Still not compiling ok

/*
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 * and open the template in the editor.
 */
package tests;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.codec.DecoderException;
import org.apache.commons.codec.binary.Hex;


/**
 *
 * @author Makerimages
 */
public class Compilertest3
{
    String S;
    String SClean;

    public Compilertest3(File f) throws IOException
    {
      //  intNames=new String[256];
      //  ints=new String[256];
         StringBuffer fileData = new StringBuffer();
        BufferedReader reader = new BufferedReader(
                new FileReader(f));
        char[] buf = new char[1024];
        int numRead=0;
        while((numRead=reader.read(buf)) != -1){
            String readData = String.valueOf(buf, 0, numRead);
            fileData.append(readData);
        }
        reader.close();
       S=fileData.toString();
    }




    public void cleanFile(String input)
    {
        String split[]=input.split("\n");
        input="\n"+input;
        split[0]=" "+split[0];
         int count = 0;
         int intCount = 0;//change this for starting vX value (default: 0)
         int funcCount=0;
                while (count < split.length) {
                        if (split[count].startsWith(" define")) {

                                split[count] = split[count].substring(8);//remove define and space

                                input = input.replaceAll(split[count].split(" ")[0], split[count].substring(split[count].split(" ")[0].length()));
                                //the above replaces the first argument with all the last arguments in the define function, in the input string
                              //  System.err.print(input);
                        }  if (split[count].startsWith(" int")) {
                               //System.out.println("int debug:");

                                split[count] = split[count].substring(4);//remove "int" and space
                                input = input.replaceAll(split[count], " v" + intCount + " ");
                              input= input.replaceAll(split[count], " v" + intCount + " ");//just in case

                                intCount++;
                        }
                        if (split[count].startsWith("func "))
                        {
                            split[count] = split[count].substring(0);
                            input = input.replaceAll(split[count], "~" + funcCount + " ");
                           // input = input.replaceAll(split[count], " ~" + funcCount + " ");//just in case
                            funcCount++;
                        }



                        count++;
                }

                input = input.replaceAll("\n int.*.\n", "\n");//this is where the added \n at start is
                input = input.replaceAll("\n func.*.\n", "\n");
                 input = input.replaceAll(" #.*.", "");
                   input = input.replaceAll("\\{", "");
                while(input.contains(" int ")==true)
                {
                        input = input.replaceAll("\n int.*.\n", "\n");
                }

                         while(input.contains(" func ")==true)
                {
                        input = input.replaceAll("\n func.*.\n", "\n");
                }
                input=input.replaceAll("(?m)^[ \t]*\r?\n", "");//clear all empty lines
                input=input.substring(0);//gets rid of the problem caused by the adding \n thing
              //  input = cleanInput(input);//cleans the input for the last time
                //System.err.print(input);
                SClean=input;
                System.err.println(SClean);
                }



    }