[Biojava-l] DistributionLogo help

[xjw2101 at columbia.edu]

Thomas,
Seems the version is different from mine. In my version  
DistributionLogo is extension of Component and there are no 
setRenderingHints(hints) or setPreferedSize() methods.


Xuegong


--- Thomas Down <td2 at sanger.ac.uk> wrote:
> 
> On 28 Jun 2004, at 21:44, xjw2101 at columbia.edu
> wrote:
> 
> >
> >
> > I am trying to use DistributionLogo class to
> represent a PSSM for a
> > transcription factor. I can generate
> DistributionLogos for each
> > position but can't merge them together to form a
> nice looking
> > single logo to be displayed on a panel.
> Basically,I don't know how
> > to control the color or the size. can someone show
> me how this
> > class works or give me some sample code of how
> this class works?
> 
> Hi Xuegong,
> 
> I generally use the following code, which creates a
> row of 
> DistributionLogo objects, for displaying a BioJava
> WeightMatrix (i.e. 
> PSSM) objects.  Can this be adapted to do what you
> want?
> 
>         Thomas.
> 
> 
> 
> import java.awt.*;
> 
> import javax.swing.*;
> 
> import org.biojava.bio.*;
> import org.biojava.bio.dist.Distribution;
> import org.biojava.bio.dp.WeightMatrix;
> import org.biojava.bio.gui.*;
> 
> public class WMPanel extends JPanel {
>      private WeightMatrix wm;
>      private DistributionLogo[] logos;
> 
>      public WMPanel(WeightMatrix wm) {
>          super();
>          this.wm = wm;
>          setBackground(Color.white);
> 
>          RenderingHints hints = new 
> RenderingHints(RenderingHints.KEY_ANTIALIASING, 
> RenderingHints.VALUE_ANTIALIAS_ON);
> 
>          try {
>              setLayout(new GridLayout(1,
> wm.columns()));
>              logos = new
> DistributionLogo[wm.columns()];
>              for (int pos = 0; pos < wm.columns();
> ++pos) {
>                  Distribution dist =
> wm.getColumn(pos);
>                  DistributionLogo dl = new
> DistributionLogo();
>                  dl.setRenderingHints(hints);
>                  dl.setBackground(Color.white);
>                  dl.setOpaque(true);
>                  dl.setDistribution(dist);
>                  dl.setPreferredSize(new
> Dimension(40, 50));
>                  dl.setLogoPainter(new
> TextLogoPainter());
>                  dl.setStyle(new DNAStyle());
>                  add(dl);
>                  logos[pos] = dl;
>              }
>          } catch (BioException ex) {
>              throw new BioError(ex);
>          }
>      }
> 
>      public static void wmViewer(WeightMatrix wm,
> String message)
>      {
>          WMPanel wmv = new WMPanel(wm);
>          JFrame frame = new JFrame("Weight matrix
> viewer" + ((message == 
> null) ? "" : (" (" + message + ")")));
>          frame.getContentPane().add(wmv);
>          frame.pack();
>          frame.setVisible(true);
>      }
> }
> 
>