[Biojava-l] Sequence Range Question

[Schreiber, Mark]

Hi -

In this case, rather than using the SequencePanel you would use a
TranslatedSequencePanel which allows you to translate (offset) the
coordinates to display the bit you want.

- Mark


> -----Original Message-----
> From: Ethan Cerami [mailto:ecerami@yahoo.com] 
> Sent: Wednesday, 15 January 2003 2:51 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Sequence Range Question
> 
> 
> 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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