[Gmod-help] Re: [Gmod-gbrowse] option='fgcolor' and option='bgcolor'
Erick Antezana
erant at psb.vib-ugent.be
Fri Feb 13 07:50:21 EST 2009
Thanks Dave, it does indeed the trick. However, it would be good that in a
near future this bug could be fixed.
cheers,
Erick
> Erick,
>
> There are two other things you can try if you don't like any of the
> named colors (see
> http://gmod.org/wiki/Image:Gbrowse_Color_Palette.pdf).
>
> 1. Build the hex string in Perl, replacing the '#' with a chr(35) call. eg
>
> fgcolor = sub {
> return chr(35) . "ABCDEF";
> }
>
> 2. At the January 2009 GMOD meeting (summarized at
> http://gmod.org/wiki/January_2009_GMOD_Meeting), Russell Smithies
> indicated you could avoid issues like this one by putting the code in
> separate file and then requiring it from the callback. I haven't
> tried that yet.
>
> Dave C.
> GMOD Help Desk
>
> Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
>
> On Tue, Feb 10, 2009 at 1:21 AM, Erick Antezana <erant at psb.vib-ugent.be>
> wrote:
>> This issue has, indeed, something to do with the '#', we also played
>> with
>> several ways to overcome it (e.g. using hex() subroutine, etc). Our
>> GBrowse 1.68 works fine. But as I mentioned, GGB 2.0 does not like the
>> '#'
>>
>> cheers,
>> Erick
>>
>>> When we upgraded to gbrowse 1.69 in December we had a similar problem
>>> with
>>> the header and foot html in the in the gbrowse conf file. It seems to
>>> be
>>> a problem with escaping the "#". When we changed the colors to names
>>> (i.e. black from #000000) we stopped getting errors. Sofia and I tried
>>> different methods of quoting, but without much luck. Changing to color
>>> names worked well enough for the colors that we use that we didn't
>>> spend
>>> much more time looking into it.
>>>
>>>
>>> ---------------
>>> Eric Ross
>>> Alejandro Sánchez Alvarado Laboratory
>>> Howard Hughes Medical Institute
>>> Department of Neurobiology and Anatomy
>>> University of Utah
>>> ejr at neuro.utah.edu
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:scott at scottcain.net]
>>> Sent: Mon 2009-02-09 8:01 AM
>>> To: erant at psb.vib-ugent.be
>>> Cc: gmod-gbrowse at lists.sourceforge.net
>>> Subject: Re: [Gmod-gbrowse] option='fgcolor' and option='bgcolor'
>>>
>>> Hi Erick,
>>>
>>> The first thing I would check is that the single quote marks around
>>> the hex color strings (ie, my $c = ['#00ff65','#00ff46', ...) are
>>> still really single quotes. Some browsers and/or operating systems
>>> and/or editing software might try to be clever and turn them into
>>> smart quotes or even apostrophes.
>>>
>>> Scott
>>>
>>>
>>> On Mon, Feb 9, 2009 at 9:51 AM, Erick Antezana <erant at psb.vib-ugent.be>
>>> wrote:
>>>> Hello,
>>>>
>>>> I am trying to understand why I have the following error messages
>>>> (from
>>>> apache) while using the config file distributed by TAIR
>>>> (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR8_genome_release/TAIR8_gff3/arabidopsis.conf):
>>>>
>>>>
>>>>
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> Use of uninitialized value in pattern match (m//) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/RegionSearch.pm
>>>> line 122.
>>>> An error occurred while evaluating the callback at section='MPSS
>>>> Flower',
>>>> option='fgcolor':
>>>> => Missing right curly or square bracket at (eval 88) line 2, at
>>>> end
>>>> of line
>>>> syntax error at (eval 88) line 2, at EOF
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='MPSS/Seed1',
>>>> option='fgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 90)
>>>> line 6.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='MPSS/Seed2',
>>>> option='fgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 114)
>>>> line 6.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='Ecker_smRNA_Gregory', option='bgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 116)
>>>> line 3.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='Ecker_smRNA',
>>>> option='bgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 152)
>>>> line 3.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at section='MPSS
>>>> Flower',
>>>> option='fgcolor':
>>>> => Missing right curly or square bracket at (eval 87) line 2, at
>>>> end
>>>> of line
>>>> syntax error at (eval 87) line 2, at EOF
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='MPSS/Seed1',
>>>> option='fgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 89)
>>>> line 6.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='MPSS/Seed2',
>>>> option='fgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 113)
>>>> line 6.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='Ecker_smRNA_Gregory', option='bgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 115)
>>>> line 3.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='Ecker_smRNA',
>>>> option='bgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 151)
>>>> line 3.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> Use of uninitialized value in pattern match (m//) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/RegionSearch.pm
>>>> line 122.
>>>> An error occurred while evaluating the callback at section='MPSS
>>>> Flower',
>>>> option='fgcolor':
>>>> => Missing right curly or square bracket at (eval 87) line 2, at
>>>> end
>>>> of line
>>>> syntax error at (eval 87) line 2, at EOF
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='MPSS/Seed1',
>>>> option='fgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 89)
>>>> line 6.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='MPSS/Seed2',
>>>> option='fgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 113)
>>>> line 6.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='Ecker_smRNA_Gregory', option='bgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 115)
>>>> line 3.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> An error occurred while evaluating the callback at
>>>> section='Ecker_smRNA',
>>>> option='bgcolor':
>>>> => Can't find string terminator "'" anywhere before EOF at (eval
>>>> 151)
>>>> line 3.
>>>> at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
>>>> line 218
>>>> Use of uninitialized value in pattern match (m//) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser/RegionSearch.pm
>>>> line 122.
>>>> An error occurred while evaluating the callback at section='MPSS
>>>> Flower',
>>>> option='fgcolor':
>>>> => Missing right curly or square bracket at (eval 88) line 2, at
>>>> end
>>>> of line
>>>> syntax error at (eval 88) line 2, at EOF
>>>>
>>>>
>>>>
>>>> Any suggestions will be very appreciated,
>>>> Erick
>>>> p.s. I am using the GGB2.0 CVS sources
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D. scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Create and Deploy Rich Internet Apps outside the browser with
>>> Adobe(R)AIR(TM)
>>> software. With Adobe AIR, Ajax developers can use existing skills and
>>> code
>>> to
>>> build responsive, highly engaging applications that combine the power
>>> of
>>> local
>>> resources and data with the reach of the web. Download the Adobe AIR
>>> SDK
>>> and
>>> Ajax docs to start building applications
>>> today-http://p.sf.net/sfu/adobe-com
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Create and Deploy Rich Internet Apps outside the browser with
>> Adobe(R)AIR(TM)
>> software. With Adobe AIR, Ajax developers can use existing skills and
>> code to
>> build responsive, highly engaging applications that combine the power of
>> local
>> resources and data with the reach of the web. Download the Adobe AIR SDK
>> and
>> Ajax docs to start building applications
>> today-http://p.sf.net/sfu/adobe-com
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
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