Two arraylists with different size, compare them!

Question

I Have a major problem now.
I have two text files that I read and split.
TableA:
AT1G01710.1     1     425     427     SKL
AT1G16730.1     1     200     202     SKL
AT1G20480.1     1     563     565     SKL
AT1G20510.1     1     544     546     SKL
AT1G20560.1     1     554     556     SKL
AT1G20560.2     1     476     478     SKL
TableC:
AT1G01710.1
AT1G16730.1
AT1G20480.1
AT1G20510.1
AT1G20510.2
AT1G20560.1
AT1G20560.2I have a database with the values in TableC. In table A I am interested in the 4th "column", The values before SKL. As you see; AT1G20510.2 doesn't exist in TableA. So for those values that does not exist in Table A, I just want to a add a null value. I want this output:
AT1G01710.1 \t 427
AT1G16730.1 \t 202
AT1G20480.1 \t 565
AT1G20510.1 \t 546
AT1G20510.2 \t null
AT1G20560.1 \t 556
AT1G20560.2 \t 478This is my code:
// Reads table C.
while ((line_tableC = br_tablec.readLine()) != null) {
     c_list.add(line_tableC);
// c_list size = 6
// Reads table A, and split around tabs and add "column" 4 to a list (list_size_aa).
while ((line_tableA = br_tablea.readLine()) != null) {
     a_tab_split = line_tableA.split("\\t", -1);
     a_list.add(a_tab_split[0]);
     list_size_aa.add(a_tab_split[3]);
// a_list size = 5
// Problem 1: a_list is smaller than c_list
for (int i = 0; i < a_list.size(); i++) {
          if (a_list.contains(c_list.get(i))) {
          x.add(list_size_aa.get(i));                         
         else {
     x.add("null");
       System.out.println(c_list.get(i) + "\t" + x.get(i));With this code I get this output:
AT1G01710.1 \t 427
AT1G16730.1 \t 202
AT1G20480.1 \t 565
AT1G20510.1 \t 546
AT1G20510.2 \t null
AT1G20560.1 \t 478
AT1G20560.2 \t 709Do you see the problem? In the output I get AT1G20560.1 with the corresponding value 478, but it should be 556! This is because when a_list doesn't contain a string from c_list, a null value will be added to x, and i will be incremented. Its hard to explain, maybe you see it better than I am to explain.
How can I solve this?
Best regards, knx

Answer 1

Last for loop should be based on table C data. In this loop your approach should be fetch each record of table C and retrieve corresponding value from table A using the key.
Here is your solution:
[*Note:* I have used HashMap to hold data of table A and also to hold result. You can use any data type of your choice, but approach will be same.]
import java.io.*;
import java.util.*;
public class Parser{
     public static void main(String[] args) throws Exception{
          System.out.println("Hello: "+System.getProperty("user.dir"));
          new Parser().parse();
     public void parse() throws Exception{
          FileReader reader1=new FileReader("TABLE_A.txt");
          BufferedReader buffer1=new BufferedReader(reader1);
          FileReader reader2=new FileReader("TABLE_C.txt");
          BufferedReader buffer2=new BufferedReader(reader2);          
          HashMap<String,String> tableAData=new HashMap<String,String>();
          List<String> tableCData=new ArrayList<String>();
          // Read data from table a          
          String data=null;
          while((data=buffer1.readLine())!=null){
               String[] temp=data.split("\\t");
               tableAData.put(temp[0],temp[3]);
          data=null;
          while((data=buffer2.readLine())!=null){               
               tableCData.add(data);
          HashMap<String, String> result=new HashMap<String, String>();          
          for(String cData: tableCData){
               if(tableAData.containsKey(cData)){
                    result.put(cData, tableAData.get(cData));
               }else{
                    result.put(cData, null);
          System.out.println("Result: "+result.toString());
}Thanks,
Mrityunjoy