Read file from directory, update contents of the each file

hai,
I could not understand how to debug the error i have now.
target
1- read the files from directory // i able ot do this part
2- for each file
for each file read the content & compare with the existing List & update the list // i able to do this part
when i try to combine both parts , i got some following error
run:
E:\java\check\100130.ixf
Error: children[i] (The system cannot find the file specified)
BUILD SUCCESSFUL (total time: 2 seconds)
i can see from the code that children[i] only gives the error when i use that in the second part of the code.
can any one help me on this??
Thanks
Priyan
the original code
import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import java.io.RandomAccessFile;
import java.util.ArrayList;
public class CompareList
     public static void main(String[] args){
         ArrayList a1 = new ArrayList();
         ArrayList a2 = new ArrayList();
         a1.add("1");
         a1.add("2");
         a1.add("3");
         a1.add("4");
         a1.add("5");
         a1.add("6");
         a1.add("7");
         a1.add("8");
         a1.add("9");
         a1.add("10");
         a1.add("11");
         a1.add("12");
         a1.add("13");
         a1.add("14");
         a1.add("15");
         a1.add("16");
         a1.add("17");
         a1.add("18");
         a1.add("19");
         a1.add("20");
         a1.add("21");
         a1.add("22");
         a1.add("23");
         a1.add("24");
         a1.add("25");
         a1.add("26");
         a1.add("27");
         a1.add("28");
         a1.add("29");
         a1.add("30");
         a1.add("31");
         a1.add("32");
         a1.add("33");
         a1.add("34");
         a1.add("35");
         a1.add("36");
         a1.add("37");
         a1.add("38");
         a1.add("39");
         a1.add("40");
         a1.add("41");
         a1.add("42");
         a1.add("43");
         a1.add("44");
         a1.add("45");
         a1.add("46");
         a1.add("47");
         a1.add("48");
         a1.add("49");
         a1.add("50");
         a1.add("51");
         a1.add("52");
          try{
                File dir = new File("E:\\java\\check");
                File[] children = dir.listFiles();
                if (children == null) {
                      System.out.println("does not exist or is not a directory");
    else {
           for (int i = 0; i < children.length; i++) {
                   System.out.println( children);
FileInputStream fstream = new FileInputStream("children[i]");
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String strLine;
while ((strLine = br.readLine()) != null)      {
String line =strLine.substring(0,2);
// Print the content on the console
//System.out.println(line);
a2.add(line);
} // end of add list2
if (a1.size() > a2.size())
int k = 0;
for (int l = 0; l < a2.size(); l++)
if (!((String)a1.get(l)).equals((String)a2.get(l)))
//System.out.println((String)a2.get(i));
// System.out.println("dd");
k = l;
k++;
for (int l = k; l < a1.size(); l++)
System.out.println((String)a1.get(l));
String str = "children[l]";
File file = new File(str);
RandomAccessFile rand = new RandomAccessFile(file,"rw");
rand.seek(file.length()); //Seek to end of file
rand.writeBytes((String)a1.get(i)); //Write end of file
rand.writeBytes("., 0.");
rand.writeBytes("\n");
}// end of comparing and updating the list2
          in.close();
catch (Exception e){//Catch exception if any
System.err.println("Error: " + e.getMessage());

thanks for the information.
i tried, the error
like this
run:
E:\java\check\100130.ixf
java.lang.StringIndexOutOfBoundsException: String index out of range: 2
        at java.lang.String.substring(String.java:1935) 
        at CompareList.main(CompareList.java:84)
BUILD SUCCESSFUL (total time: 0 seconds)this comes because in my code i used children[i] as string in the later part
    else {
           for (int i = 0; i < children.length; i++) {
                    System.out.println( children);
FileInputStream fstream = new FileInputStream(children[i]);
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String strLine;
while ((strLine = br.readLine()) != null)      {
String line =strLine.substring(0,2);
a2.add(line);
System.out.println(line);
} // end of add list2
if (a1.size() > a2.size())
int k = 0;
for (int l = 0; l < a2.size(); l++)
if (!((String)a1.get(l)).equals((String)a2.get(l)))
//System.out.println((String)a2.get(i));
// System.out.println("dd");
k = l;
k++;
for (int l = k; l < a1.size(); l++)
System.out.println((String)a1.get(l));
String str = "children[l]";
File file = new File(str);
RandomAccessFile rand = new RandomAccessFile(file,"rw");
rand.seek(file.length()); //Seek to end of file
rand.writeBytes((String)a1.get(i)); //Write end of file
rand.writeBytes("., 0.");
rand.writeBytes("\n");
rand.close();
}// end of comparing and updating the list2
          in.close();
i stil could not figure out it yet. do u have any clue with this.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           

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