LastIndexOf and java.lang.IndexOutOfBoundsException

Question

I have a string CCAATA CCGT that I'm trying to get fixed length, n, of contiguous subsequences . Then, I want to get something like this:

The index of each subsequences in that string. 0-3, 1-4, 2-5, etc.

0 thru 3 : CCAA 
1 thru 4 : CAAT 
2 thru 5 : AATA 
3 thru 6 : ATAC 
4 thru 7 : TACC 
5 thru 8 : ACCG 
6 thru 9 : CCGT 

The list size is 7. Here, I am looping thru the list and getting index & lastIndexOf. After, 3 thru 6 : ATAC , I get

Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 7, Size: 7

for (int i = 0; i < list.size(); i++) {
            System.out.println(ss.indexOf(list.get(i)) 
             + " thru " + ss.lastIndexOf(list.get(i + n - 1)) + " : " 
            + list.get(i));

Demo:

import java.util.ArrayList;

public class Subsequences {

    public static void main(String[] args) {

        String s = "CCAATA CCGT";
        ArrayList<String> list = new ArrayList<String>(); // list of subsequence

        int n = 4; // subsequences of length

        String ss = s.replaceAll("\\s+", "");
        String substr = null;

        for (int i = 0; i <= ss.length() - n; i++) {
            substr = ss.substring(i, i + n);
            list.add(substr);
        }

        for (int i = 0; i < list.size(); i++) {
            System.out.println(ss.indexOf(list.get(i)) 
             + " thru " + ss.lastIndexOf(list.get(i + n - 1)) + " : " 
            + list.get(i));

        }
    }
}

Any hints?

Answer 1

I believe your issue is in list.get(i + n - 1) . You're currently iterating such that the start of each subsequence ranges from 0 to list.size() - 1 . The last subsequence that makes sense is the n characters at positions list.size() - n through list.size() - 1 .

for (int i = 0; i < list.size() - n; i++) {
    System.out.println(ss.indexOf(list.get(i)) 
        + " thru " + ss.lastIndexOf(list.get(i + n - 1)) + " : " 
        + list.get(i));

    }

Answer 2

Remove all whitespace, loop:

String data = "CCAATA CCGT";
String replaced = data.replaceAll("\\s", "");
for (int i = 0; i < replaced.length() - 4 + 1; i++) {
    System.out.println(replaced.subSequence(i, i + 4));
}

Output:

CCAA
CAAT
AATA
ATAC
TACC
ACCG
CCGT

Answer 3

You don't need to add n to the lastIndexOf since you separated the substring by 4. Each entry in the List consist of 4 chars. Change your index check to this

(ss.lastIndexOf(list.get(i)) + n - 1)

and finally it looks like this

 for (int i = 0; i < list.size(); i++) {
        System.out.println(ss.indexOf(list.get(i))
                + " thru " + (ss.lastIndexOf(list.get(i)) + n - 1) + " : "
                + list.get(i));

    }

output:

0 thru 3 : CCAA   
1 thru 4 : CAAT   
2 thru 5 : AATA   
3 thru 6 : ATAC   
4 thru 7 : TACC   
5 thru 8 : ACCG  
6 thru 9 : CCGT   

Answer 4

In your loop

for (int i = 0; i < list.size(); i++) { 
   System.out.println(ss.indexOf(list.get(i)) 
   + " thru " + ss.lastIndexOf(list.get(i + n - 1))
   + " : " + list.get(i));
}

When you do list.get(i + n - 1) and your i is 4, the result of the addiction will be 4 + 4 - 1 = 7 and you can't get a member of a list with the same or bigger index of your list.size() , so the system throws the Exception

To have the result you expect, you can do something like this:

import java.util.ArrayList;

public class Subsequences {

public static void main(String[] args) {

    String s = "CCAATA CCGT";
    ArrayList<String> list = new ArrayList<String>(); // list of subsequence

    int n = 4; // subsequences of length

    String ss = s.replaceAll("\\s+", "");
    String substr = null;

    for (int i = 0; i <= ss.length() - n; i++) {
        substr = ss.substring(i, i + n);
        list.add(substr);
    }

    // --------Here the edits-------
    for (int i = 0; i < list.size(); i++) 
        System.println(i + " thru " + (i+n-1) + " : " + list.get(i))
    // -----------------------------

}
}

Answer 5

You can do this with a simple regex as well. Remove the whitespaces and run this regex:

(?=(.{4}))

Sample:

package com.see;

import java.util.ArrayList;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class RegexTest {

    private static final String TEST_STR = "CCAATA CCGT";

    public ArrayList<String> getMatchedStrings(String input) {
        ArrayList<String> matches = new ArrayList<String>();
        input = input.replaceAll("\\s", "");

        Pattern pattern = Pattern.compile("(?=(.{4}))");
        Matcher matcher = pattern.matcher(input);

        while (matcher.find())
            matches.add(matcher.group(1));

        return matches;
    }

    public static void main(String[] args) {
        RegexTest rt = new RegexTest();
        for (String string : rt.getMatchedStrings(TEST_STR)) {
            System.out.println(string);
        }
    }
}