[Gmod-ajax] features disappear when zoomed out (bug?)

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[Gmod-ajax] features disappear when zoomed out (bug?)

David Breimann
Hi,

I have a couple of tracks displaying clones mapped to the genome, which I load from a GFF3 file.
When I zoom in, I can see the feature fine but once I zoom out and the display changes to "clones per x bp" nothing is visible.
This is not true for my CDS track, where the histogram is shown correctly when zoomed out. The only difference I could think of between the two tracks is that clones are relatively longer than CDS and that clones have larger overlap with each other.

Best,
Dave

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Re: features disappear when zoomed out (bug?)

David Breimann
Another note: I use a variableStep wig file that actually holds information for only a couple of ranges in the genome, i.e. something like:

500 1.2
501 1.2
502 1.3
...
999 3.1
1000 3.1
95000 2.4
95001 2.5
95002 2.4
...
95999 3.4
95600 3.7

(perhaps it would be more efficient to use two fixedStep wig files, but I think it's currently impossible to load two wig files to the same track).

Anyway, the problem is that for regions in the wig file I have no data for (e.g. 1001..94999) I sometime see on the track the edges of some (transparent) graphic tile (?) - see upper track on the attached picture.


Best,
Dave

On Sat, Jul 31, 2010 at 10:01 AM, David Breimann <[hidden email]> wrote:
Hi,

I have a couple of tracks displaying clones mapped to the genome, which I load from a GFF3 file.
When I zoom in, I can see the feature fine but once I zoom out and the display changes to "clones per x bp" nothing is visible.
This is not true for my CDS track, where the histogram is shown correctly when zoomed out. The only difference I could think of between the two tracks is that clones are relatively longer than CDS and that clones have larger overlap with each other.

Best,
Dave


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Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm
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Re: features disappear when zoomed out (bug?)

Mitch Skinner
In reply to this post by David Breimann
It's tough to say what's going on without being able to see it.  If you can send a link, or at least put the generated json files up somewhere, then I'd have a better chance of understanding what's going on.

Mitch

On 07/31/2010 12:01 AM, David Breimann wrote:
Hi,

I have a couple of tracks displaying clones mapped to the genome, which I load from a GFF3 file.
When I zoom in, I can see the feature fine but once I zoom out and the display changes to "clones per x bp" nothing is visible.
This is not true for my CDS track, where the histogram is shown correctly when zoomed out. The only difference I could think of between the two tracks is that clones are relatively longer than CDS and that clones have larger overlap with each other.

Best,
Dave
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Re: features disappear when zoomed out (bug?)

Mitch Skinner
In reply to this post by David Breimann
  On 07/31/2010 12:11 AM, David Breimann wrote:
> Anyway, the problem is that for regions in the wig file I have no data
> for (e.g. 1001..94999) I sometime see on the track the edges of some
> (transparent) graphic tile (?) - see upper track on the attached picture.

Some people have mentioned this before, and I didn't know of a good
solution at the time.  I googled it again, though, and found that there
was a simple fix, which I have just committed.

I've tested it on firefox and chrome so far, please let me know if it
helps in your setup.

Mitch

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Plug-In Development Kit to bring their C/C++ apps to Palm for a share
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Re: features disappear when zoomed out (bug?)

David Breimann
Works like a charm!

On Wed, Aug 4, 2010 at 5:17 PM, Mitch Skinner <[hidden email]> wrote:
 On 07/31/2010 12:11 AM, David Breimann wrote:
Anyway, the problem is that for regions in the wig file I have no data for (e.g. 1001..94999) I sometime see on the track the edges of some (transparent) graphic tile (?) - see upper track on the attached picture.

Some people have mentioned this before, and I didn't know of a good solution at the time.  I googled it again, though, and found that there was a simple fix, which I have just committed.

I've tested it on firefox and chrome so far, please let me know if it helps in your setup.

Mitch


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Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://p.sf.net/sfu/dev2dev-palm
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