%! for use by dvi2ps Version 2.00 % $Header: tex.ps,v 2.0 88/06/07 15:12:32 peterd Rel2 $ % a start (Ha!) at a TeX mode for PostScript. % The following defines procedures assumed and used by program "dvi2ps" % and must be downloaded or sent as a header file for all TeX jobs. % By: Neal Holtz, Carleton University, Ottawa, Canada % % % June, 1985 % Last Modified: Aug 25/85 % oystr 12-Feb-1986 % Changed @dc macro to check for a badly formed bits in character % definitions. Can get a <> bit map if a character is not actually % in the font file. This is absolutely guaranteed to drive the % printer nuts - it will appear that you can no longer define a % new font, although the built-ins will still be there. % mackay 4-Jan-1988 % Changed size of character array to reflect gf usage (256 characters) % To convert this file into a downloaded file instead of a header % file, uncomment all of the lines beginning with %-% %-%0000000 % Server loop exit password %-%serverdict begin exitserver %-% systemdict /statusdict known %-% {statusdict begin 9 0 3 setsccinteractive /waittimeout 300 def end} %-% if /TeXDict 200 dict def % define a working dictionary TeXDict begin % start using it. % units are in "dots" (300/inch) /Resolution 300 def /Inch {Resolution mul} def % converts inches to internal units /Mtrx 6 array def %%%%%%%%%%%%%%%%%%%%% Page setup (user) options %%%%%%%%%%%%%%%%%%%%%%%% % dvi2ps will output coordinates in the TeX system ([0,0] 1" down and in % from top left, with y +ive downward). The default PostScript system % is [0,0] at bottom left, y +ive up. The Many Matrix Machinations in % the following code are an attempt to reconcile that. The intent is to % specify the scaling as 1 and have only translations in the matrix to % properly position the text. Caution: the default device matrices are % *not* the same in all PostScript devices; that should not matter in most % of the code below (except for lanscape mode -- in that, rotations of % -90 degrees resulted in the the rotation matrix [ e 1 ] % [ 1 e ] % where the "e"s were almost exactly but not quite unlike zeros. /@letter { letter initmatrix 72 Resolution div dup neg scale % set scaling to 1. 310 -3005 translate % move origin to top (these are not exactly 1" Mtrx currentmatrix pop % and -10" because margins aren't set exactly right) } def % note mode is like letter, except it uses less VM /@note { note initmatrix 72 Resolution div dup neg scale % set scaling to 1. 310 -3005 translate % move origin to top Mtrx currentmatrix pop } def /@landscape { letter initmatrix 72 Resolution div dup neg scale % set scaling to 1. % -90 rotate % it would be nice to be able to do this Mtrx currentmatrix 0 0.0 put % but instead we have to do things like this because what Mtrx 1 -1.0 put % should be zero terms aren't (and text comes out wobbly) Mtrx 2 1.0 put % Fie! This likely will not work on QMS printers Mtrx 3 0.0 put % (nor on others where the device matrix is not like Mtrx setmatrix % like it is on the LaserWriter). 300 310 translate % move origin to top Mtrx currentmatrix pop } def /@legal { legal initmatrix 72 Resolution div dup neg scale % set scaling to 1. 295 -3880 translate % move origin to top Mtrx currentmatrix pop } def /@manualfeed { statusdict /manualfeed true put statusdict /manualfeedtimeout 300 put % 5 minutes } def % n @copies - set number of copies /@copies { /#copies exch def } def %%%%%%%%%%%%%%%%%%%% Procedure Defintions %%%%%%%%%%%%%%%%%%%%%%%%%% /@newfont % id @newfont - -- initialize a new font dictionary { /newname exch def pop newname 7 dict def % allocate new font dictionary newname load begin /FontType 3 def /FontMatrix [1 0 0 -1 0 0] def /FontBBox [0 0 1 1] def % mackay 4-Jan-1987 changed size of array from 128 to 256 for gf fonts /BitMaps 256 array def /BuildChar {CharBuilder} def /Encoding 256 array def 0 1 255 {Encoding exch /.undef put} for end newname newname load definefont pop } def % the following is the only character builder we need. it looks up the % char data in the BitMaps array, and paints the character if possible. % char data -- a bitmap descriptor -- is an array of length 6, of % which the various slots are: /ch-image {ch-data 0 get} def % the hex string image /ch-width {ch-data 1 get} def % the number of pixels across /ch-height {ch-data 2 get} def % the number of pixels tall /ch-xoff {ch-data 3 get} def % number of pixels below origin /ch-yoff {ch-data 4 get} def % number of pixels to left of origin /ch-tfmw {ch-data 5 get} def % spacing to next character /CharBuilder % fontdict ch Charbuilder - -- image one character { /ch-code exch def % save the char code /font-dict exch def % and the font dict. /ch-data font-dict /BitMaps get ch-code get def % get the bitmap descriptor for char ch-data null eq not { ch-tfmw 0 ch-xoff neg ch-yoff neg ch-width ch-xoff sub ch-height ch-yoff sub setcachedevice ch-width ch-height true [1 0 0 1 ch-xoff ch-yoff] {ch-image} imagemask } if } def /@sf % fontdict @sf - -- make that the current font { setfont() pop } def % in the following, the font-cacheing mechanism requires that % a name unique in the particular font be generated /@dc % char-data ch @dc - -- define a new character bitmap in current font { /ch-code exch def % ++oystr 12-Feb-86++ dup 0 get length 2 lt { pop [ <00> 1 1 0 0 8.00 ] } % replace <> with null if % --oystr 12-Feb-86-- /ch-data exch def currentfont /BitMaps get ch-code ch-data put currentfont /Encoding get ch-code dup ( ) cvs cvn % generate a unique name simply from the character code put } def /@bop0 % n @bop0 - -- begin the char def section of a new page { } def /@bop1 % n @bop1 - -- begin a brand new page { pop erasepage initgraphics Mtrx setmatrix /SaveImage save def() pop } def %-- tjh sept. 87: if this page has a mac drawing on it, we have to %-- use showpage in the md dictionary. /@eop % - @eop - -- end a page { userdict /md known { userdict /md get type /dicttype eq { md /MacDrwgs known { md begin showpage end }{ showpage } ifelse }{ showpage } ifelse }{ showpage } ifelse SaveImage restore() pop } def /@start % - @start - -- start everything { @letter % (there is not much to do) } def /@end % - @end - -- done the whole shebang { end } def /p % x y p - -- move to position { moveto } def /r % x r - -- move right { 0 rmoveto } def /s % string s - -- show the string { show } def /c % ch c - -- show the character (code given) { c-string exch 0 exch put c-string show } def /c-string ( ) def /ru % dx dy ru - -- set a rule (rectangle) { /dy exch neg def % because dy is height up from bottom /dx exch def /x currentpoint /y exch def def % remember current point newpath x y moveto dx 0 rlineto 0 dy rlineto dx neg 0 rlineto closepath fill x y moveto } def %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% the \special command junk %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % The structure of the PostScript produced by dvi2ps for \special is: % @beginspecial % - any number of @hsize, @hoffset, @hscale, etc., commands % @setspecial % - the users file of PostScript commands % @endspecial % The @beginspecial command recognizes whether the Macintosh Laserprep % has been loaded or not, and redfines some Mac commands if so. % The @setspecial handles the users shifting, scaling, clipping commands %-- tjh sept. 87: made changes to allow postscript and macdrawing to %-- to be inserted with version 65 of the md dictionary. Many bugs %-- were fixed: %-- vo changed to vof, name conflict with md %-- vs changed to vsz, name conflict with md %-- substantially changed @setspecial and @MacSetUp %-- Also, made changes to allow users to specify offsets %-- and clip rectangles in inches. % The following are user settable options from the \special command. /@SpecialDefaults { /hs 8.5 72 mul def /vsz 11 72 mul def /ho 0 def /vof 0 def /hsc 1 def /vsc 1 def /CLIP false def } def % d @hsize - specify a horizontal clipping dimension % these 2 are executed before the MacDraw initializations /@hsize {72 mul /hs exch def /CLIP true def} def /@vsize {72 mul /vsz exch def /CLIP true def} def % d @hoffset - specify a shift for the drwgs /@hoffset {72 mul /ho exch def} def /@voffset {72 mul /vof exch def} def % s @hscale - set scale factor /@hscale {/hsc exch def} def /@vscale {/vsc exch def} def /@setclipper { hsc vsc scale CLIP { newpath 0 0 moveto hs 0 rlineto 0 vsz rlineto hs neg 0 rlineto closepath clip } if } def % this will be invoked as the result of a \special command (for the % inclusion of PostScript graphics). The basic idea is to change all % scaling and graphics back to defaults, but to shift the origin % to the current position on the page. Due to TeXnical difficulties, % we only set the y-origin. The x-origin is set at the left edge of % the page. /@beginspecial { gsave /SpecialSave save def % the following magic incantation establishes the current point as % the users origin, and reverts back to default scalings, rotations currentpoint transform initgraphics itransform translate @SpecialDefaults % setup default offsets, scales, sizes @MacSetUp % fix up Mac stuff } def %-- tjh: assume this is raw postscript, but save some state in case its not. /@setspecial { /specmtrx matrix currentmatrix def ho vof translate @setclipper } def /@endspecial { SpecialSave restore grestore } def % - @MacSetUp - turn-off/fix-up all the MacDraw stuff that might hurt us % we depend on 'psu' being the first procedure executed % by a Mac document. We redefine 'psu' to adjust page % translations, and to do all other the fixups required. % This stuff will not harm other included PS files /@MacSetUp { userdict /md known % if md is defined { userdict /md get type /dicttype eq % and if it is a dictionary { md begin % then redefine some stuff /psu % redfine psu to set origins, etc. /psu load % this procedure contains almost all the fixup code { % /letter {} def % it is bad manners to execute the real % /note {} def % versions of these (clears page image, etc.) % /legal {} def /MacDrwgs true def specmtrx setmatrix % restore pre-@setspecial state. initclip % ditto % change smalls to prevent page clearing. /smalls [ lnop lnop lnop lnop lnop lnop lnop lnop lnop ] def 0 0 0 0 ppr astore pop % prevents origin translation. % redifine cp, do the showpage later, see @eop /cp { pop pop pm restore } def % no printing of pages } concatprocs def /od % redefine od to translate and scale. % redfine load to set clipping region. /od load { ho vof translate hsc vsc scale CLIP { /nc /nc load { newpath 0 0 moveto hs 0 rlineto 0 vsz rlineto hs neg 0 rlineto closepath clip } concatprocs def } if } concatprocs def end } if } if } def % p1 p2 concatprocs p - concatenate procedures /concatprocs { /p2 exch cvlit def /p1 exch cvlit def /p p1 length p2 length add array def p 0 p1 putinterval p p1 length p2 putinterval p cvx } def end % revert to previous dictionary TeXDict begin @start %%Title: ted.dvi %%Creator: dvi2ps %%EndProlog 5 @bop0 [ 300 ] /cmr12.300 @newfont cmr12.300 @sf [ 24 33 -2 0 24.387] 50 @dc [<70F8F8F870> 8 5 -4 0 13.548] 46 @dc [ 32 34 -2 0 37.249] 68 @dc [<00FC000703000E00801C0040380020780020700000F00000F00000F00000F00000F00000FFFFE0F000E07000E07801E03801 C01C01C00C038007070001FC00> 24 21 -1 0 21.677] 101 @dc [<0FC1E03C2390781708F00F08F00708F00708F007087007007807003C07001E070007C70000FF000007000007000007001807 003C0E003C0C001838000FE000> 24 21 -2 0 24.387] 97 @dc [ 24 21 -1 0 18.968] 114 @dc 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(the) s 17 r (ted) s 17 r (graphical) s 17 r (in) s -1 r (terface.) s 23 r (The) s 17 r (dis-) s 164 548 p (pla) s 0 r 121 c 22 r (consists) s 24 r (of) s 23 r (the) s 24 r (con) s -1 r (trol) s 23 r (panel) s 23 r (and) s 24 r (the) s 23 r (sync) s 0 r (hronized) s 22 r (view) s 24 r (of) s 23 r (the) s 24 r (base) s 164 608 p 112 c 1 r (osition) s 19 r (information,) s 19 r (original) s 18 r (and) s 19 r (edited) s 18 r (sequence) s 19 r (data,) s 19 r (and) s 18 r (graphical) s 19 r (rep-) s 164 668 p (resen) s 0 r (tation) s 15 r (of) s 16 r (the) s 16 r (trace) s 16 r (\(with) s 16 r (eac) s 0 r 104 c 15 r 110 c -1 r (ucleotide's) s 15 r (trace) s 16 r 98 c 2 r (eing) s 16 r (represen) s -1 r (ted) s 15 r 98 c 0 r 121 c 15 r 97 c 164 729 p (di\013eren) s 0 r 116 c 16 r (color\).) s 24 r (The) s 17 r (con) s 0 r (trol) s 16 r (panel) s 17 r (allo) s 0 r (ws) s 16 r (the) s 18 r (user) s 17 r (to) s 17 r (read) s 17 r (in) s 17 r (new) s 17 r (trace) s 18 r (\014les) s 164 789 p (\(in) s 17 r (either) s 16 r 98 c 1 r (ottom) s 17 r (or) s 16 r (top) s 17 r (strand) s 17 r (orien) s -1 r (tation\)) s 16 r (as) s 16 r 119 c 0 r (ell) s 15 r (as) s 17 r (to) s 17 r (searc) s -1 r 104 c 16 r (for) s 16 r 97 c 17 r (string) s 164 849 p (of) s 15 r 110 c 0 r (ucleotides) s 15 r (or) s 15 r 97 c 15 r (certain) s 16 r (base) s 15 r 112 c 2 r (osition.) s 21 r (Scroll) s 16 r (bars) s 15 r (allo) s 0 r 119 c 14 r (the) s 16 r (user) s 15 r (to) s 15 r (adjust) s 164 909 p (the) s 15 r (magni\014cation) s 15 r (of) s 15 r (or) s 14 r (scroll) s 15 r (through) s 15 r (the) s 15 r (sequence) s 15 r (and) s 15 r (trace) s 15 r (data.) s 21 r (The) s 15 r (user) s 164 969 p (ma) s 0 r 121 c 15 r (also) s 16 r 99 c -1 r (ho) s 1 r (ose) s 16 r (to) s 16 r 99 c -1 r (hange) s 15 r (the) s 16 r 118 c 0 r (ertical) s 15 r (magni\014cation) s 16 r (of) s 16 r (the) s 16 r (trace) s 16 r (data.) s 22 r 70 c -3 r (ur-) s 164 1029 p (ther,) s 17 r (sequence) s 17 r (on) s 17 r (the) s 18 r (head) s 17 r (\(v) s -1 r (ector\)) s 16 r (or) s 17 r (tail) s 18 r (\(uncertain) s 17 r (data\)) s 17 r (of) s 17 r (the) s 17 r (sequence) s 164 1090 p (ma) s 0 r 121 c 19 r 98 c 1 r 101 c 21 r (\\cuto\013) s 3 r 34 c 20 r (using) s 21 r (the) s 20 r (adjust) s 20 r (left) s 21 r (and) s 20 r (righ) s 0 r 116 c 19 r (cuto\013) s 20 r (buttons.) s 34 r (Bases) s 20 r (can) s 164 1150 p 98 c 1 r 101 c 17 r (inserted,) s 16 r (deleted,) s 17 r (or) s 16 r (replaced) s 17 r (as) s 16 r (with) s 17 r (an) s 0 r 121 c 15 r (ordinary) s 17 r 119 c -1 r (ord-pro) s 1 r (cessor) s 16 r (in) s 17 r (the) s 164 1210 p (sequence) s 17 r (data) s 16 r (windo) s 0 r (w.) s 22 r (Finally) s -3 r 44 c 16 r (the) s 17 r (sequence) s 16 r (ma) s 0 r 121 c 16 r 98 c 1 r 101 c 17 r (written) s 16 r (to) s 17 r (an) s 17 r (ascii) s 17 r (\014le) s 164 1270 p (using) s 16 r (the) s 16 r (output) s 17 r (button) s 16 r (on) s 16 r (the) s 17 r (con) s -1 r (trol) s 15 r (panel.) s 961 2599 p 53 c @eop 4 @bop0 cmbx12.300 @sf [ 40 34 -2 0 42.317] 65 @dc [ 40 34 -2 0 38.281] 80 @dc [ 32 34 -2 0 33.669] 76 @dc [ 24 34 -1 0 20.870] 73 @dc [<0003FE0000001FFFC00000FF00F00001F800380003F0000C0007C00006000F800003001F800003003F000003803F00000180 7F000001807E000001807E00000000FE00000000FE00000000FE00000000FE00000000FE00000000FE00000000FE00000000 FE000000007E000001807E000001807F000001803F000003803F000003801F800007800F8000078007C0000F8003E0001F80 01F8003F8000FF01E380001FFF81800003FE0080> 40 34 -3 0 40.472] 67 @dc [<03FFFFF80003FFFFF8000003F800000003F800000003F800000003F800000003F800000003F800000003F800000003F80000 0003F800000003F800000003F800000003F800000003F800000003F800000003F800000003F800000003F800000003F80000 0003F800000003F80000C003F800C0C003F800C0C003F800C0C003F800C0E003F801C0E003F801C06003F801807003F80380 7803F807807E03F80F807FFFFFFF807FFFFFFF80> 40 34 -2 0 38.973] 84 @dc [<0007FC0000003FFF800000FC07E00003F001F80007E000FC000FC0007E001F80003F003F80003F803F00001F807F00001FC0 7F00001FC07E00000FC0FE00000FE0FE00000FE0FE00000FE0FE00000FE0FE00000FE0FE00000FE0FE00000FE0FE00000FE0 FE00000FE07E00000FC07E00000FC07F00001FC03F00001F803F00001F801F80003F001F80003F000FC0007E0007E000FC00 03F001F80000FC07E000003FFF80000007FC0000> 40 34 -3 0 42.086] 79 @dc [ 40 34 -2 0 43.816] 78 @dc [<80FF8000C7FFE000FF00F800FC003C00F0003C00E0001E00E0001E00C0001F00C0001F00C0001F0000003F0000003F000000 7F000003FF00003FFE0003FFFE000FFFFC001FFFF8003FFFF0007FFFC0007FFF0000FFE00000FF000000FC000000FC000C00 F8000C00F8000C0078001C0078001C007C003C003C007C001F03FC0007FF8C0001FC0400> 32 34 -3 0 31.133] 83 @dc [ 40 34 -2 0 42.951] 68 @dc [<0001FF0000000FFFE000003F80F800007E001C0000FC000E0001F800060003F800030003F000030007F000018007F0000180 07F000018007F000018007F000018007F000018007F000018007F000018007F000018007F000018007F000018007F0000180 07F000018007F000018007F000018007F000018007F000018007F000018007F000018007F000018007F000018007F0000180 07F000018007F0000180FFFF803FFCFFFF803FFC> 40 34 -2 0 43.067] 85 @dc cmr12.300 @sf [ 16 34 -2 0 17.595] 73 @dc [<0007E00000381C0000E0020001C0010003800080070000400E0000401E0000201C0000203C0000103C0000107C0000107800 001078000000F8000000F8000000F8000000F8000000F8000000F8000000F8000000F800000078000010780000107C000010 3C0000303C0000301C0000301E0000700E000070070000F0038000F001C0017000E00630003818300007E010> 32 36 -3 1 35.225] 67 @dc [ 24 35 -1 0 25.742] 107 @dc [<0003F00000001C0800000030060000006001000000E000800001C000800003C000400003C000400003800040000780002000 0780002000078000200007800020000780002000078000200007800020000780002000078000200007800020000780002000 0780002000078000200007800020000780002000078000200007800020000780002000078000200007800020000780002000 0780002000078000200007800070000FC000F800FFFC07FF00> 40 35 -2 1 36.563] 85 @dc [ 24 21 -1 0 25.742] 120 @dc [ 8 49 -5 12 13.548] 91 @dc [ 8 49 -1 12 13.548] 93 @dc cmbx12.300 @sf [<0000380000000038000000007C000000007C00000000FE00000000FE00000000FE00000001FF00000001FF00000003FD8000 0003F980000007F9C0000007F0C0000007F0C000000FF06000000FE06000001FE03000001FC03000003FC03800003F801800 003F801800007F800C00007F000C0000FF00060000FE00060001FE00070001FC00030001FC00030003F800018003F8000180 07F80000C007F00000C0FFFF800FFEFFFF800FFE> 40 34 -1 0 42.317] 86 @dc [ 40 34 -2 0 39.838] 66 @dc [<001FFFF000001FFFF0000000FE00000000FE00000000FE00000000FE00000000FE00000000FE00000000FE00000000FE0000 0000FE00000000FE00000000FE00000000FE00000001FE00000001FF00000003FF80000003FD80000007F8C000000FF0E000 000FF06000001FE07000003FC03000003FC01800007F801C0000FF000C0000FF00060001FE00070001FE00030003FC000180 07F80001C007F80000C0FFFF800FFEFFFF800FFE> 40 34 -1 0 42.317] 89 @dc cmr12.300 @sf [ 48 34 -2 0 44.692] 77 @dc [ 40 34 -2 0 37.918] 75 @dc [<000001E0000003F8000007F8000007FC000007FC00000F0E00000E0600000C0200000C02000FEC02007C3C0200E80E0003C8 1780078813C00F0801E00E0420E01E0380F03C0000783C0000787C00007C7C00007C7800003CF800003EF800003EF800003E F800003EF800003EF800003EF800003EF800003EF800003E7800003C7800003C7C00007C7C00007C3C0000783E0000F81E00 00F00E0000E00F0001E0078003C003C0078000E00E0000783C00000FE000> 32 45 -3 10 37.935] 81 @dc [ 40 34 -1 0 36.563] 88 @dc [<000FE00000783C0000E00E0003C00780078003C00F0001E00F0001E01E0000F03E0000F83C0000787C00007C7C00007C7800 003CF800003EF800003EF800003EF800003EF800003EF800003EF800003EF800003EF800003E7800003C7800003C7C00007C 7C00007C3C0000783C0000781E0000F00E0000E00F0001E0078003C003C0078000E00E0000783C00000FE000> 32 36 -3 1 37.935] 79 @dc cmbx12.300 @sf [ 40 34 -2 0 43.874] 75 @dc [<0000E0000E00000000E0000E00000000F0001E00000001F0001F00000001F0001F00000003F8003F80000003F8003F800000 03FC007F80000007FC007FC0000007FC007FC000000FF600FFE000000FE600FE6000000FE600FE6000001FE301FC3000001F C301FC3000001FC383FC3000003F8183F81800003F8183F81800007F80C7F81C00007F00C7F00C00007F00C7F00C0000FF00 6FE0060000FE006FE0060000FE007FE0060001FC003FC0030001FC003FC0030003FC003F80038003F8003F80018003F8007F 80018007F0007F0000C007F0007F0000C00FF000FF0000E0FFFF0FFFF01FFEFFFF0FFFF01FFE> 56 34 -1 0 57.883] 87 @dc [ 40 34 -2 0 36.782] 69 @dc [<0003FF00C0001FFFC3C0007F80E7C001FC003FC003F0001FC007E0001FC00FC0001FC01F80001FC03F00001FC03F00001FC0 7F00001FC07F00001FC07E000FFFFCFE000FFFFCFE00000000FE00000000FE00000000FE00000000FE00000000FE00000000 FE000000007E000000C07E000000C07F000000C03F000001C03F000001C01F800003C00FC00003C007C00007C003F0000FC0 01F8003FC0007F00F1C0001FFFC0C00003FE0040> 40 34 -3 0 44.047] 71 @dc [ 56 34 -2 0 53.156] 77 @dc cmr12.300 @sf [<70F8F8F870000000000000000000000070F8F8F870> 8 21 -4 0 13.548] 58 @dc [<07C000187000203800401C00F01E00F80E00F80F00F80F00700F00000F00000F00000F00000F00000F00000F00000F00000F 00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F00000F0000 1F0003FFF0> 24 35 -2 1 25.056] 74 @dc [<00020000800000030001800000070001C00000070001C00000070001C000000F8003E000000F8003E000000F8003E000001E 40079000001E40079000001E40079000003C200F0800003C200F0800003C200F0800007C101E04000078101E04000078101E 040000F8183E060000F0083C020000F0083C020000F0083C020001E00478010001E00478010001E00478010003C002F00080 03C002F0008003C002F00080078001E00040078001E00040078001E000400F0003C000200F0003C000200F0003C000701F80 07E000F8FFF03FFC03FE> 48 35 -1 1 50.111] 87 @dc [<01F000071C000C06001C07003803803803807803C07001C07001C07001C0F001E0F001E0F001E0F001E0F001E0F001E0F001 E0F001E0F001E0F001E0F001E0F001E0F001E0F001E07001C07001C07001C07001C03803803803801803000C0600071C0001 F000> 24 34 -2 1 24.387] 48 @dc [<01F000070C000C06001C03001803803801C03801C07001E07001E07001E0F001E0F001E0F001E0F001E0F001E0F001C0F801 C0F80380F40300F40600F30C00F0F8007000007000007800003800003800001801801C03C00E03C00601C003008001C10000 7E00> 24 34 -2 1 24.387] 54 @dc cmbx12.300 @sf [ 40 34 -2 0 41.798] 82 @dc cmr12.300 @sf [<01FFF0001F00000E00000E00000E00000E00000E00000E00000E00FFFFF8800E00400E00200E00200E00100E00100E00080E 00040E00040E00020E00020E00010E00008E00008E00004E00004E00002E00001E00001E00000E00000E00000600000200> 24 33 -1 0 24.387] 52 @dc 4 @bop1 cmbx12.300 @sf 164 307 p (APPLICA) s -4 r (TIONS) s 18 r (AND) s 19 r (CONCLUSIONS) s cmr12.300 @sf 164 400 p (In) s 18 r (the) s 18 r (C.) s 19 r (elegans) s 18 r (genome) s 18 r (sequencing) s 19 r (pro) s 2 r (ject,) s 19 r (data) s 18 r (from) s 18 r (the) s 19 r (ABI) s 18 r (or) s 18 r (A.L.F.) s 164 460 p (sequencing) s 20 r (mac) s 0 r (hines') s 19 r (computers) s 20 r (are) s 20 r (transferred) s 20 r (to) s 20 r (Sun) s 21 r 119 c -1 r (orkstations.) s 33 r (The) s 164 520 p (user) s 18 r (in) s 0 r 118 c -2 r (ok) s -1 r (es) s 17 r 97 c 18 r (Unix) s 18 r (shell) s 18 r (script) s 18 r (that) s 18 r (calls) s 18 r (ted) s 18 r (systematically) s 18 r (on) s 18 r (eac) s -1 r 104 c 17 r (of) s 18 r (the) s 164 580 p (new) s 16 r (set) s 16 r (of) s 17 r (trace) s 16 r (\014les) s 16 r (creating) s 16 r 97 c 16 r (set) s 17 r (of) s 16 r (sequence) s 16 r (\014les.) s 22 r (The) s 16 r (sequence) s 16 r (\014les) s 16 r (that) s 164 640 p (are) s 20 r (deemed) s 20 r (to) s 20 r 98 c 1 r 101 c 20 r (of) s 20 r (acceptable) s 20 r (qualit) s 0 r 121 c 19 r (are) s 20 r (then) s 20 r (en) s -1 r (tered) s 19 r (in) s 0 r (to) s 19 r (the) s 20 r (sequence) s 164 700 p (assem) s 0 r (bly) s 16 r (program) s 17 r (xdap) s 18 r ([2]) s 17 r (where) s 18 r (the) s 17 r (sequences) s 17 r (are) s 18 r (assem) s 0 r (bled) s 16 r (in) s 0 r (to) s 16 r (con) s 0 r (tigs.) s 164 761 p 80 c 0 r (ortions) s 14 r (of) s 15 r (the) s 16 r (ted) s 15 r (trace-editor) s 16 r (ha) s -1 r 118 c -1 r 101 c 14 r 98 c 2 r (een) s 15 r (incorp) s 2 r (orated) s 15 r (in) s 0 r (to) s 14 r (the) s 15 r (xdap) s 16 r (\\trace) s 164 821 p (manager,") s 19 r (whic) s 0 r 104 c 18 r (is) s 18 r (used) s 19 r (in) s 19 r (conjunction) s 18 r (with) s 19 r (the) s 19 r (con) s -1 r (tig) s 18 r (editor) s 19 r (to) s 19 r (view) s 18 r (sets) s 164 881 p (of) s 16 r (aligned) s 16 r (traces) s 17 r (at) s 16 r (sites) s 16 r (of) s 17 r (discrepancies) s 16 r (in) s 16 r (the) s 16 r (aligned) s 17 r (sequences.) s 237 941 p 84 c -3 r (ed) s 16 r (is) s 17 r (also) s 16 r (used) s 17 r (at) s 17 r (the) s 17 r (stage) s 16 r (of) s 17 r 99 c 0 r (ho) s 0 r (osing) s 17 r (oligo) s 17 r (primers) s 16 r (for) s 17 r (the) s 17 r (\\w) s -1 r (alking") s 164 1001 p (stage) s 21 r (of) s 20 r (the) s 21 r (sequencing) s 20 r (pro) s 3 r (ject.) s 35 r (It) s 20 r (can) s 21 r 98 c 1 r 101 c 21 r (in) s -1 r 118 c -1 r (ok) s -1 r (ed) s 19 r (directly) s 21 r (from) s 20 r (the) s 21 r (oligo) s 164 1062 p (selection) s 23 r (program,) s 24 r (osp) s 23 r ([3],) s 25 r (to) s 23 r (allo) s 0 r 119 c 21 r (examination) s 23 r (of) s 23 r (the) s 23 r (trace) s 23 r (data) s 23 r (in) s 23 r (the) s 164 1122 p (region) s 16 r (of) s 16 r (the) s 17 r (primers) s 16 r (so) s 16 r (that) s 17 r (in) s -1 r (tegrit) s -1 r 121 c 15 r (of) s 16 r (the) s 17 r (sequence) s 16 r (data) s 16 r (can) s 16 r 98 c 2 r 101 c 16 r 118 c 0 r (eri\014ed.) s 237 1182 p (Curren) s 0 r (tly) s -4 r 44 c 20 r (no) s 20 r (other) s 20 r (programs) s 20 r (are) s 20 r (kno) s -1 r (wn) s 19 r (to) s 20 r 98 c 2 r 101 c 20 r 97 c -1 r 118 c -2 r (ailable) s 19 r (whic) s -1 r 104 c 19 r (supp) s 2 r (ort) s 164 1242 p (editing) s 18 r (of) s 18 r (the) s 18 r (ABI) s 18 r (trace) s 18 r (data.) s 26 r 70 c -3 r (urther,) s 18 r (the) s 18 r (mo) s 1 r (dular) s 18 r (design) s 18 r (of) s 18 r (the) s 18 r (program) s 164 1302 p (should) s 18 r (allo) s 0 r 119 c 17 r (supp) s 2 r (ort) s 18 r (for) s 18 r (new) s 18 r 116 c 0 r (yp) s 0 r (es) s 19 r (of) s 18 r (sequencing) s 18 r (mac) s 0 r (hines,) s 18 r (with) s 18 r (new) s 18 r (data) s 164 1363 p (formats,) s 16 r (to) s 16 r 98 c 2 r 101 c 16 r (implemen) s 0 r (ted) s 15 r (in) s 16 r 97 c 17 r (straigh) s -1 r (tforw) s -1 r (ard) s 15 r (fashion.) s cmbx12.300 @sf 164 1492 p 65 c -5 r 86 c -6 r (AILABILITY) s cmr12.300 @sf 164 1585 p 84 c -3 r (ed) s 18 r (is) s 18 r (freely) s 19 r 97 c 0 r 118 c -3 r (ailable) s 18 r (from) s 19 r (the) s 18 r (authors) s 19 r (or) s 19 r (from) s 19 r (Ro) s 1 r (dger) s 19 r (Staden) s 18 r (and) s 19 r (Simon) s 164 1645 p (Dear) s 19 r (\(MR) s -1 r 67 c 18 r (Lab) s 1 r (oratory) s 19 r (of) s 19 r (Molecular) s 18 r (Biology) s -3 r 44 c 18 r (Hills) s 19 r (Road,) s 19 r (Cam) s 0 r (bridge,) s 18 r (UK,) s 164 1705 p (CB2) s 16 r (2QH\)) s 16 r (for) s 17 r (use) s 16 r (on) s 16 r (Sun) s 17 r 119 c -1 r (orkstations) s 15 r (running) s 17 r (X-windo) s -1 r (ws) s 16 r (\(or) s 16 r (Op) s 1 r (enLo) s 2 r (ok\).) s cmbx12.300 @sf 164 1835 p 65 c -1 r (CKNO) s -1 r (WLEDGMENTS) s cmr12.300 @sf 164 1927 p (The) s 19 r (authors) s 19 r 119 c 0 r (ould) s 18 r (lik) s 0 r 101 c 18 r (to) s 19 r (thank) s 19 r (all) s 20 r (mem) s -1 r 98 c 1 r (ers) s 19 r (of) s 19 r (the) s 19 r (C.) s 20 r (elegans) s 19 r (sequencing) s 164 1988 p (pro) s 3 r (ject) s 16 r (with) s 17 r (sp) s 2 r (ecial) s 16 r (thanks) s 17 r (to) s 17 r (the) s 16 r (follo) s 0 r (wing) s 16 r 112 c 1 r (eople:) s 23 r (John) s 17 r (Sulston,) s 16 r (Bob) s 17 r 87 c -3 r (a-) s 164 2048 p (terston,) s 16 r (Phil) s 15 r (Green,) s 16 r (Ric) s 0 r 107 c 15 r (Wilson,) s 15 r (Ric) s 0 r (hard) s 15 r (Durbin,) s 16 r (Simon) s 15 r (Dear,) s 16 r (and) s 16 r (Ro) s 1 r (dger) s 164 2108 p (Staden) s 13 r (for) s 12 r (their) s 13 r (helpful) s 13 r (suggestions) s 12 r (for) s 13 r (impro) s 0 r 118 c -2 r (emen) s -1 r (ts) s 12 r (in) s 12 r (the) s 13 r (ted) s 13 r (in) s 0 r (terface) s 11 r (and) s 164 2168 p (for) s 18 r (their) s 19 r (parts) s 18 r (in) s 18 r (the) s 19 r (dev) s -1 r (elopmen) s -1 r 116 c 17 r (of) s 19 r (ted.) s 28 r (This) s 18 r 119 c 0 r (ork) s 17 r 119 c 0 r (as) s 17 r (supp) s 1 r (orted) s 19 r 98 c -1 r 121 c 18 r (the) s 164 2228 p (Medical) s 16 r (Researc) s 0 r 104 c 15 r (Council) s 16 r (and) s 17 r (NIH) s 16 r (gran) s 0 r 116 c 15 r (R01-HG00136.) s cmbx12.300 @sf 164 2358 p (REFERENCES) s cmr12.300 @sf 164 2451 p (1.) s 22 r 87 c -3 r (aterston,) s 15 r (R.,) s 16 r (Sulston,) s 16 r (J.,) s 17 r (et) s 16 r (al.) s 22 r (\(1991\),) s 16 r (in) s 16 r (preparation.) s 961 2599 p 52 c @eop 3 @bop0 cmr12.300 @sf [<4040201010100808080878F8F8F870000000000000000000000070F8F8F870> 8 31 -4 10 13.548] 59 @dc [ 32 34 -2 0 33.185] 69 @dc [<7FF1FFCFFE07001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C00E0 07001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C00E007001C01E0 FFFFFFFFE007001C000007001C000007001C000007001C000007001C000007001C000007001C000007001C00C007003C01E0 03803E01E001801E00E000E00B0040007031C080000FC07F00> 40 35 0 0 40.645] 14 @dc 3 @bop1 cmr12.300 @sf 164 307 p (program) s 15 r (has) s 15 r 98 c 1 r (een) s 15 r (in) s 0 r 118 c -2 r (ok) s -1 r (ed.) s 20 r (Other) s 15 r (parameters) s 15 r (whic) s 0 r 104 c 14 r (the) s 15 r (user) s 15 r (ma) s -1 r 121 c 14 r (sp) s 2 r (ecify) s 15 r (on) s 164 367 p (the) s 15 r (command) s 15 r (line) s 15 r (include:) s 21 r (the) s 15 r (output) s 15 r (\014le) s 16 r (name;) s 15 r 97 c 15 r (base) s 15 r 112 c 2 r (osition) s 15 r (or) s 15 r (sequence) s 164 428 p (string) s 17 r (on) s 18 r (whic) s 0 r 104 c 16 r (the) s 17 r (trace) s 18 r (is) s 17 r (to) s 18 r 98 c 1 r 101 c 18 r (cen) s -1 r (tered;) s 17 r 97 c 18 r (default) s 17 r (trace) s 18 r (magni\014cation;) s 18 r 97 c 164 488 p (5') s 17 r 118 c -1 r (ector) s 16 r (sequence) s 16 r (for) s 17 r (automated) s 17 r (elimination) s 16 r (of) s 17 r (the) s 16 r (sequence) s 17 r (head) s 17 r (\(v) s -1 r (ector\);) s 164 548 p (top) s 16 r (or) s 17 r 98 c 1 r (ottom) s 17 r (strand) s 16 r (orien) s 0 r (tation;) s 15 r (or) s 17 r (an) s -1 r 121 c 16 r (of) s 16 r (the) s 16 r (usual) s 17 r (X-windo) s -1 r 119 c 16 r (parameters) s 164 608 p (\(e.g.) s 22 r (displa) s -1 r 121 c -4 r 44 c 15 r (geometry) s -3 r (...\).) s 237 668 p (The) s 21 r (graphics) s 21 r (displa) s -1 r 121 c 20 r (\(Figure) s 21 r (1\)) s 21 r (consists) s 21 r (of) s 21 r (the) s 21 r (con) s -1 r (trol) s 20 r (panel,) s 22 r (the) s 21 r (base) s 164 729 p 112 c 1 r (osition) s 12 r (information,) s 12 r (the) s 11 r (original) s 12 r (and) s 11 r (edited) s 12 r (sequence) s 11 r (data,) s 12 r (and) s 12 r (the) s 11 r (graphical) s 164 789 p (represen) s 0 r (tation) s 16 r (of) s 18 r (the) s 18 r (trace.) s 27 r (The) s 17 r (user) s 18 r (ma) s 0 r 121 c 17 r 98 c 1 r (egin) s 18 r 98 c 0 r 121 c 16 r (using) s 18 r (the) s 18 r (con) s 0 r (trol) s 17 r (panel) s 164 849 p (INPUT) s 11 r (button) s 12 r (to) s 11 r (input) s 12 r 97 c 11 r (new) s 11 r (trace) s 12 r (\014le) s 11 r (at) s 12 r (whic) s -1 r 104 c 11 r (time) s 11 r (the) s 11 r (user) s 12 r (selects) s 11 r (whether) s 164 909 p (to) s 21 r (view) s 21 r (the) s 21 r (sequence) s 21 r (and) s 21 r (trace) s 21 r (in) s 21 r (top) s 21 r (or) s 21 r 98 c 1 r (ottom) s 21 r (strand) s 21 r (orien) s -1 r (tation.) s 35 r (The) s 164 969 p (trace) s 18 r (\014le) s 18 r (is) s 18 r (displa) s 0 r 121 c -2 r (ed) s 17 r (and,) s 19 r (if) s 18 r 97 c 18 r (5') s 18 r 118 c 0 r (ector) s 17 r (sequence) s 18 r (has) s 18 r 98 c 1 r (een) s 18 r (sp) s 2 r (eci\014ed) s 18 r (on) s 18 r (the) s 164 1029 p (command) s 17 r (line,) s 18 r (the) s 17 r (program) s 18 r (attempts) s 17 r (to) s 17 r (select) s 18 r 97 c 17 r (cuto\013) s 17 r 112 c 2 r (oin) s -1 r 116 c 17 r (corresp) s 1 r (onding) s 164 1090 p (to) s 16 r (the) s 16 r 118 c -1 r (ector) s 15 r (sequence) s 16 r (at) s 16 r (the) s 15 r (\\head") s 16 r (of) s 16 r (the) s 16 r (trace) s 15 r (\014le.) s 22 r (The) s 16 r (bases) s 15 r 98 c 2 r (ey) s -1 r (ond) s 15 r (the) s 164 1150 p (\\cuto\013) s 3 r 34 c 17 r 112 c 1 r (oin) s 0 r 116 c 15 r (are) s 16 r (displa) s -1 r 121 c -1 r (ed) s 15 r (on) s 16 r 97 c 16 r (shaded) s 16 r (bac) s 0 r (kground.) s 21 r (The) s 16 r (user) s 16 r (ma) s -1 r 121 c 16 r (mo) s 1 r (dify) s 164 1210 p (the) s 18 r (cuto\013) s 18 r 112 c 1 r (osition) s 18 r 98 c 0 r 121 c 17 r (clic) s -1 r (king) s 17 r (on) s 18 r (the) s 18 r (\\Adj) s 18 r (left) s 18 r (cut") s 18 r (button) s 17 r (and) s 18 r (clic) s 0 r (king) s 17 r (on) s 164 1270 p (the) s 19 r 112 c 2 r (osition) s 19 r (of) s 20 r (the) s 19 r (desired) s 19 r (cuto\013.) s 31 r (Similarly) s -3 r 44 c 20 r (the) s 19 r (user) s 19 r (ma) s 0 r 121 c 18 r (adjust) s 20 r (the) s 19 r (righ) s 0 r 116 c 164 1330 p (cuto\013) s 17 r (of) s 16 r (the) s 17 r (sequence) s 17 r (\(c) s -1 r (hosen) s 16 r 98 c 0 r 121 c 15 r (starting) s 17 r (at) s 16 r (the) s 17 r (5') s 17 r (end) s 16 r (of) s 17 r (the) s 17 r (sequence) s 16 r (and) s 164 1391 p (lo) s 1 r (oking) s 20 r (for) s 19 r (the) s 19 r (\014rst) s 20 r 111 c 1 r (ccurrence) s 20 r (when) s 19 r 50 c 19 r (out) s 20 r (of) s 19 r 53 c 19 r (bases) s 20 r (are) s 19 r ('N'\)) s 19 r 98 c 0 r 121 c 18 r (scrolling) s 164 1451 p (along) s 22 r (the) s 21 r (sequence) s 22 r (to) s 22 r (that) s 21 r 112 c 2 r (oin) s -1 r (t,) s 22 r (clic) s 0 r (king) s 20 r (on) s 22 r (the) s 22 r (\\Adj) s 21 r (righ) s 0 r 116 c 21 r (cut") s 21 r (button,) s 164 1511 p (and) s 16 r (clic) s 0 r (king) s 15 r (on) s 17 r (the) s 16 r (appropriate) s 17 r (base.) s 22 r (Automation) s 16 r (of) s 17 r (the) s 16 r (\\cuto\013) s 4 r 34 c 16 r (pro) s 1 r (cess) s 17 r (is) s 164 1571 p (optional;) s 16 r (the) s 16 r (user) s 17 r (ma) s -1 r 121 c 16 r (compile) s 16 r (the) s 16 r (program) s 16 r (with) s 17 r (that) s 16 r (feature) s 16 r (turned) s 16 r (\\o\013.") s 237 1631 p (Clic) s 0 r (king) s 13 r (on) s 15 r (the) s 14 r (\\Edit) s 15 r (seq") s 15 r (button) s 14 r (allo) s 0 r (ws) s 13 r (the) s 15 r (user) s 15 r (to) s 14 r (en) s 0 r (ter) s 13 r (the) s 15 r (edit) s 14 r (mo) s 2 r (de.) s 164 1692 p (The) s 14 r (\\Searc) s 0 r (h") s 14 r (button) s 14 r (can) s 15 r 98 c 1 r 101 c 15 r (used) s 14 r (to) s 15 r (skip) s 14 r (from) s 15 r (\\problem") s 14 r (to) s 15 r (\\problem") s 14 r (\(i.e.,) s 164 1752 p (am) s 0 r (biguit) s -2 r 121 c 17 r (to) s 17 r (am) s -1 r (biguit) s -1 r (y\)) s 16 r (or) s 18 r (to) s 17 r (lo) s 1 r (ok) s 18 r (for) s 17 r (runs) s 17 r (of) s 17 r (iden) s 0 r (tical) s 16 r (bases) s 18 r (\(e.g.,) s 17 r (TTTT\)) s 164 1812 p (whic) s 0 r 104 c 15 r (are) s 16 r (often) s 16 r (mis-called) s 17 r 98 c -1 r 121 c 16 r (the) s 16 r (mac) s -1 r (hine) s 16 r (soft) s -1 r 119 c -1 r (are.) s 237 1872 p (Bases) s 20 r (can) s 20 r 98 c 1 r 101 c 20 r (inserted,) s 21 r (deleted,) s 21 r (or) s 20 r (replaced) s 20 r (as) s 20 r (with) s 20 r (an) s 0 r 121 c 19 r (ordinary) s 20 r 119 c -1 r (ord-) s 164 1932 p (pro) s 1 r (cessor.) s 26 r (In) s 18 r (di\016cult-to-read) s 17 r (areas,) s 18 r (the) s 18 r (trace) s 18 r (ma) s -1 r 121 c 17 r 98 c 1 r 101 c 18 r 118 c -1 r (ertically) s 17 r (or) s 18 r (horizon-) s 164 1992 p (tally) s 23 r (scaled) s 22 r 98 c 0 r 121 c 22 r (dragging) s 23 r (or) s 22 r (clic) s 0 r (king) s 22 r (on) s 23 r (the) s 22 r (magni\014cation) s 23 r (scroll) s 23 r (bar) s 23 r (or) s 22 r 98 c 0 r 121 c 164 2053 p (clic) s 0 r (king) s 17 r (on) s 18 r (the) s 18 r 118 c 0 r (ertical) s 17 r (scaling) s 18 r (buttons) s 18 r (\(\\Scale) s 18 r (do) s 0 r (wn",) s 17 r (\\Scale) s 18 r (up"\),) s 19 r (resp) s 1 r (ec-) s 164 2113 p (tiv) s 0 r (ely) s -4 r 46 c 19 r (Finally) s -3 r 44 c 12 r (the) s 12 r (edited) s 12 r (sequence) s 12 r (is) s 12 r (sa) s 0 r 118 c -2 r (ed) s 11 r (to) s 12 r (an) s 12 r (ascii) s 12 r (\014le) s 12 r (using) s 13 r (the) s 12 r (\\Output") s 164 2173 p (button.) s 21 r 65 c 16 r (history) s 16 r (of) s 16 r (the) s 15 r (editing) s 16 r (session) s 16 r (can) s 15 r (also) s 16 r 98 c 1 r 101 c 16 r (sa) s 0 r 118 c -2 r (ed) s 15 r (along) s 16 r (with) s 16 r (the) s 15 r (se-) s 164 2233 p (quence.) s 30 r (The) s 19 r (\\Quit") s 18 r (button) s 19 r (is) s 19 r (used) s 19 r (to) s 19 r (exit) s 19 r (the) s 19 r (program.) s 30 r (When) s 19 r (rein) s -1 r 118 c -1 r (oking) s 164 2293 p (ted) s 16 r (on) s 16 r (an) s 15 r (edited) s 16 r (trace) s 16 r (\014le) s 16 r (the) s 15 r (edited) s 16 r (base) s 16 r (sequence,) s 16 r (rather) s 16 r (than) s 15 r (the) s 16 r (original) s 164 2354 p (sequence,) s 18 r (is) s 17 r (sho) s 0 r (wn) s 16 r (in) s 18 r (the) s 17 r (edited) s 18 r (base) s 17 r (windo) s 0 r (w.) s 24 r (The) s 18 r (user) s 17 r (ma) s 0 r 121 c 17 r (in) s -1 r 118 c -1 r (ok) s -2 r 101 c 17 r (ted) s 17 r 98 c 0 r 121 c 164 2414 p (calling) s 16 r (in) s 16 r (an) s 0 r 121 c 15 r (one) s 17 r (of) s 16 r (the) s 16 r (previous) s 16 r (editing) s 17 r (sessions.) s 961 2599 p 51 c @eop 2 @bop0 cmbx12.300 @sf [ 40 34 -2 0 43.816] 72 @dc [ 300 ] /cmti12.300 @newfont cmti12.300 @sf [<00FE0000000381C0000006003000001C000800001800040000380002000070000100007000008000F000008000E000004000 E000004000E000002000E000002000E000000000F000000000F000000000F000000000F000000000F0000000007800000000 780000000078000000003C000008003C000004001E000004000E000004000F000004000700000E000380000E0001C0000E00 00E0000E000070001F000038002700000E006300000380810000007F0080> 40 36 -7 1 34.869] 67 @dc [<07C000187000301800700C00700E00700700F00780F00380F003C0F003C07801E07801E07801E03801E03C01E01C01E00E01 C00701C003818001C300007E00> 24 21 -5 0 24.906] 111 @dc [<3003001E00700700310038038030803803807080380380704038038038401C01C038201C01C01C001C01C01C001C01C01C00 0E00E00E000E00E00E000E00E00E000E00E00E00870070070087007007008780780700878078070047606606002610C10C00 1C0F80F800> 40 21 -5 0 39.850] 109 @dc [ 24 31 -1 10 24.906] 112 @dc [<07C3C00C26201C1E201C0E10180E101C0E101C07081C07001C07001C07000E03800E03800E03800703808701C08701C08381 C04381C04380E02300E01E0060> 24 21 -5 0 26.152] 117 @dc [<1E003100708070407020702038103800380038001C001C001C001C000E000E000E000E0007000700FFF80700038003800380 038001C001C001C001C000C0> 16 31 -4 0 16.189] 116 @dc [<1C00320071007080708070803840380038001C001C001C000E000E008700870087004300430023001C000000000000000000 000000000000000001C001C001E000C0> 16 33 -5 0 14.944] 105 @dc [<3003C0700620380610380E10380E083807081C07041C03801C03801C03800E01C00E01C00E01C00E01C08700E08700E08780 E08780E04740C02631C01C0F00> 24 21 -5 0 27.397] 110 @dc [<3F800060E000F03000F01800701C00000E00000E00000E0000070000070001E700061700060B800E07800E03801E03801E01 C01E01C01E01C01E01C00F00E00F00E00F00E00700E007807003807001C07001C07000E0B80030B8001F18> 24 31 -2 10 22.416] 103 @dc [ 40 34 -3 0 36.783] 68 @dc [<0F80306070186004E002E002E000E000E000E000F000F000FFE0F018780438023C021C020E02038400F8> 16 21 -6 0 22.416] 101 @dc [<1FC000203000400800E00400F00600F00600700700000700000F00003E0003FE0007FC000FF0000F00000C00000C03000C03 8004018002008001830000FC00> 24 21 -3 0 19.925] 115 @dc [<0F0780308C40305C40703C20701C20F01C20F00E10F00E00F00E00F00E007807007807007807003807003C03801C03800E03 800E03800705C00185C000F8C0> 24 21 -5 0 24.906] 97 @dc [<0F0780308C40305C40703C20701C20F01C20F00E10F00E00F00E00F00E007807007807007807003807003C03801C03800E03 800E03800705C00185C000F9C00001C00000E00000E00000E00000E000007000007000007000007000003800003800003800 03F800003C> 24 35 -5 0 24.906] 100 @dc [ 24 34 -3 0 18.772] 73 @dc [<38006400E200E200E200E200710070007000700038003800380038001C001C001C001C000E000E000E000E00070007000700 0700038003800380038001C001C001C01FC001E0> 16 35 -4 0 12.453] 108 @dc [ 8 5 -6 0 14.944] 46 @dc [<00FE0000000381C1000006002300001C0013800018000F800038000780007000078000700003C000F00003C000E00003C000 E00003C000E00001E000E00001E000E00001E000F0003FFC00F000000000F000000000F000000000F0000000007800000000 780000000078000000003C000008003C000004001E000004000E000004000F000004000700000E000380000E0001C0000E00 00E0000E000070001F000038002700000E006300000380810000007F0080> 40 36 -7 1 37.694] 71 @dc [<3000007000003800003800003800003800001C00001C00001C00001C00000E00000E00000E00000E00008700008701808703 C08783C04741C02620801C1F00> 24 21 -5 0 20.548] 114 @dc [<6003C0E00620700610700E10700E087007083807043803803803803803801C01C01C01C01C01C01C01C00E00E00E00E00F00 E00F00E007C0C0072180071F0007000003800003800003800003800001C00001C00001C00001C00000E00000E00000E0000F E00000F000> 24 35 -3 0 24.906] 104 @dc [<0FC000183000300C00700200700100F00100F00000F00000F00000F000007800007800007800003800003C00001C07800E07 8007038003018001C100007E00> 24 21 -5 0 22.416] 99 @dc [<3C00000062000000F3000000F18000007180000001C0000001C0000000C0000000E0000000E0000000E0000000E000000070 0000007000000070000000700000007000000038000000380000003800000038000000380000001C0000001C0000001C0000 001C0000001C0000000E0000000E0000000E000000FFF000000E000000070000000700000007000000070000000700000003 800000038000000380000001860000018F000000CF000000470000003E00> 32 45 2 10 14.944] 102 @dc cmr12.300 @sf [<7FF3FF8007003800070038000700380007003800070038000700380007003800070038000700380007003800070038000700 380007003800070038000700380007003800070038000700380007003800FFFFF80007003800070038000700380007003800 0700380007003800070038000700380007003800038078000180780000C0780000703800001FD800> 32 35 0 0 27.097] 13 @dc [<01800003C00003C00003C00003C00003C00003C00003C00003C00001C00001C00001C00001C00000C00000C00000E0000060 00006000006000002000003000001000000800000800000400800200800200800100C001004000807FFFC07FFFC07FFFE060 0000400000> 24 35 -3 1 24.387] 55 @dc 2 @bop1 cmr12.300 @sf 164 307 p (in) s 0 r 118 c -3 r (aluable.) s 35 r 84 c -3 r (ed) s 20 r (\(a) s 21 r 84 c -3 r (race-EDitor\)) s 21 r 119 c -1 r (as) s 20 r (dev) s 0 r (elop) s 0 r (ed) s 21 r (to) s 22 r (\014ll) s 21 r (this) s 21 r (role) s 21 r (in) s 21 r (the) s 21 r (C.) s 164 367 p (elegans) s 16 r (genome) s 16 r (sequencing) s 17 r (pro) s 2 r (ject) s 17 r ([1].) s cmbx12.300 @sf 164 497 p (METHODS) s cmti12.300 @sf 164 590 p (Computing) s 15 r (Design) s 14 r (and) s 15 r (Implementation.) s cmr12.300 @sf 21 r (When) s 13 r (designing) s 13 r (ted,) s 14 r 119 c 0 r 101 c 12 r (had) s 13 r 97 c 14 r 110 c -1 r (um-) s 164 650 p 98 c 1 r (er) s 11 r (of) s 11 r (sp) s 2 r (eci\014c) s 11 r (computing) s 11 r (goals) s 11 r (in) s 11 r (mind) s 11 r (including) s 11 r 112 c 1 r (ortabilit) s 0 r 121 c 10 r (and) s 11 r (adaptabilit) s 0 r 121 c -4 r 46 c 164 710 p 70 c -3 r (or) s 14 r 112 c 1 r (ortabilit) s 0 r 121 c -4 r 44 c 14 r 119 c -1 r 101 c 14 r 99 c 0 r (hose) s 14 r (to) s 15 r (write) s 15 r (ted) s 14 r (in) s 15 r (ANSI) s 15 r 67 c 15 r (using) s 15 r (the) s 15 r 88 c 14 r (windo) s 0 r (wing) s 14 r (sys-) s 164 770 p (tem) s 17 r (and) s 17 r (the) s 17 r (Xa) s -1 r 119 c 16 r (to) s 1 r (olkit.) s 24 r 88 c 17 r (pro) s -1 r (vides) s 16 r (basic) s 17 r (capabilities) s 17 r (for) s 17 r (the) s 17 r (creation) s 17 r (and) s 164 830 p (use) s 18 r (of) s 18 r (windo) s 0 r (ws,) s 17 r (and) s 18 r (the) s 18 r (to) s 1 r (olkit) s 18 r (con) s 0 r (tains) s 17 r 97 c 18 r 110 c 0 r (um) s -2 r 98 c 1 r (er) s 18 r (of) s 17 r (pre-pac) s 0 r 107 c -3 r (aged) s 17 r (comp) s 2 r (o-) s 164 891 p (nen) s 0 r (ts,) s 19 r (suc) s -1 r 104 c 18 r (as) s 20 r (the) s 19 r (\\sliders") s 19 r (used) s 19 r (for) s 19 r (scrolling.) s 31 r 88 c 19 r (also) s 19 r (allo) s 0 r (ws) s 18 r (site,) s 20 r (user) s 19 r (and) s 164 951 p 112 c 1 r (er-run) s 19 r (defaults) s 18 r (to) s 19 r 98 c 1 r 101 c 19 r (set.) s 28 r (Adaptabilit) s 0 r 121 c 17 r (is) s 19 r (also) s 18 r (an) s 18 r (imp) s 2 r (ortan) s -1 r 116 c 18 r (goal) s 18 r (since) s 19 r 119 c 0 r 101 c 164 1011 p (are) s 18 r (pro) s 0 r (viding) s 17 r 97 c 18 r (new) s 18 r (function) s 18 r (to) s 18 r (researc) s -1 r 104 c 17 r (groups) s 18 r (who) s 18 r (are) s 18 r (constan) s 0 r (tly) s 17 r (adding) s 164 1071 p (new) s 16 r (requiremen) s 0 r (ts.) s 237 1131 p (St) s 0 r (ylistically) s -4 r 44 c 21 r 119 c 0 r 101 c 20 r (ha) s 0 r 118 c -2 r 101 c 20 r (follo) s 0 r 119 c -1 r (ed) s 20 r (an) s 21 r (\\Abstract) s 21 r (Data) s 21 r 84 c 0 r (yp) s 0 r (e") s 22 r (discipline.) s 36 r (In) s 164 1192 p (this) s 20 r (discipline,) s 20 r 97 c 20 r (program) s 20 r (is) s 19 r (split) s 20 r (in) s 0 r (to) s 18 r 97 c 20 r 110 c 0 r (um) s -2 r 98 c 1 r (er) s 19 r (of) s 20 r (mo) s 1 r (dules) s 20 r (whic) s 0 r 104 c 18 r (pro) s 0 r (vide) s 164 1252 p (separate,) s 15 r 119 c 0 r (ell-de\014ned) s 14 r (functions.) s 22 r 87 c -3 r 101 c 14 r (separate) s 15 r (the) s 15 r (in) s 0 r (terface) s 14 r (of) s 16 r 97 c 15 r (mo) s 1 r (dule) s 15 r (from) s 164 1312 p (its) s 15 r (implemen) s 0 r (tation.) s 20 r 70 c -3 r (or) s 15 r (example,) s 15 r 97 c 16 r (uni\014ed) s 15 r (in) s 0 r (ternal) s 15 r (sequence) s 15 r (format) s 15 r (is) s 16 r 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164 2354 p (Time) s 23 r (in) s 0 r 118 c -1 r (olv) s -2 r (ed) s 22 r (in) s 24 r (sequence) s 23 r (editing) s 23 r (is) s 24 r (extensiv) s -1 r (e,) s 24 r (and) s 24 r (an) s -1 r (ything) s 22 r (easing) s 24 r (that) s 164 2414 p (burden) s 21 r (will) s 21 r (impro) s 0 r 118 c -1 r 101 c 20 r (the) s 21 r (e\016ciency) s 21 r (of) s 21 r (an) s 0 r 121 c 20 r (ma) s 3 r (jor) s 21 r (sequencing) s 21 r (pro) s 3 r (ject.) s 37 r (Ha) s -1 r (v-) s 164 2474 p (ing) s 19 r (sequence) s 19 r (and) s 19 r (trace) s 19 r (data) s 20 r 97 c -1 r 118 c -2 r (ailable) s 18 r (online) s 19 r (in) s 19 r (easily-) s 19 r (manipulable) s 19 r (form) s 19 r (is) s 961 2599 p 49 c @eop @end