57 lines
1.6 KiB
Java
57 lines
1.6 KiB
Java
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import edu.princeton.cs.introcs.BinaryStdIn;
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import edu.princeton.cs.introcs.BinaryStdOut;
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/*************************************************************************
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* Compilation: javac Genome.java
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* Execution: java Genome - < input.txt (compress)
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* Execution: java Genome + < input.txt (expand)
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* Dependencies: BinaryIn.java BinaryOut.java
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*
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* Compress or expand a genomic sequence using a 2-bit code.
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*
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* % more genomeTiny.txt
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* ATAGATGCATAGCGCATAGCTAGATGTGCTAGC
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*
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* % java Genome - < genomeTiny.txt | java Genome +
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* ATAGATGCATAGCGCATAGCTAGATGTGCTAGC
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*
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*************************************************************************/
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public class Genome {
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public static void compress() {
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Alphabet DNA = new Alphabet("ACTG");
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String s = BinaryStdIn.readString();
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int N = s.length();
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BinaryStdOut.write(N);
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// Write two-bit code for char.
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for (int i = 0; i < N; i++) {
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int d = DNA.toIndex(s.charAt(i));
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BinaryStdOut.write(d, 2);
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}
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BinaryStdOut.close();
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}
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public static void expand() {
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Alphabet DNA = new Alphabet("ACTG");
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int N = BinaryStdIn.readInt();
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// Read two bits; write char.
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for (int i = 0; i < N; i++) {
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char c = BinaryStdIn.readChar(2);
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BinaryStdOut.write(DNA.toChar(c), 8);
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}
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BinaryStdOut.close();
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}
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public static void main(String[] args) {
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if (args[0].equals("-")) compress();
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else if (args[0].equals("+")) expand();
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else throw new IllegalArgumentException("Illegal command line argument");
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}
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}
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