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prettyplot output

Peter Rice pmr at sanger.ac.uk
Fri Jul 14 05:58:59 EST 1995

In article <1995Jul13.134532.9944 at reks.uia.ac.be> przemko at reks.uia.ac.be (Przemko) writes:
>prettyplot has finally arrived to our machine.
>Thankx to Peter Rice for all those color options etc.

Thanks. But I didn't do them all. David Mathog at Caltech included his own
color options and we made them work together with mine and Jaakko Hattula's
(luckily there was no clash of qualifier names).

>But, here is my problem.
>I would like to achieve the following
>-take file in msf format (BTW, why there is no conversion from Clustal .aln to 
>.msf format?. I know I can ask Clustal to give me .msf output but not all gcg 
>programs will recognize it)

Great idea. I'll try to slip in a conversion program (probably to be called
CLUSTALTOGCG or ALNTOMSF) in a future release of EGCG.

>- color the aminoacids (including BACKGROUD - is it possible in the current 

Sorry, the GCG graphics drivers are completely unable to do that. PRETTYBOX
can do it, but it has to write Postscript directly so it is no help to you
with HPL

>If my default output is set to postscript, even if I use 
>-plot=filename option in the prettyplot, I still get ps_file NOT a HPGL file.

That is because EGCG uses exactly the same graphics controls as GCG. If you
want HPGL, you must set your graphics to be HPGL with SETPLOT or the
equivalent commands.

>Second problem arises when I get my .hpgl file (because of fiddling with the 
>setplot) and get onto my pc. PowerPoint converts it very nicely BUT it puts a 
>multiple pages onto one. In other words, if my .msf is 1000bases long then  
>I get 10 pages overlapped onto one (TOTTALY UNREADABLE). My VERY UNEDUCATED  
>GUESS is that the end-of-page command (or something like that) is missing
>from that .hpgl output of prettyplot.

Sounds like a GCG problem. Does it happen with original GCG programs
(MAPPLOT for example) on multi-page plots?

Meanwhile, you could use -BEGIN and -END to create each page one at a time

Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/   | England

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