Compressor em java

[DarkT]

Este codigo faz a compressao de um ficheiro txt.

O Bwt faz a rotaçao das frases e ordena por ordem lexicográfica e no fim retorna a ultima coluna.
O rle faz o seguinte:

aaabbbcc

3a3b2c


O seguinte codigo funciona mas no entanto demora demasiado tempo. Aceito sujestoes para o optimizar ..

import java.util.Scanner;  
import java.io.*;                            

public class compressor2
{
	
	static String rle (String mod)
	{
		int k,count = 1, flag =0;
		char c = 'e';
		String modrle;
		
		modrle = "";
		for (k=0; k<mod.length();k++){
			if (k != mod.length()-1){
				if (mod.charAt(k)== mod.charAt(k+1))
				{
				count = count+1;
				c = mod.charAt(k);
				flag = 1;
				}
				else if (flag == 0){
					c = mod.charAt(k);
					modrle = modrle + '1' + c;
					count= 1;
					flag=0;}
					else if (k==mod.length()-1 & flag == 0){
						c=mod.charAt(k);
						modrle = modrle + '1' + c;
						count=1;
						flag = 0;
					}
					else {
						c=mod.charAt(k);
						while (count>9)
						{
							modrle = modrle + '9' + c;
							count = count - 9;
						}
						modrle = modrle + count + c;
						count=1;
						flag = 0;
			}
			}
			else{
			if (flag == 0){
					c = mod.charAt(k);
					modrle = modrle + '1' + c;
					count= 1;
					flag=0;}
					else if (k==mod.length()-1 & flag == 0){
						c=mod.charAt(k);
						modrle = modrle + '1' + c;
						count=1;
						flag = 0;
					}
					else {
						c=mod.charAt(k);
						while (count>9)
						{
							modrle = modrle + '9' + c;
							count = count - 9;
						}
						modrle = modrle + count + c;
						count=1;
						flag = 0;
					}
			}		
				 
		}
		return modrle;
	}
	
	static String bwt (String[] frase, int nc)
	{
		int k,i,j,x,o;
		String v, v2, aux, mod;
		String [][] matrix = new String[nc][nc];
		
		//BWT ROTACOES
		
		for (k=0; k<nc;k++){
			if (k == nc-1)
				matrix[0][k]=String.valueOf('ß');
			else
				matrix[0][k]=frase[k];
		}
		for(i=0;i<matrix.length-1;i++){
			for (j=0;j<matrix.length;j++){
				if (j==matrix.length-1)
					matrix[i+1][0]=matrix[i][j];
				else
					matrix[i+1][j+1]=matrix[i][j];
			}
		}
		
		//BWT A ORDENAR
		
		v="";
		v2="";
		
		for (i=0;i<nc - 1;i++){

			for (k=i+1;k < nc; k++){



				for (j=0;j<nc;j++){
					v=v+matrix[i][j];
					v2=v2+matrix[k][j];
				}

				x = v.compareTo(v2);
				if (x > 0)
				{
					aux = v;
					for (o=0;o<nc;o++){
						matrix[i][o] = matrix[k][o];
						matrix[k][o] = String.valueOf(aux.charAt(o));
					}

				}
				v="";
				v2="";
			}
			
		}
		
		//BWT RESULTADO
		
		mod = "";
		for (i=0; i<matrix.length;i++){
			mod = mod + matrix[i][nc -1];
		}
		
		return mod;
		
		}

	
	
	public static void main(String[] args) throws IOException
	{
		String frase=null, mod = "", rlemod = "";
		int i = 0, j = 0, nl = 0, nc = 0, prog = 0, prog2 = 0; //nl = number of lines; nc = number of columns


		File file = new File("input.txt");
		Scanner inputFile = new Scanner(file);
		PrintWriter outputFile = new PrintWriter("compressed.txt");        


		while (inputFile.hasNext())
		{
			nl ++;    
			frase = inputFile.nextLine();    /**Lê as linhas do ficheiro "input.txt"**/
			if (frase.length() > nc)
				nc = frase.length();

		}
		inputFile.close();

		inputFile = new Scanner(file);

		String[][] texto = new String [nl][nc];

		while (inputFile.hasNext())
		{


			while (i < nl)
			{
				frase = inputFile.nextLine();
				j=0; 
				while (j < nc)
				{
					if (j < frase.length())
					{
						texto [i][j] = String.valueOf(frase.charAt(j));

						j++;
					}
					else 
					{
						texto [i][j] = null; 
						j++;
					}
				}
				i++;
			}    
		}                                
		i=0;

		int [] a =new int [nl];
		int x = 0;
		while(i<nl)
		{
			j=0;

			while(j!=nc)
			{
				if (texto[i][j]!=null)
				{
					j++;
					x = j;
				}
				else
				{
					x = j;
					j=nc;
				}

			}
			a[i]=x + 1;
			i++;
		}
		i=0;
		System.out.println();
		System.out.println();
		System.out.println("Text Files Compressor - Version 1.0");
		System.out.println();
		System.out.println();
		System.out.println();
		System.out.println("Please be patient... compression is in progress.");
		System.out.println("This could take a few minutes based on the size and line width of your text file.");
		System.out.println();
		System.out.println();
		System.out.println("Compression Progress:");
		System.out.println();
		
		while (i < nl)
		{
			mod = bwt (texto[i], a[i]);
			rlemod = rle (mod);
			prog = ((i+1)*100)/nl;
			if (prog != prog2)
				System.out.print("|");
			outputFile.println(rlemod);
			i++;
			prog2 = prog;
		}
		
		System.out.println("  " + prog + "%");
		System.out.println();

		//Fechar os ficheiros
		inputFile.close();
		outputFile.close();

	}
}

Obrigado