Create TestRNAFolding.java

Author: alexcerezo

src/test/java/com/thealgorithms/dynamicprogramming/TestRNAFolding.java

@@ -0,0 +1,124 @@
+package com.thealgorithms.dynamicprogramming;
+
+import java.io.IOException;
+import java.util.List;
+
+import es.uma.eda.AlgorithmUtil;
+import es.uma.eda.problem.combinatorial.sequence.SequenceUtil;
+import es.uma.eda.problem.combinatorial.sequence.folding.RNASecondaryStructurePredictor;
+
+/**
+ * Main class for testing RNA folding algorithms
+ * @author ccottap
+ *
+ */
+public class TestRNAFolding {
+
+	/**
+	 * Filename for storing statistics
+	 */
+	private final static String outputFilename = "folding.txt";
+	/**
+	 * how much the size of sequences is scaled-up on each step 
+	 */
+	private final static double scaleFactor = 1.5;
+	
+	/**
+	 * Finds the best folding of an RNA sequence
+	 * @param args command-line arguments (to read data from file or generate at random)
+	 * @throws IOException if data cannot be read from file or statistics cannot be written to file
+	 */
+	public static void main(String[] args) throws IOException {
+		if (args.length<1) {
+			System.out.println("java TestRNAFolding (-s|-f|-r) <arguments>");
+			System.out.println("\t-s: folds a string given as parameter");
+			System.out.println("\t-f: performs a batch test from a file");
+			System.out.println("\t-r: measures time");
+		}
+		else {
+			List<String> sequences = null;
+			RNASecondaryStructurePredictor predictor = new Nussinov();
+			
+			switch (args[0]) {
+			case "-s":
+				if (args.length < 3) {
+					System.out.println("java TestRNAFolding -s <string> <min-loop-size>");
+					System.exit(-1);
+				}
+				else {
+					String f = predictor.run(args[1], Integer.parseInt(args[2]));
+					System.out.println("Folding " + args[1] + "...");
+					System.out.println("Result:\n\t" + (int)predictor.evaluate(args[1],f) + " base pairs\n\t" +  args[1] + "\n\t" + f);
+				}
+				break;
+				
+			case "-f":
+				if (args.length < 3) {
+					System.out.println("java TestRNAFolding -f <filename> <min-loop-size>");
+					System.exit(-1);
+				}
+				else {
+					sequences = SequenceUtil.readSequencesFromFile(args[1]);
+					predictor.setVerbosity(false);
+					for (String s: sequences) {
+						String f = predictor.run(s, Integer.parseInt(args[2]));
+						System.out.println((int)predictor.evaluate(s, f));
+					}
+				}
+				break;
+				
+			case "-r":
+				if (args.length < 5) {
+					System.out.println("java TestRNAFolding -r <initial-lenght> <doublings> <tests-per-length> <min-loop-size>");
+					System.exit(-1);
+				}
+				else {
+					int initialLength = Integer.parseUnsignedInt(args[1]);
+					int doublings = Integer.parseUnsignedInt(args[2]);
+					int testsPerLength = Integer.parseUnsignedInt(args[3]);
+					int minLoopSize = Integer.parseUnsignedInt(args[4]);
+					double[][] statistics = runTimer(predictor, initialLength, doublings, testsPerLength, minLoopSize);
+					AlgorithmUtil.writeStats(outputFilename, statistics);
+				}
+				break;
+				
+			default:
+				System.out.println("Wrong argument: " + args[0]);
+				System.exit(-1);
+			}
+		}
+
+	}
+
+	/**
+	 * Performs a series of timed experiments with sequences of different sizes
+	 * @param predictor the structure prediction algorithm	 
+	 * @param initialLength initial length of sequences
+	 * @param doublings number of times the sequence length is doubled
+	 * @param testsPerLength number of tests per sequence length
+	 * @param minLoopSize minimum number of nucleotides enclosed in loops
+	 * @return a matrix with computational times (one row per size, one column per test).
+	 */
+	private static double[][] runTimer(RNASecondaryStructurePredictor predictor , int initialLength, int doublings, int testsPerLength, int minLoopSize) {
+		final String alphabet = "ACGU";
+		double[][] statistics = new double[doublings][testsPerLength+1];
+		double interval;
+		
+		predictor.setVerbosity(false);
+		for (int l = initialLength, dup = 0; dup < doublings; l *= scaleFactor, dup++) {
+			statistics[dup][0] = l;
+	        System.out.println("Trying sequences of length " + l);
+			for (int j=0; j<testsPerLength; j++) {
+				String s = SequenceUtil.randomString(l, alphabet);
+				predictor.run(s, minLoopSize);
+		        interval = predictor.getTime();
+		        statistics[dup][j+1] = interval;
+		        System.out.println(predictor.getName() + " took " + interval + "s");
+			}
+		}
+		
+		return statistics;
+		
+	}
+
+}