This program won't work for some reason

Question

I'm having trouble with getting this program to do what I want. It reads in a file and identifies certain parts that follow the rules I've given. The first version below is one that works. It simply prints out the string if it meets the conditions in the if statements. The second one will compile but shows no data. I know it stores the values in the arrays sortstem and sortdg becuase I put the println statement directly after the code for storing them and it worked. However, when I put it where it is now, it will not work. Any suggestions? Also, I get an error after the program runs for both versions: It says exception in thread "main" Java.lang.NullPointerException at tokens.main(tokens.java.69) (this was for the first program).
import java.io.*;
import java.util.*;
class tokens {
     public static void main(String args[]) throws IOException {
          int i;                                                       //int to read in the data from the text file
          int count = -1;
          int countt = -1;
          int countc = 0;                                                  //int to put data into a char array
          FileInputStream fin;                                             //input stream
          char array[] = new char[10000];                                        //array to hold chars from the text file
          String s;                                                  //chars are transfered to this String
          int index;                                                  //index of the names I'm searching for in the string
          String tokens[] = new String[10000];                    
          try {
               fin = new FileInputStream(args[0]);
          } catch (FileNotFoundException e) {
               System.out.println("File not Found");
               return;
          } catch (ArrayIndexOutOfBoundsException e) {
               System.out.println("Usage: ShowFile File");
               return;
          do {
               i = fin.read();
               if (i != -1) {
                    if (count==array.length-1) {                              //this expands the array if more space is needed
                         char temp[] = new char[array.length+5000];
                         for (int j = 0; j < array.length; j++) temp[j] = array[j];
                         array = temp;
                         array[++count] = (char) i;
                    else
                         array[++count] = (char) i;                         
          } while(i != -1);
          fin.close();
          s = new String(array);
          StringTokenizer st = new StringTokenizer(s);                                                            
          while (st.hasMoreTokens()) {
               if (countt==tokens.length-1) {                              //this expands the array if more space is needed
                         String temp1[] = new String[tokens.length+5000];
                         for (int j = 0; j < tokens.length; j++) temp1[j] = tokens[j];
                         tokens = temp1;
                         tokens[++countt] = st.nextToken();
                    else
                         tokens[++countt] = st.nextToken();     
          if (tokens[4].startsWith("stem")) {
               if (tokens[4].equals(tokens[201])) {      //Skip this one
               else
                    if ((tokens[9].equals("32")) && (tokens[15].equals("31"))
                    && (tokens[21].equals("30")) && (tokens[27].equals("29"))
                    && (tokens[33].equals("28")) && (tokens[39].equals("27"))) {
                         System.out.println(tokens[4]);
          for (int k = 201; k < tokens.length-198; k++) {
               if (tokens[k].startsWith("stem")) {
                    if ((tokens[k].equals(tokens[k+197])) || (tokens[k].equals(tokens[k-197]))) {
                         //Skip this one
                    else
                         if ((tokens[k+5].equals("32")) && (tokens[k+11].equals("31"))
                         && (tokens[k+17].equals("30")) && (tokens[k+23].equals("29"))
                         && (tokens[k+29].equals("28")) && (tokens[k+35].equals("27"))) {
                              System.out.println(tokens[k]);
}This one below compiles but doesn't print to the screen.
import java.io.*;
import java.util.*;
class tokenstest {
     public static void main(String args[]) throws IOException {
          int i;                                                       //int to read in the data from the text file
          int count = -1;
          int countt = -1;
          int countc = 0;                                                  //int to put data into a char array
          FileInputStream fin;                                             //input stream
          char array[] = new char[1000000];                                        //array to hold chars from the text file
          String s;                                                  //chars are transfered to this String
          int index;                                                  //index of the names I'm searching for in the string
          String tokens[] = new String[200000];
          String sortdg[] = new String[500];     
          String sortstem[] = new String[500];                         
          try {
               fin = new FileInputStream(args[0]);
          } catch (FileNotFoundException e) {
               System.out.println("File not Found");
               return;
          } catch (ArrayIndexOutOfBoundsException e) {
               System.out.println("Usage: ShowFile File");
               return;
          do {
               i = fin.read();
               if (i != -1) {
                    if (count==array.length-1) {                              //this expands the array if more space is needed
                         char temp[] = new char[array.length+5000];
                         for (int j = 0; j < array.length; j++) temp[j] = array[j];
                         array = temp;
                         array[++count] = (char) i;
                    else
                         array[++count] = (char) i;                         
          } while(i != -1);
          fin.close();
          s = new String(array);
          StringTokenizer st = new StringTokenizer(s);                                                            
          while (st.hasMoreTokens()) {
               if (countt==tokens.length-1) {                              //this expands the array if more space is needed
                         String temp1[] = new String[tokens.length+5000];
                         for (int j = 0; j < tokens.length; j++) temp1[j] = tokens[j];
                         tokens = temp1;
                         tokens[++countt] = st.nextToken();
                    else
                         tokens[++countt] = st.nextToken();     
          if (tokens[4].startsWith("stem")) {
               if (tokens[4].equals(tokens[201])) {      //Skip this one
               else
                    if ((tokens[9].equals("32")) && (tokens[15].equals("31"))
                    && (tokens[21].equals("30")) && (tokens[27].equals("29"))
                    && (tokens[33].equals("28")) && (tokens[39].equals("27"))) {
                         sortstem[countc] = tokens[4];
                         sortdg[countc] = tokens[3];
                         countc++;
          for (int k = 201; k < tokens.length-198; k++) {
               if (tokens[k].startsWith("stem")) {
                    if ((tokens[k].equals(tokens[k+197])) || (tokens[k].equals(tokens[k-197]))) {
                         //Do nothing
                    else
                         if ((tokens[k+5].equals("32")) && (tokens[k+11].equals("31"))
                         && (tokens[k+17].equals("30")) && (tokens[k+23].equals("29"))
                         && (tokens[k+29].equals("28")) && (tokens[k+35].equals("27"))) {
                              sortstem[countc] = tokens[k];
                              sortdg[countc] = tokens[k-1];
                              countc++;
          for (int z = 0; z < countc; z++) {
               System.out.println(sortstem[z]);
          for (int z = 0; z < countc; z++) {
               for (int y = z+1; y < countc; y++) {
                    if (sortdg[z].compareTo(sortdg[z]) > 0) {
                         String tdg = sortdg[z];
                         String tstem = sortstem[z];
                         sortdg[z] = sortdg[y];
                         sortstem[z] = sortstem[y];
                         sortdg[y] = tdg;
                         sortstem[y] = tstem;
          for (int j = 0; j < 20; j++) {
               System.out.println(sortstem[j] + ": dG = " + sortdg[j]);
          System.out.println("Test");
}

Answer 1

I'm still having trouble with the println in this program. For some reason, in this section of the code, if I put System.out.println(sortstem[0]); inside the for loop, it works fine. But if I try to do it ouside of this loop, it will not work. The only thing I can think of is that the variable is only available inside the loop but I just can't figure it out. Can anyone enlighten me?
for (int k = 201; k < tokens.length-198; k++) {
               if (tokens[k].startsWith("stem")) {
                    if ((tokens[k].equals(tokens[k+197])) || (tokens[k].equals(tokens[k-197]))) {
                         //Do nothing
                    else
                         if ((tokens[k+5].equals("32")) && (tokens[k+11].equals("31"))
                         && (tokens[k+17].equals("30")) && (tokens[k+23].equals("29"))
                         && (tokens[k+29].equals("28")) && (tokens[k+35].equals("27"))) {
                              sortstem[countc] = tokens[k];
                              sortdg[countc] = tokens[k-1];
                              countc++;
[code/]