options [:cipher, :key])
            (or (contains? options :message)
                (contains? options :message-file))
            (or (contains? options :encrypt)
                (contains? options :decrypt)))
       (cond
+        (and (= (:cipher options) "Caesar")
+             (false? (ps/int-string? (:key options))))
+        {:exit-message (error-msg ["Please, use the key format: [+-](integer)!!! Example: 10, +9, -7."])}
+
+        (and (= (:cipher options) "Gamma")
+             (false? (gamma-ps/key? (:key options))))
+        {:exit-message (error-msg ["Please, use the key format: [+-](integer),[+-](integer),[+-](integer) !!! Example: 10,+9,-7."])}
+
+
         (contains? options :encrypt)
         {:options options :arguments arguments :action-type :encrypt}
 
@@ -113,8 +127,10 @@
 (defn set-symbols
   "Set defaults symbols for a language."
   [options]
-  (set-option options :symbols
-              (sf/default-symbol-factory (:language options))))
+  (if (contains? options :language)
+    (set-option options :symbols
+                (sf/default-symbol-factory (:language options)))
+    options))
 
 (defn load-and-set-option
   "Load the option and set it."
@@ -129,36 +145,36 @@
       (set-symbols)
       (load-and-set-option :message)))
 
-(defn cracking-actions
-  [options arguments action-type]
-  (let [message (:message options)
-        symbols (:symbols options)
-        frequencies symbol-frequences/english-letter-frequences]
-    (cond
-      (= action-type :cracking)
-      (caesar-analyzers/get-plaintext message symbols frequencies)
-      )))
+(defn save-output
+  "Save the output to a file"
+  [output options]
+  (let [file-path (:output-file options)]
+    (file/write-file file-path output)))
 
-(defn crypt-actions
-  [options arguments action-type]
-  (let [message (:message options)
-        key (Integer/parseInt (:key options))
-        symbols (:symbols options)]
-    (cond
-      (= action-type :encrypt)
-      (caesar/encrypt-message message key symbols)
-
-      (= action-type :decrypt)
-      (caesar/decrypt-message message key symbols))))
+(defn show-and-save-output
+  "Print and save the output to a file if needed"
+  [output options]
+  (when (contains? options :output-file)
+    (save-output output options))
+  (println output))
 
 (defn actions
   [options arguments action-type]
   (let [options (load-all-options options)]
-    (println
+    (->
      (cond
        (contains? #{:encrypt :decrypt} action-type)
-       (crypt-actions options arguments action-type)
+       (cryptography/cryptography-actions options arguments action-type)
 
        (= action-type :cracking)
-       (cracking-actions options arguments action-type)))))
+       (cracking/cracking-actions options arguments action-type))
+
+     (show-and-save-output options))))
+
+(defn cli-main
+  [args]
+  (let [{:keys [options arguments action-type exit-message ok?]} (validate-args args)]
+    (if exit-message
+      (exit exit-message ok?)
+      (actions options arguments action-type))))
 

src/cipher_analytical_machine/cli/file.clj

@@ -1,4 +1,4 @@
-(ns cipher-analytical-machine.file
+(ns cipher-analytical-machine.cli.file
   (:require [clojure.java.io :as io])
   (:gen-class))
 
@@ -16,3 +16,6 @@
 (defn read-file [file-path]
   (slurp file-path))
 
+(defn write-file [file-path content]
+  (spit file-path content))
+

src/cipher_analytical_machine/cli/options.clj

@@ -0,0 +1,65 @@
+(ns cipher-analytical-machine.cli.options
+  (:require
+   [cipher-analytical-machine.symbols.factories :as sf]
+   [clojure.string :as cs])
+  (:gen-class))
+
+(defn option-values-as-row
+  "Return the formatted string of values for an option."
+  [option values]
+  (str option ": " (cs/join ", " values)))
+
+(defn option-values-as-list
+  "Return the formatted string of values for an option as a multiline list."
+  [option values]
+  (str option ": \n - " (cs/join "\n - " values)))
+
+(defn map-of-option-value-as-list
+  "Return the formatted string of values for an option as a multiline list.
+   The values are a map of pairs (suboption and its options)."
+  [option values]
+  (let [values (map #(apply option-values-as-row %) values)]
+    (option-values-as-list option values)))
+
+(def cipher-options
+  #{"Caesar" "Simple substitution and Caesar" "Gamma"})
+
+(def default-cipher "Caesar")
+
+(defn get-available-cipher-options-as-string
+  "Return the formatted string of analyzers options."
+  []
+  (option-values-as-row "Ciphers" cipher-options))
+
+(def analyzers-options
+  {"Caesar" #{"Chi^2" "Frequency"}
+   "Simple substitution and Caesar" #{"Chi^2" "Frequency"}})
+
+(defn get-available-analyzers-options-as-string
+  "Return the formatted string of analyzers options."
+  []
+  (map-of-option-value-as-list "Analyzers" analyzers-options))
+
+(def language-options
+  #{"en", "uk"})
+
+(def default-symbols
+  (sf/default-symbol-factory "en"))
+
+(def cli-options
+  [["-m" "--message MESSAGE" "The message will be encrypted or decrypted."]
+   ["-M" "--message-file MESSAGE-FILE" "The file contains the message that will be encrypted or decrypted."]
+   ["-k" "--key KEY" "The key will be used to encrypt or decrypt."]
+   ["-c" "--cipher CIPHER" "The cipher will be used to encrypt or decrypt a message."
+    :default default-cipher]
+   ["-e" "--encrypt" "Encrypt the message."]
+   ["-d" "--decrypt" "Decrypt the message."]
+   ["-s" "--symbols SYMBOLS" "The string will be used as a set of symbols for a cipher."
+    :default default-symbols]
+   ["-l" "--language CODE" "The string will be used to set a default symbols for a cipher."
+    :validate [#(contains? language-options %) "Must be a code from the list: en, uk!!!"]]
+   ["-C" "--cracking" "Cracking the encrypted message."]
+   ["-a" "--analyzer ANALYZER" "The way of cracking."]
+   ["-O" "--output-file OUTPUT-FILE" "Save the program output to a file."]
+   ["-h" "--help"]])
+

src/cipher_analytical_machine/core.clj

@@ -1,12 +1,9 @@
 (ns cipher-analytical-machine.core
   (:require
-   [cipher-analytical-machine.cli :as cli])
+   [cipher-analytical-machine.cli.cli :as cli])
   (:gen-class))
 
 (defn -main
   [& args]
-  (let [{:keys [options arguments action-type exit-message ok?]} (cli/validate-args args)]
-    (if exit-message
-      (cli/exit exit-message ok?)
-      (cli/actions options arguments action-type))))
+  (cli/cli-main args))
 

src/cipher_analytical_machine/parsers/gamma.clj

@@ -0,0 +1,9 @@
+(ns cipher-analytical-machine.parsers.gamma
+  (:gen-class))
+
+(defn key?
+  "Return true if the string is an key of three integers."
+  [str]
+  (if (re-matches #"[+-]?\b\d+\b,[+-]?\b\d+\b,[+-]?\b\d+\b" str)
+    true false))
+

src/cipher_analytical_machine/parsers/parsers.clj

@@ -0,0 +1,29 @@
+(ns cipher-analytical-machine.parsers.parsers
+  (:require [cheshire.core :as cc])
+  (:gen-class))
+
+(defn unsigned-int-string?
+  "Return true if the string is an unsigned integer."
+  [str]
+  (if (re-matches #"\d+" str)
+    true false))
+
+(defn int-string?
+  "Return true if the string is an signed integer."
+  [str]
+  (if (re-matches #"[+-]?\b\d+\b" str)
+    true false))
+
+(defn parse-unsigned-int
+  "Return an integer if the argument is an integer."
+  [str-or-int]
+  (cond
+    (int? str-or-int)
+    str-or-int
+
+    (unsigned-int-string? str-or-int)
+    (Integer/parseInt str-or-int)
+
+    :else
+    nil))
+

src/cipher_analytical_machine/parsers/simple_substitution.clj

@@ -0,0 +1,54 @@
+(ns cipher-analytical-machine.parsers.simple-substitution
+  (:require
+   [cipher-analytical-machine.ciphers.simple-substitution :as ss]
+   [cipher-analytical-machine.parsers.parsers :as ps]
+   [clojure.set :as set]
+   [cheshire.core :as cc])
+  (:gen-class))
+
+(defn encode-key-and-substitution-table-to-json
+  [key substitution-table]
+  (-> {"key" key}
+      (assoc "table" substitution-table)
+      (cc/generate-string)))
+
+(defn decode-key
+  "Returns the first character if the string is a char. Return the number if the string is a number."
+  [str]
+  (if (ps/unsigned-int-string? str)
+    (Integer/parseInt str)
+    (first str)))
+
+(defn decode-pair
+  "Decode a numbers as a string and a char as a string"
+  [acc [key value]]
+  (if (ps/unsigned-int-string? key)
+    (assoc acc (decode-key key) (decode-key value))
+    (assoc acc (decode-key key) value)))
+
+(defn decode-substitution-table
+  [substitution-table-map-from-json]
+  (reduce decode-pair {} substitution-table-map-from-json))
+
+(defn decode-key-and-substitution-table-from-json
+  [json]
+  (let [data (cc/parse-string json)]
+    (assoc data "table" (decode-substitution-table (get data "table")))))
+
+(defn generate-table-or-decode-json
+  "It generate the table and return map with the key and the table if the argument is a key. Else it decode the json."
+  [key-or-json symbols]
+  (if (ps/unsigned-int-string? key-or-json)
+    (-> {"key" key-or-json}
+        (assoc "table" (ss/generate-substitution-table symbols)))
+    (decode-key-and-substitution-table-from-json key-or-json)))
+
+(defn invert-table-in-map
+  "Invert the table in a decoded json (key, table)"
+  [decoded-json]
+  (->>
+   (-> decoded-json
+       (get "table")
+       (set/map-invert))
+   (assoc decoded-json "table")))
+

src/cipher_analytical_machine/symbols/factories.clj

@@ -1,4 +1,4 @@
-(ns cipher-analytical-machine.symbol-factories
+(ns cipher-analytical-machine.symbols.factories
   (:require [clojure.string :as cs])
   (:gen-class))
 

src/cipher_analytical_machine/symbols/frequencies.clj

@@ -1,7 +1,17 @@
-(ns cipher-analytical-machine.symbol-frequences
+(ns cipher-analytical-machine.symbols.frequencies
   (:gen-class))
 
-(def english-letter-frequences {
+(defn map-to-string
+  "Convert the map of frequencies to the frequency string. Letters are sorted by frequency in descending order."
+  [frequency-map]
+  (->> frequency-map
+       (reduce (fn [acc el] (conj acc el)) [])
+       (sort-by last)
+       (map first)
+       (reverse)
+       (apply str)))
+
+(def english-letter-frequencies {
    \a 0.0804
    \b 0.0154
    \c 0.0306
@@ -30,7 +40,7 @@
    \z 0.0009
 })
 
-(def ukrainian-letter-frequences {
+(def ukrainian-letter-frequencies {
    \а 0.064
    \б 0.013
    \в 0.046
@@ -67,3 +77,16 @@
    \  0.138
 })
 
+(defn default-frequency-factory
+  "Returns a default map of letter frequencies for a language"
+  [language-code]
+  (cond
+    (= language-code "en")
+    english-letter-frequencies
+
+    (= language-code "uk")
+    ukrainian-letter-frequencies
+
+    :else
+    english-letter-frequencies))
+

src/main/java/cipher_analytical_machine/analyzers/caesar/FrequencyAnalyzer.java

@@ -0,0 +1,53 @@
+package cipher_analytical_machine.analyzers.caesar;
+
+import cipher_analytical_machine.analyzers.caesar.IsNonsense;
+import cipher_analytical_machine.ciphers.caesar.Decrypted;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+
+public class FrequencyAnalyzer {
+    private String ciphertext;
+    private String symbols;
+    private String symbol_frequences;
+    private Decrypted decryptor;
+    private IsNonsense isNonsense;
+
+    public FrequencyAnalyzer(String ciphertext, String symbols, String symbol_frequences, Decrypted decryptor, IsNonsense isNonsense) {
+	    this.ciphertext = ciphertext;
+        this.symbol_frequences = symbol_frequences;
+        this.symbols = symbols;
+	    this.decryptor = decryptor;
+	    this.isNonsense = isNonsense;
+    }
+
+    public String crack() {
+        // Знаходимо кількість літер
+        Map<Character, Integer> encryptedLetterCounts = new HashMap<>();
+
+        for (char c : ciphertext.toLowerCase().toCharArray()) {
+            encryptedLetterCounts.put(c, encryptedLetterCounts.getOrDefault(c, 0) + 1);
+        }
+
+        // Знаходимо букву, яка зустрічається найчастіше
+        char mostFrequentEncryptedLetter = ' ';
+        int mostFrequentEncryptedLetterCount = 0;
+
+        for (Entry<Character, Integer> entry : encryptedLetterCounts.entrySet()) {
+            if (entry.getValue() > mostFrequentEncryptedLetterCount) {
+                mostFrequentEncryptedLetter = entry.getKey();
+                mostFrequentEncryptedLetterCount = entry.getValue();
+            }
+        }
+
+        // Обчислимо зміщення
+        int size = symbols.length();
+        int indexOfMostFrequentEncryptedLetter = symbols.indexOf(mostFrequentEncryptedLetter);
+        int indexOfMostFrequentLetter = symbols.indexOf(symbol_frequences.charAt(0));
+        int shift = (indexOfMostFrequentEncryptedLetter - indexOfMostFrequentLetter) % size;
+
+        return decryptor.decrypt(ciphertext, shift, symbols);
+    }
+}
+

src/main/java/cipher_analytical_machine/analyzers/caesar/IsNonsense.java

@@ -0,0 +1,6 @@
+package cipher_analytical_machine.analyzers.caesar;
+
+public interface IsNonsense {
+    boolean isNonsense(String message);
+}
+

src/main/java/cipher_analytical_machine/ciphers/caesar/Decrypted.java

@@ -0,0 +1,6 @@
+package cipher_analytical_machine.ciphers.caesar;
+
+public interface Decrypted {
+    String decrypt(String message, int key, String symbols);
+}
+

test/cipher_analytical_machine/analyzers/analyzers_test.clj

@@ -0,0 +1,47 @@
+(ns cipher-analytical-machine.analyzers.analyzers-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.analyzers.analyzers :refer :all]))
+
+(deftest count-characters-test
+  (testing "Count two dublicates and one uniq character from a string."
+    (is (= {\a 2 \b 1}
+           (count-characters "aba")))))
+
+(deftest reverse-count-characters-test
+  (testing "The symbols must be grouped as a vector and the count must be a key."
+    (are [count-map expected-map]
+        (= expected-map (reverse-count-characters count-map))
+      {\a 1 \b 2 \c 1} {1 [\a \c] 2 [\b]}
+      {\a 1 \b 2 \c 3} {1 [\a] 2 [\b] 3 [\c]})))
+
+(deftest chi-squared-letter-statistic-test
+  (testing "If the frequence of A is 0.1, the text length is 100 and contains 20 times, then the chi-squared is 10."
+    (is (= 10.0
+           (chi-squared-letter-statistic 20 0.1 100))))
+
+  (testing "If the frequence of A is 0.1, the text length is 10 and contains 5 times, then the chi-squared is 16.0."
+    (is (= 16.0
+           (chi-squared-letter-statistic 5 0.1 10)))))
+
+(deftest chi-squared-statistic-test
+  (let [text "aaaaabbbbb"]
+  (testing "If the frequencies of a and b is 0.1, the text length is 10 and contains them 5 times, then score is 32."
+    (is (= 32.0
+           (chi-squared-statistic text {\a 0.1 \b 0.1}))))))
+
+(deftest sort-map-by-count-test
+  (testing "Test the sort in descending order."
+    (is (= [[\b 3] [\a 2] [\c 1]]
+           (sort-map-by-count {\a 2 \b 3 \c 1} )))))
+
+(deftest table-to-string-test
+  (testing "Test the sort in descending order."
+    (is (= "bac"
+           (table-to-string [[\b 3] [\a 2] [\c 1]])))))
+
+(deftest symbol-frequency-table-test
+  (testing "Test the sort in descending order."
+    (is (= {\d \b, \e \a, \f \c}
+           (symbol-frequency-table {\d 3 \e 2 \f 1} {\b 3 \a 2 \c 1})))))
+

test/cipher_analytical_machine/analyzers/caesar_test.clj

@@ -1,9 +1,9 @@
-(ns cipher-analytical-machine.caesar-analyzers-test
+(ns cipher-analytical-machine.analyzers.caesar-test
   (:require
    [clojure.test :refer :all]
-   [cipher-analytical-machine.caesar-analyzers :refer :all]
-   [cipher-analytical-machine.symbol-frequences :as sf]
-   [cipher-analytical-machine.cipher-analyzers :as ca]
+   [cipher-analytical-machine.analyzers.caesar :refer :all]
+   [cipher-analytical-machine.symbols.frequencies :as sf]
+   [cipher-analytical-machine.analyzers.analyzers :as ca]
    [clojure.string :as cs]))
 
 (deftest get-all-texts-test
@@ -25,9 +25,9 @@
   (testing "There're 27 combinations for a 'Hello World'."
     (let [ciphertext "khoorczruog"
           symbols "abcdefghijklmnopqrstuvwxyz "
-          frequences sf/english-letter-frequences
+          frequencies sf/english-letter-frequencies
           text-pairs (get-all-texts ciphertext symbols)]
-      (is (= 27 (count (get-all-scores frequences text-pairs)))))))
+      (is (= 27 (count (get-all-scores frequencies text-pairs)))))))
 
 (deftest get-min-score-pair-test
   (testing "If a key is one, then the min score pair is 15."
@@ -40,37 +40,37 @@
         ciphertext "khoorczruog"
         key 3
         symbols "abcdefghijklmnopqrstuvwxyz "
-        frequences sf/english-letter-frequences]
+        frequencies sf/english-letter-frequencies]
     (testing "The plaintext is encrypted with 3 as the key."
-      (is (= key (get-key ciphertext symbols frequences)))))
+      (is (= key (get-key ciphertext symbols frequencies)))))
 
   (let [; З поеми "Кавказ" Тараса Григоровича Шевченка:
         plaintext "Борітеся – поборете, Вам Бог помагає! За вас правда, за вас слава. І воля святая!"
         ciphertext "жхчощйшде–ецхжхчйщй,езєуежхиецхуєиєк!емєезєшецчєзїє,емєезєшештєзє.еоезхтдешздщєд!"
         key 7
         symbols "абвгґдеєжзиіїйклмнопрстуфхцчшщьюя "
-        frequences sf/ukrainian-letter-frequences]
+        frequencies sf/ukrainian-letter-frequencies]
     (testing "The plaintext is encrypted with 3 as the key."
-      (is (= key (get-key ciphertext symbols frequences))))))
+      (is (= key (get-key ciphertext symbols frequencies))))))
 
 (deftest get-plaintext-test
   (let [plaintext "hello world"
         ciphertext "khoorczruog"
         symbols "abcdefghijklmnopqrstuvwxyz "
-        frequences sf/english-letter-frequences]
+        frequencies sf/english-letter-frequencies]
     (testing "The plaintext is encrypted with 3 as the key."
-      (is (= plaintext (get-plaintext ciphertext symbols frequences))))
+      (is (= plaintext (get-plaintext ciphertext symbols frequencies))))
 
     (testing "The ciphertext is case-insensitive."
-      (is (= plaintext (get-plaintext "KhoorcZruog" symbols frequences)))))
+      (is (= plaintext (get-plaintext "KhoorcZruog" symbols frequencies)))))
 
   (let [; З поеми "Кавказ" Тараса Григоровича Шевченка:
         plaintext "Борітеся – поборете, Вам Бог помагає! За вас правда, за вас слава. І воля святая!"
         ciphertext "жхчощйшде–ецхжхчйщй,езєуежхиецхуєиєк!емєезєшецчєзїє,емєезєшештєзє.еоезхтдешздщєд!"
         key 7
         symbols "абвгґдеєжзиіїйклмнопрстуфхцчшщьюя "
-        frequences sf/ukrainian-letter-frequences]
+        frequencies sf/ukrainian-letter-frequencies]
     (testing "The ciphertext is case-insensitive."
       (is (= (cs/lower-case plaintext)
-             (get-plaintext ciphertext symbols frequences))))))
+             (get-plaintext ciphertext symbols frequencies))))))
 

test/cipher_analytical_machine/analyzers/language_test.clj

@@ -1,7 +1,7 @@
-(ns cipher-analytical-machine.language-analyzer-test
+(ns cipher-analytical-machine.analyzers.language-test
   (:require
    [clojure.test :refer :all]
-   [cipher-analytical-machine.language-analyzer :refer :all]
+   [cipher-analytical-machine.analyzers.language :refer :all]
   ))
 
 (deftest detect-language-test

test/cipher_analytical_machine/analyzers/simple_substitution_test.clj

@@ -0,0 +1,50 @@
+(ns cipher-analytical-machine.analyzers.simple-substitution-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.symbols.frequencies :as sf]
+   [cipher-analytical-machine.ciphers.simple-substitution :as ss]
+   [cipher-analytical-machine.analyzers.simple-substitution :refer :all])
+  (:gen-class))
+
+(deftest get-possible-keys-vector-test
+  (testing "The vector must be ordered by symbols"
+    (are [possible-keys-map symbols expected-key-vector]
+        (= expected-key-vector (get-possible-key-vector possible-keys-map symbols))
+      {\a [\a \b] \b [\b \a] \c [\a \c]} "abc" [[\a \b] [\b \a] [\a \c]]
+      {\a [\a \b] \c [\b \a] \b [\a \c]} "abc" [[\a \b] [\a \c] [\b \a]])))
+
+(deftest get-possible-key-vector-from-reversed-count-map-test
+  (testing "The block order must be in descending order"
+    (are [reversed-count-map expected-key-vector]
+        (= expected-key-vector (get-possible-key-vector-from-reversed-count-map reversed-count-map))
+      {1 [\a \c] 2 [\b]}     [[\b] [\a \c]]
+      {2 [\a] 1 [\b] 3 [\c]} [[\c] [\a] [\b]])))
+
+(deftest get-all-permutation-for-block-test
+  (testing "It must return all permutations"
+    (are [symbols expected-permutations]
+        (= expected-permutations (get-all-permutation-for-block symbols))
+      [\a \b]    ["ab" "ba"]
+      [\a \b \c] ["abc" "acb" "bac" "bca" "cab" "cba"])))
+
+(deftest get-all-combinations-for-blocks-test
+  (testing "The keys must be the all combinations of blocks"
+    (are [possible-keys-vector expected-keys]
+        (= expected-keys (get-all-combinations-for-blocks possible-keys-vector))
+      [[\a \b] [\f] [\a \c] [\g]] '("afag" "afcg" "bfag" "bfcg")
+      [[\a \b] [\a \c]] '("aa" "ac" "ba" "bc")
+      [[\a \b \c] [\a \c] [\b \c]] '("aab" "aac" "acb" "acc" "bab" "bac" "bcb" "bcc" "cab" "cac" "ccb" "ccc"))))
+
+(deftest get-possible-key-combinations-test
+  (testing "The keys must be the all combinations, but the blocks must create a permutations which will be joined as a combination"
+    (are [possible-keys-vector expected-keys]
+        (= expected-keys (get-possible-key-combinations possible-keys-vector))
+      [[\a \b] [\f] [\e \c] [\g]] '("abfecg" "abfceg" "bafecg" "bafceg")
+      [[\a \b] [\a \c]] '("abac" "abca" "baac" "baca")
+      [[\a \b \c] [\a \c] [\b \c]] '("abcacbc" "abcaccb" "abccabc" "abccacb"
+                                     "acbacbc" "acbaccb" "acbcabc" "acbcacb"
+                                     "bacacbc" "bacaccb" "baccabc" "baccacb"
+                                     "bcaacbc" "bcaaccb" "bcacabc" "bcacacb"
+                                     "cabacbc" "cabaccb" "cabcabc" "cabcacb"
+                                     "cbaacbc" "cbaaccb" "cbacabc" "cbacacb"))))
+

test/cipher_analytical_machine/cipher_analyzers_test.clj

@@ -1,25 +0,0 @@
-(ns cipher-analytical-machine.cipher-analyzers-test
-  (:require
-   [clojure.test :refer :all]
-   [cipher-analytical-machine.cipher-analyzers :refer :all]))
-
-(deftest count-characters-test
-  (testing "Count two dublicates and one uniq character from a string."
-    (is (= {\a 2 \b 1}
-           (count-characters "aba")))))
-
-(deftest chi-squared-letter-statistic-test
-  (testing "If the frequence of A is 0.1, the text length is 100 and contains 20 times, then the chi-squared is 10."
-    (is (= 10.0
-           (chi-squared-letter-statistic 20 0.1 100))))
-
-  (testing "If the frequence of A is 0.1, the text length is 10 and contains 5 times, then the chi-squared is 16.0."
-    (is (= 16.0
-           (chi-squared-letter-statistic 5 0.1 10)))))
-
-(deftest chi-squared-statistic-test
-  (let [text "aaaaabbbbb"]
-  (testing "If the frequences of a and b is 0.1, the text length is 10 and contains them 5 times, then score is 32."
-    (is (= 32.0
-           (chi-squared-statistic text {\a 0.1 \b 0.1}))))))
-

test/cipher_analytical_machine/ciphers/caesar_test.clj

@@ -1,7 +1,7 @@
-(ns cipher-analytical-machine.caesar-test
+(ns cipher-analytical-machine.ciphers.caesar-test
   (:require
    [clojure.test :refer :all]
-   [cipher-analytical-machine.caesar :refer :all]
+   [cipher-analytical-machine.ciphers.caesar :refer :all]
   ))
 
 (deftest calculate-char-index-test

test/cipher_analytical_machine/ciphers/gamma_test.clj

@@ -0,0 +1,62 @@
+(ns cipher-analytical-machine.ciphers.gamma-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.ciphers.gamma :refer :all]))
+
+(deftest add-mod-test
+  (testing "The remainder must be as expected."
+    (are [a b module expected]
+        (= expected (add-mod a b module))
+      5 2 4 3
+      1 2 3 0
+      2 2 3 1)))
+
+(deftest generate-seq-test
+  (testing "Checking that the next element of a sequence is calculated by (e[i-1] + e[i-3] % mod)."
+    (are [a b c module size expected]
+        (= expected (take size (generate-seq a b c module)))
+      4 32 15 33 10 [4 32 15 19 18 0 19 4 4 23]
+      1 2  3  3  9  [1 2 3 1 0 0 1 1 1])))
+
+(deftest generate-gamma-seq-test
+  (testing "Checking that the next element of a sequence is calculated by (s[i] + s[i+1] % mod)."
+    (are [acc seq module expected]
+        (= expected (generate-gamma-seq acc seq module))
+      [] [4 32 15 19 18 0 19 4 4 23] 33 [3 14 1 4 18 19 23 8 27]
+      [] [1 2 3 1 0 0 1 1 1]         3  [0 2 1 1 0 1 2 2])))
+
+(deftest generate-gamma-test
+  (testing "Checking that the gamma is generated as expected."
+    (are [a b c module size expected]
+        (= expected (generate-gamma a b c module size))
+      4 32 15 33 10 [3 14 1 4 18 19 23 8 27 17]
+      1 2  3  3  9  [0 2 1 1 0 1 2 2 0])))
+
+(deftest encrypt-array-test
+  (testing "Checking that the message is encrypted as expected: (msg+gamma)%module."
+    (are [key module array expected]
+        (= expected (encrypt-array key module array))
+      [4 32 15] 33 [3 14 1 4 18 19 23 8 27 17] [6 28 2 8 3 5 13 16 21 1]
+      [1 2  3 ] 3  [0 2 1 1 0 1 2 2 0]         [0 1 2 2 0 2 1 1 0])))
+
+(deftest encrypt-message-test
+  (testing "Checking that the message is encrypted as expected"
+    (are [key symbols message expected]
+        (= expected (encrypt-message key symbols message))
+      [4 32 15] "абвгґдеєжзиіїйклмнопрстуфхцчшщьюя" "гкбґопужчн" "ешвжгдймсб"
+      [1 2  3 ] "абв"  "авббабвва"  "абввавбба")))
+
+(deftest decrypt-array-test
+  (testing "Checking that the message is decrypted as expected."
+    (are [key module array expected]
+        (= expected (decrypt-array key module array))
+      [4 32 15] 33 [6 28 2 8 3 5 13 16 21 1] [3 14 1 4 18 19 23 8 27 17]
+      [1 2  3 ] 3  [0 1 2 2 0 2 1 1 0]       [0 2 1 1 0 1 2 2 0])))
+
+(deftest decrypt-message-test
+  (testing "Checking that the message is decrypted as expected"
+    (are [key symbols message expected]
+        (= expected (decrypt-message key symbols message))
+      [4 32 15] "абвгґдеєжзиіїйклмнопрстуфхцчшщьюя" "ешвжгдймсб" "гкбґопужчн"
+      [1 2  3 ] "абв" "абввавбба" "авббабвва")))
+

test/cipher_analytical_machine/ciphers/simple_substitution_test.clj

@@ -0,0 +1,85 @@
+(ns cipher-analytical-machine.ciphers.simple-substitution-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.ciphers.simple-substitution :refer :all]))
+
+(deftest find-value-in-table-test
+  (let [table {\a 1 \b 2 \c 3}
+        rtable {1 \a 2 \b 3 \c}]
+    (testing "If the symbol is in the table as a key, then the result won't nil."
+      (are [key expected]
+          (= expected (find-value-in-table key table))
+        \a 1
+        \d nil
+        1 nil
+        5 nil))
+
+    (testing "If the digit is in the reversed table as a key, then the result won't nil."
+      (are [key expected]
+          (= expected (find-value-in-table key rtable))
+        \a nil
+        \d nil
+        1 \a
+        5 nil))))
+
+(deftest generate-sorted-substitution-table-test
+  (testing "If the symbol is in the table as a key, then the result won't nil."
+    (are [symbols expected-table]
+        (= expected-table (generate-sorted-substitution-table symbols))
+      "abc" {0 \a 1 \b 2 \c}
+      "a" {0 \a})))
+
+(deftest encrypt-message-test
+  (let [symbols "abc"
+        table {\a 1 \b 2 \c 3}]
+    (testing "The function must encrypt the message and remove unknown symbols."
+      (are [message expected]
+          (= expected (encrypt-message message table))
+        "abc" "1,2,3"
+        "aDbdc" "1,2,3"))))
+
+(deftest encrypt-message-with-caesar-test
+  (let [symbols "abc"
+        table {\a 1 \b 2 \c 3}]
+    (testing "The function must encrypt the message and remove unknown symbols."
+      (are [message key expected]
+          (= expected (encrypt-message-with-caesar message key table symbols))
+        "abc" 0 "1,2,3"
+        "abc" 1 "2,3,1"
+        "aDbdc" 0 "1,2,3"))))
+
+(deftest decrypt-by-table-test
+  (let [table {\d \a \e \b \f \c}]
+    (testing "The function must decrypt the message by the table."
+      (are [message expected]
+          (= expected (decrypt-by-table table message))
+        "def" '(\a \b \c)
+        "abf" '(nil nil \c)
+        "fed" '(\c \b \a)))))
+
+(deftest decrypt-message-by-symbol-table-test
+  (let [table {\d \a \e \b \f \c}]
+    (testing "The function must decrypt the message and remove unknown numbers."
+      (are [message expected]
+          (= expected (decrypt-message-by-symbol-table table message))
+        "def" "abc"
+        "daef" "abc"))))
+
+(deftest decrypt-message-test
+  (let [table {1 \a 2 \b 3 \c}]
+    (testing "The function must decrypt the message and remove unknown numbers."
+      (are [message expected]
+          (= expected (decrypt-message message table))
+        "1,2,3" "abc"
+        "1,12,2,3" "abc"))))
+
+(deftest decrypt-message-with-caesar-test
+  (let [symbols "abc"
+        table {1 \a 2 \b 3 \c}]
+    (testing "The function must decrypt the message and remove unknown numbers."
+      (are [message key expected]
+          (= expected (decrypt-message-with-caesar message key table symbols))
+        "1,2,3" 0 "abc"
+        "2,3,1" 1 "abc"
+        "1,12,2,3" 0 "abc"))))
+

test/cipher_analytical_machine/parsers/gamma_test.clj

@@ -0,0 +1,20 @@
+(ns cipher-analytical-machine.parsers.gamma-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.parsers.gamma :refer :all]))
+
+(deftest key?-test
+  (testing "The function return true only if the key in the format '%d,%d,%d'."
+    (are [str expected]
+        (= expected
+           (key? str))
+      "9"         false
+      "9,10"      false
+      "10,9,8"    true
+      "-10,9,-8"  true
+      "-10,-9,-8" true
+      "asd 10 "   false
+      " 10 "      false
+      "-10"       false
+      "abc"       false)))
+

test/cipher_analytical_machine/parsers/parsers_test.clj

@@ -0,0 +1,40 @@
+(ns cipher-analytical-machine.parsers.parsers-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.parsers.parsers :refer :all]))
+
+(deftest unsigned-int-string?-test
+  (testing "The function return true only for an unsingned integer as a string."
+    (are [str expected]
+        (= expected
+           (unsigned-int-string? str))
+      "9" true
+      "9" true
+      "10" true
+      "asd 10 " false
+      " 10 " false
+      "-10" false
+      "abc" false)))
+
+(deftest int-string?-test
+  (testing "The function return true only for an singned integer as a string."
+    (are [str expected]
+        (= expected
+           (int-string? str))
+      "9" true
+      "10" true
+      "-10" true
+      "asd -10 " false
+      " -10 " false
+      "abc" false)))
+
+(deftest parse-unsigned-int-test
+  (testing "The function parse the integer if the string is an integer."
+    (are [str-or-int expected]
+        (= expected
+           (parse-unsigned-int str-or-int))
+      "9"   9
+      9     9
+      "10"  10
+      "-10" nil
+      "abc" nil)))

test/cipher_analytical_machine/parsers/simple_substitution_test.clj

@@ -0,0 +1,49 @@
+(ns cipher-analytical-machine.parsers.simple-substitution-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.parsers.simple-substitution :refer :all]))
+
+(deftest encode-key-and-substitution-table-to-json-test
+  (testing "The encoder must parse the map and create a json."
+    (are [key table expected-json]
+        (= expected-json
+           (encode-key-and-substitution-table-to-json key table))
+      1 {0 \a 1 \b 2 \c} "{\"key\":1,\"table\":{\"0\":\"a\",\"1\":\"b\",\"2\":\"c\"}}"
+      2 {\a 0 \b 1 \c 2} "{\"key\":2,\"table\":{\"a\":0,\"b\":1,\"c\":2}}")))
+
+(deftest decode-key-and-substitution-table-from-json-test
+  (testing "The decoder must parse the json and create a map."
+    (are [json expected-data]
+        (= expected-data
+           (decode-key-and-substitution-table-from-json json))
+      "{\"key\":1, \"table\":{\"0\":\"a\",\"1\":\"b\",\"2\":\"c\"}}" {"key" 1 "table" {0 \a 1 \b 2 \c}}
+      "{\"key\":2, \"table\":{\"a\":0,\"b\":1,\"c\":2}}" {"key" 2 "table" {\a 0 \b 1 \c 2}})))
+
+(deftest generate-table-or-decode-json-test
+  (let [symbols "abc"]
+    (testing "The function decodes the json."
+      (are [json expected-data]
+          (= expected-data
+             (generate-table-or-decode-json json symbols))
+        "{\"key\":1, \"table\":{\"0\":\"a\",\"1\":\"b\",\"2\":\"c\"}}" {"key" 1 "table" {0 \a 1 \b 2 \c}}
+        "{\"key\":2, \"table\":{\"a\":0,\"b\":1,\"c\":2}}" {"key" 2 "table" {\a 0 \b 1 \c 2}}))
+
+    (testing "The function generates the table, because the argument is a key."
+      (are [json expected-data]
+          (let [data (generate-table-or-decode-json json symbols)]
+            (and (= (get expected-data "key")
+                    (get data "key"))
+                 (= (keys (get expected-data "table"))
+                    (keys (get data "table"))))
+             (generate-table-or-decode-json json symbols))
+        "1" {"key" 1 "table" {0 \a 1 \b 2 \c}}
+        "2" {"key" 2 "table" {\a 0 \b 1 \c 2}}))))
+
+(deftest invert-table-in-map-test
+  (testing "The function invert the table in a decoded json."
+    (are [decoded-json expected-data]
+        (= expected-data
+           (invert-table-in-map decoded-json))
+      {"key" 1 "table" {0 \a 1 \b 2 \c}} {"key" 1 "table" {\a 0 \b 1 \c 2}}
+      {"key" 2 "table" {\a 0 \b 1 \c 2}} {"key" 2 "table" {0 \a 1 \b 2 \c}})))
+

test/cipher_analytical_machine/symbols/factories_test.clj

@@ -1,7 +1,7 @@
-(ns cipher-analytical-machine.symbol-factories-test
+(ns cipher-analytical-machine.symbols.factories-test
   (:require
    [clojure.test :refer :all]
-   [cipher-analytical-machine.symbol-factories :refer :all]
+   [cipher-analytical-machine.symbols.factories :refer :all]
   ))
 
 (deftest english-alphabet-factory-test

test/cipher_analytical_machine/symbols/frequencies_test.clj

@@ -0,0 +1,21 @@
+(ns cipher-analytical-machine.symbols.frequencies-test
+  (:require
+   [clojure.test :refer :all]
+   [cipher-analytical-machine.symbols.frequencies :refer :all]))
+
+(deftest map-to-string-test
+  (let [symbol-map english-letter-frequencies]
+    (testing "The map must be converted to 'etaoinsrhldcumfpgwybvkxjqz'"
+      (is (= "etaoinsrhldcumfpgwybvkxjqz"
+             (map-to-string symbol-map))))))
+
+(deftest default-frequency-factory-test
+  (testing "Factory supports languages: English (en), Ukrainian (uk). If language code is unidentified, then it must have the 'en'."
+    (are [language-code expected-map-size]
+        (->> (default-frequency-factory language-code)
+             count
+             (= expected-map-size))
+      "en"           26
+      "uk"           34
+      "Maybe a code" 26)))
+