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<[EMAIL PROTECTED]>
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From: "hywang" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: Re: How to Use SixFrameRenderer and related classes?
Date: Thu, 07 Aug 2003 10:49:38 +0800
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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.
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