[Biojava-l] AlignmentRenderer works with TranslatedSequencePanel but not SequencePanel???

[Mark Southern]

The attached example code renders an alignment when used with a
TranslatedSequencePanel but not with a SequencePanel - the SequencePanel
remains blank.

A diff of TranslatedSequencePanel and SequencePanel shows they are quite
different. I am not sure what is going on.


Can anyone give me some pointers as to how to get this to work in a
SequencePanel? I would prefer this since SequencePanel can be scrolled in a
JScrollPane and TranslatedSequencePanel cannot.

Cheers,

Mark.


import java.awt.*;
import java.io.*;
import javax.swing.*;
import java.util.*;

import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;



public class Test{
    
    /** Creates a new instance of Test */
    private Test() {
    }
    
    public static void main(String[] args) throws Exception{
        JFrame f = new JFrame();
        f.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
        // doesn't work with a SequencePanel
        SequencePanel v = new SequencePanel();
        v.setFont( new Font("Courier",Font.PLAIN, 12));
        f.getContentPane().add(v, java.awt.BorderLayout.CENTER);
        BufferedReader br = new BufferedReader( new FileReader( new File(
args[0] ) ) );
        Alignment a = (Alignment)SeqIOTools.fileToBiojava(
AlignIOConstants.MSF_AA, br);
        v.setSequence(a);
        MultiLineRenderer mlr = new MultiLineRenderer();
        SymbolSequenceRenderer ssr = new SymbolSequenceRenderer();
        for(Iterator it = a.getLabels().iterator(); it.hasNext(); ){
            Object o = it.next();
            AlignmentRenderer ar = new AlignmentRenderer();
            ar.setLabel(o);
            ar.setRenderer(ssr);
            mlr.addRenderer(ar);
        }
        v.setRenderer(mlr);
        f.pack();
        f.setVisible(true);
    }
    
}