BTreeProject/GeneBankSearch.java at master · maxrichie5/BTreeProject · GitHub

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import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.RandomAccessFile;

public class GeneBankSearch {

static private Boolean cacheSearch = false;
	static private String bTreeFile = "";
	static private String queryFile = "";
	static private int cacheSizeSearch = 0;
	static private int debugLevelSearch = 2;

	public static void main(String[] args) {

		long startTime = System.nanoTime();

		if (args.length > 5 || args.length < 3) {
			correctOutput();
		}
		if (args[0].equals("1")) {
			cacheSearch = true;
		} else if (!(args[0].equals("0"))) {
			correctOutput();
		}
		bTreeFile = args[1];
		queryFile = args[2];
		if (args.length > 3 && cacheSearch) {
			try {
				cacheSizeSearch = Integer.valueOf(args[3]);
			}catch(Exception e) {
				correctOutput();
			}
		}
		if (args.length > 4 && cacheSearch) {
			try {
				debugLevelSearch = Integer.valueOf(args[4]);
			}catch(Exception e) {
				correctOutput();
			}
		}
		if (args.length > 3 && !cacheSearch) {
			try {
				debugLevelSearch = Integer.valueOf(args[3]);
			}catch(Exception e) {
				correctOutput();
			}
		}
		if (debugLevelSearch != 0 && debugLevelSearch != 1) {
			debugLevelSearch = 0;
		}

		try {
			search();
		} catch (Exception e) {
			e.printStackTrace();
			System.err.println("RUN UNSUCCESSFUL");
			System.exit(0);
		}

		long endTime   = System.nanoTime();
		long totalTime = endTime - startTime;
		double seconds = totalTime/1000000000.0;
		double minutes = seconds/60;
		System.out.println("Runtime:");
		System.out.println("Seconds: "+seconds);
		System.out.println("Minutes: "+minutes);

		System.out.println("\nRun Successful.");
	}

	private static void correctOutput() {
		System.out.println( "CL arguments: <0/1(no/with Cache> <btree file> <query file> [<cache size>] [<debug level>]");
		System.exit(0);
	}

	private static void search() throws ClassNotFoundException, IOException {
		//Create file from query file
		File file = new File(queryFile);

		//Parse the file
		QueryParser parser = new QueryParser(file);

		//Get the string from the parser
		String[] geneStringArray = parser.getGeneStringArray();

		//Create GeneConverter
		GeneConverter gc = new GeneConverter();

		//Create BTree
		BTree bt = new BTree(bTreeFile, debugLevelSearch, cacheSizeSearch);

		//Create a dump for query results
		BufferedWriter bw = null;
		if(debugLevelSearch == 1) {
			String dumpFileName = "btree.search."+queryFile+"_result";
			File dumpFile = new File(dumpFileName);
			if(!dumpFile.exists()) {
				try {
					file.createNewFile();
				} catch (IOException e) {
					e.printStackTrace();
				}
			}
			bw = new BufferedWriter(new FileWriter(dumpFileName));
		}

		//search btree
		for (String queryString: geneStringArray) {
			queryString = queryString.toLowerCase();
			if(queryString.equals("ttttttt")) {
				System.out.print("");;
			}
			long key = gc.convertStringToLong(queryString);
			int frequency = bt.search(key);
			if(frequency != 0) {
				if(debugLevelSearch == 1) { //make query dump
					bw.write(queryString+": "+frequency+"\n");
				} else { //print query result to stdout
					System.out.println(queryString+": "+frequency);
				}
			}
		}
		if(bw != null) {
			bw.close();
		}
	}

}