Saving an output in a file

Question

Hi all, i am having problems with an assignment that i have. I have to prompt the user for a dna sequence and a description of that sequence and then save it to a file., but when i go to look at the file that i created, it give me the memory address of that sequence and then the description always returns null like i never set it. Can anyone help.
Sequence.java(you shouldn't need this but in case you do)
public class Sequence
    // instance variables - replace the example below with your own
    public String sequence;
    public String description;
    public double energy;
    public int number;
    public int temp;
    public double boltzman;
    public final double gasConstant = 1.9872;
     * Constructor for objects of class sequence
    public Sequence()
        // initialise instance variables
        sequence = " not set";
        description = "  not set";
        energy = 0;
        number = 0;
        temp = 0;
        boltzman = 0;
     /**initialize variables
     public Sequence(String aSequence, String aDescription)
         sequence = aSequence;
         description = aDescription;
     /** Sets the sequence
     public void setSequence(String aSequence){
         sequence = aSequence;
     /** Returns the sequence
     public String getSequence(){
         return this.sequence;
     /** Sets the description
     public void setDescription(String aDescription){
         description = aDescription;
     /** Returns the description
     public String getDescription(){
         return this.description;
     /** sets the energy
     public void setEnergy(double aEnergy){
         energy = aEnergy;
     /** returns the energy
     public double getEnergy(){
         return this.energy;
     /** sets number
     public void setNumber(int aNumber){
         number = aNumber;
     /** returns that number
     public double getNumber(){
         return this.number;
     /** sets temp
     public void setTemp(int aTemp){
         temp = aTemp;
     /** returns temp
     public int getTemp(){
         return this.temp;
      /** calculates the number of A's and T's
    public int countATs(){
        int count = 0;
        String at = "AT";
        for (int i=0; i < sequence.length(); i++)
            char ch = Character.toUpperCase(sequence.charAt(i));
            if(at.indexOf(ch) >= 0)
            count++;
        return count;
  /** calculates the number of C's and G's
    public int countCGs(){
        sequence = this.sequence;
        int count = 0;
        String cg = "CG";
        for (int i= 0; i < sequence.length(); i++)
            char ch = Character.toUpperCase(sequence.charAt(i));
            if(cg.indexOf(ch) >= 0)
            count++;
        return count;
     /** calculates boltzmann factor
     public double calculateBoltzman(){
        boltzman = Math.exp(-(energy)/(gasConstant*temp));
        return boltzman;
    /** calculates number-- number overflows when the integer exceeds 32-bits...(i.e. 4^200000000000)
    public int calculateNumber(){
        number = (int)Math.pow(sequence.length(),4);
        return number;
     * ToString method that returns the sequence.
     public String toString(){
         return super.toString()+" The Sequence is  "+ "\n"+this.sequence+"\n"+" The Description is "+"\n"+ this.description+"\n";
}SequenceTest.java <---where my problem is
import java.io.FileWriter;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.*;
* A Class to Sequence.
* @author (Corbin Blake)
* @version (10/20/04)
public class SequenceTest
public static String desc;  
public static String[] b;   
     public static void main(String[] args) throws IOException
      while (true)
          System.out.println("Welcome to my program!");
          try
              System.out.println();
              System.out.println("Enter d to enter a new DNA sequence, s to save the entered sequence to a file, and x to exit:  ");
              BufferedReader console = new BufferedReader(new InputStreamReader(System.in));
              String input = console.readLine();
              Sequence aSequence = new Sequence();
              String[] sequenceArray = new String[10];
              if (input.equalsIgnoreCase("d"))
                //keeps track of exactly how many elements are being used in the array
                int sequenceSize = 0;
                // asks the user for an input
                System.out.println("Enter a DNA Sequence: ");
                // gets the input string from the user
                String input0 = console.readLine();
                //stores that input as an array
                sequenceArray = new String[input0.length()];
                String[] b = sequenceArray;
                //checks to see if arraysize needs to be doubled and doubles it if necessary
                if(sequenceSize >= sequenceArray.length)
                    MyUtilities.myarraycopy(sequenceArray);
                //enters a description
                System.out.println("Enter a Description of the Sequence: ");
                //gets input from the user
                String input1 = console.readLine();
                String desc = input1;
              else if (input.equalsIgnoreCase("s"))
                   //asks to save information
                   System.out.println("Enter the name of the file( as a .txt file):");
                   String input2 = console.readLine();
                   //saves the information to the filename of the users chosing.
                   FileOutputStream out;//declares a fileoutput object
                   //declares a printstream object
                   PrintStream p;
                   String [] x = sequenceArray;
                   try
                       //creates a new file output stream connected to the user input
                       out = new FileOutputStream(input2);
                       //connect the printstream to the output stream
                       p = new PrintStream(out);
                       p.println("The saved DNA sequence is: " + b +"/n"+ "The Description is: "+ desc);
                       // exit
                       p.close();
                    catch (Exception e)
                        System.err.println ("Error writing to file");
              else if (input.equalsIgnoreCase("x"))
                  break;
              else
                  System.out.println("You have entered an invalid letter, please try again");
                  continue;
    catch (IOException e)
                  break;
          System.out.println("Thank you for using the application");
}

Answer 1

I guess we are discussing this line:
p.println("The saved DNA sequence is: " + b +"/n"+ "The Description is: "+ desc);b is a String[] and arrays don't have overridden toString(). You can use Arrays.asList(b) to get a better String representation or make your own method that lists array to String.
As far as the null desctiption is concerned - is is possible that there is no more input and readLine returns null?
HTH
Mike