[Biojava-l] Multiple alignment display issues

[Russ Kepler]

Further in my efforts in using the FlexibleAlignment class in conjunction with 
the display the alignments I have created some test code, reproduced below.  
The sequences are all displaying, but not in the alignment range.  Am I 
simply missing something simple here, like a symbol renderer that handles a 
range?  Or should someone be rewriting the context before the renderer is 
called?  

(Apologies for the form - I've had to maintain this in a development 
environment to use my modified BioJava ).

import java.awt.*;
import java.util.*;
import java.util.List;

import javax.swing.*;

import org.biojava.bio.alignment.*;
import org.biojava.bio.gui.sequence.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;

public class MultiAlignViewerDemo {
  public static void main(String[] args) {
    //MultiAlignViewer multialignviewer = new MultiAlignViewer();
    try {

      MultiLineRenderer mlr = new MultiLineRenderer();
      SequenceRenderer subSeqRend = new SymbolSequenceRenderer();
      GappedRenderer seqRend = new GappedRenderer(subSeqRend);

      // make three random sequences
      SymbolList res1 = createSymbolList(10);
      SymbolList res2 = createSymbolList(10);
      SymbolList res3 = createSymbolList(10);

      // think of three names
      String name1 = "pigs";
      String name2 = "dogs";
      String name3 = "cats";

      // create list with reference sequence
      ArrayList list = new ArrayList(1);
      SymbolList refSeq = createSymbolList(30);
      list.add(new SimpleAlignmentElement("reference", refSeq, new 
RangeLocation(1, 30)));
      // create the alignment with the reference sequence
      FlexibleAlignment alignment = new FlexibleAlignment(list);

      list = new ArrayList(3);

      // add the sequences as alignments
      alignment.addSequence(new SimpleAlignmentElement(name1, res1, new 
RangeLocation(1, 10)));
      AlignmentRenderer ar1 = new AlignmentRenderer();
      ar1.setLabel("pigs");
      ar1.setRenderer(seqRend);
      mlr.addRenderer(ar1);
      alignment.addSequence(new SimpleAlignmentElement(name2, res2, new 
RangeLocation(11, 20)));
      AlignmentRenderer ar2 = new AlignmentRenderer();
      ar2.setLabel("dogs");
      ar2.setRenderer(seqRend);
      mlr.addRenderer(ar2);
      alignment.addSequence(new SimpleAlignmentElement(name3, res3, new 
RangeLocation(21, 30)));
      AlignmentRenderer ar3 = new AlignmentRenderer();
      ar3.setLabel("cats");
      ar3.setRenderer(seqRend);
      mlr.addRenderer(ar3);

      // add the reference sequence to the render list
      AlignmentRenderer arRef = new AlignmentRenderer();
      arRef.setLabel("reference");
      arRef.setRenderer(seqRend);
      mlr.addRenderer(arRef);
      mlr.addRenderer(new RulerRenderer());

      // we will display this in a window
      JFrame frame = new JFrame("Multialign Viewer Demo");
      frame.setSize(400, 300);

      TranslatedSequencePanel sp = new TranslatedSequencePanel();
      sp.setSequence(alignment);
      sp.setScale(7.0);
      sp.setDirection(TranslatedSequencePanel.HORIZONTAL);
      sp.setRenderer(mlr);
      frame.getContentPane().setLayout(new BorderLayout());
      frame.getContentPane().add(sp, BorderLayout.CENTER);

      frame.setVisible(true);
    } catch (Exception ex) {
      ex.printStackTrace(System.err);
      System.exit(1);
    }
  }
  /**
   * Common stuff that the demos rely on.
   *
   * @author Matthew Pocock
   */

    public static SymbolList createSymbolList(int length) throws 
IllegalSymbolException {
      List l = new ArrayList(length);
      for (int i = 0; i < length; i++) {
        l.add(DNATools.forIndex((int) (4.0 * Math.random())));
      }
      return new SimpleSymbolList(DNATools.getDNA(), l);
    }

}
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