BioJava:CookBook:Interfaces:Features

From BioJava

How do I display Features?

Features are displayed by implementations of the FeatureRenderer interface. FeatureRenderers work in much the same way as SequenceRenderers and handle the drawing of the Features from a Sequence that is held in a SequenceRenderContext.

A SequenceRenderContext has no way of interacting directly with a FeatureRenderer so a FeatureBlockSequenceRenderer is used to wrap up the FeatureRenderer and act as a proxy.

The use of a FeatureBlockSequenceRenderer and a FeatureRenderer is demonstrated in the program below. A screen shot follows the program.

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.symbol.*;
 
public class FeatureView extends JFrame {
  private Sequence seq;
  private JPanel jPanel1 = new JPanel();
 
  private MultiLineRenderer mlr = new MultiLineRenderer();
  private FeatureRenderer featr = new BasicFeatureRenderer();
  private SequenceRenderer seqR = new SymbolSequenceRenderer();
  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 feature from 10 to 25
      StrandedFeature.Template temp = new StrandedFeature.Template();
      temp.annotation = Annotation.EMPTY_ANNOTATION;
      temp.location = new RangeLocation(10,25);
      temp.source = "";
      temp.strand = StrandedFeature.POSITIVE;
      temp.type = "";
 
      //create another from 30 to 35
      Feature f = seq.createFeature(temp);
      temp = (StrandedFeature.Template)f.makeTemplate();
      temp.location = new RangeLocation(30,35);
      temp.strand = StrandedFeature.NEGATIVE;
      seq.createFeature(temp);
 
      //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(jPanel1, BorderLayout.CENTER);
    jPanel1.add(seqPanel, null);
 
    //Register the FeatureRenderer with the FeatureBlockSequenceRenderer
    fbr.setFeatureRenderer(featr);
 
    //add Renderers to the MultiLineRenderer
    mlr.addRenderer(fbr);
    mlr.addRenderer(seqR);
 
    //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);
    }
  }
}