Minimal AV engine

MainClass.java

import java.io.*;
import java.nio.file.Files;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;

public class MainClass {
	
	public static void main(String args[]) {
		
		try {
			BufferedReader sigReader = new BufferedReader(new InputStreamReader(new FileInputStream("Signature.DAT")));
			String sigLine = null;
			
			//Reading all the signatures
			try {
				while ((sigLine = sigReader.readLine()) != null){
					ArrayList<String> detected = detection(sigLine);
					
					
					//Printing the List of detected files
					if(!detected.isEmpty()){
						System.out.println("Signature " + sigLine +" detected in :");
						for(Iterator<String> it = detected.iterator(); it.hasNext(); ){
							System.out.println(it.next());
						}
					} else {
						System.out.println("No detection for signature " + sigLine);
					}
				}
			} catch (IOException e) {
				e.printStackTrace();
			}
			
		} catch (FileNotFoundException e) {
			e.printStackTrace();
		}
		
		
	}
	
	public static ArrayList<String> detection(String signature) {
		ArrayList<String> result = new ArrayList<String>();
		
		//Listings the files in program
		File folder = new File("Programs");
		ArrayList<File> suspects = new ArrayList<File>(Arrays.asList(folder.listFiles()));
		
		for (Iterator<File> it = suspects.iterator(); it.hasNext();){
			
			File current = it.next();
			
			switch(signature.length()){
			case 32 :
				if(md5(signature, current)){
					result.add(current.getName());
				}
				break;
				
			case 40:
				if(sha1(signature, current)){
					result.add(current.getName());
				}
				break;
				
			default :
				if(sigInFile(signature, current)) {
					result.add(current.getName());
				}
				break;
			}

		}
		
		return result;
	}

	
	/*
	 * Checks if every line in the file contains the signature
	 */
	public static boolean sigInFile(String signature, File suspect) {
		try {
			BufferedReader fileReader = new BufferedReader(new InputStreamReader(new FileInputStream(suspect)));
			String line = null;
			
			try {
				while((line = fileReader.readLine()) != null){
					if(line.contains(signature)){
						return true;
					}
				}
				fileReader.close();
			} catch (IOException e) {
				e.printStackTrace();
			}
		} catch (FileNotFoundException e) {
			e.printStackTrace();
		}
		return false;
	}
	
	//Compares the signature with the md5
	public static boolean md5(String signature, File suspect) {
        MessageDigest md;
        try {
            md = MessageDigest.getInstance("MD5");
            byte[] fileArray;
            try {
                fileArray = Files.readAllBytes(suspect.toPath());
                md.update(fileArray);
                byte[] md5filearray = md.digest();
                String result = "";
                for (int i=0; i < md5filearray.length; i++) {
                   result += Integer.toString( ( md5filearray[i] & 0xff ) + 0x100, 16).substring( 1 );
                }
                result = result.toUpperCase();
                if(signature.contains(result)){
                	return true;
                }
            } catch (IOException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
           
        } catch (NoSuchAlgorithmException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return false;
	}
	
	//Compare the signature with the SHA1
	public static boolean sha1(String signature, File suspect) {
           
	    try {
	        MessageDigest md = MessageDigest.getInstance("SHA-1");
	        byte[] fileArray;
	        try {
	            fileArray = Files.readAllBytes(suspect.toPath());
	            md.update(fileArray);
	            byte[] sha1filearray = md.digest();
	            String result = "";
	            for (int i=0; i < sha1filearray.length; i++) {
	               result += Integer.toString( ( sha1filearray[i] & 0xff ) + 0x100, 16).substring( 1 );
	            }
	            result = result.toUpperCase();
	            if(signature.contains(result)){
	            	return true;
	            }
	        } catch (IOException e) {
	            // TODO Auto-generated catch block
	            e.printStackTrace();
	        }
	       
	    } catch (NoSuchAlgorithmException e) {
	        // TODO Auto-generated catch block
	        e.printStackTrace();
	    }
	    return false;
	}

}