[Biojava-l] Sequence Range Question

[Ethan Cerami]

Ok, based on the feedback I got yesterday, I have made
much progress :-)  Right now, I am trying to create a
bare bones gene viewer that can render gene features
via a SequencePanel object.  For example, the code
below renders the Adam2 gene on chromosome 8.

Adam2 is located at:  Chromosome 8:  38997645 -
39047541 bp.  To render it, I have a 1MB dummy
sequence that starts at 1.  How do I create a dummy
sequence that starts at 38995000 so that I can show
the correct location?  Is there some way to create a
virtual offset?

Sample code is below.  Thanks again for any help!

Ethan 

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.impl.SimpleSequence;
import org.biojava.bio.seq.genomic.Gene;
import org.biojava.bio.symbol.*;
import org.biojava.utils.ChangeVetoException;

/**
 * Simple Gene Browser
 */
public class FeatureView extends JFrame {
	private final static int WINDOW = 1000000;  //  1
Million BP
	private Sequence sequence;
	private JPanel panel = new JPanel ();
	private MultiLineRenderer mlr = new MultiLineRenderer
();
	private RectangularBeadRenderer featr = new
RectangularBeadRenderer ();
	private RulerRenderer ruler = new RulerRenderer ();
	private SequencePanel seqPanel = new SequencePanel
();
	private FeatureBlockSequenceRenderer fbr =
			new FeatureBlockSequenceRenderer ();

	/**
	 * Constructor
	 */
	public FeatureView () throws Exception {
		sequence = createSequence ();
		addGenes (sequence);
		createGUI ();
	}

	/**
	 * Creates a Dummy Sequence
	 */
	private Sequence createSequence () {
		SymbolList dummyList = new DummySymbolList
(DNATools.getDNA (),
				WINDOW);
		Sequence sequence = new SimpleSequence (dummyList,
"ensembl", "ensembl",
				Annotation.EMPTY_ANNOTATION);
		return sequence;
	}

	/**
	 * Creates Multiple Genes
	 */
	private void addGenes (Sequence sequence)
			throws BioException, ChangeVetoException {
		//  Add Adam2 Gene
		//  Location:  Chromosome 8:  38997645 - 39047541 bp
		//  int adam2_start = 38997645;  this doesn't work
b/c
		//								 it's out of range
		int adam2_start = 20000;
		int adam2_length = 49896;
		Gene.Template gene = new Gene.Template ();
		gene.type = "gene";
		gene.source = "ensembl";
		gene.location = new RangeLocation (adam2_start,
adam2_start
				+ adam2_length);
		gene.annotation = Annotation.EMPTY_ANNOTATION;
		gene.strand = StrandedFeature.POSITIVE;
		sequence.createFeature (gene);

	}

	/**
	 * Create the User Interface
	 */
	private void createGUI () throws Exception {
		this.setTitle ("Gene Viewer");
		Container contentPane = this.getContentPane ();
		contentPane.add (panel, BorderLayout.CENTER);
		panel.add (seqPanel);

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

		// Add Renderers to the MultiLineRenderer
		mlr.addRenderer (fbr);
		mlr.addRenderer (ruler);
		seqPanel.setRenderer (mlr);

		// Set the Sequence to Render
		seqPanel.setSequence (sequence);
		seqPanel.setRange (new RangeLocation (1, WINDOW));
		seqPanel.setScale (.0007);
	}

	/**
	 * 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);
		}
	}

	/**
	 * Main Method
	 */
	public static void main (String[] args) throws
Exception {
		FeatureView featureView = new FeatureView ();
		featureView.pack ();
		featureView.show ();
	}

}



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