[Gmod-gbrowse] Semantic zooming

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[Gmod-gbrowse] Semantic zooming

Wes Barris
Is semantic zooming broken or am I doing something silly?

[test1]
feature       = EST_match:bcmcontig
glyph         = segments
key           = testing

[test1:100000]
feature       = EST_match:bcmcontig
glyph         = box

The above stanzas result in one track with all features duplicated.

gbrowse2.06
bio-graphics-2.08
--
Wes Barris

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Re: [ExternalEmail] Semantic zooming

Wes Barris
Wes Barris wrote:

> Is semantic zooming broken or am I doing something silly?
>
> [test1]
> feature       = EST_match:bcmcontig
> glyph         = segments
> key           = testing
>
> [test1:100000]
> feature       = EST_match:bcmcontig
> glyph         = box
>
> The above stanzas result in one track with all features duplicated.
>
> gbrowse2.06
> bio-graphics-2.08
Perhaps with another example someone might respond?

If I take the yeast_simple.conf file and add this stanza:

[Genes:10000]
feature      = gene
glyph        = gene

The "Named gene" track displays duplicated features.  See the attached
image.

--
Wes Barris

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Re: [ExternalEmail] Semantic zooming

Lincoln Stein
I was able to confirmed this behavior briefly and then it vanished mysteriously and semantic zooming is working properly for me. I will try to get it to happen again.

Lincoln

On Mon, May 24, 2010 at 1:39 AM, Wes Barris <[hidden email]> wrote:
Wes Barris wrote:
Is semantic zooming broken or am I doing something silly?

[test1]
feature       = EST_match:bcmcontig
glyph         = segments
key           = testing

[test1:100000]
feature       = EST_match:bcmcontig
glyph         = box

The above stanzas result in one track with all features duplicated.

gbrowse2.06
bio-graphics-2.08

Perhaps with another example someone might respond?

If I take the yeast_simple.conf file and add this stanza:

[Genes:10000]
feature      = gene
glyph        = gene

The "Named gene" track displays duplicated features.  See the attached
image.

--
Wes Barris

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: [ExternalEmail] Semantic zooming

Lincoln Stein
In reply to this post by Wes Barris
Ok, there is a bug but it is an easy one to work around. If you repeat the "feature" line in the semantic stanza, and the value of that line is identical to what it is in the non-semantic stanza, then you will get this peculiar doubling. It should never be necessary to repeat the feature line unless you are changing the value to another feature type.

I will track down the underlying cause and fix it.

Lincoln

On Mon, May 24, 2010 at 1:39 AM, Wes Barris <[hidden email]> wrote:
Wes Barris wrote:
Is semantic zooming broken or am I doing something silly?

[test1]
feature       = EST_match:bcmcontig
glyph         = segments
key           = testing

[test1:100000]
feature       = EST_match:bcmcontig
glyph         = box

The above stanzas result in one track with all features duplicated.

gbrowse2.06
bio-graphics-2.08

Perhaps with another example someone might respond?

If I take the yeast_simple.conf file and add this stanza:

[Genes:10000]
feature      = gene
glyph        = gene

The "Named gene" track displays duplicated features.  See the attached
image.

--
Wes Barris

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: [ExternalEmail] Semantic zooming

Wes Barris
Lincoln Stein wrote:
> Ok, there is a bug but it is an easy one to work around. If you repeat
> the "feature" line in the semantic stanza, *and* the value of that line
> is identical to what it is in the non-semantic stanza, then you will get
> this peculiar doubling. It should never be necessary to repeat the
> feature line unless you are changing the value to another feature type.

Thanks Lincoln.

> I will track down the underlying cause and fix it.
>
> Lincoln
>
> On Mon, May 24, 2010 at 1:39 AM, Wes Barris <[hidden email]> wrote:
>
>     Wes Barris wrote:
>
>         Is semantic zooming broken or am I doing something silly?
>
>         [test1]
>         feature       = EST_match:bcmcontig
>         glyph         = segments
>         key           = testing
>
>         [test1:100000]
>         feature       = EST_match:bcmcontig
>         glyph         = box
>
>         The above stanzas result in one track with all features duplicated.
>
>         gbrowse2.06
>         bio-graphics-2.08
>
>
>     Perhaps with another example someone might respond?
>
>     If I take the yeast_simple.conf file and add this stanza:
>
>     [Genes:10000]
>     feature      = gene
>     glyph        = gene
>
>     The "Named gene" track displays duplicated features.  See the attached
>     image.
>
>     --
>     Wes Barris
>
>     ------------------------------------------------------------------------------
>
>
>     _______________________________________________
>     Gmod-gbrowse mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]
> <mailto:[hidden email]>>


--
Wes Barris

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