orffinder, error in object translator

import java.awt.event.*;
import javax.swing.*;
import java.io.*;
import java.util.*;
import javax.swing.border.*;
import java.text.StringCharacterIterator;
import java.text.CharacterIterator;

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;

public class orffinder{
    public static void main (String args[]){
        View view = new View();
        view.showMain();
    }
}

class View extends JFrame implements ActionListener{
    JPanel root = new JPanel();
    Box topbox = Box.createVerticalBox();
    JPanel input_panel = new JPanel();
    JPanel output_panel = new JPanel();
    JTextArea input = new JTextArea(10,30);
    JTextArea output = new JTextArea(10,30);

    JMenuBar menubar = new JMenuBar();
    JMenu filemenu = new JMenu("file");
    JMenu helpmenu = new JMenu("help");
    JMenuItem item_open = new JMenuItem("open");
    JMenuItem item_run = new JMenuItem("run");
    JMenuItem item_about = new JMenuItem("about");

    TitledBorder title_input = BorderFactory.createTitledBorder("input sequence(DNA)");
    TitledBorder title_output = BorderFactory.createTitledBorder("output sequence(protein)");

    //variables
    Sequence input_sequence = null;

    public void showMain(){
        output.setEditable(false);
        input.setEditable(true);
        JScrollPane input_scrollpane = new JScrollPane(input);
        JScrollPane output_scrollpane = new JScrollPane(output);
        this.setName("ORF finder");

        item_open.addActionListener(this);
        item_run.addActionListener(this);
        item_about.addActionListener(this);

        filemenu.add(item_open);
        filemenu.add(item_run);
        helpmenu.add(item_about);
        menubar.add(filemenu);
        menubar.add(helpmenu);
        this.setJMenuBar(menubar);

        input_panel.add(input_scrollpane);
        input_panel.setBorder(title_input);
        output_panel.add(output_scrollpane);
        output_panel.setBorder(title_output);

        topbox.add(input_panel);
        topbox.add(output_panel);
        root.add(topbox);
        this.setResizable(false);
        this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        this.setContentPane(root);
        this.pack();
        this.setVisible(true);

    }
    public void actionPerformed(ActionEvent e){
        if(e.getSource().equals(item_open)){
            JFileChooser filechooser = new JFileChooser();
            int returnVal = filechooser.showOpenDialog(this);
            FastaParser file = new FastaParser();
            if(returnVal == JFileChooser.APPROVE_OPTION) {
                file.setFile(filechooser.getSelectedFile());
            }
            Object[] options = file.getIDs().toArray();
            Object dialog = null;
            dialog = JOptionPane.showInputDialog(this,
            "wich sequence do u want to use?",
            "choose sequence",
            JOptionPane.QUESTION_MESSAGE,
            null,
            options,
            null);
            input_sequence = file.getSequence(dialog);
            CharacterIterator it = new StringCharacterIterator(input_sequence.seqString());
            String temp = "";
            int i = 0;
            for (char ch=it.first(); ch != CharacterIterator.DONE; ch=it.next()){
                temp += ch;
                i += 1;
                if (i == 37){
                    temp += '\n';
                    i = 0;
                }
            }
            input.setText(temp);
        }
        if(e.getSource().equals(item_run)){
            Translator translator = new Translator();
            translator.setSequence(input_sequence);
            Sequence output_sequence = translator.run();
            output.setText(output_sequence.getName());
            output.append("\n");
            String temp = null;
            int i = 0;
            CharacterIterator it = new StringCharacterIterator(output_sequence.seqString());
            for (char ch=it.first(); ch != CharacterIterator.DONE; ch=it.next()){
                temp += ch;
                i += 1;
                if (i == 37){
                    temp += '\n';
                    i = 0;
                }
            }
            output.append(temp);
        }
    }
}

class FastaParser{
    static SequenceDB sequences;
    public static void setFile(File fastafile){
        try{
            BufferedInputStream input = new BufferedInputStream(new FileInputStream(fastafile));
            Alphabet alpha = AlphabetManager.alphabetForName("PROTEIN");
            sequences = SeqIOTools.readFasta(input, alpha);
        }catch (BioException ex){
        //not in fasta format or wrong alphabet
        ex.printStackTrace();
        }catch (NoSuchElementException ex){
        //no fasta sequences in the file
        ex.printStackTrace();
        }catch (FileNotFoundException ex){
        //problem reading file
        ex.printStackTrace();
        }
    }
    public Set getIDs(){
        return sequences.ids();
    }
    public Sequence getSequence(Object id){
        Object[] ids = sequences.ids().toArray();
        int x = 0;
        Sequence sequence = null;
        SequenceIterator iterator = sequences.sequenceIterator();
        for(int i = 0;i < ids.length;i++){
            try{
                sequence = iterator.nextSequence();
            }catch(BioException ex){
                ex.printStackTrace();
            }
            if(ids[i] == id){
                break;
            }
        }
        return sequence;
    }
}

class Translator{
    Sequence seq;
    ArrayList<Sequence> output = new ArrayList<Sequence>();
    Sequence temp;
    public void setSequence(Sequence input){
        seq = input;
    }
    public Sequence run(){
        // for each frame
        for (int i = 0; i < 3; i++){
            try{
                SymbolList prot;
                // take the reading frame
                // remember that in a SymbolList the first element has
                // index= 1
                // remember that if the length of the list evenly divisible
                // by three an IllegalArgumentException will be thrown
                SymbolList syms = seq.subList(i + 1, seq.length()
                - (seq.length() - i) % 3);
                // if it is DNA transcribe it to RNA
                if(syms.getAlphabet() == DNATools.getDNA()){
                    syms = DNATools.toRNA(syms);
                }
                SymbolList codons = SymbolListViews.windowedSymbolList(syms, 3);
                prot = SymbolListViews.translate(codons,RNATools.getGeneticCode("UNIVERSAL"));
                // System.out.println(syms.seqString());
                output.add(SequenceTools.createSequence(prot, "", seq.getName()
                + "TranslationFrame: +" + i,Annotation.EMPTY_ANNOTATION));
                syms = RNATools.reverseComplement(syms);
                prot = SymbolListViews.translate(codons,RNATools.getGeneticCode("UNIVERSAL"));
                output.add(SequenceTools.createSequence(prot, "", seq.getName()
                + " TranslationFrame: -" + i,Annotation.EMPTY_ANNOTATION));
            }catch(IllegalAlphabetException ex){
                ex.printStackTrace();
            }catch(Exception ex){
                ex.printStackTrace();
            }
        }
        for(int i = 0;i < output.size();i++){
            for(int x = 0;x < output.size();x++){
                if(output.get(i).seqString().length() > output.get(x).seqString().length()){
                    temp = output.get(i);
                }
            }
        }
    return temp;
    }
}