Remove stop words from the file content and count the no of occurrences of words

Question 1

Just print your map outside of the while loop.

Question 2

Move your map after finish the while loop. See below code.

import java.util.Map;
import java.util.Scanner;
import java.util.TreeMap;

/**
 *
 * @author Masud
 */
public class UserRepository {

    public static void main(String[] args) {
        String[] stopwords = {"a", "about", "above", "above", "across", "after", "afterwards", "again", "against", "all", "almost",
            "alone", "along", "already", "also", "although", "always", "am", "among", "amongst", "amoungst", "amount", "an", "and",
            "another", "any", "anyhow", "anyone", "anything", "anyway", "anywhere", "are", "around", "as", "at", "back", "be", "became",
            "because", "become", "becomes", "becoming", "been", "before", "beforehand", "behind", "being", "below", "beside", "besides",
            "between", "beyond", "bill", "both", "bottom", "but", "by", "call", "can", "cannot", "cant", "co", "con", "could", "couldnt",
            "cry", "de", "describe", "detail", "do", "done", "down", "due", "during", "each", "eg", "eight", "either", "eleven", "else",
            "elsewhere", "empty", "enough", "etc", "even", "ever", "every", "everyone", "everything", "everywhere", "except", "few",
            "fifteen", "fify", "fill", "find", "fire", "first", "five", "for", "former", "formerly", "forty", "found", "four", "from",
            "front", "full", "further", "get", "give", "go", "had", "has", "hasnt",
            "have", "he", "hence", "her", "here", "hereafter", "hereby", "herein", "hereupon", "hers", "herself",
            "him", "himself", "his", "how", "however", "hundred", "ie", "if", "in", "inc", "indeed", "interest", "into",
            "is", "it", "its", "itself", "keep", "last", "latter", "latterly", "least", "less", "ltd", "made", "many",
            "may", "me", "meanwhile", "might", "mill", "mine", "more", "moreover", "most", "mostly", "move", "much", "must",
            "my", "myself", "name", "namely", "neither", "never", "nevertheless", "next", "nine", "no", "nobody", "none",
            "noone", "nor", "not", "nothing", "now", "nowhere", "of", "off", "often", "on", "once", "one", "only", "onto",
            "or", "other", "others", "otherwise", "our", "ours", "ourselves", "out", "over", "own", "part", "per", "perhaps",
            "please", "put", "rather", "re", "same", "see", "seem", "seemed", "seeming", "seems", "serious", "several", "she",
            "should", "show", "side", "since", "sincere", "six", "sixty", "so", "some", "somehow", "someone", "something",
            "sometime", "sometimes", "somewhere", "still", "such", "system", "take", "ten", "than", "that", "the", "their",
            "them", "themselves", "then", "thence", "there", "thereafter", "thereby", "therefore", "therein", "thereupon",
            "these", "they", "thickv", "thin", "third", "this", "those", "though", "three", "through", "throughout", "thru",
            "thus", "to", "together", "too", "top", "toward", "towards", "twelve", "twenty", "two", "un", "under", "until",
            "up", "upon", "us", "very", "via", "was", "we", "well", "were", "what", "whatever", "when", "whence", "whenever",
            "where", "whereafter", "whereas", "whereby", "wherein", "whereupon", "wherever", "whether", "which", "while",
            "whither", "who", "whoever", "whole", "whom", "whose", "why", "will", "with", "within", "without", "would", "yet",
            "you", "your", "yours", "yourself", "yourselves", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "1.", "2.", "3.", "4.", "5.", "6.", "11",
            "7.", "8.", "9.", "12", "13", "14", "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z",
            "terms", "CONDITIONS", "conditions", "values", "interested.", "care", "sure", ".", "!", "@", "#", "$", "%", "^", "&", "*", "(", ")", "{", "}", "[", "]", ":", ";", ",", "<", ".", ">", "/", "?", "_", "-", "+", "=",
            "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z",
            "contact", "grounds", "buyers", "tried", "said,", "plan", "value", "principle.", "forces", "sent:", "is,", "was", "like",
            "discussion", "tmus", "diffrent.", "layout", "area.", "thanks", "thankyou", "hello", "bye", "rise", "fell", "fall", "psqft.", "http://", "km", "miles"};

        Scanner fip1 = new Scanner(new String("contains java"));

        Map map = new TreeMap();

        Integer ONE = new Integer(1);
        while (fip1.hasNext()) {
            int flag = 1;
            String s1 = fip1.next();
            s1 = s1.toLowerCase();
            for (int i = 0; i < stopwords.length; i++) {
                if (s1.equals(stopwords[i])) {
                    flag = 0;
                }
            }
            if (flag != 0) {
                if (s1.length() > 0) {

                    Integer frequency = (Integer) map.get(s1);
                    if (frequency == null) {
                        frequency = ONE;
                    } else {
                        int value = frequency.intValue();
                        frequency = new Integer(value + 1);
                    }
                    map.put(s1, frequency);
                }
            }
        }
        System.out.println(map);
    }
}

Question 3

Remove System.out.println(map); from while loop and pring map outside while loop

Question 4

Print the map outside of the while(fip1.hasNext) loop.

while(fip1.hasNext) {
....
        map.put(s1, frequency);               
        }                     
    }
}
System.out.println(map);