Merge pull request #403 from VerisimilitudeX/deepsource-transform-56a…

…054c8 format code with autopep8 and google-java-format
VerisimilitudeX · Jun 8, 2023 · b863d7f · b863d7f
2 parents 93b25b6 + 8f44c11
commit b863d7f
Showing 1 changed file with 65 additions and 62 deletions.
diff --git a/src/main/java/DNAnalyzer/data/Parser.java b/src/main/java/DNAnalyzer/data/Parser.java
@@ -9,86 +9,89 @@
  * @version 3.0.0-beta.0
  */
 public class Parser {
-    /**
-     * Parses a FASTA file and returns the DNA sequence.
-     *
-     * @param file File to parse
-     * @return DNA sequence
-     * @throws IOException
-     */
-    private static String parseFasta(File file) throws IOException {
-        BufferedReader rd = new BufferedReader(new FileReader(file));
-        StringBuilder dna = new StringBuilder();
-        while (true) {
-            String line = rd.readLine();
-            if (line == null) break;
-
-            // Extra info
-            if (line.startsWith(">")) { // File descriptor
-                System.out.println("Reading DNA: " + line.substring(1).trim());
-                continue;
-            }
-            if (line.startsWith(";")) { // Comment
-                continue;
-            }
-
-            // Read file
-            boolean stop = false;
-            if (line.endsWith("*")) {
-                line = line.replace("*", "");
-                stop = true;
-            }
-            line = line.toLowerCase();
-            dna.append(line);
-            if (stop) break;
-        }
+  /**
+   * Parses a FASTA file and returns the DNA sequence.
+   *
+   * @param file File to parse
+   * @return DNA sequence
+   * @throws IOException
+   */
+  private static String parseFasta(File file) throws IOException {
+    BufferedReader rd = new BufferedReader(new FileReader(file));
+    StringBuilder dna = new StringBuilder();
+    while (true) {
+      String line = rd.readLine();
+      if (line == null) break;
 
-        rd.close();
+      // Extra info
+      if (line.startsWith(">")) { // File descriptor
+        System.out.println("Reading DNA: " + line.substring(1).trim());
+        continue;
+      }
+      if (line.startsWith(";")) { // Comment
+        continue;
+      }
 
-        return dna.toString();
+      // Read file
+      boolean stop = false;
+      if (line.endsWith("*")) {
+        line = line.replace("*", "");
+        stop = true;
+      }
+      line = line.toLowerCase();
+      dna.append(line);
+      if (stop) break;
     }
 
-    /**
-     * Parses a FASTQ file and returns the DNA sequence.
-     *
-     * @param file File to parse
-     * @return DNA sequence
-     * @throws IOException
-     */
-    private static String parseFastq(File file) throws IOException {
-        BufferedReader br = new BufferedReader(new FileReader(file));
+    rd.close();
+
+    return dna.toString();
+  }
 
-        // Read SEQ id
-        System.out.println("Reading DNA: " + br.readLine().substring(1).trim());
+  /**
+   * Parses a FASTQ file and returns the DNA sequence.
+   *
+   * @param file File to parse
+   * @return DNA sequence
+   * @throws IOException
+   */
+  private static String parseFastq(File file) throws IOException {
+    BufferedReader br = new BufferedReader(new FileReader(file));
 
-        // Read DNA
-        String dna = br.readLine();
-        br.close();
+    // Read SEQ id
+    System.out.println("Reading DNA: " + br.readLine().substring(1).trim());
 
-        if (dna == null) {
-            return "No DNA found";
-        }
+    // Read DNA
+    String dna = br.readLine();
+    br.close();
 
-        // TODO: Read field 3 (just a "+"), and then parse the quality data in Field 4
-        return dna.toLowerCase();
+    if (dna == null) {
+      return "No DNA found";
     }
 
+    // TODO: Read field 3 (just a "+"), and then parse the quality data in Field 4
+    return dna.toLowerCase();
+  }
 
-    /**
+  /**
    * Parses a file and returns the DNA sequence.
    *
    * @param file File to parse
    * @return DNA sequence
    * @throws IOException
    */
   public static String parseFile(File file) throws IOException {
-      if (file.getName().endsWith(".fa")) { // Regular FASTA file, this implementation only reads the first DNA sequence
-          return parseFasta(file);
-      }
-      if (file.getName().endsWith(".fastq")) { // Regular FASTA file, this implementation only reads the first DNA sequence
-          return parseFastq(file);
-      }
+    if (file.getName()
+        .endsWith(
+            ".fa")) { // Regular FASTA file, this implementation only reads the first DNA sequence
+      return parseFasta(file);
+    }
+    if (file.getName()
+        .endsWith(".fastq")) { // Regular FASTA file, this implementation only reads the first DNA
+      // sequence
+      return parseFastq(file);
+    }
 
-      return null; // TODO: Error handling, handle more types of files
+    return null; // TODO: Error handling, handle more types of files
   }
 }