Reading, comparing and appending two files is taking lot of time

Question

public static void main(String args[])
     BufferedReader bSource = null;
     String sSource="";
     String sSourceData="";
     BufferedReader bDestination = null;
     String sDestination="";
     String sDestinationData="";
     try
          bSource = new BufferedReader(new FileReader("C:/TEMP/Source.map"));
          while((sSource = bSource.readLine()) != null)
               sSourceData+=sSource;
          bDestination = new BufferedReader(new FileReader("D:/TEMP/Destination.map"));
          while((sDestination = bDestination.readLine()) != null)
               sDestinationData+=sDestination;
     catch(IOException ioe)
          System.out.println(ioe.getMessage());
     finally
          try
               bSource.close();
               bDestination.close();
          catch(Exception e)
     if(sDestinationData.contains(sSourceData))
          fDestinationFlag=false;
     else
          fDestinationFlag=true;
     if(fDestinationFlag)
          BufferedReader br2 = null;
          BufferedWriter bw2 = null;
          try
               br2 = new BufferedReader(new FileReader("C:/TEMP/Source.map"));     
               bw2 = new BufferedWriter(new FileWriter("D:/TEMP/Destination.map",true));
               while((line2 = br2.readLine()) != null)
                    bw2.write(line2);
                    bw2.newLine();
                    bw2.flush(); 
          catch(IOException ioe)
               System.out.println(ioe.getMessage());
          finally
               try
                    br2.close();
               catch(Exception e)
               try
                    bw2.close();
               catch(Exception e)
}I am comparing the contents of the two files Source.map (containing 3 lines) and Destination.map (containing 5000+ lines). The contents of the Source.map gets appended in the Destination.map only if it does not contain the same.
Now my program is doing the necessary, but it is taking lot of time. It's taking 1 min 26 seconds.
Could anyone please tell me what do I modify in may program to make it execute much faster.

Answer 1

1) Just compare the byte content - no need to convert to Strings.
2) Compare a block (say 256K bytes) at a time - no need to read the whole file into memory.
3) Compare the file lengths first - if they are different then the content cannot be the same.
4) When appending one file to the other, set the 'append' flag in the constructor of FileOutputStream to true.