Fortunately the friendly BioJava team have made the FeatureTree class to let you see where all that structure goes. The FeatureTree extends the JTree component and can easily be used in a GUI. The data used by the tree is supplied in the form of a SequenceDB that can be made by reading a text file.

The following program demonstrates the use of a FeatureTree. It takes two arguments. The first is the name of a file containing sequence data. The second is a number specifying the format of the data.

import java.awt.*;
import java.awt.event.*;
import java.io.*;

import javax.swing.*;

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

public class TreeFrame extends JFrame {
  private JPanel jPanel = new JPanel();
  private JScrollPane jScrollPane1 = new JScrollPane();
  private BorderLayout borderLayout = new BorderLayout();
  private FeatureTree featureTree = new FeatureTree();

  public TreeFrame() {
    try {
      init();
    }
    catch(Exception e) {
      e.printStackTrace();
    }
  }

  /**
   * This program will read files supported by SeqIOTools and display its
   * Sequence, Annotations and Features as a Tree. It takes three
   * arguments, the first is the file name the second is the file type
   * and the third is the alphabet type
   *
   */
  public static void main(String[] args) throws Exception{

    //read the sequence flat file
    BufferedReader br = new BufferedReader(new FileReader(args[0]));
    //get the format type from the command line
    String format = args[1];
    //get the alphabet from the command line
    String alpha = args[2];

    //read the sequences into a DB that will serve as the model for the tree
    SequenceDB db = new HashSequenceDB();
    SequenceIterator iter =
        (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br);
    while(iter.hasNext()){
      db.addSequence(iter.nextSequence());
    }
    UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
    TreeFrame treeFrame = new TreeFrame();
    //set the SequenceDB to serve as the data model
    treeFrame.getFeatureTree().setSequenceDB(db);
    treeFrame.pack();
    treeFrame.show();
  }

  private void init() throws Exception {
    jPanel.setLayout(borderLayout);
    this.setTitle("FeatureTree Demo");
    this.getContentPane().add(jPanel, BorderLayout.CENTER);
    jPanel.add(jScrollPane1,  BorderLayout.CENTER);
    jScrollPane1.getViewport().add(featureTree, null);
  }

  public FeatureTree getFeatureTree() {
    return featureTree;
  }

  protected void processWindowEvent(WindowEvent we){
    if(we.getID() == WindowEvent.WINDOW_CLOSING){
      System.exit(0);
    }else{
      super.processWindowEvent(we);
    }
  }
}