baseline translator

Main.java

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.math.BigDecimal;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Random;
import java.util.TreeMap;

public class Main {
	static String read3CharsFromBuffer(BufferedReader bfr) throws Exception {
		StringBuilder sb = new StringBuilder();
		for(int i = 0;i < 3;i++) {
			int ch = bfr.read();
			if(ch >= 0)	sb.append((char)ch);
			else	return null;
		}
		return sb.toString();
	}
	static void generateInputs(final int NUM_INPUT,final int SIZE) throws Exception {
		final char[] ARR = {'A','U','G','C'};
		Random rand = new Random();
		BufferedWriter bfw;
		for(int i = 0;i < NUM_INPUT;i++) {
			bfw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(String.format("in%03d.txt",i + 1))));
			System.out.println("Generating file " + (i + 1) + " out of " + NUM_INPUT);
			for(int k = 0;k < SIZE;k++)
				bfw.append(ARR[rand.nextInt(4)]);
			bfw.flush();
			bfw.close();
			System.out.println("Done generating file " + (i + 1) + " out of " + NUM_INPUT);
		}
	}
	static void process_map(final int NUM_INPUT,final int SIZE,final Map<String,String> map) throws Exception {
		BufferedReader bfr;
		BufferedWriter bfw;
		long time;
		BigDecimal overallTime = BigDecimal.ZERO;
		BigDecimal minTime = BigDecimal.TEN.pow(20);
		BigDecimal maxTime = BigDecimal.ZERO;
		for(int i = 0;i < NUM_INPUT;i++) {
			time = System.currentTimeMillis();
			bfr = new BufferedReader(new InputStreamReader(new FileInputStream(String.format("in%03d.txt",i + 1))));
			bfw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(String.format("out%03d.txt",i + 1))));
//			System.out.println("Processing file " + (i + 1) + " out of " + NUM_INPUT);
			String tmp;
			while((tmp = read3CharsFromBuffer(bfr)) != null) {
				bfw.append(map.get(tmp).charAt(0));
			}
			bfr.close();
			bfw.flush();
			bfw.close();
//			System.out.println("Done processing file " + (i + 1) + " out of " + NUM_INPUT);
			BigDecimal tmpTime = BigDecimal.valueOf((System.currentTimeMillis() - time) / 1000.0);
			overallTime = overallTime.add(tmpTime);
			minTime = minTime.min(tmpTime);
			maxTime = maxTime.max(tmpTime);
		}
		System.out.println("Data structure: " + map.getClass().getSimpleName());
		System.out.println("Average time used: " + overallTime.divide(BigDecimal.valueOf(NUM_INPUT)) + " seconds");
		System.out.println("Min time used: " + minTime + " seconds");
		System.out.println("Max time used: " + maxTime + " seconds");
	}
	static void process_array(final int NUM_INPUT,final int SIZE,final Map<String,String> map) throws Exception {
		BufferedReader bfr;
		BufferedWriter bfw;
		int charMap[] = new int[26];
		charMap['A' - 'A'] = 0;
		charMap['U' - 'A'] = 1;
		charMap['G' - 'A'] = 2;
		charMap['C' - 'A'] = 3;
		String mapper[][][] = new String[4][4][4];
		long time;
		BigDecimal overallTime = BigDecimal.ZERO;
		BigDecimal minTime = BigDecimal.TEN.pow(20);
		BigDecimal maxTime = BigDecimal.ZERO;
		for(Entry<String,String> entry:map.entrySet()) {
			String key = entry.getKey();
			mapper[charMap[key.charAt(0) - 'A']][charMap[key.charAt(1) - 'A']][charMap[key.charAt(2) - 'A']] = entry.getValue();
		}
		for(int i = 0;i < NUM_INPUT;i++) {
			time = System.currentTimeMillis();
			bfr = new BufferedReader(new InputStreamReader(new FileInputStream(String.format("in%03d.txt",i + 1))));
			bfw = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(String.format("out%03d.txt",i + 1))));
//			System.out.println("Processing file " + (i + 1) + " out of " + NUM_INPUT);
			String tmp;
			while((tmp = read3CharsFromBuffer(bfr)) != null) {
				bfw.append(mapper[charMap[tmp.charAt(0) - 'A']][charMap[tmp.charAt(1) - 'A']][charMap[tmp.charAt(2) - 'A']]);
			}
			bfr.close();
			bfw.flush();
			bfw.close();
//			System.out.println("Done processing file " + (i + 1) + " out of " + NUM_INPUT);
			BigDecimal tmpTime = BigDecimal.valueOf((System.currentTimeMillis() - time) / 1000.0);
			overallTime = overallTime.add(tmpTime);
			minTime = minTime.min(tmpTime);
			maxTime = maxTime.max(tmpTime);
		}
		System.out.println("Data structure: " + charMap.getClass().getSimpleName());
		System.out.println("Average time used: " + overallTime.divide(BigDecimal.valueOf(NUM_INPUT)) + " seconds");
		System.out.println("Min time used: " + minTime + " seconds");
		System.out.println("Max time used: " + maxTime + " seconds");
	}
	public static void main(String args[]) throws Exception {
		final int SIZE = 1000000000;
		final int NUM_INPUT = 10;
		
		generateInputs(NUM_INPUT,SIZE);
		Map<String,String> map;
		map = new HashMap<String,String>();
		map.put("UUU","F"); map.put("UUC","F"); map.put("UUA","L"); map.put("UUG","L"); map.put("UCU","S"); map.put("UCC","S"); map.put("UCA","S"); map.put("UCG","S");
		map.put("UAU","Y"); map.put("UAC","Y"); map.put("UAA"," "); map.put("UAG"," "); map.put("UGU","C"); map.put("UGC","C"); map.put("UGA"," "); map.put("UGG","W");
		map.put("CUU","L"); map.put("CUC","L"); map.put("CUA","L"); map.put("CUG","L"); map.put("CCU","P"); map.put("CCC","P"); map.put("CCA","P"); map.put("CCG","P");
		map.put("CAU","H"); map.put("CAC","H"); map.put("CAA","Q"); map.put("CAG","Q"); map.put("CGU","R"); map.put("CGC","R"); map.put("CGA","R"); map.put("CGG","R");
		map.put("AUU","I"); map.put("AUC","I"); map.put("AUA","I"); map.put("AUG","M"); map.put("ACU","T"); map.put("ACC","T"); map.put("ACA","T"); map.put("ACG","T");
		map.put("AAU","N"); map.put("AAC","N"); map.put("AAA","K"); map.put("AAG","K"); map.put("AGU","S"); map.put("AGC","S"); map.put("AGA","R"); map.put("AGG","R");
		map.put("GUU","V"); map.put("GUC","V"); map.put("GUA","V"); map.put("GUG","V"); map.put("GCU","A"); map.put("GCC","A"); map.put("GCA","A"); map.put("GCG","A");
		map.put("GAU","D"); map.put("GAC","D"); map.put("GAA","E"); map.put("GAG","E"); map.put("GGU","G"); map.put("GGC","G"); map.put("GGA","G"); map.put("GGG","G");
		process_map(NUM_INPUT,SIZE,map);
		
		map = new TreeMap<String,String>(map);
		process_map(NUM_INPUT,SIZE,map);
		
		process_array(NUM_INPUT,SIZE,map);
	}
}