trying biojava 3

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.biojava3.core.sequence.*;
import org.biojava3.core.sequence.io.*;
import org.biojava3.core.sequence.compound.*;
import org.biojava3.core.sequence.transcription.*;

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
    DNASequence input_sequence;

    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)){
            LinkedHashMap<String, DNASequence> inputSequences = null;
            JFileChooser filechooser = new JFileChooser();
            int returnVal = filechooser.showOpenDialog(this);
            FastaParser file = new FastaParser();
            if(returnVal == JFileChooser.APPROVE_OPTION) {
                try{
                        inputSequences = file.readFastaDNASequence(filechooser.getSelectedFile());
                }catch(Exception ex){}
            }
            Object[] options = inputSequences.keySet().toArray();
            Object dialog = null;
            dialog = JOptionPane.showInputDialog(this,
            "wich sequence do you want to use?",
            "choose sequence",
            JOptionPane.QUESTION_MESSAGE,
            null,
            options,
            null);
            input_sequence = file.getSequence(dialog);
            CharacterIterator it = new StringCharacterIterator(input_sequence.getSequenceAsString());
            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);
            ProteinSequence output_sequence = translator.run();
            output.setText(output_sequence.getOriginalHeader());
            output.append("\n");
            String temp = null;
            int i = 0;
            CharacterIterator it = new StringCharacterIterator(output_sequence.getSequenceAsString());
            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{
    LinkedHashMap<String, DNASequence> dnaSequences = null;
    public LinkedHashMap<String, DNASequence> readFastaDNASequence(InputStream inStream) throws Exception{
        FastaReader<DNASequence, NucleotideCompound> fastaReader = new FastaReader<DNASequence, NucleotideCompound>(
        inStream,new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
        new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
        return fastaReader.process();
    }
    public LinkedHashMap<String, DNASequence> readFastaDNASequence(File file) throws Exception{
        FileInputStream inStream = new FileInputStream(file);
        dnaSequences = readFastaDNASequence(inStream);
        inStream.close();
        return dnaSequences;
    }
    public DNASequence getSequence(Object sequenceID){
        return dnaSequences.get(sequenceID);
    }
}

class Translator{
    DNASequence seq;
    ArrayList<ProteinSequence> output = new ArrayList<ProteinSequence>();
    ProteinSequence temp;
    Frame frame;
    public void setSequence(DNASequence input){
        seq = input;
    }
    public ProteinSequence run(){
        for (int i = 0; i < 3; i++){
            if(i == 0){
                frame = frame.ONE;
            }if(i == 1){
                frame = frame.TWO;
            }if(i == 2){
                frame = frame.THREE;
            }
            ProteinSequence prot_forward = seq.getRNASequence(frame).getProteinSequence();
            prot_forward.setOriginalHeader(seq.getOriginalHeader() + "TranslationFrame: +" + i);
            //ProteinSequence prot_reversecomplement = seq.getRNASequence(frame).getReverseComplement().getProteinSequence();
            //prot_reversecomplement.setOriginalHeader(seq.getOriginalHeader() + "TranslationFrame: +" + i);
            output.add(prot_forward);
            //output.add(prot_reversecomplement);
        }
        for(int i = 0;i < output.size();i++){
            for(int x = 0;x < output.size();x++){
                if(output.get(i).getSequenceAsString().length() > output.get(x).getSequenceAsString().length()){
                    temp = output.get(i);
                }
            }
        }
    return temp;
    }
}