craigw@aecom.YU.EDU (Craig Werner) (06/29/88)
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Measurement:
inch - converts from inches to points (usually used in combination)
Example: 4.25 inch 5.5 inch CENTER
cm - converts from centimeters to points
degree - optional (for readability)
point - optional (for readability)
General Definition:
DEFINE - synonym of PostScript's "def"
Usage: /Variable-name value DEFINE
Example: /Site 2545 DEFINE
percentBLACK -sets grayscale for filled segments
Usage: value [0-100] percentBLACK
Example: 20 percentBLACK
ZEROPOINT - determines which base position is at "12:00"
Usage: site [bp] ZEROPOINT
Example: 396 ZEROPOINT
PLASMIDLENGTH - total length of plasmid (for scaling maps to 360 degrees)
Usage: length [bp] PLASMIDLENGTH
Example: 2868 PLASMIDLENGTH
PHAGELENGTH - synonym of PLASMIDLENGTH
WIDTH -specifies the half width of a segment (dr)
ticLENGTH -specifes distance from center of segment to end of tic (dR)
textDISTANCE -specifies distance from center of segment to label text (dT)
textLENGTH - synonym of textDISTANCE
spanDISTANCE -distance of span line from main map (dS)
POINTSIZE -Specifies the Point Size for text (PS) but DOES NOT reset font.
SETFONT -Specifies the font, and resets typeface.
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Circular Map Defintion:
RADIUS -specifies the radius of the map (R)
CENTER -specifies center of the map (X,Y)
Usage: X-position Y-position CENTER
Example: 4.25 inch 5.5 inch CENTER
XCENTER -specifies X coordinate of map center (X)
YCENTER -specifies Y coordinate of map center (Y)
extLENGTH -length of an extension for extRESITE (dE)
extARC -absolute angle (degrees, not bp) of the extension (aE)
EXTENSION -sets both extLENGTH and extARC
Circular Map Drawing Routines:
arcSEGMENT -draws a circular map segment
Usage: site-1 [bp] site-2 [bp] arcSEGMENT
Example: 2120 3050 arcSEGMENT
Notes: modified by WIDTH, percentBLACK, ZEROPOINT, among others
will go across 0, i.e. 3050 120 arcSEGMENT will work
arcTIC -draws a tic at a site
Usage: site [bp] arcTIC
Example: 0 arcTIC
arcTICi -same as arcTIC, only inside the arc
arcLABEL -puts a label centered on a site
Usage (Text) site arcLABEL
Example: (ORI) 800 arcLABEL
arcRESITE -draws a tic and labels it at specified site
Example: (EcoRI) 396 arcRESITE
arcARROWc -draws a clockwise arrow from specified site with given length
Usage: site [bp] length [bp] arcARROWc
Example: 1500 100 arcARROWc
Note: For promoter symbol, combine it with arcTIC
arcARROWci -clockwise arrow, inside the circle
arcARROWcc -counterclockwise arrow
arcARROWcci -counterclockwise arrow inside the circle
WEDGE
extension
exttic
extREsite
Don't ask:
CenterPText -Centers Text on a point
Usage: (text) xpoint ypoint CenterPText
Example (pUC18) X Y CenterPText % X,Y are map center.
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Linear Maps
Definition:
percentBLACK
YPOSITION - sets vertical position on which linear map is centered
LEFTMARGIN - sets left margin
Note: LEFTMARGIN actually sets the horizontal position
of the ZeroPoint (ZEROPOINT). Hence setting the left
margin to the middle of the page will allow one to
center diagrams on a particular restriction site.
This is particularly nice for maps of nested deletions.
To make it work correctly however. The PLASMIDLENGTH
should not be changed for the deletions, as this will
cause scaling of the base pairs.
RIGHTMARGIN - set right margin
Note: Actually is position of the base defined as
PLASMIDLENGTH. Similar tricks can be played.
WIDTH -- thickness of segment
ticLENGTH -- distance from center of segment of end of tic
textLENGTH -- distance from center of segment to text
spanLENGTH -- distance from center of segment to span line
ZEROPOINT -- the base which is aligned with the left margin
PLASMIDLENGTH -- in base pairs
PHAGELENGTH -- PLASMIDLENGTH and PHAGELENGTH are interchangable
POINTSIZE -- a POINTSIZE and SETFONT are usually used together
SETFONT >> in fact POINTSIZE only changes with SETFONT
Linear Map Routines:
linSEGMENT -- draws a DNA segment
Usage: position1 position2 linSEGMENT
Example: 0 1134 linSEGMENT
linTIC -- a vertical line above segment to mark a position
linTICd -- same, only below (down) the segment
linLABEL -- places text above a position
linLABELd -- same, only below
Example: (Promoter) 100 linLABELd
linCLABEL -- a label above segment centered between two sites
linCLABELd -- a label below segment
linRESITEh -- for restriction enzyme sites, places a tic and label
linRESITEhd -- " horizontal below
linRESITEv -- " vertical above
linRESITEvd -- " vertical below
Example: (HindIII) 450 linRESITEh
linARROWr -- draws a rightward arrow (a tic length above segment)
linARROWl -- leftward arrow
linARROWrd -- rightward arrow below segment
linARROWld -- leftward arrow below segment
Usage: start length linARROW*
Note: the standard promoter notation can be drawn by combining
a TIC with the appropriate ARROW.
Example: 1500 300 linARROW
1500 linTIC
(Direction of Transcription) linLABELd
linSPAN -- draws a spanning line spanLENGTH above a segment
linSPANd -- draws a spanning line below segment
Usage: start finish linSPAN*
Note: modified by spanDISTANCE, which can be positive
or negative, which makes linSPANd slighly superfluous.
linNSPAN -- a spanning line with its length [bp] above it.
linNSPANd -- a spanning line with its length below it.
Note 1: The length is computed by the program, usage is
same as linSPAN
Note 2: The d (for down) refers to the position of the
label with regards to the span line, not the span line
in relation to the mapped SEGMENT.
linLSPAN -- a spanning line with a label above it
linLSPANd -- a spanning line with a label below it
Usage: (text) start finish linLSPAN*
These can be combined, as in:
Example: 235 1000 linNSPAN
(deleted in pCW16) 235 1000 linLSPANd
% the net effect is the length above the span line
and the comment below - note the 'd'.
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Craig Werner (Lognames: werner, craigw)
"This is no social crisis, just another tricky day for you."