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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