MuscleWrapper.java

package aliview.aligner;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.math.BigInteger;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.SimpleDateFormat;

import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;

import utils.OSNativeUtils;


	public class MuscleWrapper {
		
	public static void main(String[] args) {
		getMusclePath();
	}
	
	private static final Logger logger = Logger.getLogger(MuscleWrapper.class);
	
	public static File getMusclePath(){
		
		// get predefined path
		
		// if no predefined path create one for distributed program
		File localMuscleBinFile = new File(getAliViewUserDataDirectory(), "/binaries" + File.separator + getMuscleBinDependingOnOS());
		
		//logger.info("localMuscleBinFile.lastModified()" + localMuscleBinFile.lastModified());
		//SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd HH:mm:ss");
		//System.out.println("After Format : " + sdf.format(localMuscleBinFile.lastModified()));
		
		// check if file exist if not extract it from jar
		if(! localMuscleBinFile.exists() || localMuscleBinFile.length() == 0 || localMuscleBinFile.lastModified() < 1395868152000L){ // modified date = 20140326 22:09:12 (this is the date when saving file problem finally was resolved)
				ClassLoader cl = MuscleWrapper.class.getClassLoader();	
				try {
					boolean fileISOK = false;
					int nTries = 0;
					while(! fileISOK && nTries <=3){
						nTries ++;
						InputStream muscleStreamFromJar = cl.getResourceAsStream(localMuscleBinFile.getName());
						logger.info(muscleStreamFromJar);
						copyMuscleFileToLocalDir(muscleStreamFromJar, localMuscleBinFile);
						// reopen stream
						muscleStreamFromJar = cl.getResourceAsStream(localMuscleBinFile.getName());
						fileISOK = verifyMD5(muscleStreamFromJar, localMuscleBinFile);
						if(! fileISOK){
							FileUtils.deleteQuietly(localMuscleBinFile);
						}else{
							localMuscleBinFile.setExecutable(true);
						}
					}
					
				} catch (IOException e) {
					// TODO Auto-generated catch block
					e.printStackTrace();
					// TODO Maybe notify something went wrong with installing muscle
				}
			
		}
		
		logger.info(localMuscleBinFile);		
		return localMuscleBinFile;
		
	}
	
	
	private static boolean verifyMD5(InputStream streamFromJar,File localMuscleBinFile) throws FileNotFoundException {
		boolean checksumOK = false;
		String checksum1 = checkSum(streamFromJar);
		String checksum2 = checkSum(new FileInputStream(localMuscleBinFile));
		logger.info(checksum1);
		logger.info(checksum2);
		if(checksum1 != null && checksum2 != null && checksum1.equals(checksum2)){
			checksumOK = true;
		}
		return checksumOK;
	}


	private static void copyMuscleFileToLocalDir(InputStream muscleStreamFromJar, File localMuscleBinFile) throws IOException {
		FileUtils.forceMkdir(localMuscleBinFile.getParentFile());
		FileUtils.copyInputStreamToFile(muscleStreamFromJar, localMuscleBinFile);		
	}


	public static final String getAliViewUserDataDirectory() {
	    return System.getProperty("user.home") + File.separator + ".AliView";
	}
	
	
	
	public static final String getMuscleBinDependingOnOS() {
		
		String binName = "";
		// 64-bit
		if(OSNativeUtils.is64BitOS()){
			if(OSNativeUtils.isMac()){
				binName = "muscle3.8.31_i86darwin64";
			}
			else if(OSNativeUtils.isLinuxOrUnix()){
				binName = "muscle3.8.425_i86linux64";
			}
			// default
			else{
				binName = "muscle3.8.425_win32.exe";
			}
		// 32-bit
		}else{
			if(OSNativeUtils.isMac()){
				if(OSNativeUtils.isPowerPC()){
					binName = "muscle3.8.31_macppc";
				}
				else{
					binName = "muscle3.8.31_i86darwin32";
				}
			}
			else if(OSNativeUtils.isLinuxOrUnix()){
				binName = "muscle3.8.425_i86linux32";
			}
			// default
			else{
				binName = "muscle3.8.425_win32.exe";
			}
		}
		
		return binName;

	}
	
	/*
     * Calculate checksum of a File using MD5 algorithm
     */
    public static String checkSum(InputStream instream){
        String checksum = null;
        
            try {
				BufferedInputStream bis = new BufferedInputStream(instream);
				MessageDigest md = MessageDigest.getInstance("MD5");
        
				//Using MessageDigest update() method to provide input
				byte[] buffer = new byte[8192];
				int numOfBytesRead;
				while( (numOfBytesRead = bis.read(buffer)) > 0){
				    md.update(buffer, 0, numOfBytesRead);
				}
				byte[] hash = md.digest();
				checksum = new BigInteger(1, hash).toString(16); //don't use this, truncates leading zero
			} catch (FileNotFoundException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			} catch (NoSuchAlgorithmException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			} catch (IOException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			}

       return checksum;
    }


}