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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
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From: anja <fri...@ho...> - 2010-10-06 12:14:21
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sent
There is something else I noticed by looking at your visualisation. For example are the first 3 variants small, but have the same size as a tall motif. The second tall motif is not displayed, there is just the grey line... What can be the reason for this?
Anja
Date: Wed, 6 Oct 2010 05:09:33 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)
It has to be close. Do this:
cd /var/www
tar czf taro.tar.gz *
and send me the taro.tar.gz.
Mitch
On 10/06/2010 04:59 AM, anja wrote:
yes
Date: Wed, 6 Oct 2010 04:56:55 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: data are not displayed even though they were loaded
(JBrowse)
The genome-2.css file is in /var/www?
On 10/06/2010 04:51 AM, anja wrote:
fixed
everything but now I have a blank page...
Anja
Date: Wed, 6 Oct 2010 04:33:30 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: data are not displayed even though they were loaded
(JBrowse)
Hmmm, I know that we're very close, I tried out the data from
your taro-tracks.tar.gz:
http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat
I noticed two things when I was setting that up; one was that
the CSS file that you sent was named genome-2.css. The
index.html file has to refer to the correct CSS file. In the
index.html file, there's a line like this:
<link rel="stylesheet" type="text/css"
href="genome.css"></link>
I put your genome-2.css file in the same directory as the
original genome.css, and changed that line in index.html to:
<link rel="stylesheet" type="text/css"
href="genome-2.css"></link>
Also, in the CSS file you sent, there was a line like this:
.minus-tall_orange, {
which has an extra comma; it shouldn't have that comma at the
end, like this:
.minus-tall_orange {
or, if the data is unstranded, it should look like this:
.tall_orange {
Also, some of the CSS classes were missing the "." at the
beginning.
Mitch
On 10/06/2010 12:43 AM, Anja Friedrich wrote:
Thank
you very much for your time and help.
I was afraid something like this will happen when I change it.
But as I don't know whether they are stranded or not, I
thought its better to mark it as unknown...
I changed all the classes but it still won't display the
motifs. Do I have to change it somewhere in addition?
Anja
Date: Tue, 5 Oct 2010 18:31:31 -0700
From: [hidden
email]
To: [hidden
email]; [hidden
email]
Subject: Re: [Gmod-ajax] data are not displayed even though
they were loaded (JBrowse)
Okay, one of the GFF files that you sent earlier had strand
information for the motifs. I didn't notice that your later
GFF files listed the motifs as being unstranded.
That's why, in the CSS example I sent earlier, the CSS classes
were all listed with separate "plus-" and "minus-" versions.
If the motifs don't have strand information, then the CSS file
should have CSS class names without those "plus-" and "minus-"
prefixes. For example, in the earlier example CSS file I
sent, I had this:
=====
.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-tall_blue,
.plus-tall_purple,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-tall_blue,
.minus-tall_purple {
position: absolute;
cursor: pointer;
z-index: 10;
min-width: 1px;
}
.plus-small_red, .minus-small_red {
background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.plus-small_blue, .minus-small_blue {
background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_purple {
background-color: #7322BF; height: 6px; margin-top: -1px;
}
.plus-tall_blue, .minus-tall_blue {
background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.plus-tall_purple, .minus-tall_purple {
background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====
but if your motifs are unstranded, you could have this
instead:
=====
.small_red,
.small_blue,
.small_purple,
.tall_blue,
.tall_purple {
position: absolute;
cursor: pointer;
z-index: 10;
min-width: 1px;
}
.small_red {
background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.small_blue {
background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.small_purple {
background-color: #7322BF; height: 6px; margin-top: -1px;
}
.tall_blue {
background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.tall_purple {
background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====
Or, if your data has both stranded and unstranded features,
you could include both stranded and unstranded versions of
your CSS classes.
Mitch
On 10/05/2010 03:39 PM, Anja Friedrich wrote:
done
> Date: Tue, 5 Oct 2010 15:37:01 -0700
> From: [hidden
email]
> To: [hidden
email]; [hidden
email]
> Subject: Re: [Gmod-ajax] data are not displayed even
though they were loaded (JBrowse)
>
> Can you do this:
>
> cd /var/www
> tar czf taro-tracks.tar.gz data/tracks
>
> That will create a file named taro-tracks.tar.gz, with
your generated
> data. Then can you email the file to me? That should
help me figure
> out what's going on.
>
> Mitch
>
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