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Line length limit for Pretty?

T. Mark Reboul MARK at CUCCFA.CCC.COLUMBIA.EDU
Thu Jan 13 08:21:05 EST 1994


Keith Robison writes:

> I've been trying to use Pretty to format some alignments, and seem
> to have run into a limit of 110 residues per line.  Has anyone else
> experienced this?  This limit does not appear to be documented.

If you look in the GCG source file GenSource:Pretty.For, in the code 
for the Subroutine PrettyOut, you will see a statement restricting 
the variable LineSize's value (changeable from the default 50 via 
command-line option) to the range [1,110]:

	  LineSize  = CLRetInt('LINesize', 1, 110, LineSize) 

I'll guess that the program authors assumed most users would never 
choose to generate an output file containing lines longer than 132 
characters, and they chose the 110 limit to allow sufficient space 
at the beginning of lines to accommodate reasonably long sequence 
identifiers. Yes, that limit does not seem to be documented outside 
the code itself.

In that same section of code, it looks to me as if the character 
array used for assembling lines of Pretty'd sequence output is 
declared large enough to hold about 256 characters. In principle, 
you could change the Pretty source code, raising the LineSize upper 
limit to a value somewhat higher than 110, recompile, relink, and 
rerun. However, without studying the full Pretty code carefully for 
delicate dependencies, it probably makes sense to ask the GCG folks 
about it first.

	Mark Reboul
	Columbia-Presbyterian Cancer Center Computing Facility
	mark at cuccfa.ccc.columbia.edu



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