craigw@aecom.YU.EDU (Craig Werner) (06/29/88)
[Note: this part of the introduction is a general one for people who
don't know PostScript. For those reading this article in
comp.lang.postscript rather than sci.bio, I apologize.]
.nf
A Plasmid Description Language for PostScript Printers
Version 0, Edition 13
Craig Werner
This is a highly preliminary version of a program that allows one to
specify publication quality maps in a text based format. When combined
with the appropriate prologue and epilogue and printed out on a printer
that supports the page description language PostScript (such as the
Apple LaserWriter and the PSjet+), the graphic map is printed rather
than the text description.
General notes:
Since this is based on the PostScript Language, and has not advanced
sufficiently to shed many of the conventions of PostScript, I should explain
some of those conventions.
1. PostScript uses a Post-Fix notation (presumably why it was named
PostScript). If you use an HP calculator, you should feel right at home.
Otherwise, it may seem odd.
For instance, adding two numbers together is not 1 + 2, or 1 add 2,
but rather 1 2 add.
2. PostScript uses a stack. Hence the order of arguments is important.
(EcoRI) 450 REsite will print out a restriction site labeled EcoRI.
450 (EcoRI) REsite will do something bizarre and inexplicable.
3. PostScript uses a % to mark a comment. Anything on a line after
a % character is not interpreted.
4. The four arithmetic operators are: add, sub, mul, and div, in case
you need them.
5. Variables. When defined they need to be preceded by a slash (/),
although they are used simply by name after that. And all definitions
end with the word def.
For example, if you want all Restriction sites in an insert
in terms of itself, you can define a variable as the cloning site number
and then add, i.e.,
/Site 450 def
(BglII) Site 100 add REsite % "Site 100 add" treated as 1 number.
(SspI) Site 350 add REsite
This is also a way of adjusting all vector sites after an insert, rather
than recalculating. The command /insert 2500 def followed
by lines of the form (XmnI) 2294 insert add REsite
instead of (XmnI) 4694 REsite
1750 insert add 2450 insert add arcSEGMENT %ampR
instead of 3250 4950 arcSEGMENT %ampR
means that you don't have to edit the whole vector for different inserts,
jusr redefine the variable "insert."
6. Text
I haven't had a chance to simplify this yet. You have to specify a
font and a pointsize in an elaborate line. Just memorize the following
two lines and insert them by rote:
8 POINTSIZE
/Times-Roman SETFONT
If you change the pointsize , you need to type in the entire second line
as well. There are other fonts, but stick to Times-Roman for now.
7. Measurement.
PostScript measures all distances in points, which is a typesetting
unit. I have defined two conversion units: cm and inch. Thus you need
not know that the center of a typical page is 306 points over and 396 points
up. The center of an 8.5 by 11 page can be 4.25 inch and 5.5 inch.
The measurement, by the way, is from the lower left corner. The page
is the 1st quadrant of a graph (X and Y axis positive).
Another conversion routine allows most distances to be defined in
base pairs, although this varies depending on plasmid size.
Now that I dealt with preliminaries, the rest of the description is of
the PostScript procedures that form the plasmid description language.
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Craig Werner (Lognames: werner, craigw)
"This is no social crisis, just another tricky day for you."