Initial data commit
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Ingy döt Net
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199087 changed files with 3378941 additions and 0 deletions
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Random;
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class Program {
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List<Character> sequence;
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Random random;
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SequenceMutation() {
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sequence = new ArrayList<>();
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random = new Random();
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}
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void generate(int amount) {
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for (int count = 0; count < amount; count++)
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sequence.add(randomBase());
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}
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void mutate(int amount) {
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int index;
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for (int count = 0; count < amount; count++) {
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index = random.nextInt(0, sequence.size());
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switch (random.nextInt(0, 3)) {
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case 0 -> sequence.set(index, randomBase());
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case 1 -> sequence.remove(index);
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case 2 -> sequence.add(index, randomBase());
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}
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}
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}
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private char randomBase() {
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return switch (random.nextInt(0, 4)) {
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case 0 -> 'A';
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case 1 -> 'C';
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case 2 -> 'G';
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case 3 -> 'T';
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default -> '?';
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};
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}
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private Base count(String string) {
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int a = 0, c = 0, g = 0, t = 0;
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for (char base : string.toCharArray()) {
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switch (base) {
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case 'A' -> a++;
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case 'C' -> c++;
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case 'G' -> g++;
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case 'T' -> t++;
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}
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}
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return new Base(a, c, g, t);
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}
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/* used exclusively for count totals */
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private record Base(int a, int c, int g, int t) {
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int total() {
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return a + c + g + t;
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}
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@Override
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public String toString() {
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return "[A %2d, C %2d, G %2d, T %2d]".formatted(a, c, g, t);
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}
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}
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@Override
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public String toString() {
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StringBuilder string = new StringBuilder();
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StringBuilder stringB = new StringBuilder();
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String newline = System.lineSeparator();
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for (int index = 0; index < sequence.size(); index++) {
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if (index != 0 && index % 50 == 0)
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string.append(newline);
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string.append(sequence.get(index));
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stringB.append(sequence.get(index));
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}
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try {
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BufferedReader reader = new BufferedReader(new StringReader(string.toString()));
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string = new StringBuilder();
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int count = 0;
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String line;
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while ((line = reader.readLine()) != null) {
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string.append(count++);
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string.append(" %-50s ".formatted(line));
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string.append(count(line));
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string.append(newline);
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}
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} catch (IOException exception) {
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/* ignore */
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}
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string.append(newline);
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Base bases = count(stringB.toString());
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int total = bases.total();
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string.append("Total of %d bases%n".formatted(total));
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string.append("A %3d (%.2f%%)%n".formatted(bases.a, ((double) bases.a / total) * 100));
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string.append("C %3d (%.2f%%)%n".formatted(bases.c, ((double) bases.c / total) * 100));
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string.append("G %3d (%.2f%%)%n".formatted(bases.g, ((double) bases.g / total) * 100));
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string.append("T %3d (%.2f%%)%n".formatted(bases.t, ((double) bases.t / total) * 100));
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return string.toString();
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}
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}
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@ -0,0 +1,113 @@
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import java.util.Arrays;
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import java.util.Random;
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public class SequenceMutation {
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public static void main(String[] args) {
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SequenceMutation sm = new SequenceMutation();
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sm.setWeight(OP_CHANGE, 3);
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String sequence = sm.generateSequence(250);
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System.out.println("Initial sequence:");
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printSequence(sequence);
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int count = 10;
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for (int i = 0; i < count; ++i)
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sequence = sm.mutateSequence(sequence);
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System.out.println("After " + count + " mutations:");
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printSequence(sequence);
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}
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public SequenceMutation() {
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totalWeight_ = OP_COUNT;
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Arrays.fill(operationWeight_, 1);
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}
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public String generateSequence(int length) {
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char[] ch = new char[length];
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for (int i = 0; i < length; ++i)
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ch[i] = getRandomBase();
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return new String(ch);
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}
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public void setWeight(int operation, int weight) {
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totalWeight_ -= operationWeight_[operation];
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operationWeight_[operation] = weight;
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totalWeight_ += weight;
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}
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public String mutateSequence(String sequence) {
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char[] ch = sequence.toCharArray();
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int pos = random_.nextInt(ch.length);
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int operation = getRandomOperation();
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if (operation == OP_CHANGE) {
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char b = getRandomBase();
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System.out.println("Change base at position " + pos + " from "
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+ ch[pos] + " to " + b);
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ch[pos] = b;
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} else if (operation == OP_ERASE) {
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System.out.println("Erase base " + ch[pos] + " at position " + pos);
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char[] newCh = new char[ch.length - 1];
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System.arraycopy(ch, 0, newCh, 0, pos);
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System.arraycopy(ch, pos + 1, newCh, pos, ch.length - pos - 1);
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ch = newCh;
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} else if (operation == OP_INSERT) {
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char b = getRandomBase();
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System.out.println("Insert base " + b + " at position " + pos);
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char[] newCh = new char[ch.length + 1];
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System.arraycopy(ch, 0, newCh, 0, pos);
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System.arraycopy(ch, pos, newCh, pos + 1, ch.length - pos);
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newCh[pos] = b;
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ch = newCh;
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}
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return new String(ch);
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}
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public static void printSequence(String sequence) {
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int[] count = new int[BASES.length];
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for (int i = 0, n = sequence.length(); i < n; ++i) {
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if (i % 50 == 0) {
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if (i != 0)
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System.out.println();
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System.out.printf("%3d: ", i);
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}
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char ch = sequence.charAt(i);
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System.out.print(ch);
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for (int j = 0; j < BASES.length; ++j) {
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if (BASES[j] == ch) {
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++count[j];
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break;
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}
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}
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}
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System.out.println();
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System.out.println("Base counts:");
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int total = 0;
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for (int j = 0; j < BASES.length; ++j) {
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total += count[j];
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System.out.print(BASES[j] + ": " + count[j] + ", ");
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}
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System.out.println("Total: " + total);
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}
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private char getRandomBase() {
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return BASES[random_.nextInt(BASES.length)];
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}
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private int getRandomOperation() {
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int n = random_.nextInt(totalWeight_), op = 0;
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for (int weight = 0; op < OP_COUNT; ++op) {
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weight += operationWeight_[op];
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if (n < weight)
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break;
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}
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return op;
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}
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private final Random random_ = new Random();
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private int[] operationWeight_ = new int[OP_COUNT];
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private int totalWeight_ = 0;
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private static final int OP_CHANGE = 0;
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private static final int OP_ERASE = 1;
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private static final int OP_INSERT = 2;
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private static final int OP_COUNT = 3;
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private static final char[] BASES = {'A', 'C', 'G', 'T'};
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}
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