style: format code with Autopep8 and Google Java Format

src/main/java/DNAnalyzer/core/DNAAnalysis.java

@@ -11,18 +11,18 @@
 
 package DNAnalyzer.core;
 
-import java.io.PrintStream;
-import java.util.List;
 import static java.util.Optional.ofNullable;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import DNAnalyzer.data.codon.CodonFrame;
 import DNAnalyzer.utils.core.BasePairCounter;
 import DNAnalyzer.utils.core.DNATools;
 import DNAnalyzer.utils.core.ReadingFrames;
 import DNAnalyzer.utils.protein.ProteinAnalysis;
 import DNAnalyzer.utils.protein.ProteinFinder;
+import java.io.PrintStream;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 /**
  * Provides functionality to analyze the DNA
@@ -111,7 +111,7 @@ public void configureReadingFrames(final int minCount, final int maxCount, Print
   // used as helper method for output codons, handles protein decisions
   public void proteinSequence(PrintStream out) {
     final String dnaValue = this.dna.getDna();
-  
+
     if (protein != null) {
       final Pattern p = Pattern.compile(protein);
       final Matcher m = p.matcher(dnaValue);

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

@@ -10,15 +10,15 @@
  */
 package DNAnalyzer.core;
 
-import java.io.PrintStream;
-import java.util.Arrays;
-import java.util.List;
-import java.util.stream.IntStream;
+import static DNAnalyzer.core.DNAAnalysis.countBasePairs;
 
 import DNAnalyzer.core.DNAAnalysis.BasePairIndex;
-import static DNAnalyzer.core.DNAAnalysis.countBasePairs;
 import DNAnalyzer.data.aminoAcid.AminoAcid;
 import DNAnalyzer.data.aminoAcid.AminoAcidFactory;
+import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.IntStream;
 
 /**
  * Prints the list of proteins and their respective properties found in the DNA.
@@ -28,175 +28,171 @@
  */
 public class Properties {
 
-    /**
-     * Gets the version of the application.
-     *
-     * @return The version of the application
-     * @category Properties
-     */
-    public static String getVersion() {
-        return "3.0.0-beta.0";
+  /**
+   * Gets the version of the application.
+   *
+   * @return The version of the application
+   * @category Properties
+   */
+  public static String getVersion() {
+    return "3.0.0-beta.0";
+  }
+
+  /**
+   * Prints the list of proteins found in the DNA.
+   *
+   * @param proteinList The list of proteins to be printed
+   * @param aminoAcid The amino acid to be searched for {@code @category} Output
+   */
+  public static void printProteinList(
+      final List<String> proteinList, final String aminoAcid, PrintStream out) {
+
+    // Changes the 1 letter or 3 letter abbreviation of the amino acids into the
+    // full name
+    final AminoAcid acid = AminoAcidFactory.getAminoAcid(aminoAcid);
+
+    out.println("Proteins coded for " + acid.getFullName() + ": ");
+    out.println("----------------------------------------------------");
+    short count = 1;
+    for (final String gene : proteinList) {
+      out.println(count + ". " + gene);
+      count++;
     }
-
-    /**
-     * Prints the list of proteins found in the DNA.
-     *
-     * @param proteinList The list of proteins to be printed
-     * @param aminoAcid The amino acid to be searched for {@code @category}
-     * Output
-     */
-    public static void printProteinList(
-            final List<String> proteinList, final String aminoAcid, PrintStream out) {
-
-        // Changes the 1 letter or 3 letter abbreviation of the amino acids into the
-        // full name
-        final AminoAcid acid = AminoAcidFactory.getAminoAcid(aminoAcid);
-
-        out.println("Proteins coded for " + acid.getFullName() + ": ");
-        out.println("----------------------------------------------------");
-        short count = 1;
-        for (final String gene : proteinList) {
-            out.println(count + ". " + gene);
-            count++;
-        }
-    }
-
-    /**
-     * Gets the GC content of a gene.
-     *
-     * @param dna The DNA sequence to be analyzed
-     * @return The GC content of the DNA sequence
-     * @category Properties
-     * @see
-     * "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gc-content"
-     */
-    public static float getGCContent(String dna) {
-        float gcContent = 0;
-        if (dna.length() == 0) {
-            return gcContent;
-        }
-
-        dna = dna.toLowerCase();
-        float gcLen = (float) calculateLengthOfCG(dna);
-        gcContent = gcLen / dna.length();
-
-        return gcContent;
-    }
-
-    /**
-     * Calculate the total number of characters that are 'g' or 'c' of a given
-     * DNA String
-     *
-     * @param dna The DNA sequence that was analyzed
-     * @category Property
-     */
-    public static int calculateLengthOfCG(String dna) {
-        int gcLength = 0;
-        char[] dnaCharArray = dna.toCharArray();
-
-        for (char letter : dnaCharArray) {
-            if (letterIsCorG(letter)) {
-                gcLength++;
-            }
-        }
-
-        return gcLength;
+  }
+
+  /**
+   * Gets the GC content of a gene.
+   *
+   * @param dna The DNA sequence to be analyzed
+   * @return The GC content of the DNA sequence
+   * @category Properties
+   * @see
+   *     "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/gc-content"
+   */
+  public static float getGCContent(String dna) {
+    float gcContent = 0;
+    if (dna.length() == 0) {
+      return gcContent;
     }
 
-    /**
-     * Checks if a letter is either 'c' or 'g'
-     *
-     * @param aLetter The letter to check
-     * @category Property
-     */
-    public static boolean letterIsCorG(char aLetter) {
-        return (aLetter == 'c') || (aLetter == 'g');
+    dna = dna.toLowerCase();
+    float gcLen = (float) calculateLengthOfCG(dna);
+    gcContent = gcLen / dna.length();
+
+    return gcContent;
+  }
+
+  /**
+   * Calculate the total number of characters that are 'g' or 'c' of a given DNA String
+   *
+   * @param dna The DNA sequence that was analyzed
+   * @category Property
+   */
+  public static int calculateLengthOfCG(String dna) {
+    int gcLength = 0;
+    char[] dnaCharArray = dna.toCharArray();
+
+    for (char letter : dnaCharArray) {
+      if (letterIsCorG(letter)) {
+        gcLength++;
+      }
     }
 
-    /**
-     * Prints the nucleotide count of the DNA sequence.
-     *
-     * @param dna The DNA sequence that was analyzed {@code @category} Output
-     */
-    public static void printNucleotideCount(final String dna, PrintStream out) {
-        out.println("Nucleotide count:");
-        long[] counts = countBasePairs(dna);
-        out.println(
-                "A"
-                + ": "
-                + counts[BasePairIndex.ADENINE]
-                + " ("
-                + (float) counts[BasePairIndex.ADENINE] / dna.length() * 100
-                + "%)");
-        out.println(
-                "T"
-                + ": "
-                + counts[BasePairIndex.THYMINE]
-                + " ("
-                + (float) counts[BasePairIndex.THYMINE] / dna.length() * 100
-                + "%)");
-        out.println(
-                "G"
-                + ": "
-                + counts[BasePairIndex.GUANINE]
-                + " ("
-                + (float) counts[BasePairIndex.GUANINE] / dna.length() * 100
-                + "%)");
-        out.println(
-                "C"
-                + ": "
-                + counts[BasePairIndex.CYTOSINE]
-                + " ("
-                + (float) counts[BasePairIndex.CYTOSINE] / dna.length() * 100
-                + "%)");
-        out.println(
-                "N"
-                + ": "
-                + counts[BasePairIndex.UNKNOWN]
-                + " ("
-                + (((float) counts[BasePairIndex.UNKNOWN] / dna.length()) * 100)
-                + "%)");
-        out.println("Total: " + dna.length());
-    }
-
-    /**
-     * Checks if the DNA sequence is random or not.
-     *
-     * @param dna The DNA sequence that was analyzed
-     * @return Whether the DNA sequence is random or not {@code @category}
-     * Properties
-     */
-    public static boolean isRandomDNA(final String dna) {
-        long[] nucleotideCount = countBasePairs(dna);
-        int[] percentages
-                = Arrays.stream(nucleotideCount).mapToInt(c -> nucleotidePercentage(c, dna)).toArray();
-
-        int a = percentages[BasePairIndex.ADENINE];
-        int t = percentages[BasePairIndex.THYMINE];
-        int g = percentages[BasePairIndex.GUANINE];
-        int c = percentages[BasePairIndex.CYTOSINE];
-
-        IntStream diffs
-                = IntStream.of(
-                        Math.abs(a - t),
-                        Math.abs(a - g),
-                        Math.abs(a - c),
-                        Math.abs(t - g),
-                        Math.abs(t - c),
-                        Math.abs(g - c));
-
-        return diffs.allMatch(diff -> diff <= 2);
-    }
-
-    /**
-     * Calculates the percentage of given amount of nucleotide in the dna
-     * sequence/
-     *
-     * @param nucleotideCount Number of nucleotides (int)
-     * @param dna DNA sequence
-     * @return the percentage of nucleotides in that DNA sequence
-     */
-    private static int nucleotidePercentage(final long nucleotideCount, final String dna) {
-        return (int) (((float) nucleotideCount) / dna.length() * 100);
-    }
+    return gcLength;
+  }
+
+  /**
+   * Checks if a letter is either 'c' or 'g'
+   *
+   * @param aLetter The letter to check
+   * @category Property
+   */
+  public static boolean letterIsCorG(char aLetter) {
+    return (aLetter == 'c') || (aLetter == 'g');
+  }
+
+  /**
+   * Prints the nucleotide count of the DNA sequence.
+   *
+   * @param dna The DNA sequence that was analyzed {@code @category} Output
+   */
+  public static void printNucleotideCount(final String dna, PrintStream out) {
+    out.println("Nucleotide count:");
+    long[] counts = countBasePairs(dna);
+    out.println(
+        "A"
+            + ": "
+            + counts[BasePairIndex.ADENINE]
+            + " ("
+            + (float) counts[BasePairIndex.ADENINE] / dna.length() * 100
+            + "%)");
+    out.println(
+        "T"
+            + ": "
+            + counts[BasePairIndex.THYMINE]
+            + " ("
+            + (float) counts[BasePairIndex.THYMINE] / dna.length() * 100
+            + "%)");
+    out.println(
+        "G"
+            + ": "
+            + counts[BasePairIndex.GUANINE]
+            + " ("
+            + (float) counts[BasePairIndex.GUANINE] / dna.length() * 100
+            + "%)");
+    out.println(
+        "C"
+            + ": "
+            + counts[BasePairIndex.CYTOSINE]
+            + " ("
+            + (float) counts[BasePairIndex.CYTOSINE] / dna.length() * 100
+            + "%)");
+    out.println(
+        "N"
+            + ": "
+            + counts[BasePairIndex.UNKNOWN]
+            + " ("
+            + (((float) counts[BasePairIndex.UNKNOWN] / dna.length()) * 100)
+            + "%)");
+    out.println("Total: " + dna.length());
+  }
+
+  /**
+   * Checks if the DNA sequence is random or not.
+   *
+   * @param dna The DNA sequence that was analyzed
+   * @return Whether the DNA sequence is random or not {@code @category} Properties
+   */
+  public static boolean isRandomDNA(final String dna) {
+    long[] nucleotideCount = countBasePairs(dna);
+    int[] percentages =
+        Arrays.stream(nucleotideCount).mapToInt(c -> nucleotidePercentage(c, dna)).toArray();
+
+    int a = percentages[BasePairIndex.ADENINE];
+    int t = percentages[BasePairIndex.THYMINE];
+    int g = percentages[BasePairIndex.GUANINE];
+    int c = percentages[BasePairIndex.CYTOSINE];
+
+    IntStream diffs =
+        IntStream.of(
+            Math.abs(a - t),
+            Math.abs(a - g),
+            Math.abs(a - c),
+            Math.abs(t - g),
+            Math.abs(t - c),
+            Math.abs(g - c));
+
+    return diffs.allMatch(diff -> diff <= 2);
+  }
+
+  /**
+   * Calculates the percentage of given amount of nucleotide in the dna sequence/
+   *
+   * @param nucleotideCount Number of nucleotides (int)
+   * @param dna DNA sequence
+   * @return the percentage of nucleotides in that DNA sequence
+   */
+  private static int nucleotidePercentage(final long nucleotideCount, final String dna) {
+    return (int) (((float) nucleotideCount) / dna.length() * 100);
+  }
 }