CompressedGene.java

// CompressedGene.java
// From Classic Computer Science Problems in Java Chapter 1
// Copyright 2020 David Kopec
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

package chapter1;

import java.util.BitSet;

public class CompressedGene {
	private BitSet bitSet;
	private int length;

	public CompressedGene(String gene) {
		compress(gene);
	}

	private void compress(String gene) {
		length = gene.length();
		// reserve enough capacity for all of the bits
		bitSet = new BitSet(length * 2);
		// convert to upper case for consistency
		final String upperGene = gene.toUpperCase();
		// convert String to bit representation
		for (int i = 0; i < length; i++) {
			final int firstLocation = 2 * i;
			final int secondLocation = 2 * i + 1;
			switch (upperGene.charAt(i)) {
			case 'A': // 00 are next two bits
				bitSet.set(firstLocation, false);
				bitSet.set(secondLocation, false);
				break;
			case 'C': // 01 are next two bits
				bitSet.set(firstLocation, false);
				bitSet.set(secondLocation, true);
				break;
			case 'G': // 10 are next two bits
				bitSet.set(firstLocation, true);
				bitSet.set(secondLocation, false);
				break;
			case 'T': // 11 are next two bits
				bitSet.set(firstLocation, true);
				bitSet.set(secondLocation, true);
				break;
			default:
				throw new IllegalArgumentException("The provided gene String contains characters other than ACGT");
			}
		}
	}

	public String decompress() {
		if (bitSet == null) {
			return "";
		}
		// create a mutable place for characters with right capacity
		StringBuilder builder = new StringBuilder(length);
		for (int i = 0; i < (length * 2); i += 2) {
			final int firstBit = (bitSet.get(i) ? 1 : 0);
			final int secondBit = (bitSet.get(i + 1) ? 1 : 0);
			final int lastBits = firstBit << 1 | secondBit;
			switch (lastBits) {
			case 0b00: // 00 is 'A'
				builder.append('A');
				break;
			case 0b01: // 01 is 'C'
				builder.append('C');
				break;
			case 0b10: // 10 is 'G'
				builder.append('G');
				break;
			case 0b11: // 11 is 'T'
				builder.append('T');
				break;
			}
		}
		return builder.toString();
	}

	public static void main(String[] args) {
		final String original = "TAGGGATTAACCGTTATATATATATAGCCATGGATCGATTATATAGGGATTAACCGTTATATATATATAGCCATGGATCGATTATA";
		CompressedGene compressed = new CompressedGene(original);
		final String decompressed = compressed.decompress();
		System.out.println(decompressed);
		System.out.println("original is the same as decompressed: " + original.equalsIgnoreCase(decompressed));
	}

}