package edu.princeton.cs.algs4.ch55;
import edu.princeton.cs.algs4.ch51.Alphabet;
import edu.princeton.cs.introcs.*;
/*************************************************************************
* Compilation: javac Genome.java
* Execution: java Genome - < input.txt (compress)
* Execution: java Genome + < input.txt (expand)
* Dependencies: BinaryIn.java BinaryOut.java
*
* Compress or expand a genomic sequence using a 2-bit code.
*
* % more genomeTiny.txt
* ATAGATGCATAGCGCATAGCTAGATGTGCTAGC
*
* % java Genome - < genomeTiny.txt | java Genome +
* ATAGATGCATAGCGCATAGCTAGATGTGCTAGC
*
*************************************************************************/
public class Genome {
public static void compress() {
Alphabet DNA = new Alphabet("ACTG");
String s = BinaryStdIn.readString();
int N = s.length();
BinaryStdOut.write(N);
// Write two-bit code for char.
for (int i = 0; i < N; i++) {
int d = DNA.toIndex(s.charAt(i));
BinaryStdOut.write(d, 2);
}
BinaryStdOut.close();
}
public static void expand() {
Alphabet DNA = new Alphabet("ACTG");
int N = BinaryStdIn.readInt();
// Read two bits; write char.
for (int i = 0; i < N; i++) {
char c = BinaryStdIn.readChar(2);
BinaryStdOut.write(DNA.toChar(c), 8);
}
BinaryStdOut.close();
}
public static void main(String[] args) {
if (args[0].equals("-")) compress();
else if (args[0].equals("+")) expand();
else throw new IllegalArgumentException("Illegal command line argument");
}
}
/*************************************************************************
* Copyright 2002-2012, Robert Sedgewick and Kevin Wayne.
*
* This file is part of algs4-package.jar, which accompanies the textbook
*
* Algorithms, 4th edition by Robert Sedgewick and Kevin Wayne,
* Addison-Wesley Professional, 2011, ISBN 0-321-57351-X.
* http://algs4.cs.princeton.edu
*
*
* algs4-package.jar is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* algs4-package.jar is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with algs4-package.jar. If not, see http://www.gnu.org/licenses.
*************************************************************************/