Merge pull request #159 from Verisimilitude11/deepsource-transform-83…

…7fd95a

Format code with autopep8 and google-java-format

src/DNAnalyzer/CmdArgs.java

@@ -6,26 +6,37 @@
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 import picocli.CommandLine.Parameters;
 
-@Command(name="DNAnalyzer", mixinStandardHelpOptions = true, description = "A program to analyze DNA sequences.")
+@Command(
+    name = "DNAnalyzer",
+    mixinStandardHelpOptions = true,
+    description = "A program to analyze DNA sequences.")
 public class CmdArgs implements Runnable {
-  @Option(required=true, names = {"--amino"}, description = "The amino acid representing the start of a gene.")
+  @Option(
+      required = true,
+      names = {"--amino"},
+      description = "The amino acid representing the start of a gene.")
   String aminoAcid;
 
-  @Option(names = {"--min"}, description = "The minimum count of the reading frame.")
+  @Option(
+      names = {"--min"},
+      description = "The minimum count of the reading frame.")
   int minCount = 0;
 
-  @Option(names = {"--max"}, description = "The maximum count of the reading frame.")
+  @Option(
+      names = {"--max"},
+      description = "The maximum count of the reading frame.")
   int maxCount = 0;
 
-  @Parameters(paramLabel = "DNA", description = "The FASTA file to be analyzed.") 
+  @Parameters(paramLabel = "DNA", description = "The FASTA file to be analyzed.")
   File dnaFile;
 
-  @Option(names = {"--find"}, description = "The DNA sequence to be found within the FASTA file.")
+  @Option(
+      names = {"--find"},
+      description = "The DNA sequence to be found within the FASTA file.")
   File proteinFile;
 
   String readFile(File file) throws IOException {
@@ -65,9 +76,11 @@ public void run() {
     System.out.println("\nGC-content (genome): " + gcContent + "\n");
     Properties.printNucleotideCount(dna);
 
-    // Output the number of codons based on the reading frame the user wants to look at, and minimum and maximum filters
+    // Output the number of codons based on the reading frame the user wants to look at, and minimum
+    // and maximum filters
     final short READING_FRAME = 1;
-    final ReadingFrames aap = new ReadingFrames(new CodonFrame(dna, READING_FRAME, minCount, maxCount));
+    final ReadingFrames aap =
+        new ReadingFrames(new CodonFrame(dna, READING_FRAME, minCount, maxCount));
     System.out.print("\n");
     aap.printCodonCounts();
 
@@ -76,7 +89,8 @@ public void run() {
       Pattern p = Pattern.compile(protein);
       Matcher m = p.matcher(dna);
       if (m.find()) {
-        System.out.println("\nProtein sequence found at index " + m.start() + " in the DNA sequence.");
+        System.out.println(
+            "\nProtein sequence found at index " + m.start() + " in the DNA sequence.");
       } else {
         System.out.println("\nProtein sequence not found in the DNA sequence.");
       }