We used the 'postgrid' option from the Bio::Graphics::Panel to draw
callback-generated images onto the panel's background after the grid
line are drawn. Please have a look at the following thread about custom
background images,
http://sourceforge.net/mailarchive/message.php?msg_id=12116755
I hope it is helpful and please let me know if you have questions.
-Haiming
Smithies, Russell wrote:
> On a slightly different note, how have you created the syntenic
> alignments on cryptodb?
> It's something we're interested in doing but don't want to go the whole
> hog with Synbrowse.
>
> Thanx,
>
> Russell Smithies
> Bioinformatics Software Developer
> Invermay Research Centre
> Puddle Alley,
> Mosgiel,
> New Zealand
> http://www.agresearch.co.nz
>
>
>> -----Original Message-----
>> From: gmod-gbrowse-bounces@...
>> [mailto:gmod-gbrowse-bounces@...] On Behalf
>> Of Haiming Wang
>> Sent: Wednesday, 28 June 2006 6:55 a.m.
>> To: Jim Hu
>> Cc: Scott Cain; Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] mouseover
>>
>> There are customizable popup windows implemented by CryptoDB
>> and PlasmoDB. Please have a look at the following examples,
>>
>> http://cryptodb.org/cgi-bin/gbrowse/cryptodb/?name=AAEE0100000
>> 2%3A106357-116356
>>
>> and
>> http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/
>>
>> In a nutshell, a javascript library is included in your
>> config file and a subroutine, using HTML::Template, is
>> defined in the init_code section to format the data.
>>
>> -Haiming
>>
>> p.s.
>> you can download this javascript popup library at
>> http://www.walterzorn.com/tooltip/tooltip_e.htm
>>
>> Jim Hu wrote:
>>> Scott (or anyone else),
>>>
>>> Can you point to someone who has instructions for how to do
>> the popup
>>> menus with javascript? It seems like this would be a good
>> way to do
>>> linkout to external sites, instead of going to another page
>> that lists
>>> them. This may be trivial, but my javascript knowledge is
>> even worse
>>> than my Perl.
>>>
>>> Jim Hu
>>> =====================================
>>> Jim Hu
>>> Associate Professor and Associate Head for Graduate
>> Programs Dept. of
>>> Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>>
>>> On May 26, 2006, at 9:03 AM, Scott Cain wrote:
>>>
>>>> Jianjun,
>>>>
>>>> I think you may be mixing apples and oranges a little bit. The
>>>> Bio::DB::GFF schema can be run in many RDMS. The most common is
>>>> MySQL, but I use PostgreSQL, and an Oracle adaptor exists as well.
>>>>
>>>> But that should matter anyway; even if you were using
>> another adaptor
>>>> (like the Chado adaptor), you can still write callbacks
>> like the ones
>>>> in that section.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Fri, 2006-05-26 at 09:42 -0400, Jianjun Wang wrote:
>>>>> Thank you, Scott. I think I can go by without Javascript. But the
>>>>> COMPUTED OPTIONS part seems to apply only to Bio::DB::GFF schema,
>>>>> what should I do with other databases, such as Oracle?
>>>>>
>>>>> cheers,
>>>>> Jianjun
>>>>>
>>>>>
>> ______________________________________________________________
>>>>> From: Scott Cain [mailto:cain@...]
>>>>> To: Jianjun Wang [mailto:jwang@...]
>>>>> Cc: gmod-gbrowse@...
>>>>> Sent: Thu, 25 May 2006 11:21:58 -0400
>>>>> Subject: Re: [Gmod-gbrowse] mouseover
>>>>>
>>>>> Hi Jianjun,
>>>>>
>>>>> I'm not sure what you are asking about; if you
>> just want to
>>>>> customize
>>>>> the text that is in the 'tooltip' window that
>> pops up, see the
>>>>> entry for
>>>>> 'title' in the CONFIGURE_HOWTO, B2. The [TRACK DEFAULTS]
>>>>> section. The
>>>>> title option can be used in both the track defaults and
>>>>> individual track
>>>>> definitions.
>>>>>
>>>>> If, on the other hand, you want a more sophisticated popup
>>>>> when you
>>>>> mouseover a feature, you need javascript. While
>> people have
>>>>> used
>>>>> javascript to create cool things like popup menus, I
>>>>> personally haven't
>>>>> done that, but it is possible by inserting the
>> javascript in
>>>>> the "head="
>>>>> section of the conf file.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Thu, 2006-05-25 at 09:54 -0400, Jianjun Wang wrote:
>>>>>> Could someone please enlighten me on the mouseover mechanism
>>>>> in
>>>>>> GBrowse, in the context of customizing the mouseover
>>>>> contents and
>>>>>> creating new tracks? It doesn't seem to be handled in the
>>>>> glyph
>>>>>> object.
>>>>>>
>>>>>> Thanks in advance,
>>>>>>
>>>>>> Jianjun
>>>>> --
>>>>>
>>>>>
>> --------------------------------------------------------------
>> ----------
>>>>> Scott Cain, Ph. D. cain@...
>>>>> GMOD Coordinator (http://www.gmod.org/) 216-392-3087
>>>>> Cold Spring Harbor Laboratory
>>>>>
>> ---------------------------------------------------------------------
>>>> -----
>>>>
>>>> Scott Cain, Ph. D.
>> cain@...
>>>> GMOD Coordinator (http://www.gmod.org/)
>> 216-392-3087
>>>> Cold Spring Harbor Laboratory
>>>
>>>
>>> =====================================
>>> Jim Hu
>>> Associate Professor and Associate Head for Graduate
>> Programs Dept. of
>>> Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>>
>>>
>>>
>>>
>> ----------------------------------------------------------------------
>>> --
>>>
>>> Using Tomcat but need to do more? Need to support web
>> services, security?
>>> Get stuff done quickly with pre-integrated technology to
>> make your job
>>> easier Download IBM WebSphere Application Server v.1.0.1 based on
>>> Apache Geronimo
>>>
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216
>>> 42
>>>
>>>
>>>
>> ----------------------------------------------------------------------
>>> --
>>>
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse@...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> Using Tomcat but need to do more? Need to support web
>> services, security?
>> Get stuff done quickly with pre-integrated technology to make
>> your job easier Download IBM WebSphere Application Server
>> v.1.0.1 based on Apache Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&;
>> dat=121642
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
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