filterDifferenceInLists

Script

import java.io.BufferedOutputStream;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Scanner;

// get the scanner from the input file URL(our protein list)
Scanner getSequence =new Scanner(new File(filename));			
// get the scanner from the input file URL
Scanner getComSequence =new Scanner(new File(filename1));
			//get the outcome file location and assign a filewriter for that
			FileOutputStream out = null;
			File outcome = new File(filename2);
// if the output file doesn't exist, create it
			if(!outcome.exists())
            {
				outcome.createNewFile();
            }
            out = new FileOutputStream(outcome);
		
	//create a list for storing our protein hits
            List FastaList = new ArrayList();
	//create a list for storing comparision protein hits
            List ComList = new ArrayList();
          	// copy all the our protein hits to the list  
	String s = getSequence.next();
			while (getSequence.hasNext())
			{
				FastaList.add(s);
				s = getSequence.next();
			}
			FastaList.add(s);
	// copy all the comparision proteins to the list	
	String s = getComSequence.next();
			while (getComSequence.hasNext())
			{
				ComList.add(s);
				s = getComSequence.next();
			}
			ComList.add(s);
	
		//temporary virable
			int i, j;
			String abc = null;
			String bcd= null;
				Iterator test = FastaList.iterator();
	// filter all the proteins in both lists , only leave with 
	// the proteins in our list but not in the comparision list, 	
		for(i=FastaList.size()-1;i>=0;i--)
			{
				for (j= ComList.size()-1; j >= 0; j--)
				
					{
					
					abc = FastaList.get(i);
					bcd = ComList.get(j);
						if(abc.equals(bcd))
						{
							FastaList.remove(i);
							break;
						}

					}
				
			}
	//write the result protein list to the output scream	
			out1 = new String();
	
			for(i=0;i