Hashtable dict= new  Hashtable();
...
много-много put
...
StringBuffer res =  new  StringBuffer();

 for  ( int  i =  0 ; i < src.length(); ++i) {
      res.append(dicе.get(src.subSequence(i,i+ 1 ) ) );
}

 public   class  test2 {
     public   static  String[] f = {"А", "Б", "В", "Г", "Д", "Е", "Ё", "Ж", "З", "И", "Й", "К", "Л", "М", "Н", "О", "П", "Р", "С", "Т", "У", "Ф", "Х", "Ч", "Ц", "Ш", "Щ", "Э", "Ю", "Я", "Ы", "Ъ", "Ь", "а", "б", "в", "г", "д", "е", "ё", "ж", "з", "и", "й", "к", "л", "м", "н", "о", "п", "р", "с", "т", "у", "ф", "х", "ч", "ц", "ш", "щ", "э", "ю", "я", "ы", "ъ", "ь"};
     public   static  String[] t = {"A", "B", "V", "G", "D", "E", "Jo", "Zh", "Z", "I", "J", "K", "L", "M", "N", "O", "P", "R", "S", "T", "U", "F", "H", "Ch", "C", "Sh", "Csh", "E", "Ju", "Ja", "Y", "`", "'", "a", "b", "v", "g", "d", "e", "jo", "zh", "z", "i", "j", "k", "l", "m", "n", "o", "p", "r", "s", "t", "u", "f", "h", "ch", "c", "sh", "csh", "e", "ju", "ja", "y", "`", "'"};
     public   static   void  main(String[] args) {
           try  {
             long  i;
            i = System.currentTimeMillis();
             for  ( int  n =  0 ; n <  1000 ; n++) {
                BufferedReader fin =  new  BufferedReader( new  FileReader("file"));
                String line;
                String translit;
                 while  ((line = fin.readLine()) !=  null ) {
                    translit = toTranslit(line);
                }
            }
            System.out.println((i - System.currentTimeMillis()) /  1000 );
        }  catch  (FileNotFoundException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }  catch  (IOException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
    }
     private   static  String toTranslit(String src) {
         if  (src ==  null ) {
             return  "";
        }
        StringBuffer res =  new  StringBuffer();
         for  ( int  i =  0 ; i < src.length(); ++i) {
             char  add = src.charAt(i);
             for  ( int  j =  0 ; j < f.length; j++) {
                 if  (f[j].length() ==  1  && f[j].charAt( 0 ) == add) {
                    res.append(t[j]);
                     break ;
                }  else  {
                     if  (j == f.length -  1 ) {
                        res.append(add); //unknown input char found - insert as is.
                    }
                }
            }
        }
         return  res.toString();
    }
}

ublic  class  test {
     static  Hashtable dic =  new  Hashtable();
     public   static   void  dict() {
 dic.put("Й", "J");
      ...
куча put
...
  dic.put("ё", "jo");
    }
     public   static   void  main(String[] args) {
        dict();
         try  {
             long  i;
            i = System.currentTimeMillis();
             for  ( int  n =  0 ; n <  1000 ; n++) {
                BufferedReader fin =  new  BufferedReader( new  FileReader("NB-balance1.csv"));
                String line;
                String translit;
                 while  ((line = fin.readLine()) !=  null ) {
                    translit = cyr2lat(line);
                }
            }
            System.out.println((i - System.currentTimeMillis()) /  1000 );
        }  catch  (FileNotFoundException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }  catch  (IOException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        }
    }
     public   static  String cyr2lat(String src) {
        StringBuffer res =  new  StringBuffer();
         for  ( int  i =  0 ; i < src.length(); ++i) {
             if  (dic.get(src.subSequence(i, i +  1 )) !=  null ) {
                res.append(dic.get(src.subSequence(i, i +  1 )));
            }  else  {
                res.append(src.subSequence(i, i +  1 ));
            }
        }
         return  res.toString();
    }
}

  try  {
             long  i;
            i = System.currentTimeMillis();
dict()