[Biojava-l] (Re)How to Use SixFrameRenderer and related classes? (fwd)

[hywang]

References: <Pine.SOL.3.96.1030802134841.1208A-100000 at virgo.cus.cam.ac.uk>
           <20030803024828.28387.qmail at scbit.org>
           <200308041525.52802.smh1008 at cus.cam.ac.uk>
In-Reply-To: <200308041525.52802.smh1008 at cus.cam.ac.uk>
From: "hywang" <hywang at scbit.org>
To: smh1008 at cus.cam.ac.uk
Subject: Re: How to Use SixFrameRenderer and related classes?
Date: Thu, 07 Aug 2003 10:49:38 +0800
Mime-Version: 1.0
Content-Type: text/plain; format=flowed; charset="gb2312"
Content-Transfer-Encoding: 7bit 

Hi, 

Thanks a lot for your help and the bug of StopRendereris fixed out. But I am 
still in some trouble of SixFrame rendering 

When I render a sequence in the six frame mode, just as the method below: 

   SixFrameRenderer sixFramePane = new SixFrameRenderer();
   SixFrameZiggyRenderer sixZig = new SixFrameZiggyRenderer(sixFramePane);
   FeatureFilter cdsFilter = new FeatureFilter.ByType("transcript");
   FeatureBlockSequenceRenderer featureBin = new 
FeatureBlockSequenceRenderer(sixZig);
   zml.addRenderer(new OverlayRendererWrapper(new 
FilteringRenderer(featureBin, cdsFilter, true))); 

   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
0, StrandedFeature.POSITIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
1, StrandedFeature.POSITIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
2, StrandedFeature.POSITIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
0, StrandedFeature.NEGATIVE)));
   zml.addRenderer(new OverlayRendererWrapper(new StopRenderer(sixFramePane, 
1, StrandedFeature.NEGATIVE)));
   zml.addRenderer(new StopRenderer(sixFramePane, 2, 
StrandedFeature.NEGATIVE)); 

   zml.addRenderer(new SymbolSequenceRenderer());
   zml.addRenderer(new RulerRenderer());
... 

The main result is all right but compare to the six frame view of Artemis, 
there's only a line of DNA base symbols renderered overlayedwrapped in the 
first row. But I think we should got the result that each row should be 
wrapped with amino symbols just like Artemis has done. 

Can I achieve the goal with biojava? 

Haiyan Wang, 

 

David Huen: 

> OK, a fix for that bug has been committed to developer CVS.  It may take up 
> to 2 hours to get sync'd to the public CVS.  
> 
> Regards,
> David Huen
> P.S. I will not be available tomorrow so don't expect a reply to further 
> queries tomorrow.  
>