Initial data commit

Task/Bioinformatics-Sequence-mutation/Java/bioinformatics-sequence-mutation-1.java

@@ -0,0 +1,104 @@
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
+
+class Program {
+    List<Character> sequence;
+    Random random;
+
+    SequenceMutation() {
+        sequence = new ArrayList<>();
+        random = new Random();
+    }
+
+    void generate(int amount) {
+        for (int count = 0; count < amount; count++)
+            sequence.add(randomBase());
+    }
+
+    void mutate(int amount) {
+        int index;
+        for (int count = 0; count < amount; count++) {
+            index = random.nextInt(0, sequence.size());
+            switch (random.nextInt(0, 3)) {
+                case 0 -> sequence.set(index, randomBase());
+                case 1 -> sequence.remove(index);
+                case 2 -> sequence.add(index, randomBase());
+            }
+        }
+    }
+
+    private char randomBase() {
+        return switch (random.nextInt(0, 4)) {
+            case 0 -> 'A';
+            case 1 -> 'C';
+            case 2 -> 'G';
+            case 3 -> 'T';
+            default -> '?';
+        };
+    }
+
+    private Base count(String string) {
+        int a = 0, c = 0, g = 0, t = 0;
+        for (char base : string.toCharArray()) {
+            switch (base) {
+                case 'A' -> a++;
+                case 'C' -> c++;
+                case 'G' -> g++;
+                case 'T' -> t++;
+            }
+        }
+        return new Base(a, c, g, t);
+    }
+
+    /* used exclusively for count totals */
+    private record Base(int a, int c, int g, int t) {
+        int total() {
+            return a + c + g + t;
+        }
+
+        @Override
+        public String toString() {
+            return "[A %2d, C %2d, G %2d, T %2d]".formatted(a, c, g, t);
+        }
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder string = new StringBuilder();
+        StringBuilder stringB = new StringBuilder();
+        String newline = System.lineSeparator();
+        for (int index = 0; index < sequence.size(); index++) {
+            if (index != 0 && index % 50 == 0)
+                string.append(newline);
+            string.append(sequence.get(index));
+            stringB.append(sequence.get(index));
+        }
+        try {
+            BufferedReader reader = new BufferedReader(new StringReader(string.toString()));
+            string = new StringBuilder();
+            int count = 0;
+            String line;
+            while ((line = reader.readLine()) != null) {
+                string.append(count++);
+                string.append(" %-50s ".formatted(line));
+                string.append(count(line));
+                string.append(newline);
+            }
+        } catch (IOException exception) {
+            /* ignore */
+        }
+        string.append(newline);
+        Base bases = count(stringB.toString());
+        int total = bases.total();
+        string.append("Total of %d bases%n".formatted(total));
+        string.append("A %3d (%.2f%%)%n".formatted(bases.a, ((double) bases.a / total) * 100));
+        string.append("C %3d (%.2f%%)%n".formatted(bases.c, ((double) bases.c / total) * 100));
+        string.append("G %3d (%.2f%%)%n".formatted(bases.g, ((double) bases.g / total) * 100));
+        string.append("T %3d (%.2f%%)%n".formatted(bases.t, ((double) bases.t / total) * 100));
+        return string.toString();
+    }
+}