how to make changing title

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how to make changing title

Mikhail Pachkov
Hello All!

I would like to make gbrowse to show description+score on the mouse
over. When I try to make my own function like: sub {...} it just show
code in the popup. Is it possible in any other way?

Thank you in advance!

Good luck!

Mikhail


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Re: how to make changing title

Don Gilbert

Mikhail,

This is from one of my gbrowse configs, it shows score and best "name"
along with feature type and location in the link title. Put this above
'### TRACK CONFIGURATION ####' in gbrowse.conf to apply to all.
I'm not sure about description - it may be $f->description.

title = sub { my $f= shift;
  my $loc= $f->seq_id .':'.$f->start."..".$f->end;
  my $ftype= $f->method; if ($ftype =~ /^match/) { $ftype= $f->source(); }
  my ($nm)= ($f->attributes('Name'), $f->attributes('Alias'),
             $f->attributes('symbol'), $f->attributes('name'), $f->name() );
  my $sc= $f->score; $nm .= " p=$sc" if ($sc =~ /\d/);
  return $ftype .":". $nm . " ". $loc;
  }

- Don


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Re: how to make changing title

Lincoln Stein-2
In reply to this post by Mikhail Pachkov
Here's an excerpt from the yeast_chr1.conf file that shows how to attach a
fortune-of-the-day popup to each member of the "named genes" track:

[Genes]
feature      = gene:sgd
glyph        = generic
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
strand_arrow = 1
height       = 6
description  = 1
title        = sub { `/usr/games/fortune` }
key          = Named gene

Lincoln

On Tuesday 06 September 2005 11:34 am, Mikhail Pachkov wrote:

> Hello All!
>
> I would like to make gbrowse to show description+score on the mouse
> over. When I try to make my own function like: sub {...} it just show
> code in the popup. Is it possible in any other way?
>
> Thank you in advance!
>
> Good luck!
>
> Mikhail
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT [hidden email]


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Re: how to make changing title

Mikhail Pachkov-2
Thank you guys! It is working!

Is it possible to do the same not in the .conf file but in a .gff file
I want to upload? Or I should submit that to 'feature request' list?

Good luck!

Mikhail


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Re: how to make changing title

Mikhail Pachkov
In reply to this post by Lincoln Stein-2
Thank you guys!

Unfortunately it is working only for tracks defined in .conf file.
When I upload my own annotation (.gff file with track settings
included), it use title settings from somewhere else not from .conf.
If I try to specify 'title = sub {'/usr/games/fortune'} in gff file it
shows popup "sub {'/usr/games/fortune'}" on the mouse over.

Is it possible to do the same not in the .conf file but in a .gff file
I want to upload? Or I should submit that to 'feature request' list?

Good luck!

Mikhail


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Re: how to make changing title

Scott Cain-2
Mikhail,

Sorry, you can't do that.  Allowing anonymous subs to be executed from
an uploaded file would be a rather large security hole, and is therefore
disabled.

Scott


On Wed, 2005-09-07 at 12:01 +0200, Mikhail Pachkov wrote:

> Thank you guys!
>
> Unfortunately it is working only for tracks defined in .conf file.
> When I upload my own annotation (.gff file with track settings
> included), it use title settings from somewhere else not from .conf.
> If I try to specify 'title = sub {'/usr/games/fortune'} in gff file it
> shows popup "sub {'/usr/games/fortune'}" on the mouse over.
>
> Is it possible to do the same not in the .conf file but in a .gff file
> I want to upload? Or I should submit that to 'feature request' list?
>
> Good luck!
>
> Mikhail
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
--
------------------------------------------------------------------------
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GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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Re: how to make changing title

Mikhail Pachkov
> Sorry, you can't do that.  Allowing anonymous subs to be executed from
> an uploaded file would be a rather large security hole, and is therefore
> disabled.

True. What a pity.
How I can force the same 'title' in uploaded annotation as specified
in .conf file, at least?  I tried Don's example and it works well for
all tracks defined in the config. But not for the uploaded annotation!

Good luck!

Mikhail

P.S. Have you received my letter about help with internationalization?


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Re: how to make changing title

Scott Cain-2
On Wed, 2005-09-07 at 15:43 +0200, Mikhail Pachkov wrote:
> > Sorry, you can't do that.  Allowing anonymous subs to be executed from
> > an uploaded file would be a rather large security hole, and is therefore
> > disabled.
>
> True. What a pity.
> How I can force the same 'title' in uploaded annotation as specified
> in .conf file, at least?  I tried Don's example and it works well for
> all tracks defined in the config. But not for the uploaded annotation!

I don't think so; the idea would be that you would set a default title
for uploaded tracks?
>
> Good luck!
>
> Mikhail
>
> P.S. Have you received my letter about help with internationalization?

Yes--I'm going to send you a separate email with directions.

>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                         [hidden email]
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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Re: how to make changing title

Lincoln Stein-2
In reply to this post by Mikhail Pachkov
Please submit a feature request. It should be possible to do this
automatically with a per-feature attribute.

Lincoln

On Wednesday 07 September 2005 09:43 am, Mikhail Pachkov wrote:

> > Sorry, you can't do that.  Allowing anonymous subs to be executed from
> > an uploaded file would be a rather large security hole, and is therefore
> > disabled.
>
> True. What a pity.
> How I can force the same 'title' in uploaded annotation as specified
> in .conf file, at least?  I tried Don's example and it works well for
> all tracks defined in the config. But not for the uploaded annotation!
>
> Good luck!
>
> Mikhail
>
> P.S. Have you received my letter about help with internationalization?
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT [hidden email]


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