Merge branch 'main' of https://github.com/VerisimilitudeX/DNAnalyzer

.vscode/launch.json

@@ -1,5 +1,6 @@
 {
   "configurations": [
+
     {
       "type": "java",
       "name": "DNADataUploader",
@@ -20,7 +21,7 @@
       "request": "launch",
       "mainClass": "DNAnalyzer.Main",
       "projectName": "DNAnalyzer",
-      "args": "assets/dna/random/dnalong.fa --amino=ser --min=16450 --max=520218 -r --rcomplement --version"
+      "args": "assets/dna/random/dnalong.fa --amino=ser --min=16450 --max=520218 -r --rcomplement --version --mutate 10"
     }
   ]
 }

src/main/java/DNAnalyzer/adapter/ApiKeyController.java

@@ -1,7 +1,7 @@
 package DNAnalyzer.adapter;
 
+import DNAnalyzer.core.ApiKeyService;
 import java.util.Map;
-
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.CrossOrigin;
@@ -11,53 +11,46 @@
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
-import DNAnalyzer.core.ApiKeyService;
-
-/**
- * REST controller for managing OpenAI API key.
- */
+/** REST controller for managing OpenAI API key. */
 @RestController
 @RequestMapping("/api-key")
 @CrossOrigin(origins = "*")
 public class ApiKeyController {
 
-    private final ApiKeyService apiKeyService;
-
-    @Autowired
-    public ApiKeyController(ApiKeyService apiKeyService) {
-        this.apiKeyService = apiKeyService;
-    }
-
-    /**
-     * Get the current API key status.
-     *
-     * @return Response indicating if API key is configured
-     */
-    @GetMapping
-    public ResponseEntity<ApiKeyResponse> getApiKeyStatus() {
-        boolean hasKey = apiKeyService.hasApiKey();
-        return ResponseEntity.ok(new ApiKeyResponse(hasKey));
-    }
-
-    /**
-     * Set a new API key.
-     *
-     * @param request Request containing the new API key
-     * @return Response indicating success
-     */
-    @PostMapping
-    public ResponseEntity<?> setApiKey(@RequestBody SetApiKeyRequest request) {
-        try {
-            apiKeyService.setApiKey(request.getApiKey());
-            return ResponseEntity.ok(Map.of(
-                "status", "success",
-                "message", "API key updated successfully"
-            ));
-        } catch (IllegalArgumentException e) {
-            return ResponseEntity.badRequest().body(Map.of(
-                "status", "error",
-                "message", e.getMessage()
-            ));
-        }
+  private final ApiKeyService apiKeyService;
+
+  @Autowired
+  public ApiKeyController(ApiKeyService apiKeyService) {
+    this.apiKeyService = apiKeyService;
+  }
+
+  /**
+   * Get the current API key status.
+   *
+   * @return Response indicating if API key is configured
+   */
+  @GetMapping
+  public ResponseEntity<ApiKeyResponse> getApiKeyStatus() {
+    boolean hasKey = apiKeyService.hasApiKey();
+    return ResponseEntity.ok(new ApiKeyResponse(hasKey));
+  }
+
+  /**
+   * Set a new API key.
+   *
+   * @param request Request containing the new API key
+   * @return Response indicating success
+   */
+  @PostMapping
+  public ResponseEntity<?> setApiKey(@RequestBody SetApiKeyRequest request) {
+    try {
+      apiKeyService.setApiKey(request.getApiKey());
+      return ResponseEntity.ok(
+          Map.of(
+              "status", "success",
+              "message", "API key updated successfully"));
+    } catch (IllegalArgumentException e) {
+      return ResponseEntity.badRequest().body(Map.of("status", "error", "message", e.getMessage()));
     }
+  }
 }

src/main/java/DNAnalyzer/adapter/ApiKeyResponse.java

@@ -1,16 +1,14 @@
 package DNAnalyzer.adapter;
 
-/**
- * Response object for API key status.
- */
+/** Response object for API key status. */
 public class ApiKeyResponse {
-    private final boolean configured;
+  private final boolean configured;
 
-    public ApiKeyResponse(boolean configured) {
-        this.configured = configured;
-    }
+  public ApiKeyResponse(boolean configured) {
+    this.configured = configured;
+  }
 
-    public boolean isConfigured() {
-        return configured;
-    }
+  public boolean isConfigured() {
+    return configured;
+  }
 }

src/main/java/DNAnalyzer/adapter/SetApiKeyRequest.java

@@ -1,16 +1,14 @@
 package DNAnalyzer.adapter;
 
-/**
- * Request object for setting API key.
- */
+/** Request object for setting API key. */
 public class SetApiKeyRequest {
-    private String apiKey;
+  private String apiKey;
 
-    public String getApiKey() {
-        return apiKey;
-    }
+  public String getApiKey() {
+    return apiKey;
+  }
 
-    public void setApiKey(String apiKey) {
-        this.apiKey = apiKey;
-    }
+  public void setApiKey(String apiKey) {
+    this.apiKey = apiKey;
+  }
 }

src/main/java/DNAnalyzer/adapter/StatusController.java

@@ -1,22 +1,22 @@
 package DNAnalyzer.adapter;
 
+import java.util.Map;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
-import java.util.Map;
 
 @RestController
 @RequestMapping("/api")
 @CrossOrigin(origins = "*")
 public class StatusController {
-
-    @GetMapping("/status")
-    public ResponseEntity<?> getStatus() {
-        return ResponseEntity.ok(Map.of(
+
+  @GetMapping("/status")
+  public ResponseEntity<?> getStatus() {
+    return ResponseEntity.ok(
+        Map.of(
             "status", "online",
-            "version", "1.0.0"
-        ));
-    }
-}
+            "version", "1.0.0"));
+  }
+}

src/main/java/DNAnalyzer/core/DNAMutation.java

@@ -0,0 +1,112 @@
+package DNAnalyzer.core;
+
+import DNAnalyzer.utils.core.DNATools;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintStream;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.Random;
+
+/** This class provides provides functionality for generating mutated DNA sequences. */
+public class DNAMutation {
+
+  private static final char[] BASES = {'A', 'T', 'C', 'G', 'N'};
+  private static Random random = new Random();
+
+  /**
+   * Generates a list of 10 mutated DNA sequences based on the specified number of base mutations
+   * and prints them to the console.
+   *
+   * @param dnaString Original DNA sequence to mutate
+   * @param numMutations The number of base mutations to apply to each mutated sequence
+   */
+  public static void generateAndWriteMutatedSequences(
+      String dnaString, int numMutations, PrintStream out) {
+    List<String> mutatedSequences = new ArrayList<>();
+
+    out.println("\nMutating DNA sequence...");
+
+    // Generate 10 mutated sequences
+    for (int i = 0; i < 10; i++) {
+      DNATools mutatedDna = new DNATools(mutate(dnaString, numMutations));
+      mutatedSequences.add(mutatedDna.dna()); // Store the mutated DNA sequence to the list
+    }
+
+    // Dynamically generate the file name based on the current timestamp
+    String timestamp = new SimpleDateFormat("yyyyMMdd_HHmmss").format(new Date());
+    String fileName = "mutated_dna_" + timestamp + ".fa";
+
+    // Write the mutated sequences to a file
+    try (FileWriter writer = new FileWriter(fileName)) {
+      for (int i = 0; i < mutatedSequences.size(); i++) {
+        writer.write(">mutation_" + (i + 1) + "\n"); // Write a header for each mutated sequence
+        String mutatedSequence = mutatedSequences.get(i);
+
+        // Write the sequence over multiple lines (e.g., 80 characters per line)
+        for (int j = 0; j < mutatedSequence.length(); j += 80) {
+          writer.write(
+              mutatedSequence.substring(j, Math.min(j + 80, mutatedSequence.length())) + "\n");
+        }
+      }
+      out.println("Mutated DNA sequences have been written to: " + fileName + "\n");
+    } catch (IOException e) {
+      out.println("Error writing to file: " + e.getMessage() + "\n");
+    }
+  }
+
+  /**
+   * Mutates a DNA sequence with a specified number of random base mutations.
+   *
+   * @param dnaString Original DNA sequence to mutate
+   * @param numMutations The number of mutations (substitutions) to apply to the sequence
+   * @return A new mutated DNA sequence
+   */
+  private static String mutate(String dnaString, int numMutations) {
+    StringBuilder mutatedDna = new StringBuilder(dnaString);
+
+    if (numMutations > mutatedDna.length()) {
+      System.out.println(
+          "Warning: Number of requested mutations exceeds DNA length. Limiting to "
+              + mutatedDna.length());
+      numMutations = mutatedDna.length();
+    }
+
+    // Create a list of all possible positions
+    List<Integer> availablePositions = new ArrayList<>();
+    for (int i = 0; i < dnaString.length(); i++) {
+      availablePositions.add(i);
+    }
+
+    // Perform mutations
+    for (int i = 0; i < numMutations; i++) {
+      // Select a random position from the available positions
+      int randomPosition = random.nextInt(availablePositions.size());
+      int position = availablePositions.remove(randomPosition);
+
+      char originalBase = dnaString.charAt(position);
+      char mutatedBase = getDifferentBase(originalBase);
+
+      mutatedDna.setCharAt(position, mutatedBase);
+    }
+
+    return mutatedDna.toString();
+  }
+
+  /**
+   * Returns a random base different from the original base.
+   *
+   * @param originalBase Original base to mutate from
+   * @return A mutated base (different from the original)
+   */
+  private static char getDifferentBase(char originalBase) {
+    int index = new String(BASES).indexOf(originalBase);
+
+    // Pick a random index that isn’t the same as the original
+    int newIndex = (index + 1 + random.nextInt(BASES.length - 1)) % BASES.length;
+
+    return BASES[newIndex];
+  }
+}

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

@@ -11,16 +11,17 @@
 
 package DNAnalyzer.ui.cli;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.Objects;
+import static DNAnalyzer.data.Parser.parseFile;
 
 import DNAnalyzer.core.DNAAnalysis;
+import DNAnalyzer.core.DNAMutation;
 import DNAnalyzer.core.Properties;
-import static DNAnalyzer.data.Parser.parseFile;
 import DNAnalyzer.ui.gui.DNAnalyzerGUI;
 import DNAnalyzer.utils.core.DNATools;
 import DNAnalyzer.utils.core.Utils;
+import java.io.File;
+import java.io.IOException;
+import java.util.Objects;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
@@ -89,6 +90,13 @@ public class CmdArgs implements Runnable {
       description = "Prints the complement of the DNA sequence.")
   boolean rcomplement;
 
+  @Option(
+      names = {"--mutate"},
+      description =
+          "Generates 10 mutations of the DNA sequence, each with the specified number of mutations,"
+              + " and saves them to a file.")
+  int mutationCount = 0;
+
   @Option(
       names = {"--verbose", "-V"},
       description = "Enable verbose mode (detailed output)")
@@ -127,6 +135,11 @@ public void run() {
     } else {
       DNAAnalysis dnaAnalyzer = dnaAnalyzer(aminoAcid).isValidDna().replaceDNA("u", "t");
 
+      if (mutationCount > 0) {
+        DNAMutation.generateAndWriteMutatedSequences(
+            dnaAnalyzer.dna().getDna(), mutationCount, System.out);
+      }
+
       if (reverse) {
         dnaAnalyzer = dnaAnalyzer.reverseDna();
       }