Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[Mitch S. <mit...@be...>]

  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: mit...@be...
> To: fri...@ho...; gmo...@li...
> 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: mit...@be... <mailto:mit...@be...>
>     > To: gmo...@li...
>     <mailto:gmo...@li...>;
>     fri...@ho... <mailto:fri...@ho...>
>     > 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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