[Biojava-l] FeatureTree

[Schreiber, Mark]

Hi -

I have added a new GUI component to org.biojava.bio.gui called feature
tree. It uses and inner class as its tree model and displays a database
of sequences together with their features and annotations as a nested
tree. The critical method for the tree is the setSequenceDB() method.

Here is an example of a Frame that renders the tree, add a main method
and hey presto!

import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import org.biojava.bio.gui.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.symbol.*;

public class TreeDemoFrame extends JFrame {
  JPanel contentPane;
  BorderLayout borderLayout1 = new BorderLayout();
  JPanel jPanel1 = new JPanel();
  JScrollPane jScrollPane1 = new JScrollPane();
  FeatureTree featureTree1 = new FeatureTree();
  BorderLayout borderLayout2 = new BorderLayout();

  /**Construct the frame*/
  public TreeDemoFrame() {
    enableEvents(AWTEvent.WINDOW_EVENT_MASK);
    try {
      jbInit();
    }
    catch(Exception e) {
      e.printStackTrace();
    }
  }
  /**Component initialization*/
  private void jbInit() throws Exception  {
 
//setIconImage(Toolkit.getDefaultToolkit().createImage(TreeDemoFrame.cla
ss.getResource("[Your Icon]")));
    contentPane = (JPanel) this.getContentPane();
    contentPane.setLayout(borderLayout1);
    this.setSize(new Dimension(400, 300));
    this.setTitle("FeatureTreeDemo");
    jPanel1.setLayout(borderLayout2);
    contentPane.add(jPanel1, BorderLayout.CENTER);
    jPanel1.add(jScrollPane1, BorderLayout.CENTER);
    jScrollPane1.getViewport().add(featureTree1, null);
    initializeTree();
  }

  private void initializeTree() throws Exception{
    SequenceDB db = new HashSequenceDB();

    //make Annotations
    Annotation aa = new SimpleAnnotation();
    aa.setProperty("date_submitted","28/6/00");
    aa.setProperty("source","foo beast");

    Annotation ab = new SimpleAnnotation(aa);
    ab.setProperty("vector", "pBar");

    //make sequences
    Sequence sa = new
SimpleSequence(DNATools.createDNA("accgggccccatcgacgctagc"),
       "","sequence a",aa);
    Sequence sb = new
SimpleSequence(DNATools.createDNA("ttttacacaagagggaatannn"),
       "","sequence b",ab);

    //make features
    StrandedFeature.Template ft = new StrandedFeature.Template();
    Annotation fa = new SimpleAnnotation();
    fa.setProperty("algorithm","foobar");
    fa.setProperty("score","0.01");
    ft.annotation = fa;
    ft.location = new RangeLocation(4,14);
    ft.source = "foo_detector";
    ft.strand = StrandedFeature.POSITIVE;
    ft.type = "foo motif";

    Feature f = sa.createFeature(ft);
    ft = (StrandedFeature.Template)f.makeTemplate();
    ft.annotation = Annotation.EMPTY_ANNOTATION;
    ft.location = new PointLocation(12);
    ft.source = "";
    ft.strand = StrandedFeature.POSITIVE;
    ft.type = "key_residue";
    f.createFeature(ft);

    db.addSequence(sa);
    db.addSequence(sb);
    featureTree1.setSequenceDB(db);
  }

  /**Overridden so we can exit when window is closed*/
  protected void processWindowEvent(WindowEvent e) {
    super.processWindowEvent(e);
    if (e.getID() == WindowEvent.WINDOW_CLOSING) {
      System.exit(0);
    }
  }
}

Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739


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