VerisimilitudeX · VerisimilitudeX · Dec 29, 2022 · Dec 29, 2022 · Dec 29, 2022
diff --git a/.classpath b/.classpath
@@ -1,3 +1,14 @@
+<!--
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ -->
+
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
 	<classpathentry kind="src" output="bin/main" path="src/main/java">

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 ![DNAnalyzer Logo](https://user-images.githubusercontent.com/96280466/186224441-46dd2029-b9dc-4b3d-aad8-bfd1e1e62f2e.png)
 
-<p align=center><img src="https://img.shields.io/badge/copyright-2022-blue" alt="Copyright"> <img src="https://wakatime.com/badge/github/Verisimilitude11/DNAnalyzer.svg" alt="WakaTime"> <img src="https://img.shields.io/github/v/release/VERISIMILITUDE11/DNAnalyzer" alt="Releases"> <img src="https://img.shields.io/github/repo-size/Verisimilitude11/DNAnalyzer" alt="Repository Size"> <img src="https://img.shields.io/tokei/lines/github/verisimilitude11/DNAnalyzer" alt="Lines of Code"> <img src="https://hits.dwyl.com/verisimilitude11/DNAnalyzer.svg?style=flat" alt="Hits Counter">  <img src="https://github.com/Verisimilitude11/DNAnalyzer/actions/workflows/gradle.yml/badge.svg" alt=""> 
+<p align=center><img src="https://img.shields.io/badge/copyright-2023-blue" alt="Copyright"> <img src="https://wakatime.com/badge/github/Verisimilitude11/DNAnalyzer.svg" alt="WakaTime"> <img src="https://img.shields.io/github/v/release/VERISIMILITUDE11/DNAnalyzer" alt="Releases"> <img src="https://img.shields.io/github/repo-size/Verisimilitude11/DNAnalyzer" alt="Repository Size"> <img src="https://img.shields.io/tokei/lines/github/verisimilitude11/DNAnalyzer" alt="Lines of Code"> <img src="https://hits.dwyl.com/verisimilitude11/DNAnalyzer.svg?style=flat" alt="Hits Counter">  <img src="https://github.com/Verisimilitude11/DNAnalyzer/actions/workflows/gradle.yml/badge.svg" alt=""> 
 <a href="https://discord.gg/X3YCvGf2Ug"><img src="https://img.shields.io/discord/1033196198816915516" alt=""></a>
 <a href="https://deepsource.io/gh/Verisimilitude11/DNAnalyzer/?ref=repository-badge}"><img src="https://deepsource.io/gh/Verisimilitude11/DNAnalyzer.svg/?label=active+issues&amp;show_trend=true&amp;token=9NBX3zsf0IZ3Nii3AApiX1Wa" alt="DeepSource" title="DeepSource"></a></p>
 
@@ -164,4 +164,4 @@ View our in-line citations in the [Citations](docs/citations.md) document.
 
 You are entirely responsible for the use of this application, including any and all activities that occur. While the DNAnalyzer Team strives to fix all major bugs that may be either reported by a user or discovered while debugging, they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances. For further inquiries, please contact the following email address: `[email protected]`
 
-##### Copyright © 2022 Piyush Acharya and DNAnalyzer. This is an open source project. Some rights reserved.
+##### Copyright © Piyush Acharya 2023. This is an open-source project with code available to inspect and modify.
diff --git a/src/main/java/DNAnalyzer/Main.java b/src/main/java/DNAnalyzer/Main.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/core/DNAAnalysis.java b/src/main/java/DNAnalyzer/core/DNAAnalysis.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/core/Properties.java b/src/main/java/DNAnalyzer/core/Properties.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.
@@ -8,6 +8,7 @@
  *
  * For further inquiries, please reach out to [email protected]
  */
+
 package DNAnalyzer.core;
 
 import static DNAnalyzer.core.DNAAnalysis.countBasePairs;

diff --git a/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcid.java b/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcid.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.
@@ -8,6 +8,7 @@
  *
  * For further inquiries, please contact reach out to [email protected]
  */
+
 package DNAnalyzer.data.aminoAcid;
 
 import java.util.List;

diff --git a/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcidFactory.java b/src/main/java/DNAnalyzer/data/aminoAcid/AminoAcidFactory.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.
@@ -8,6 +8,7 @@
  *
  * For further inquiries, please contact reach out to [email protected]
  */
+
 package DNAnalyzer.data.aminoAcid;
 
 import java.util.Arrays;

diff --git a/src/main/java/DNAnalyzer/data/codon/CodonDataConstants.java b/src/main/java/DNAnalyzer/data/codon/CodonDataConstants.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.
@@ -8,6 +8,7 @@
  *
  * For further inquiries, please reach out to [email protected]
  */
+
 package DNAnalyzer.data.codon;
 
 import java.util.*;

diff --git a/src/main/java/DNAnalyzer/data/codon/CodonDataUtils.java b/src/main/java/DNAnalyzer/data/codon/CodonDataUtils.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/data/codon/CodonFrame.java b/src/main/java/DNAnalyzer/data/codon/CodonFrame.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/ui/cli/CmdArgs.java b/src/main/java/DNAnalyzer/ui/cli/CmdArgs.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.
@@ -8,6 +8,7 @@
  *
  * For further inquiries, please reach out to [email protected]
  */
+
 package DNAnalyzer.ui.cli;
 
 import DNAnalyzer.Main;

diff --git a/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUI.java b/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUI.java
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 package DNAnalyzer.ui.gui;
 
 import javafx.application.Application;

diff --git a/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUIFXMLController.java b/src/main/java/DNAnalyzer/ui/gui/DNAnalyzerGUIFXMLController.java
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 package DNAnalyzer.ui.gui;
 
 import DNAnalyzer.core.DNAAnalysis;

diff --git a/src/main/java/DNAnalyzer/utils/core/BasePairCounter.java b/src/main/java/DNAnalyzer/utils/core/BasePairCounter.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.
@@ -8,6 +8,7 @@
  *
  * For further inquiries, please contact reach out to [email protected]
  */
+
 package DNAnalyzer.utils.core;
 
 import java.util.Optional;

diff --git a/src/main/java/DNAnalyzer/utils/core/DNATools.java b/src/main/java/DNAnalyzer/utils/core/DNATools.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/utils/core/ReadingFrames.java b/src/main/java/DNAnalyzer/utils/core/ReadingFrames.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/utils/core/Utils.java b/src/main/java/DNAnalyzer/utils/core/Utils.java
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 package DNAnalyzer.utils.core;
 
 import java.io.File;

diff --git a/src/main/java/DNAnalyzer/utils/protein/ProteinAnalysis.java b/src/main/java/DNAnalyzer/utils/protein/ProteinAnalysis.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/utils/protein/ProteinFinder.java b/src/main/java/DNAnalyzer/utils/protein/ProteinFinder.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/main/java/DNAnalyzer/utils/traits/Traits.java b/src/main/java/DNAnalyzer/utils/traits/Traits.java
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 package DNAnalyzer.utils.traits;
 
 import java.util.HashMap;

diff --git a/src/test/java/DNAnalyzer/CodonDataUtilsTest.java b/src/test/java/DNAnalyzer/CodonDataUtilsTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022 DNAnalyzer. Some rights reserved.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * You are entirely responsible for the use of this application, including any and all activities that occur.

diff --git a/src/test/java/DNAnalyzer/DNAAnalysisTest.java b/src/test/java/DNAnalyzer/DNAAnalysisTest.java
@@ -1,7 +1,14 @@
 /*
- * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
- * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
  */
+
 package DNAnalyzer;
 
 import java.io.IOException;

diff --git a/src/test/java/DNAnalyzer/MainTest.java b/src/test/java/DNAnalyzer/MainTest.java
@@ -1,6 +1,14 @@
 /*
- * This Java source file was generated by the Gradle 'init' task.
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
  */
+
 package DNAnalyzer;
 
 import org.junit.jupiter.api.Test;

diff --git a/src/test/java/DNAnalyzer/ProteinFinderTest.java b/src/test/java/DNAnalyzer/ProteinFinderTest.java
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 package DNAnalyzer;
 
 import static org.junit.jupiter.api.Assertions.assertArrayEquals;

diff --git a/web/about/about.css b/web/about/about.css
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 @import url('https://fonts.googleapis.com/css2?family=Poppins&display=swap');
 
 * > * {

diff --git a/web/about/about.html b/web/about/about.html
@@ -1,3 +1,14 @@
+<!--
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+-->
+
 <!DOCTYPE html>
 <html lang="en">
 

diff --git a/web/about/about.js b/web/about/about.js
@@ -1,4 +1,14 @@
-// select toggle button
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 const toggle = document.getElementById("mode");
 
 toggle.addEventListener("click", () => {

diff --git a/web/index.html b/web/index.html
@@ -1,3 +1,14 @@
+<!--
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+-->
+
 <!DOCTYPE html>
 <html lang="en-us">
 

diff --git a/web/style.css b/web/style.css
@@ -1,3 +1,14 @@
+/*
+ * Copyright © 2023 DNAnalyzer. Some rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * You are entirely responsible for the use of this application, including any and all activities that occur.
+ * While DNAnalyzer strives to fix all major bugs that may be either reported by a user or discovered while debugging,
+ * they will not be held liable for any loss that the user may incur as a result of using this application, under any circumstances.
+ *
+ * For further inquiries, please reach out to [email protected]
+ */
+
 @import url('https://fonts.googleapis.com/css2?family=Poppins&display=swap');
 
 *>* {