Re: [Artemis-users] Hide forward and reverse frame lines

[Tim Carver]

Ok. This has been done now and so will reach the development version on the
Artemis site in the next couple of weeks.

Regards
Tim


On 5/24/10 2:41 PM, "Shahar ."  wrote:

> This would be great.
> These lines take most of the space in my Artemis window and since I rarely use
> them, the first thing I usually do is to manually close them.
> 
> On Mon, May 24, 2010 at 4:23 PM, Tim Carver  wrote:
>> Hi Shahar
>> 
>> No there isn¹t an option for this in the options file. If it would be useful
>> I can add the options :
>> 
>> show_forward_lines
>> 
>> and
>> 
>> show_reverse_lines
>> 
>> so that these can be controlled from the options file. This would control
>> both the zoomed out and zoomed in feature displays.
>> 
>> Regards
>> Tim 
>> 
>> 
>> 
>> On 5/24/10 1:53 PM, "Shahar ." http://shahar.id/> @gmail.com
>>  > wrote:
>> 
>>> Hello,
>>>  
>>> Is it possible to hide the forward and reverse frame lines both in the
>>> overview and DNA view windows by default?
>>>  
>>> Thanks,
>>> Shahar
>>> 
>>> 
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>>> Artemis-users mailing list
>>> Artemis-users@sanger.ac.uk
>>> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
>> 
>> 
>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a company
>> registered in England with number 2742969, whose registered office is 215
>> Euston Road, London, NW1 2BE.
> 
> 


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Re: [Artemis-users] Hide forward and reverse frame lines

[Shahar .]

This would be great.
These lines take most of the space in my Artemis window and since I rarely
use them, the first thing I usually do is to manually close them.

On Mon, May 24, 2010 at 4:23 PM, Tim Carver  wrote:

> Hi Shahar
>
> No there isn’t an option for this in the options file. If it would be
> useful I can add the options :
>
> show_forward_lines
>
> and
>
> show_reverse_lines
>
> so that these can be controlled from the options file. This would control
> both the zoomed out and zoomed in feature displays.
>
> Regards
> Tim
>
>
>
> On 5/24/10 1:53 PM, "Shahar ."  wrote:
>
>   Hello,
>
> Is it possible to hide the forward and reverse frame lines both in the
> overview and DNA view windows by default?
>
> Thanks,
> Shahar
>
> --
> ___
> Artemis-users mailing list
> Artemis-users@sanger.ac.uk
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>
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Re: [Artemis-users] Hide forward and reverse frame lines

[Tim Carver]

Hi Shahar

No there isn¹t an option for this in the options file. If it would be useful
I can add the options :

show_forward_lines

and

show_reverse_lines

so that these can be controlled from the options file. This would control
both the zoomed out and zoomed in feature displays.

Regards
Tim


On 5/24/10 1:53 PM, "Shahar ."  wrote:

> Hello,
>  
> Is it possible to hide the forward and reverse frame lines both in the
> overview and DNA view windows by default?
>  
> Thanks,
> Shahar
> 
> 
> ___
> Artemis-users mailing list
> Artemis-users@sanger.ac.uk
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users


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[Artemis-users] Hide forward and reverse frame lines

[Shahar .]

Hello,

Is it possible to hide the forward and reverse frame lines both in the
overview and DNA view windows by default?

Thanks,
Shahar
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Re: [Artemis-users] User plot legend

[Tim Carver]

Hi Simon

Unfortunately you can¹t add your own text. The main issue is obviously space
which is why they are just numbered at the moment across the top. In the
future I can return to this and perhaps allow the user to set the text and
position of the legend.

Regards
Tim


On 5/24/10 6:17 AM, "simon.glad...@csiro.au"  wrote:

> Hi there,
>  
> I was wondering if I could give the legend in a user plot labels of my choice.
>  For example I¹ve got a user plot as follows:
>  
> # BASE    VAL1    VAL2    VAL3
> # colour X:X:X Y:Y:Y   Z:Z:Z
> 100   1  2  3
> 200   2  3  4
> 300   3  4  5
> 400   4  5  6
> 500   5  6  7
>  
> etc
>  
> When I add this to artemis I get a lovely coloured graph with a little legend
> in the top right with 1, 2, 3 as the labels.  Can I change the labels to
> something more meaningful?
>  
> Cheers,
>  
> Simon.
> 
> 
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Re: [Artemis-users] HTML version of Artemis manual?

[Tim Carver]

Hi Torsten

Thanks for that, it isn't browsable from the new Sanger website
unfortunately but you can download the html from here if you want a local
copy:

ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v12/artemis_manual_ht
ml.zip

Regards
Tim


On 5/24/10 1:02 AM, "Torsten Seemann"  wrote:

> Tim et al,
> 
> Since the recent update to the Sanger web site, I no longer seem to be
> able to locate the HTML/online version of the Artemis manual, only the
> PDF one. This makes it difficult to point people to relevant sections
> to read with a URL. Does it still exist somewhere publicly available?
> 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
> University, AUSTRALIA
> 
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[Artemis-users] HTML version of Artemis manual?

[Torsten Seemann]

Tim et al,

Since the recent update to the Sanger web site, I no longer seem to be
able to locate the HTML/online version of the Artemis manual, only the
PDF one. This makes it difficult to point people to relevant sections
to read with a URL. Does it still exist somewhere publicly available?

--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA

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Re: [Artemis-users] Customized Genbank file - differentially color genes?

[Torsten Seemann]

Shahar,

> I wrote a customized genbank file with my genes of interest with notes etc.
> I wonder if it's possible to control the display color for different genes.
> I have a few different groups of genes, and it would be wonderful if I could
> make them visually distinguishable, e.g., by setting the display color for
> each gene in the genbank file.

Yes you can, just use the /colour tag (English spelling, yay!) in your feature:

/colour="0 255 128"
/product="DnaA protein"
/gene="dnaA"

The "0 255 128" is the "R G B" value to use - in this case a bright greeny blue.

We use this a lot eg. COG group colouring, Enzyme class, similarity score etc.

Also, the latest "User Plot" format also allows multiple plots on the
same panel, each with a different colour (user can specify in
.userplot file) and a legend/key automatically displayed.

--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
University, AUSTRALIA

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