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

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gmod-ajax

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

From: Anja F. <fri...@ho...> - 2010-10-04 18:52:12

Hi all, 

I was using SeqFeature Store to load data and display them in JBrowse. But I an't see anything. They are not displayed at all like they don't exist... Do I activate it wrong? I was looking under  http://localhost/jbrowse/
I used this commandos and it looks as if the data were loaded...
anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d "dbi:Pg:dbname=test" --a DBI::Pg --c taro.gff
loading taro.gff...

98 features loaded in  0.41s                                                    Building object tree... 0.02s
load time:  0.46s
anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs NC_010109.1

anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json

working on refseq NC_010109.1
working on track nested_tandem_repeat
got 1 features for nested_tandem_repeat
anou@anou-laptop:/var/www$ bin/generate-names.pl 

Anja

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

From: Mitch S. <mit...@be...> - 2010-10-05 21:15:22

  I'm not totally sure what's going on for you, but here's my best guess:

Usually, web servers are set up so that one particular path (e.g., 
/var/www) becomes the "root" of the space on the web server.  So, for 
example, if you put a file named "foo.html" into /var/www, so that the 
full path is /var/www/foo.html, then it'll show up in the web server as 
/foo.html.  So if you're accessing the web server on your laptop, you 
can see that HTML page by going to http://localhost/foo.html.

Different linux distributions put the "root" of the web server space in 
different places; in ubuntu (and distributions based on ubuntu, like 
Mint), it's /var/www.  In distributions derived from Red Hat, it's 
/var/www/html.

In your case, it looks like it's /var/www, so if you want to see what's 
in /var/www, you can visit http://localhost/ in your web browser.  If 
you look there, do you see your data?

Mitch

On 10/04/2010 11:52 AM, Anja Friedrich wrote:
> Hi all,
>
> I was using SeqFeature Store to load data and display them in JBrowse. 
> But I an't see anything. They are not displayed at all like they don't 
> exist... Do I activate it wrong? I was looking under 
> http://localhost/jbrowse/
> I used this commandos and it looks as if the data were loaded...
>
> anou@anou-laptop:/var/www$ bp_seqfeature_load.pl 
> <http://bp_seqfeature_load.pl/?by-user=t> --d "dbi:Pg:dbname=test" --a 
> DBI::Pg --c taro.gff
> loading taro.gff...
> 98 features loaded in  
> 0.41s                                                    Building 
> object tree... 0.02s
> load time:  0.46s
> anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl 
> <http://prepare-refseqs.pl/?by-user=t> --conf taro.json --refs NC_010109.1
> anou@anou-laptop:/var/www$ bin/biodb-to-json.pl 
> <http://biodb-to-json.pl/?by-user=t> --conf taro.json
>
> working on refseq NC_010109.1
> working on track nested_tandem_repeat
> got 1 features for nested_tandem_repeat
> anou@anou-laptop:/var/www$ bin/generate-names.pl
>
> Anja
>
>
> ------------------------------------------------------------------------------
> Virtualization is moving to the mainstream and overtaking non-virtualized
> environment for deploying applications. Does it make network security
> easier or more difficult to achieve? Read this whitepaper to separate the
> two and get a better understanding.
> http://p.sf.net/sfu/hp-phase2-d2d
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

From: anja <fri...@ho...> - 2010-10-05 21:24:51


Hi Mitch, 

when I visit http://localhost/ then I see the surface of JBrowse and the track as a grey line, so no motifs at all... more then before I guess

Anja

Date: Tue, 5 Oct 2010 14:15:32 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)





  
    
    E-Mail-Text
  
  
    I'm not totally sure what's going on for you, but here's my best
    guess:

    

    Usually, web servers are set up so that one particular path (e.g.,
    /var/www) becomes the "root" of the space on the web server.  So,
    for example, if you put a file named "foo.html" into /var/www, so
    that the full path is /var/www/foo.html, then it'll show up in the
    web server as /foo.html.  So if you're accessing the web server on
    your laptop, you can see that HTML page by going to
    http://localhost/foo.html.

    

    Different linux distributions put the "root" of the web server space
    in different places; in ubuntu (and distributions based on ubuntu,
    like Mint), it's /var/www.  In distributions derived from Red Hat,
    it's /var/www/html.

    

    In your case, it looks like it's /var/www, so if you want to see
    what's in /var/www, you can visit http://localhost/ in your web
    browser.  If you look there, do you see your data?

    

    Mitch

    

    On 10/04/2010 11:52 AM, Anja Friedrich wrote:
    
      
      Hi all, 

      

      I was using SeqFeature Store to load data and display them in
      JBrowse. But I an't see anything. They are not displayed at all
      like they don't exist... Do I activate it wrong? I was looking
      under http://localhost/jbrowse/

      I used this commandos and it looks as if the data were loaded...
      

        anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d
        "dbi:Pg:dbname=test" --a DBI::Pg --c taro.gff

        loading taro.gff...

      
      98 features loaded in 
      0.41s                                                    Building
      object tree... 0.02s

      load time:  0.46s

      anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs
      NC_010109.1

      anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json

      

      working on refseq NC_010109.1

      working on track nested_tandem_repeat

      got 1 features for nested_tandem_repeat

      anou@anou-laptop:/var/www$ bin/generate-names.pl 

      

      Anja

      
------------------------------------------------------------------------------
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environment for deploying applications. Does it make network security 
easier or more difficult to achieve? Read this whitepaper to separate the 
two and get a better understanding.
http://p.sf.net/sfu/hp-phase2-d2d
      
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

    
    

  


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

From: Mitch S. <mit...@be...> - 2010-10-05 21:55:32

  Do the motifs show up if you zoom in?

The motifs should show up, assuming that:

1. you have "subfeatures": true and "subfeature_classes" in your config 
file, like this:

       "subfeatures": true,
       "subfeature_classes": {
         "motif1_small_a": "small_red",
         "motif1_small_b": "small_blue",
         "motif1_small_c": "small_purple",
         "motif1_tall_a": "tall_blue",
         "motif1_tall_b": "tall_purple"
       }

and 2. /var/www/genome.css has a listing for all of the values in the 
"subfeature_classes" setting.

If have both of those things, then my best guess for what's going on is 
this: by default, subfeatures like your motifs are only shown once you 
zoom in beyond a certain level.

The threshold where they show up is controlled by the "subfeatureScale" 
setting in the "clientConfig" part of the config file, so you can add 
something like this:

       "clientConfig": {
           "subfeatureScale": 40
       },

The default is 80, and if you want the subfeatures to still show up when 
you're more zoomed out, set it lower.

The actual units for the "subfeatureScale" setting are pixels/feature.  
That value is multiplied by the average feature density in features/base 
units (i.e., the number of features in the track / the refseq length) to 
get the scale threshold in pixels per base.  For example, if the 
subfeatureScale is 2, and a track has 100 features, then subfeatures 
will be shown if you're zoomed in far enough that the entire refseq 
would be at least 200 pixels wide.

Hope this helps,
Mitch

On 10/05/2010 02:24 PM, anja wrote:
> Hi Mitch,
>
> when I visit http://localhost/ then I see the surface of JBrowse and 
> the track as a grey line, so no motifs at all... more then before I guess

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

From: anja <fri...@ho...> - 2010-10-05 22:02:35


I zoomed in as much as possible (and it is far enough when I look at the "ruler") but I still can't see anything. Only the DNA track was added. I hope the config file and genome.css are right... but I attached them

Date: Tue, 5 Oct 2010 14:55:40 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)



  Do the motifs show up if you zoom in?


The motifs should show up, assuming that:


1. you have "subfeatures": true and "subfeature_classes" in your config 

file, like this:


       "subfeatures": true,

       "subfeature_classes": {

         "motif1_small_a": "small_red",

         "motif1_small_b": "small_blue",

         "motif1_small_c": "small_purple",

         "motif1_tall_a": "tall_blue",

         "motif1_tall_b": "tall_purple"

       }


and 2. /var/www/genome.css has a listing for all of the values in the 

"subfeature_classes" setting.


If have both of those things, then my best guess for what's going on is 

this: by default, subfeatures like your motifs are only shown once you 

zoom in beyond a certain level.


The threshold where they show up is controlled by the "subfeatureScale" 

setting in the "clientConfig" part of the config file, so you can add 

something like this:


       "clientConfig": {

           "subfeatureScale": 40

       },


The default is 80, and if you want the subfeatures to still show up when 

you're more zoomed out, set it lower.


The actual units for the "subfeatureScale" setting are pixels/feature.  

That value is multiplied by the average feature density in features/base 

units (i.e., the number of features in the track / the refseq length) to 

get the scale threshold in pixels per base.  For example, if the 

subfeatureScale is 2, and a track has 100 features, then subfeatures 

will be shown if you're zoomed in far enough that the entire refseq 

would be at least 200 pixels wide.


Hope this helps,

Mitch


On 10/05/2010 02:24 PM, anja wrote:

> Hi Mitch,

>

> when I visit http://localhost/ then I see the surface of JBrowse and 

> the track as a grey line, so no motifs at all... more then before I guess



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html, body {
    height: 98%;
}

.nav {
    vertical-align: middle;
    z-index: 10;
}

input.icon {
    display: -moz-inline-stack;
    display: inline-block;
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}

div.container {
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div.locationTrap {
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}

div.locationThumb {
    position: absolute;
    top: 0px;
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    border: 2px solid red;
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    cursor: url("openhand.cur");
}

div.locationThumb.dojoMoveItem {
    cursor: url("closedhand.cur");
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div.overview {
    width: 100%;
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    z-index: -5;
}

div.block {
    position: absolute;
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div.track {
    position: absolute;
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}

.track.dojoDndItemOver {
    cursor: inherit;
}

.track.dojoDndItemBefore {
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}

.track.dojoDndItemAfter {
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}

div#static_track {
    top: 0px;
    position: absolute;
    background-color: #f0f0f0;
    z-index: 20;
}

div.gridline {
    position: absolute;
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    height: 100%;
    border-style: none none none solid;
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}

div.pos-label {
    position: absolute;
    left: 0px;
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    padding: 4px;
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}

div.overview-pos {
    position: absolute;
    left: 0px;
    color: black;
    padding-left: 4px;
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}

div.blank-block {
    font: sans-serif;
    position: absolute;
    overflow: visible;
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div.sequence {
    position: absolute;
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    letter-spacing: 2px;
    padding-left: 2px;
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/*
div.minus-feature:before {
    content: attr(fName);
    display: block;
}

div.plus-feature:before {
    content: attr(fName);
    display: inline;
}
*/

div.track-label {
    font-family: sans-serif;
    z-index: 20;
    background-color: #BDD7FF;
    border: 2px #2b434c solid;
    color: #2b434c;
    padding: 5px;
    cursor: pointer;
}

div.tracklist-label {
    font-family: sans-serif;
    z-index: 20;
    background-color: #BDD7FF;
    border: 2px #2b434c solid;
    color: #2b434c;
    cursor: pointer;
    padding: 3px;
}

/* commented for now, multi-select too confusing?
.tracklist-container.dojoDndItemSelected {
    background: #ddf;
}

.tracklist-container.dojoDndItemAnchor {
    background: #ddf;
}
*/

div.tracklist-container {
    padding: 5px;
    margin-top: -3px;
    margin-bottom: -3px;
}

.tracklist-container.dojoDndItemBefore {
    border-top: 3px solid #999;
    padding-top: 2px;
}

.tracklist-container.dojoDndItemAfter {
    border-bottom: 3px solid #999;
    padding-bottom: 2px;
}

.feature-label {
    position: absolute;
    font-family: monospace;
    border: 0px;
    margin: -2px 0px 0px 0px;
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    padding: 0px 0px 0px 0px;
    /* font-size: 80%; */
    white-space: nowrap;
    background-color: #eee;
    z-index: 10;
    cursor: pointer;
}

.basic,
.plus-basic,
.minus-basic {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

div.basic-hist {
    position: absolute;
    z-index: 10;
}

.plus-feature,
.minus-feature {
    position:absolute;
    height: 8px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
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}

.plus-feature { background-image: url('img/plus-chevron3.png'); }

.minus-feature { background-image: url('img/minus-chevron3.png'); }

div.feature-hist {
    position: absolute;
    background-color: blue;
    border-color: lightblue;
    border-style: solid;
    border-width: 1px;
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}

.plus-feature2,
.minus-feature2 {
    position:absolute;
    height: 15px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
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}

.plus-feature2 { background-image: url('img/plus-herringbone16.png'); }

.minus-feature2 { background-image: url('img/minus-herringbone16.png'); }

div.feature2-hist {
    position: absolute;
    background-color: #9f9;
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.minus-feature3 {
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.plus-feature3 { background-image: url('img/plus-chevron.png'); }

.minus-feature3 { background-image: url('img/minus-chevron.png'); }

div.feature3-hist {
    position: absolute;
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    border-color: black;
    border-style: solid;
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    z-index: 10;
}

.plus-feature4,
.minus-feature4 {
    position:absolute;
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    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
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}

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div.feature4-hist {
    position: absolute;
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    border-color: black;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-feature5,
.minus-feature5 {
    position:absolute;
    height: 8px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
    z-index: 10;
}

.plus-feature5 { background-image: url('img/plus-chevron2.png'); }

.minus-feature5 { background-image: url('img/minus-chevron2.png'); }

div.feature5-hist {
    position: absolute;
    background-color: blue;
    border-color: lightblue;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

div.exon-hist {
    position: absolute;
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    border-color: #00f;
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}

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    position: absolute;
    height: 5px;
    background-color: #4B76E8;
    border-style: solid;
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    cursor: pointer;
    z-index: 10;
}

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    position: absolute;
    background-color: #ED9185;
    border-style: solid;
    border-color: #c33;
    border-width: 1px;
    z-index: 10;
}

.plus-est,
.minus-est {
    position: absolute;
    height: 5px;
    background-color: #ED9185;
    border-style: solid;
    border-color: #c33;
    border-width: 1px;
    cursor: pointer;
    z-index: 10;
}

.plus-dblhelix,
.minus-dblhelix {
    position:absolute;
    height: 11px;
    background-image: url('img/dblhelix-red.png');
    background-repeat: repeat-x;
    min-width: 1px;
    cursor: pointer;
    z-index: 10;
}

div.dblhelix-hist {
    position: absolute;
    background-color: #fcc;
    border-color: #daa;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-helix,
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    position:absolute;
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    z-index: 10;
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.loops {
    position:absolute;
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    cursor: pointer;
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.minus-cds0 { background-image: url('img/minus-cds0.png'); }
.minus-cds1 { background-image: url('img/minus-cds1.png'); }
.minus-cds2 { background-image: url('img/minus-cds2.png'); }

div.cds-hist {
    position: absolute;
    background-color: #fcc;
    border-color: #daa;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.topbracket {
    position:absolute;
    height: 8px;
    border-style: solid solid none solid;
/*    border-width: 2px 2px 0px 2px; */
    border-width: 2px;
    border-color: orange;
/*    margin-top: 2px */
    cursor: pointer;
}

.bottombracket {
    position:absolute;
    height: 8px;
    border-style: none solid solid solid;
    border-width: 2px;
    border-color: green;
    cursor: pointer;
}

.hourglass {
    position:absolute;
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    border-style: solid;
    border-width: 6px 3px 6px 3px;
    cursor: pointer;
}

.plus-triangle {
    position:absolute;
    height: 0px;
    border-style: solid;
    border-width: 6px 3px 0px 3px;
    cursor: pointer;
}

.minus-triangle {
    position:absolute;
    height: 0px;
    border-style: solid;
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    cursor: pointer;
}

.triangle {
    position:absolute;
    height: 0px;
    border-style: solid;
    border-width: 6px 0px 0px 0px;
    cursor: pointer;
}

.hgred {
    border-color: #f99 white #f99 white;
}
div.hgred-hist {
    position: absolute;
    background-color: #daa;
    border-color: #d44;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.hgblue {
    border-color: #99f white #99f white;
}
div.hgblue-hist {
    position: absolute;
    background-color: #aad;
    border-color: #99f;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.ibeam {
    position:absolute;
    height: 2px;
    background-color: blue;
    border-style: solid;
    border-width: 8px 4px 8px 4px;
    border-color: white blue white blue;
    cursor: pointer;
}

div.transcript-hist {
    position: absolute;
    background-color: #ddd;
    border-color: #FF9185;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.transcript,
.plus-transcript,
.minus-transcript {
    position: absolute;
    height: 4px;
    margin-top: 4px;
    margin-bottom: 4px;
    background-color: #999;
    z-index: 6;
    min-width: 1px;
    cursor: pointer;
}

.plus-transcript-arrowhead {
    position: absolute;
/*  border stuff seems slow
    height: 0px;
    width: 0px;
    margin-top: -4px;
    border-style: solid;
    border-color: white white white #999;
    border-width: 6px 0px 6px 10px; */
    margin-top: -4px;
    width: 12px;
    height: 12px;
    background-image: url('img/plus-transcript-head.png');
    background-repeat: no-repeat;
}

.minus-transcript-arrowhead {
    position: absolute;
/*  border stuff seems slow
    height: 0px;
    width: 0px;
    margin-top: -4px;
    border-style: solid;
    border-color: white #999 white white;
    border-width: 6px 10px 6px 0px; */
    margin-top: -4px;
    width: 12px;
    height: 12px;
    background-image: url('img/minus-transcript-head.png');
    background-repeat: no-repeat;
}

.plus-transcript-CDS,
.minus-transcript-CDS {
    position: absolute;
    height: 12px;
    margin-top: -4px;
    background-image: url('img/cds.png');
    background-repeat: repeat-x;
/*  border-width: 2px 0px 3px 0px;
    border-style: solid;
    border-color: white;
    background-color: #FF9185;
    border-style: solid;
    border-color: #00f;
    border-width: 1px;*/
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.plus-transcript-exon,
.minus-transcript-exon,
.plus-transcript-UTR, 
.minus-transcript-UTR,
.plus-transcript-five_prime_UTR,
.minus-transcript-five_prime_UTR,
.plus-transcript-three_prime_UTR,
.minus-transcript-three_prime_UTR {
    position: absolute;
    height: 4px;
    margin-top: -2px;
    background-color: #B66;
    border-style: solid;
    border-color: #D88;
    border-width: 2px 0px 2px 0px;
    z-index: 8;
    min-width: 1px;
    cursor: pointer;
}

.generic_parent,
.plus-generic_parent,
.minus-generic_parent {
    position: absolute;
    height: 4px;
    margin-top: 2px;
    margin-bottom: 2px;
    background-color: #AAA;
    z-index: 6;
    min-width: 1px;
    cursor: pointer;
}

div.generic_parent-hist {
    position: absolute;
    background-color: #ddd;
    border-color: #555;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.match_part,
.plus-match_part,
.minus-match_part {
    position: absolute;
    height: 4px;
    margin-top: -2px;
    background-color: #66B;
    border-style: solid;
    border-color: #88D;
    border-width: 2px 0px 2px 0px;
    z-index: 8;
    min-width: 1px;
    cursor: pointer;
}

.generic_part_a,
.plus-generic_part_a,
.minus-generic_part_a {
    position: absolute;
    height: 4px;
    margin-top: -2px;
    background-color: #6B6;
    border-style: solid;
    border-color: #8D8;
    border-width: 2px 0px 2px 0px;
    z-index: 8;
    min-width: 1px;
    cursor: pointer;
}

.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-small_green,
.plus-small_orange,
.plus-small_black,
.plus-small_pink,
.plus-small_brown,
.plus-small_yellow,
.plus-small_violet,
.plus-small_aqua,
.plus-small_fuchsia,
.plus-tall_blue,
.plus-tall_purple,
.plus-tall_red,
.plus-tall_yellow,
.plus-tall_brown,
.plus-tall_orange,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-small_green,
.minus-small_orange,
.minus-small_black,
.minus-small_pink,
.minus-small_brown,
.minus-small_yellow,
.minus-small_violet,
.minus-small_aqua,
.minus-small_fuchsia,
.minus-tall_blue,
.minus-tall_purple
.minus-tall_red,
.minus-tall_yellow,
.minus-tall_brown,
.minus-tall_orange, {
    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-small_purple, .minus-small_green {
    background-color: #008000; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_orange {
    background-color: #FFA500; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_black {
    background-color: #000000; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_pink {
    background-color: #FFC0CB; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_brown {
    background-color: #A52A2A; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_yellow {
    background-color: #FFFF00; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_violet {
    background-color: #C71585; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_aqua {
    background-color: #00FFFF; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_fuchsia {
    background-color: #FF00FF; 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;
}
plus-tall_blue, .minus-tall_yellow {
    background-color: #FFFF00; height: 10px; margin-top: -3px;
}
plus-tall_blue, .minus-tall_brown {
    background-color: #A52A2A; height: 10px; margin-top: -3px;
}
plus-tall_blue, .minus-tall_orange {
    background-color: #FFA500; height: 10px; margin-top: -3px;
}

 

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

From: Mitch S. <mit...@be...> - 2010-10-05 22:37:09

  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

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

From: anja <fri...@ho...> - 2010-10-06 11:52:06


fixed everything but now I have a blank page...

Anja

Date: Wed, 6 Oct 2010 04:33:30 -0700
From: ml-...@n3...
To: fri...@ho...
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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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

From: anja <fri...@ho...> - 2010-10-06 11:59:36


yes

Date: Wed, 6 Oct 2010 04:56:55 -0700
From: ml-...@n3...
To: fri...@ho...
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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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

From: anja <fri...@ho...> - 2010-10-06 12:14:21


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

From: Mitch S. <cra...@ar...> - 2010-10-06 22:56:03

  On 10/06/2010 05:14 AM, anja wrote:
> sent

I haven't received it; it might be too large to email.  If you can put 
it online (this is your eventual goal, right?) then I could look to see 
what's going on.  Otherwise, you can compare your setup to mine and see 
what the differences are.

> 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?

It's a typo in your CSS; the second tall motif is being displayed at the 
beginning, making the first 3 variants look tall.  The second tall motif 
is a "tall purple" one, and in the CSS there's this:

=====
.tall_blue,
.tall_purple
.tall_red,
=====

That missing comma for tall_purple is what's causing it.

Mitch

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

From: Anja F. <fri...@ho...> - 2010-10-06 07:43:10

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...

      > To: gmo...@li...;
      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

      >

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

From: Mitch S. <mit...@be...> - 2010-10-06 12:09:22

  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] </user/SendEmail.jtp?type=node&node=1641991&i=0>
> To: [hidden email] </user/SendEmail.jtp?type=node&node=1641991&i=1>
> 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]
>     <http:///user/SendEmail.jtp?type=node&node=1641965&i=0&by-user=t>
>     To: [hidden email]
>     <http:///user/SendEmail.jtp?type=node&node=1641965&i=1&by-user=t>
>     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
>     <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]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=0>
>         To: [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=1>;
>         [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=2>
>         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]
>             <http:///user/SendEmail.jtp?type=node&node=1641912&i=3>
>             > To: [hidden email]
>             <http:///user/SendEmail.jtp?type=node&node=1641912&i=4>;
>             [hidden email]
>             <http:///user/SendEmail.jtp?type=node&node=1641912&i=5>
>             > 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
>             >
>
>
>
>         ------------------------------------------------------------------------------
>         Beautiful is writing same markup. Internet Explorer 9 supports
>         standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>         Spend less time writing and  rewriting code and more time creating great
>         experiences on the web. Be a part of the beta today.
>         http://p.sf.net/sfu/beautyoftheweb
>
>
>         _______________________________________________
>         Gmod-ajax mailing list
>         [hidden email]  <http:///user/SendEmail.jtp?type=node&node=1641912&i=6>
>         https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
>     ------------------------------------------------------------------------------
>
>     Beautiful is writing same markup. Internet Explorer 9 supports
>     standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>     Spend less time writing and  rewriting code and more time creating
>     great
>     experiences on the web. Be a part of the beta today.
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[Gmod-ajax] FW: data are not displayed even though they were loaded (JBrowse)

From: Anja F. <fri...@ho...> - 2010-10-06 20:41:01



From: fri...@ho...
To: cra...@ar...
Subject: RE: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
Date: Wed, 6 Oct 2010 22:31:56 +0200








upload here

http://www.file-upload.net/download-2871690/taro.tar.gz.html

Anja


> Date: Wed, 6 Oct 2010 13:08:33 -0700
> From: cra...@ar...
> To: fri...@ho...
> CC: gmo...@li...
> Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
> 
>   On 10/06/2010 05:14 AM, anja wrote:
> > sent
> 
> I haven't received it; it might be too large to email.  If you can put 
> it online (this is your eventual goal, right?) then I could look to see 
> what's going on.  Otherwise, you can compare your setup to mine and see 
> what the differences are.
> 
> > 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?
> 
> It's a typo in your CSS; the second tall motif is being displayed at the 
> beginning, making the first 3 variants look tall.  The second tall motif 
> is a "tall purple" one, and in the CSS there's this:
> 
> =====
> .tall_blue,
> .tall_purple
> .tall_red,
> =====
> 
> That missing comma for tall_purple is what's causing it.
> 
> Mitch
>

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

From: Mitch S. <mit...@be...> - 2010-10-06 11:56:47

  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] </user/SendEmail.jtp?type=node&node=1641965&i=0>
> To: [hidden email] </user/SendEmail.jtp?type=node&node=1641965&i=1>
> 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 
> <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]
>     <http:///user/SendEmail.jtp?type=node&node=1641912&i=0>
>     To: [hidden email]
>     <http:///user/SendEmail.jtp?type=node&node=1641912&i=1>; [hidden
>     email] <http:///user/SendEmail.jtp?type=node&node=1641912&i=2>
>     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]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=3>
>         > To: [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=4>;
>         [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=5>
>         > 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
>         >
>
>
>
>     ------------------------------------------------------------------------------
>     Beautiful is writing same markup. Internet Explorer 9 supports
>     standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>     Spend less time writing and  rewriting code and more time creating great
>     experiences on the web. Be a part of the beta today.
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>     Gmod-ajax mailing list
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>
>
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>
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> Spend less time writing and  rewriting code and more time creating great
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> ------------------------------------------------------------------------
> View this message in context: RE: data are not displayed even though 
> they were loaded (JBrowse) 
> <http://gmod.827538.n3.nabble.com/Gmod-ajax-data-are-not-displayed-even-though-they-were-loaded-JBrowse-tp1631655p1641965.html>
> Sent from the JBrowse mailing list archive 
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>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

From: Mitch S. <mit...@be...> - 2010-10-06 01:31:41

  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...
> > To: gmo...@li...; 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
> >

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

From: Mitch S. <mit...@be...> - 2010-10-06 11:33:18

  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
>     >
>
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

From: anja <fri...@ho...> - 2010-10-06 11:41:39


Oh great, thanks. I will fix it immediately.

Anja

Date: Wed, 6 Oct 2010 04:33:30 -0700
From: ml-...@n3...
To: fri...@ho...
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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