[Biojava-l] User interface example for Cookbook
Jolyon Holdstock
jolyon.holdstock at ogt.co.uk
Fri Apr 17 10:27:16 UTC 2009
Hi,
I've been meaning to generate an updated example of code for displaying
a sequence (with some additional functionality) for the cookbook and
finally got off my backside to do it.
Code is below; I hope it's of use - feel free to point out errors,
improvements etc...
Cheers,
Jolyon
//Code starts
------------------------------------------------------------------------
-------------------
//Java libraries
import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;
import javax.swing.*;
//BioJava libraries
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.gui.sequence.*;
//BioJava extension libraries
import org.biojavax.*;
import org.biojavax.ontology.*;
import org.biojavax.bio.seq.*;
public class DisplaySequenceFile extends JFrame implements
SequenceViewerMotionListener {
private TranslatedSequencePanel tsp = new TranslatedSequencePanel();
private MultiLineRenderer mlr = new MultiLineRenderer();
private RulerRenderer rr = new RulerRenderer();
private SequenceRenderer seqR = new SymbolSequenceRenderer();
private FeatureBlockSequenceRenderer fbsr;
private RichSequence richSeq;
private Container con;
private JPanel controlPanel;
private JButton mvLeft, mvRight, zoomIn, zoomOut;
private double sequenceScale = 0.05;
private int windowWidth = 1200;
private int windowHeight = 200;
public DisplaySequenceFile(String fileName){
//Load the sequence file
try {
richSeq = RichSequence.IOTools.readEMBLDNA(new BufferedReader(new
FileReader(new File(fileName))), null).nextRichSequence();
}
catch (BioException bioe){
System.err.println("Not an EMBL sequence" + bioe);
}
catch(FileNotFoundException fnfe){
System.err.println("FileNotFoundException: " + fnfe);
}
catch (IOException ioe){
System.err.println("IOException: " + ioe);
}
//Define the appearance of the rendered Features
BasicFeatureRenderer bfr = new BasicFeatureRenderer();
GradientPaint gradient = new GradientPaint(0, 10, Color.RED, 0, 0,
Color.white, true);
bfr.setFill(gradient);
bfr.setOutline(Color.RED);
//Form a bridge between Sequence rendering and Feature rendering
fbsr = new FeatureBlockSequenceRenderer(bfr);
fbsr.setCollapsing(false);
//Filter for CDS features on the forward strand
SequenceRenderer fwd_sr = new FilteringRenderer(fbsr,
new FeatureFilter.And(new FeatureFilter.ByType("CDS"),
new FeatureFilter.StrandFilter(StrandedFeature.POSITIVE)),
true);
//Filter for CDS features on the reverse strand
SequenceRenderer rev_sr = new FilteringRenderer(fbsr,
new FeatureFilter.And(new FeatureFilter.ByType("CDS"),
new FeatureFilter.StrandFilter(StrandedFeature.NEGATIVE)),
true);
//Add the renderers to the MultiLineRenderer
mlr.addRenderer(fwd_sr);
mlr.addRenderer(rr);
mlr.addRenderer(rev_sr);
mlr.addRenderer(seqR);
//Set the sequence renderer for the TranslatedSequencePanel
tsp.setRenderer(mlr);
//Set the sequence to render
tsp.setSequence(richSeq);
//Set the position of the displayed sequence
tsp.setSymbolTranslation(1);
//Set the scale as pixels per Symbol.
tsp.setScale(sequenceScale);
//Add a sequence viewer motion listener to the
TranslateSequencePanel
tsp.addSequenceViewerMotionListener(this);
//Generate the control panel
controlPanel = new JPanel();
controlPanel.setBackground(Color.lightGray);
//Move along the sequence towards 5' end
mvLeft = new JButton("<<");
mvLeft.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent ae){
int rightSide = tsp.getRange().getMax();
int leftSide = tsp.getRange().getMin();
int newStartPoint = leftSide - (rightSide - leftSide);
if (newStartPoint < 1){
newStartPoint = 1;
}
tsp.setSymbolTranslation(newStartPoint);
}
});
//Move along the sequence towards 3' end
mvRight = new JButton(">>");
mvRight.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent ae){
int rightSide = tsp.getRange().getMax();
int leftSide = tsp.getRange().getMin();
int screenWidth = rightSide - leftSide;
if ((rightSide + screenWidth) >= richSeq.length()){
tsp.setSymbolTranslation(richSeq.length() - screenWidth);
}
else {
tsp.setSymbolTranslation(rightSide);
}
}
});
//Increase sequence scale
zoomIn = new JButton("+");
zoomIn.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent ae){
sequenceScale = sequenceScale * 2;
//if sequence scale = 12 the bases are rendered
//no need to zoom in further so disable the button.
if (sequenceScale > 12){
sequenceScale = 12;
zoomIn.setEnabled(false);
}
tsp.setScale(sequenceScale);
}
});
//Reduce sequence scale
zoomOut = new JButton("-");
zoomOut.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent ae){
sequenceScale = sequenceScale / 2;
//if sequence scale is below 12 the enable zoomIn button
if (sequenceScale < 12){
zoomIn.setEnabled(true);
}
//If the scale allows more than the sequence to be displayed
//display the whole sequence
if (sequenceScale <
((double)tsp.getWidth()/(double)richSeq.length())){
sequenceScale =
(double)tsp.getWidth()/(double)richSeq.length();
tsp.setSymbolTranslation(1);
}
tsp.setScale(sequenceScale);
//If the new scale coupled with the current SymbolTranslation
means the
//displayed can't fill the TranslatedSequencePanel then reset
the SymbolTranlstion
if(tsp.getRange().getMax() >= richSeq.length()){
int tmp = (int)((double)tsp.getWidth()/sequenceScale);
tsp.setSymbolTranslation(richSeq.length() - tmp);
}
}
});
controlPanel.add(mvLeft);
controlPanel.add(mvRight);
controlPanel.add(zoomIn);
controlPanel.add(zoomOut);
con = new Container();
con = getContentPane();
con.setLayout(new BorderLayout());
con.add(controlPanel, BorderLayout.NORTH);
con.add(tsp, BorderLayout.CENTER);
setLocation(50,50);
setSize(windowWidth,windowHeight);
setVisible(true);
setResizable(false);
}
/**
* Detect mouse dragged events
* @param sve
*/
public void mouseDragged(SequenceViewerEvent sve) {
}
/**
* Detect mouse movement events
* If the mouse moves over a CDS feature create a tooltiptext stating
the
* the name of the gene associated with the CDS feature.
* @param sve
*/
public void mouseMoved(SequenceViewerEvent sve) {
//Manage the tooltip
ToolTipManager ttm = ToolTipManager.sharedInstance();
ttm.setDismissDelay(2000);
//If the mouse have moved over a SimpleFeatureHolder
if (sve.getTarget() instanceof SimpleFeatureHolder){
ComparableTerm gene =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");
SimpleFeatureHolder sfh = (SimpleFeatureHolder)sve.getTarget();
FeatureHolder fh = sfh.filter(new FeatureFilter.ByType("CDS"));
Iterator <RichFeature> i = fh.features();
while(i.hasNext()){
RichFeature rf = i.next();
RichAnnotation anno = (RichAnnotation) rf.getAnnotation();
Set annotationNotes = anno.getNoteSet();
for (Iterator <Note> it = annotationNotes.iterator();
it.hasNext();) {
Note note = it.next();
if (note.getTerm().equals(gene)) {
tsp.setToolTipText("Gene: " + note.getValue());
}
}
}
}
else {
//Remove the tooltip
ttm.setDismissDelay(10);
}
}
/**
* Main method
* @param args
*/
public static void main(String args []){
if (args.length == 1){
new DisplaySequenceFile(args[0]);
}
else {
System.out.println("Usage: java SequenceViewer <Genbank file>");
System.exit(1);
}
}
}
//Code ends
------------------------------------------------------------------------
-------------------
Dr. Jolyon Holdstock
Senior Computational Biologist,
Oxford Gene Technology,
Begbroke Science Park,
Sandy Lane, Yarnton,
Oxford, OX5 1PF, UK.
T: +44 (0)1865 856 852
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