style: format code with Autopep8 and Google Java Format

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/web/AnalyzerController.java

@@ -1,10 +1,11 @@
 package DNAnalyzer.web;
 
+import DNAnalyzer.core.DNAAnalysis;
+import DNAnalyzer.utils.core.DNATools;
 import java.io.ByteArrayOutputStream;
 import java.io.PrintStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
-
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.CrossOrigin;
@@ -14,113 +15,110 @@
 import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.multipart.MultipartFile;
 
-import DNAnalyzer.core.DNAAnalysis;
-import DNAnalyzer.utils.core.DNATools;
-
 @RestController
 @RequestMapping("/api")
 @CrossOrigin(origins = "*")
 public class AnalyzerController {
 
-    @PostMapping(value = "/analyze", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
-    public ResponseEntity<String> analyzeDNA(
-            @RequestParam("dnaFile") MultipartFile dnaFile,
-            @RequestParam(value = "amino", defaultValue = "M") String amino,
-            @RequestParam(value = "minCount", defaultValue = "1") int minCount,
-            @RequestParam(value = "maxCount", defaultValue = "100") int maxCount,
-            @RequestParam(value = "reverse", defaultValue = "false") boolean reverse,
-            @RequestParam(value = "rcomplement", defaultValue = "false") boolean rcomplement,
-            @RequestParam(value = "codons", defaultValue = "false") boolean codons,
-            @RequestParam(value = "coverage", defaultValue = "false") boolean coverage,
-            @RequestParam(value = "longest", defaultValue = "false") boolean longest,
-            @RequestParam(value = "format", defaultValue = "text") String format) {
-
-        try {
-            // Create temporary file
-            Path tempFile = Files.createTempFile("dna-", ".fa");
-            dnaFile.transferTo(tempFile.toFile());
-
-            // Capture console output
-            ByteArrayOutputStream baos = new ByteArrayOutputStream();
-            PrintStream ps = new PrintStream(baos);
-            PrintStream old = System.out;
-            System.setOut(ps);
-
-            try {
-                // Read DNA sequence
-                String dnaSequence = new String(Files.readAllBytes(tempFile));
-
-                // Run analysis
-                DNAAnalysis analysis = new DNAAnalysis(new DNATools(dnaSequence), null, amino);
-
-                if (reverse) {
-                    analysis = analysis.reverseDna();
-                }
-                if (rcomplement) {
-                    analysis = analysis.reverseComplement();
-                }
-
-                if (codons) {
-                    analysis.outPutCodons(minCount, maxCount, System.out);
-                }
-                if (coverage) {
-                    analysis.printHighCoverageRegions(System.out);
-                }
-                if (longest) {
-                    analysis.printLongestProtein(System.out);
-                }
-
-                // Get output
-                String output = baos.toString();
-
-                // Format output
-                if ("json".equals(format)) {
-                    output = formatAsJson(output);
-                } else if ("csv".equals(format)) {
-                    output = formatAsCsv(output);
-                }
-
-                return ResponseEntity.ok(output);
-
-            } finally {
-                // Restore console output and cleanup
-                System.setOut(old);
-                Files.deleteIfExists(tempFile);
-            }
-
-        } catch (Exception e) {
-            return ResponseEntity.badRequest().body("Error analyzing DNA: " + e.getMessage());
+  @PostMapping(value = "/analyze", consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
+  public ResponseEntity<String> analyzeDNA(
+      @RequestParam("dnaFile") MultipartFile dnaFile,
+      @RequestParam(value = "amino", defaultValue = "M") String amino,
+      @RequestParam(value = "minCount", defaultValue = "1") int minCount,
+      @RequestParam(value = "maxCount", defaultValue = "100") int maxCount,
+      @RequestParam(value = "reverse", defaultValue = "false") boolean reverse,
+      @RequestParam(value = "rcomplement", defaultValue = "false") boolean rcomplement,
+      @RequestParam(value = "codons", defaultValue = "false") boolean codons,
+      @RequestParam(value = "coverage", defaultValue = "false") boolean coverage,
+      @RequestParam(value = "longest", defaultValue = "false") boolean longest,
+      @RequestParam(value = "format", defaultValue = "text") String format) {
+
+    try {
+      // Create temporary file
+      Path tempFile = Files.createTempFile("dna-", ".fa");
+      dnaFile.transferTo(tempFile.toFile());
+
+      // Capture console output
+      ByteArrayOutputStream baos = new ByteArrayOutputStream();
+      PrintStream ps = new PrintStream(baos);
+      PrintStream old = System.out;
+      System.setOut(ps);
+
+      try {
+        // Read DNA sequence
+        String dnaSequence = new String(Files.readAllBytes(tempFile));
+
+        // Run analysis
+        DNAAnalysis analysis = new DNAAnalysis(new DNATools(dnaSequence), null, amino);
+
+        if (reverse) {
+          analysis = analysis.reverseDna();
+        }
+        if (rcomplement) {
+          analysis = analysis.reverseComplement();
         }
-    }
 
-    private String formatAsJson(String output) {
-        // Convert output to JSON format
-        StringBuilder json = new StringBuilder();
-        json.append("{\"results\": [");
-
-        String[] lines = output.split("\n");
-        for (int i = 0; i < lines.length; i++) {
-            json.append("\"").append(lines[i].replace("\"", "\\\"")).append("\"");
-            if (i < lines.length - 1) {
-                json.append(",");
-            }
+        if (codons) {
+          analysis.outPutCodons(minCount, maxCount, System.out);
+        }
+        if (coverage) {
+          analysis.printHighCoverageRegions(System.out);
+        }
+        if (longest) {
+          analysis.printLongestProtein(System.out);
         }
-
-        json.append("]}");
-        return json.toString();
-    }
 
-    private String formatAsCsv(String output) {
-        // Convert output to CSV format
-        StringBuilder csv = new StringBuilder();
-
-        String[] lines = output.split("\n");
-        for (String line : lines) {
-            // Replace any commas in the data with semicolons
-            line = line.replace(",", ";");
-            csv.append(line).append(",\n");
+        // Get output
+        String output = baos.toString();
+
+        // Format output
+        if ("json".equals(format)) {
+          output = formatAsJson(output);
+        } else if ("csv".equals(format)) {
+          output = formatAsCsv(output);
         }
-
-        return csv.toString();
+
+        return ResponseEntity.ok(output);
+
+      } finally {
+        // Restore console output and cleanup
+        System.setOut(old);
+        Files.deleteIfExists(tempFile);
+      }
+
+    } catch (Exception e) {
+      return ResponseEntity.badRequest().body("Error analyzing DNA: " + e.getMessage());
+    }
+  }
+
+  private String formatAsJson(String output) {
+    // Convert output to JSON format
+    StringBuilder json = new StringBuilder();
+    json.append("{\"results\": [");
+
+    String[] lines = output.split("\n");
+    for (int i = 0; i < lines.length; i++) {
+      json.append("\"").append(lines[i].replace("\"", "\\\"")).append("\"");
+      if (i < lines.length - 1) {
+        json.append(",");
+      }
     }
-}
+
+    json.append("]}");
+    return json.toString();
+  }
+
+  private String formatAsCsv(String output) {
+    // Convert output to CSV format
+    StringBuilder csv = new StringBuilder();
+
+    String[] lines = output.split("\n");
+    for (String line : lines) {
+      // Replace any commas in the data with semicolons
+      line = line.replace(",", ";");
+      csv.append(line).append(",\n");
+    }
+
+    return csv.toString();
+  }
+}

src/test/java/DNAnalyzer/core/ApiKeyServiceTest.java

@@ -1,27 +1,28 @@
 package DNAnalyzer.core;
 
 import static org.junit.jupiter.api.Assertions.*;
+
 import org.junit.jupiter.api.Test;
 
 class ApiKeyServiceTest {
 
-    private ApiKeyService apiKeyService = new ApiKeyService();
+  private ApiKeyService apiKeyService = new ApiKeyService();
 
-    @Test
-    void shouldSetAndGetApiKey() {
-        String newKey = "test-api-key";
-        apiKeyService.setApiKey(newKey);
-        assertEquals(newKey, apiKeyService.getApiKey());
-    }
+  @Test
+  void shouldSetAndGetApiKey() {
+    String newKey = "test-api-key";
+    apiKeyService.setApiKey(newKey);
+    assertEquals(newKey, apiKeyService.getApiKey());
+  }
 
-    @Test
-    void shouldReturnFalseWhenNoKeySet() {
-        assertFalse(apiKeyService.hasApiKey());
-    }
+  @Test
+  void shouldReturnFalseWhenNoKeySet() {
+    assertFalse(apiKeyService.hasApiKey());
+  }
 
-    @Test
-    void shouldReturnTrueWhenKeySet() {
-        apiKeyService.setApiKey("test-key");
-        assertTrue(apiKeyService.hasApiKey());
-    }
+  @Test
+  void shouldReturnTrueWhenKeySet() {
+    apiKeyService.setApiKey("test-key");
+    assertTrue(apiKeyService.hasApiKey());
+  }
 }