[Jalview-discuss] issues when exporting EPS from jalview

[Jim Procter]

Hi there, Fernan.

Thanks for your comments and bug report concerning the EPS export; and 
I'm sorry it has taken me so long to reply to this - life was a little 
busy when you posted to the list.

You have raised a number of interesting points - so I've just commented 
on each one :

On 19/01/2010 21:36, Fernan Aguero wrote:
> I'm trying to prepare a figure using Jalview, and as per the
> instructions, I'm activating the wrapping in the alignment, and after
> removing columns to the left and right of the desired region, and
> resizing the jalview window to obtain a nice alignment (I'd like to
> have blocks of ~ 60 columns) and then printing to a .ps file, I find
> that the output is always wrapped at the same column (residue 71 of
> the 1st seq), no matter what I do.
>
> The only way of getting close to what I want is by altering the
> margins when printing ... which doesn't give me a good control to wrap
> my alignment exactly where I want ...
>    
Could you send me an example where this is happening ?  As far as I can 
tell, the wrapped EPS export seems to honour the displayed wrap width in 
the alignment window, but it does have its limitations. The layout 
algorithm is fairly simple (it's 'nearly' the same one as used on 
screen), and doesn't 'posterise' the alignment; that is, it doesn't span 
a block of rows vertically over multiple pages. This may be what's 
causing you problems.

> Other issues I've noticed:
>
> * when printing I have to select the largest possible paper otherwise
> the output is truncated. In this case I've chosen A3 paper for
> printing. It'd be nice if jalview offered a custom paper size
>    
The page setup box is from the standard Java printing system, and these 
settings are only relevant when you are sending data to a printer; 
Jalview doesn't use them at all when you export to an EPS file.

If your printing device supports it (ie using Adobe Distiller or some 
other kind of virtual printer), then you should be able to set a custom 
page size. But, you normally have to delve into the OS printer 
configuration dialog, and my brief experiments on windows XP suggest 
that the settings that you change in the dialog that appears after 
pressing the 'Printer..' button on the Page setup dialog are not carried 
over to the Print dialog (which is also pretty annoying - since you have 
to set the printer again, and check that its custom page definition 
still exists and is selected).

With regards to your comments above Rather than simply offer a custom 
paper size, it actually sounds like you want a 'fit alignment to paper' 
(you specify paper and jalview scales). Alternately, you might want 
jalview to try to 'fit paper to alignment' - that is, selecting a paper 
sufficiently large to fit the alignment with the current rendering 
settings.(jalview produces EPS with custom bounding box).
> * It'd also be nice if we could specify a % enlargement/reduction when
> printing, so we that we could avoid tweaking font sizes, and just say
> 50% when printing (belvu supports this nicely). With jalview the only
> way of reducing the output is by changing the font size or later by
> editing the ps file in inkscape or illustrator.
>    
Jalview was originally designed to be strictly WYSIWIG, and one of the 
reasons that we introduced the multiple view mechanism was to enable 
different font sizes to be chosen for the same alignment diagram. The 
workaround would be to press 'ctrl+T' to duplicate your current view, 
and then change the fontsize. However, I agree that having a scale 
factor setting in an 'export layout settings' dialog would be simpler.

> * when trying to print again to a file, I need to specify the path and
> name of the output file. When trying to print again in the same
> session, using the same file (i.e after changing something, like when
> resizing the window), jalview opens the dialog sitting at the default
> dir (it forgets the previous path) and I have to navigate *again* to
> the my current workdir. After 2-3 times, it gets annoying to repeat
> this.
>    
This sounds like an issue with your installation, since the last viewed 
directory should always be remembered - even after you close Jalview and 
re-open it again. Can you follow the instructions on the faq about 
getting the output of Jalview's StdOut and StdErr (the java console 
output - http://www.jalview.org/faq.html#reportbug ) and send me the 
contents of the console after you try to save your file a few times ?  
This should help me diagnose the problem.
> Hope this helps! And thanks for a great piece of software!
>    
Thanks!  You're very welcome...

all the best.
Jim.

-- 
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.