Merge pull request #369 from VerisimilitudeX/ai

New Feature - AI Analysis

.github/FUNDING.yml

@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-# github: [ Verisimilitude11 ]
+# github: [ VerisimilitudeX ]
 patreon: # Replace with a single Patreon username
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username

.vscode/settings.json

@@ -1,4 +1,5 @@
 {
   "java.configuration.updateBuildConfiguration": "automatic",
-  "java.compile.nullAnalysis.mode": "automatic"
+  "java.compile.nullAnalysis.mode": "automatic",
+  "java.jdt.ls.vmargs": "-XX:+UseParallelGC -XX:GCTimeRatio=4 -XX:AdaptiveSizePolicyWeight=90 -Dsun.zip.disableMemoryMapping=true -Xmx2G -Xms100m -Xlog:disable"
 }

CITATION.cff

@@ -7,4 +7,4 @@ date-released: 2022-10-10
 message: "If you use this software, please cite it using these metadata."
 title: "Revolutionizing DNA analysis and making it accessible to all through innovative analysis and interpretive tools"
 version: "2.0.0"
-url: "https://github.com/Verisimilitude11/DNAnalyzer"
+url: "https://github.com/VerisimilitudeX/DNAnalyzer"

Contributing_Guidelines.md

@@ -33,15 +33,15 @@ community looks forward to your contributions. 🎉
 ## I Have a Question
 
 > If you want to ask a question, we assume that you have read the
-> available [Documentation](https://github.com/Verisimilitude11/DNAnalyzer/blob/main/README.md).
+> available [Documentation](https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/README.md).
 > Before you ask a question, it is best to search for
-> existing [Issues](https://github.com/Verisimilitude11/DNAnalyzer/issues) that might help you. In case you have found a
+> existing [Issues](https://github.com/VerisimilitudeX/DNAnalyzer/issues) that might help you. In case you have found a
 > suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search
 > the internet for answers first.
 
 If you then still feel the need to ask a question and need clarification, we recommend the following:
 
-- Open an [Issue](https://github.com/Verisimilitude11/DNAnalyzer/issues/new).
+- Open an [Issue](https://github.com/VerisimilitudeX/DNAnalyzer/issues/new).
 - Provide as much context as you can about what you're running into.
 - Provide project and platform versions (nodejs, npm, etc), depending on what seems relevant.
 
@@ -95,7 +95,7 @@ Click on fork to create a copy of project to your account. This creates a separa
 You have forked the project you want to contribute to your GitHub account. To get this project on your development
 machine we use clone command of git.
 
-`$ git clone https://github.com/Verisimilitude11/DNAnalyzer.git` <br/>
+`$ git clone https://github.com/VerisimilitudeX/DNAnalyzer.git` <br/>
 Now you have the project on your local machine.
 
 <br />
@@ -106,7 +106,7 @@ Remote means the remote location of project on GitHub. By cloning, we have a rem
 forked repository. Now we will add a remote to the original repository from where we had forked.
 
 `$ cd <your-forked-project-folder>`
-`$ git remote add upstream https://github.com/Verisimilitude11/DNAnalyzer.git` <br/>
+`$ git remote add upstream https://github.com/VerisimilitudeX/DNAnalyzer.git` <br/>
 You will see the benefits of adding remote later.
 
 <br />
@@ -183,7 +183,7 @@ following steps in advance to help us fix any potential bug as fast as possible.
 - Make sure that you are using the latest version.
 - Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment
   components/versions (Make sure that you have read
-  the [documentation](https://github.com/Verisimilitude11/DNAnalyzer/blob/main/README.md). If you are looking for
+  the [documentation](https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/README.md). If you are looking for
   support, you might want to check [this section](#i-have-a-question)).
 - To see if other users have experienced (and potentially already solved) the same issue you are having, check if there
   is not already a bug report existing for your bug or error in the _**bug tracker**_.
@@ -207,7 +207,7 @@ following steps in advance to help us fix any potential bug as fast as possible.
 
 We use GitHub issues to track bugs and errors. If you run into an issue with the project:
 
-- Open an [Issue](https://github.com/Verisimilitude11/DNAnalyzer/issues/new). (Since we can't be sure at this point
+- Open an [Issue](https://github.com/VerisimilitudeX/DNAnalyzer/issues/new). (Since we can't be sure at this point
   whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.)
 - Explain the behavior you would expect and the actual behavior.
 - Please provide as much context as possible and describe the _reproduction steps_ that someone else can follow to
@@ -238,9 +238,9 @@ to understand your suggestion and find related suggestions.
 
 - Make sure that you are using the latest version.
 
-- Read the [documentation](https://github.com/Verisimilitude11/DNAnalyzer/blob/main/README.md) carefully and find out if
+- Read the [documentation](https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/README.md) carefully and find out if
   the functionality is already covered, maybe by an individual configuration.
-- Perform a [search](https://github.com/Verisimilitude11/DNAnalyzer/issues) to see if the enhancement has already been
+- Perform a [search](https://github.com/VerisimilitudeX/DNAnalyzer/issues) to see if the enhancement has already been
   suggested. If it has, add a comment to the existing issue instead of opening a new one.
 - Find out whether your idea fits with the scope and aims of the project. It's up to you to make a strong case to
   convince the project's developers of the merits of this feature. Keep in mind that we want features that will be
@@ -251,7 +251,7 @@ to understand your suggestion and find related suggestions.
 
 #### How Do I Submit a Good Enhancement Suggestion?
 
-Enhancement suggestions are tracked as [GitHub issues](https://github.com/Verisimilitude11/DNAnalyzer/issues).
+Enhancement suggestions are tracked as [GitHub issues](https://github.com/VerisimilitudeX/DNAnalyzer/issues).
 
 - Use a **clear and descriptive title** for the issue to identify the suggestion.
 - Provide a **step-by-step description of the suggested enhancement** in as many details as possible.

README.md

@@ -65,7 +65,7 @@ A [video tutorial](https://youtu.be/dOwkInn6eDw) covering the instructions below
 
 ### Build & Run
 
-* Note: Ensure you have Java [17](https://www.oracle.com/java/technologies/downloads/#jdk17-windows) or higher installed and a `JAVA_HOME` path variable set for the program to function correctly.
+The easiest way to run the program on Windows is by using the executable file located in the [releases](https://github.com/VerisimilitudeX/DNAnalyzer/releases/latest) section to install the program, build gradle and run the GUI.
 
 * We use [Gradle](https://gradle.org) for building. The Gradle wrapper takes care of downloading dependencies, testing, compiling, linking, and packaging the code.
 <details>
@@ -238,9 +238,9 @@ View our in-line citations in the [Citations](docs/citations.md) document.
 
 ## Contributing
 
-* [Contributing Guidelines](https://github.com/Verisimilitude11/DNAnalyzer/blob/main/docs/Contribution%20Guideline/Contribution_Guideline.md)
+* [Contributing Guidelines](https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/docs/Contribution%20Guideline/Contribution_Guideline.md)
 
-* [How To Use Git](https://github.com/Verisimilitude11/DNAnalyzer/blob/main/docs/contributing/CONTRIBUTING.md)
+* [How To Use Git](https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/docs/contributing/CONTRIBUTING.md)
 
 ## Terms of Use
 

build.gradle

@@ -43,6 +43,10 @@ dependencies {
 
     // OpenAI-GPT-3
     implementation group: 'com.github.plexpt', name: 'chatgpt', version: '4.0.1'
+    implementation 'com.theokanning.openai-gpt3-java:service:0.11.1'
+
+    // JSON Parser
+    implementation 'org.json:json:20210307'
 }
 
 application {
@@ -54,7 +58,7 @@ publishing {
     repositories {
         maven {
             name = "Github"
-            url = uri("https://maven.pkg.github.com/Verisimilitude11/DNAnalyzer")
+            url = uri("https://maven.pkg.github.com/VerisimilitudeX/DNAnalyzer")
             credentials {
                 username = project.findProperty("gpr.user") ?: System.getenv("GITHUB_USERNAME")
                 password = project.findProperty("gpr.key") ?: System.getenv("GITHUB_TOKEN")
@@ -69,7 +73,7 @@ publishing {
             artifactId = 'dnanalyzer'
             version = '2.0.0'
             pom {
-                url.set("https://github.com/Verisimilitude11/DNAnalyzer.git")
+                url.set("https://github.com/VerisimilitudeX/DNAnalyzer.git")
             }
         }
     }

docs/citations.md

@@ -4,9 +4,9 @@
 
 <h4>DNAnalyzer was developed with the help of the following people:
 <h4>
-<a href="https://github.com/Verisimilitude11/DNAnalyzer/graphs/contributors">
+<a href="https://github.com/VerisimilitudeX/DNAnalyzer/graphs/contributors">
 
-<img src="https://contrib.rocks/image?repo=Verisimilitude11/DNAnalyzer&&max=817"  alt=""/>
+<img src="https://contrib.rocks/image?repo=VerisimilitudeX/DNAnalyzer&&max=817"  alt=""/>
 
 <h2 align="left" id="citations">Citations
 </h2>

docs/contributing/CONTRIBUTING.md

@@ -2,7 +2,7 @@
 
 ## 1. Fork it 🍴
 
-You can get your own fork (copy) of [DNAnalyzer](https://github.com/Verisimilitude11/DNAnalyzer) by using the `Fork`
+You can get your own fork (copy) of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork`
 button at the top right of this page.
 
 ![Fork Button](https://github-images.s3.amazonaws.com/help/bootcamp/Bootcamp-Fork.png)

docs/contributing/Contribution_Guidelines.md

@@ -3,8 +3,8 @@
 - Drop a :star: on the GitHub repository (It's optional)<br/>
 
 - Before Contribute Please
-  read [Contributing_Guidelines.md]((https://github.com/Verisimilitude11/DNAnalyzer/blob/main/Contributing_Guidelines.md))
-  and [CODE_OF_CONDUCT.md]((https://github.com/Verisimilitude11/DNAnalyzer/blob/main/CODE_OF_CONDUCT.md)).
+  read [Contributing_Guidelines.md]((https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/Contributing_Guidelines.md))
+  and [CODE_OF_CONDUCT.md]((https://github.com/VerisimilitudeX/DNAnalyzer/blob/main/CODE_OF_CONDUCT.md)).
 
 - Create an issue of the project or a feature you would like to add in the project and get the task assigned for
   yourself.(Issue can be any bug fixes or any feature you want to add in this project).
@@ -13,7 +13,7 @@
 
 - Clone the Repo by going to your local Git Client in a particular local folder in your local machine by using this
   command with your forked repository link in place of below given link: <br/>
-  `git clone https://github.com/Verisimilitude11/DNAnalyzer`
+  `git clone https://github.com/VerisimilitudeX/DNAnalyzer`
 - Create a branch using below command.
   `git branch <your branch name>`
 - Checkout to your branch.

docs/wiki-Home.md

@@ -8,15 +8,15 @@ Welcome to the DNAnalyzer wiki!
 > developing a Command-Line-Interface (CLI) and Graphical User Interface (GUI) that will enable physicians to quickly and
 > more easily interact with the software, enabling them to identify genetic mutations that may cause disease.
 
-# [Documents](https://github.com/Verisimilitude11/DNAnalyzer/tree/main/docs)
+# [Documents](https://github.com/VerisimilitudeX/DNAnalyzer/tree/main/docs)
 
 ## Contributing
 
 ### Steps to follow 📜
 
 #### 1. Fork it 🍴
 
-You can get your own fork (copy) of [DNAnalyzer](https://github.com/Verisimilitude11/DNAnalyzer) by using the `Fork`
+You can get your own fork (copy) of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork`
 button at the top right of this page.
 
 ![Fork Button](https://github-images.s3.amazonaws.com/help/bootcamp/Bootcamp-Fork.png)
@@ -142,7 +142,7 @@ provide a title and description, with brevity, that describe your much-appreciat
 
 - Clone the Repo by going to your local Git Client in a particular local folder in your local machine by using this
   command with your forked repository link in place of below given link: <br/>
-  `git clone https://github.com/Verisimilitude11/DNAnalyzer`
+  `git clone https://github.com/VerisimilitudeX/DNAnalyzer`
 - Create a branch using below command.
   `git branch <your branch name>`
 - Checkout to your branch.
@@ -190,12 +190,12 @@ A program to analyze DNA sequences.
 
 ## Reports
 
-[Key Personnel and Knowledge Distribution](https://github.com/Verisimilitude11/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf)
+[Key Personnel and Knowledge Distribution](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf)
 
-[Technical Health Overview](https://github.com/Verisimilitude11/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf)
+[Technical Health Overview](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf)
 
-[Trend Report](https://github.com/Verisimilitude11/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf)
+[Trend Report](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf)
 
 ## Samples
 
-[Serine DNAlong](https://github.com/Verisimilitude11/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md)
+[Serine DNAlong](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md)

src/main/java/DNAnalyzer/Main.java

@@ -11,41 +11,20 @@
 
 package DNAnalyzer;
 
-import java.io.ByteArrayOutputStream;
 import java.io.IOException;
-import java.io.PrintStream;
-
-import com.plexpt.chatgpt.*;
-
-import DNAnalyzer.ui.cli.CmdArgs;
-import picocli.CommandLine;
+import DNAnalyzer.utils.ai.PathRouter;
 
 /**
  * Main Class for the DNAnalyzer program.
  *
- * @author Piyush Acharya (@Verisimilitude11)
+ * @author Piyush Acharya (@VerisimilitudeX)
  * @version 1.2.1
  * @see <a href=
- *      "https://www.genome.gov/about-genomics/fact-sheets/Genomic-Data-Science">...</a>
+ *      "https://www.genome.gov/about-genomics/fact-sheets/Genomic-Data-Science">Genomic
+ *      Datasheet</a>
  */
 public class Main {
 
-    /**
-     * Clears the console screen based on the operating system.
-     *
-     * @throws InterruptedException Necessary for clearing the screen
-     * @throws IOException          Necessary for clearing the screen
-     *                              {@code @category} User Experience
-     */
-    public static void clearTerminal() throws InterruptedException, IOException {
-        if (System.getProperty("os.name").contains("Windows")) { // if the os is Windows
-            new ProcessBuilder("cmd", "/c", "cls").inheritIO().start().waitFor();
-        } else {
-            System.out.print("\u001b[H\u001b[2J"); // unicode string to clear everything logged above this
-            System.out.flush();
-        }
-    }
-
     /**
      * Main method for the DNAnalyzer program (run this).
      *
@@ -55,53 +34,12 @@ public static void clearTerminal() throws InterruptedException, IOException {
      * @throws InterruptedException
      */
     public static void main(final String[] args) throws InterruptedException, IOException {
-        // Clear the console screen
-        clearTerminal();
-
-        System.out.println(
-                "Welcome to DNAnalyzer! Please allow up to 15 seconds for the analysis to complete (note: the time may vary based on your hardware).");
-
         String apiKey = System.getenv("OPENAI_API_KEY");
         if (apiKey == null) {
-            clearTerminal();
-            new CommandLine(new CmdArgs()).execute(args);
-            System.out
-                    .println("\n**Please set your OPENAI_API_KEY environment variable for an AI analysis of the DNA**");
-            System.exit(1);
+            PathRouter.regular(args);
         } else {
-
-            // Create a ByteArrayOutputStream to hold the console output
-            ByteArrayOutputStream baos = new ByteArrayOutputStream();
-            PrintStream ps = new PrintStream(baos);
-
-            // Save the old System.out
-            PrintStream old = System.out;
-
-            // Set the new System.out to the PrintStream
-            System.setOut(ps);
-
-            new CommandLine(new CmdArgs()).execute(args);
-
-            // Restore the old System.out
-            System.out.flush();
-            System.setOut(old);
-
-            // Get the captured console output as a string
-            String output = baos.toString();
-
-            // Do something with the captured output
-            ChatGPT chatGPT = ChatGPT.builder()
-                    .apiKey(apiKey)
-                    .build()
-                    .init();
-
-            String res = chatGPT.chat(
-                    "From the perspective of a biological researcher, I would like you to provide a comprehensive understanding of the DNA analysis that goes beyond the surface-level information. I expect you to use technical terms but make it meaningful and tangible enough that I can learn about the DNA. In one paragraph for each topic, please explain the results of this DNA analysis to me, assuming I am an experienced biotechnology researcher. It is crucial that you avoid stating that DNA cannot be analyzed and offer more in-depth insights into the analysis: "
-                            + output + ". End by summarizing the results of the analysis.");
-
-            System.out.println(output + "\n-----------------------\n\nAI Analysis:\n");
-            System.out.println(res);
-            System.exit(0);
+            PathRouter.runGptAnalysis(args);
         }
+
     }
 }

src/main/java/DNAnalyzer/core/Properties.java

@@ -24,7 +24,7 @@
 /**
  * Prints the list of proteins and their respective properties found in the DNA.
  *
- * @author Piyush Acharya (@Verisimilitude11)
+ * @author Piyush Acharya (@VerisimilitudeX)
  * @version 1.2.1
  */
 public class Properties {

src/main/java/DNAnalyzer/data/codon/CodonDataConstants.java

@@ -18,7 +18,7 @@
 /**
  * Declares the codon data for the 20 amino acids
  *
- * @author Piyush Acharya (@Verisimilitude11)
+ * @author Piyush Acharya (@VerisimilitudeX)
  * @version 1.2.1
  * @see "https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables"
  */

src/main/java/DNAnalyzer/data/codon/CodonDataUtils.java

@@ -18,7 +18,7 @@
 /**
  * provide function to access codon data from amino acid.
  *
- * @author Piyush Acharya (@Verisimilitude11)
+ * @author Piyush Acharya (@VerisimilitudeX)
  * @version 1.2.1
  * @see "https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables"
  */

src/main/java/DNAnalyzer/data/codon/CodonFrame.java

@@ -16,7 +16,7 @@
 /**
  * Declares the codon frame
  *
- * @author Piyush Acharya (@Verisimilitude11)
+ * @author Piyush Acharya (@VerisimilitudeX)
  * @version 1.2.1
  * @see "https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables"
  */

src/main/java/DNAnalyzer/ui/cli/CmdArgs.java

@@ -11,11 +11,11 @@
 
 package DNAnalyzer.ui.cli;
 
-import DNAnalyzer.Main;
 import DNAnalyzer.core.DNAAnalysis;
 import DNAnalyzer.core.Properties;
 import DNAnalyzer.ui.gui.DNAnalyzerGUI;
 import DNAnalyzer.utils.core.DNATools;
+import DNAnalyzer.utils.core.Utils;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
@@ -96,7 +96,7 @@ public void run() {
     private DNAAnalysis dnaAnalyzer(final String aminoAcid) {
         try {
             String protein = null;
-            Main.clearTerminal();
+            Utils.clearTerminal();
             final String dna = readFile(dnaFile);
             if (proteinFile != null) {
                 protein = readFile(proteinFile);