java indexOf function complexity is O(n*m) where n is length of the text and m is a length of pattern
here is indexOf original code

   /**
     * Returns the index within this string of the first occurrence of the
     * specified substring. The integer returned is the smallest value
     * <i>k</i> such that:
     * <blockquote><pre>
     * this.startsWith(str, <i>k</i>)
     * </pre></blockquote>
     * is <code>true</code>.
     *
     * @param   str   any string.
     * @return  if the string argument occurs as a substring within this
     *          object, then the index of the first character of the first
     *          such substring is returned; if it does not occur as a
     *          substring, <code>-1</code> is returned.
     */
    public int indexOf(String str) {
    return indexOf(str, 0);
    }

    /**
     * Returns the index within this string of the first occurrence of the
     * specified substring, starting at the specified index.  The integer
     * returned is the smallest value <tt>k</tt> for which:
     * <blockquote><pre>
     *     k &gt;= Math.min(fromIndex, this.length()) && this.startsWith(str, k)
     * </pre></blockquote>
     * If no such value of <i>k</i> exists, then -1 is returned.
     *
     * @param   str         the substring for which to search.
     * @param   fromIndex   the index from which to start the search.
     * @return  the index within this string of the first occurrence of the
     *          specified substring, starting at the specified index.
     */
    public int indexOf(String str, int fromIndex) {
        return indexOf(value, offset, count,
                       str.value, str.offset, str.count, fromIndex);
    }

    /**
     * Code shared by String and StringBuffer to do searches. The
     * source is the character array being searched, and the target
     * is the string being searched for.
     *
     * @param   source       the characters being searched.
     * @param   sourceOffset offset of the source string.
     * @param   sourceCount  count of the source string.
     * @param   target       the characters being searched for.
     * @param   targetOffset offset of the target string.
     * @param   targetCount  count of the target string.
     * @param   fromIndex    the index to begin searching from.
     */
    static int indexOf(char[] source, int sourceOffset, int sourceCount,
                       char[] target, int targetOffset, int targetCount,
                       int fromIndex) {
    if (fromIndex >= sourceCount) {
            return (targetCount == 0 ? sourceCount : -1);
    }
        if (fromIndex < 0) {
            fromIndex = 0;
        }
    if (targetCount == 0) {
        return fromIndex;
    }

        char first  = target[targetOffset];
        int max = sourceOffset + (sourceCount - targetCount);

        for (int i = sourceOffset + fromIndex; i <= max; i++) {
            /* Look for first character. */
            if (source[i] != first) {
                while (++i <= max && source[i] != first);
            }

            /* Found first character, now look at the rest of v2 */
            if (i <= max) {
                int j = i + 1;
                int end = j + targetCount - 1;
                for (int k = targetOffset + 1; j < end && source[j] ==
                         target[k]; j++, k++);

                if (j == end) {
                    /* Found whole string. */
                    return i - sourceOffset;
                }
            }
        }
        return -1;
    }

you can simply implements the KMP algorithm without using of indexOf Like this

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.Scanner;


public class Main{
    int failure[];
    int i,j;
    BufferedReader in=new BufferedReader(new InputStreamReader(System.in));
    PrintWriter out=new PrintWriter(System.out);
    String pat="",str="";
    public Main(){
            try{

            int patLength=Integer.parseInt(in.readLine());
            pat=in.readLine();
            str=in.readLine();
            fillFailure(pat,patLength);
            match(str,pat,str.length(),patLength);
            out.println();
            failure=null;}catch(Exception e){}

        out.flush();
    }
    public void fillFailure(String pat,int patLen){
        failure=new int[patLen];
        failure[0]=-1;
        for(i=1;i<patLen;i++){
            j=failure[i-1];
            while(j>=0&&pat.charAt(j+1)!=pat.charAt(i))
                j=failure[j];
            if(pat.charAt(j+1)==pat.charAt(i))
                failure[i]=j+1;
            else
                failure[i]=-1;
        }
    }
    public void match(String str,String pat,int strLen,int patLen){
        i=0;
        j=0;
        while(i<strLen){
            if(str.charAt(i)==pat.charAt(j)){
                i++;
                j++;
                if(j==patLen){
                    out.println(i-j);
                    j=failure[j-1]+1;
                }
            } else if (j==0){
                    i++;
            }else{
                j=failure[j-1]+1;
            }

        }
    }
    public static void main(String[] args) {
        new Main();
    }
}

You have taken a complicated approach. Try this:

int count = str.split("the", -1).length - 1;

If you absolutely must use indexOf():

str = str.toLowerCase();
int count = 0;
for (int i = str.indexOf("the"); i >= 0; i = str.indexOf("the", i + 1))
    count++;

You can use Regex.

Matcher matcher = Pattern.compile("(state)(\(.*?\))").matcher(text);
String state = matcher.group(2);

Well, if it helps, you can think of "FOO" as "" + "FOO".