Mine

import java.io.*;

public class smithwaterman
{
  private static void help()
  {
    System.out.println("Usage:\nEither\nsmithwaterman Patternfile1 Patternfile2 B\nOr\nsmithwaterman Patternfile1 Patternfile2 E matchscore mismatchscore gapscore\n\nWhere B uses the Blowsum Matrix for evaluation and E lets you specify which values will be applied for scoring");
    System.exit(1);
  }

  //just a debugging function!
  private static void help(int id)
  {
    System.out.println("Call from "+id);
    System.exit(1);
  }

  public smithwaterman(){}//

  public static void main(String[] args)
  {
    if(args.length<3)help();
    /*
    if(args[2]=="B"||args[2]=="E"){System.out.println("["+args[2]+"]");help(1);}
    if(args[2]=="E"&&args.length!=6)help(2);
    */

    float gap=8;//gap penality 

    switch(args[2].codePointAt(0))
    {
      case 69://let's do our own scoring
        if(args.length<7)help();
	edit algo=new edit(getFloat(args[3]),getFloat(args[4]));
        gap=getFloat(args[5]);
      break;
      
      case 66://use Blosum Matrix
        blosum algo=new blosum();
      break;

      default:help();
    }

    String A=fasFile(args[0]);
    String B=fasFile(args[1]);

  }

  public static String fasFile(String datei)
  {
    BufferedReader in;
    try
    {
      in=new BufferedReader(new FileReader(datei));
    }
    catch(IOException e)
    {
      System.out.println("Can not open file "+datei);
      System.exit(1);
    }
    StringBuilder sb=new StringBuilder();
    String line=in.readLine();//drop first line
    while((line=in.readLine())!=null)
    {
      sb.append(line);
    }
    in.close();
    return sb.toString();
  }

 static float getFloat(String i)
 {
   float f;
   try
   {
     f=Float.parseFloat(i);
   }
   catch(NumberFormatException e)
   {
     System.out.println("Error: "+i+" is not a valid floating-point value!");
     System.exit(1);
   }
   return f;
 }
    

    
}