[Biojava-l] Rendering Questions

[Ethan Cerami]

Hi Everyone,

I am new to BioJava, and had a few questions regarding
rendering of features.  First off, I started with the
feature rendering code from BioJava in Anger (thanks
for doing this -- these cookbook recipes are
enormously helpful.)

Right now, I am just modifying the code to display
exons.  The complete code is below.  And, I am using
the following jar file:  biojava-20020823.jar.

Here are my questions:

1.  I am using the ZiggyFeatureRenderer, and I had
expected to see boxes separated by ziggy lines,
therefore indicating exons and introns.  But, I don't
see any ziggy lines, just boxes.  What am I doing
wrong?

2.  I want to be able to render the same features
without having its actual sequence.  How do I do this?

Any help would be most appreciated.

Ethan Cerami

Code follows below:
----------------------------------------

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

import javax.swing.*;

import org.biojava.bio.*;
import org.biojava.bio.gui.sequence.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.genomic.Exon;
import org.biojava.bio.symbol.*;

public class FeatureView extends JFrame {
	private Sequence seq;
	private JPanel jPanel = new JPanel();

	private MultiLineRenderer mlr = new
MultiLineRenderer();
	private ZiggyFeatureRenderer featr = new
ZiggyFeatureRenderer();
	private SequenceRenderer seqR = new
SymbolSequenceRenderer();
	private RulerRenderer ruler = new RulerRenderer();

	private SequencePanel seqPanel = new SequencePanel();
	//the proxy between featr and seqPanel
	private FeatureBlockSequenceRenderer fbr = new
FeatureBlockSequenceRenderer();

	public FeatureView() {
		try {
			seq = DNATools.createDNASequence(
					"atcgcgcatgcgcgcgcgcgcgcgctttatagcgatagagatata",
					"dna 1");

			// create multiple exons
			for (int i=10; i<=30; i+=10) {
				Exon.Template exon = new Exon.Template();
				exon.annotation = Annotation.EMPTY_ANNOTATION;
				exon.location = new RangeLocation(i, i+5);
				exon.strand = StrandedFeature.POSITIVE;
				seq.createFeature(exon);
			}
			//setup GUI
			init();
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

	public static void main(String[] args) {
		FeatureView featureView = new FeatureView();
		featureView.pack();
		featureView.show();
	}

	/**
	 * initialize GUI components
	 */
	private void init() throws Exception {
		this.setTitle("FeatureView");
		this.getContentPane().add(jPanel,
BorderLayout.CENTER);
		jPanel.add(seqPanel, null);

		//Register the FeatureRenderer with the
FeatureBlockSequenceRenderer
		fbr.setFeatureRenderer(featr);

		//add Renderers to the MultiLineRenderer
		mlr.addRenderer(fbr);
		mlr.addRenderer(seqR);
		mlr.addRenderer(ruler);

		//set the MultiLineRenderer as the SequencePanels
renderer
		seqPanel.setRenderer(mlr);

		//set the Sequence to Render
		seqPanel.setSequence(seq);

		//display the whole Sequence
		seqPanel.setRange(new RangeLocation(1,
seq.length()));
	}

	/**
	 * Overridden so program terminates when window
closes
	 */
	protected void processWindowEvent(WindowEvent we) {
		if (we.getID() == WindowEvent.WINDOW_CLOSING) {
			System.exit(0);
		} else {
			super.processWindowEvent(we);
		}
	}
}




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