6258 lines
398 KiB
PostScript
Executable file
6258 lines
398 KiB
PostScript
Executable file
%!
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%%Title: "Laser Prep -- The Apple PostScript Dictionary (md)"
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%%Creator: Apple Software Engineering
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%%CreationDate: Thursday, March 19, 1987
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%{appledict version #70 0
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% ) CopyRight Apple Computer, Inc. 1984-89 All Rights Reserved.
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%%EndComments
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%%BeginProcSet: "(AppleDict md)" 70 0
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statusdict begin product(LaserWriter II NT)eq revision 1 eq and
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{userdict begin/oldcds/cleardictstack load def/cleardictstack{31 sendpcmd 4 eq tonerlight/oldcds load exec}bind def
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end
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currentfile eexec
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}{save currentfile 359 string readhexstring pop pop restore}ifelse
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35de8eabfc7fa5eac0431edc501ad43f5fcbdf9fdd321cce93b525f4439dd94696bf56ac13a0a2aad1e6bcf444711e941d7217138d20ae0500145f815439cc14e697ad201df728ea4ccad4ac
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331aa03a7aacde10760bf4ee12bbf73c77cdcbf1796f26f0dd255d2407e1ac41
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d27489a69d6b69c6a841468b46720b75ad65650700e0c528e7af61e7e3e821b59445c44b69831ebc9deaf0e3aecc14b7a1c2e18bc1fa42a59219f1e36f236e3d6c89114b1f231999c3dbce6b43f3e2918fcb85575941a9d1e65c86aa08e6eea86cc66ce90e5e4add57f2585e
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7b1c0b5203cfc46868d6e3c0d66db79174e7091e32e307679732da062e440e41dabd36a161b611a7e4523a49694026206803dbfd5be5c5fe433f0f18a40057db6f1302848c8da4a10a7f14c6
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3d512806362b1be092ad5dbd36d75fe63e4cae2ba9b72390f580cac344a08bdf6eb9e36ec45bad2a0b82829a72e0efa2d87332c482196e690361168271c55053341ab3
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end
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/sc {60 45 {abs exch abs 2 copy add 1 gt{1.0 sub dup mul exch 1.0 sub dup mul add 1.0 sub}{dup mul exch dup mul add 1.0 exch sub}
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ifelse}setscreen} bind def statusdict begin product(LaserWriter II)anchorsearch end
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{pop pop/letter [/letter load /exec load /sc load /exec load]cvx def/legal [/legal load /exec load /sc load /exec load]cvx def/a4 [/a4 load /exec load /sc load /exec load]cvx def/b5 [/b5 load /exec load /sc load /exec load]cvx def
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/lettersmall [/lettersmall load /exec load /sc load /exec load]cvx def/a4small [/a4small load /exec load /sc load /exec load]cvx def/note [/note load /exec load /sc load /exec load]cvx def}{pop}ifelse
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systemdict/currentpacking known{currentpacking true setpacking}if
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/LW{save statusdict/product get(LaserWriter)anchorsearch
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exch pop{length 0 eq{1}{2}ifelse}{0}ifelse exch restore}bind def
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/LW+{LW 2 eq}bind def
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/ok{systemdict/statusdict known dup{LW 0 gt and}if}bind def
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ok{statusdict begin 9 sccinteractive 3 ne exch 0 ne or{9 0 3 setsccinteractive}if end}if
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/md 270 dict def md begin
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/av 0 def
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/T true def/F false def/mtx matrix def/s75 75 string def/sa8 8 string def/sb8 8 string def
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/sc8 8 string def/sd8 8 string def/s1 ( ) def/pxs 1 def/pys 1 def
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/ns false def
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1 0 mtx defaultmatrix dtransform exch atan/pa exch def/nlw .24 def/ppr [-32 -29.52 762 582.48] def
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/pgr [0 0 0 0] def
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/pgs 1 def/por true def/xb 500 array def/so true def/tso true def/fillflag false def/pnm 1 def/fmv true def
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/sfl false def/ma 0 def/invertflag false def/dbinvertflag false def/xflip false def/yflip false def/noflips true def/scaleby96 false def/fNote true def/fBitStretch true def
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/4colors false def/3colors false def/2colors false def
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/wtkey false def
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statusdict begin/waittimeout where{pop waittimeout 300 lt{md /wtkey true put}if}if end
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wtkey{statusdict begin/setdefaulttimeouts where{pop 0 60 300 setdefaulttimeouts}if end}if
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/fg (Rvd\001\001\000\000\177) def
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/bdf{bind def}bind def
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/xdf{exch def}bdf
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/xl{neg exch neg translate}bdf
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/fp{pnsh 0 ne pnsv 0 ne and}bdf
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/nop{}bdf/lnop[/nop load]cvx bdf
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/vrb[
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{fp{fg 6 get 0 ne{gsave stroke grestore}{gsave 1 setlinewidth pnsh pnsv scale stroke grestore}ifelse}if newpath}bind
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/eofill load
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dup
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/newpath load
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2 index
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dup
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{clip newpath}bind
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{}bind
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dup
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2 copy
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]def
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systemdict/currentcolorscreen known{currentcolorscreen/dkspf xdf/dkrot xdf/dkfreq xdf/dyspf xdf/dyrot xdf/dyfreq xdf/dmspf xdf/dmrot xdf/dmfreq xdf
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/dcspf xdf/dcrot xdf/dcfreq xdf}{currentscreen/spf xdf/rot xdf/freq xdf}ifelse
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/doop{vrb exch get exec}bdf
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/psu{/udf xdf/tso xdf /fNote xdf/fBitStretch xdf/scaleby96 xdf/yflip xdf/xflip xdf
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/invertflag xdf/dbinvertflag invertflag statusdict begin version cvr 47.0 ge product (LaserWriter) eq not and end invertflag and {not}if def
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xflip yflip or{/noflips false def}if
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/pgs xdf 2 index .72 mul exch div/pys xdf div .72 mul/pxs xdf ppr astore pop pgr astore pop/por xdf sn and/so xdf}bdf
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/tab{statusdict /11x17 known{statusdict begin /11x17 load end}{statusdict /setpage known{statusdict begin 792 1224 1 setpage end}{statusdict /setpageparams known{statusdict begin 792 1224 0 1 setpageparams end}if}ifelse}ifelse}bdf
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/a3Size{statusdict /a3 known{statusdict begin /a3 load end}{statusdict /setpageparams known{statusdict begin 842 1191 0 1 setpageparams end}if}ifelse}bdf
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/txpose{fNote{smalls}{bigs}ifelse pgs get exec pxs pys scale ppr aload pop por{noflips{pop exch neg exch translate pop 1 -1 scale}if
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xflip yflip and{pop exch neg exch translate 180 rotate 1 -1 scale ppr 3 get ppr 1 get neg sub neg ppr 2 get ppr 0 get neg sub neg translate}if
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xflip yflip not and{pop exch neg exch translate pop 180 rotate ppr 3 get ppr 1 get neg sub neg 0 translate}if yflip xflip not and{ppr 1 get neg ppr 0 get neg translate}if}
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{noflips{translate pop pop 270 rotate 1 -1 scale}if xflip yflip and{translate pop pop 90 rotate 1 -1 scale ppr 3 get ppr 1 get neg sub neg ppr 2 get ppr 0 get neg sub neg translate}if
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xflip yflip not and{translate pop pop 90 rotate ppr 3 get ppr 1 get neg sub neg 0 translate}if yflip xflip not and{translate pop pop 270 rotate ppr 2 get ppr 0 get neg sub neg 0 exch translate}if}ifelse
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wtkey{statusdict/waittimeout 300 put}if
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scaleby96{ppr aload pop 4 -1 roll add 2 div 3 1 roll add 2 div 2 copy translate .96 dup scale neg exch neg exch translate}if}bdf
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/fr{4 copy pgr aload pop 3 -1 roll add 3 1 roll exch add 6 2 roll 3 -1 roll
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sub 3 1 roll exch sub 3 -1 roll exch div 3 1 roll div exch scale pop pop xl}bdf
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/obl{{0.212557 mul}{pop 0}ifelse}bdf
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/sfd{ps fg 5 -1 roll get mul 100 div 0 ps 5 -1 roll obl ps neg 0 0 6a astore makefont setfont}bdf
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/fnt{findfont sfd}bdf
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/bt{sa 3 1 roll 3 index and put}bdf
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/sa(\000\000\000\000\000\000\000\000\000\000)def
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/fs{0 1 bt 1 2 bt 2 4 bt 3 8 bt 4 16 bt 5 32 bt 6 64 bt 7 128 bt sa exch 8 exch put}bdf
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/mx1 matrix def
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/mx2 matrix def
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/mx3 matrix def
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/bu{currentpoint 4colors{currentcmykcolor}{currentrgbcolor}ifelse currentlinewidth currentlinecap currentlinejoin
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currentdash exch aload length fg 5 sfl{1}{0}ifelse put pnsv pnsh
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2t aload pop 3a aload pop mx2 aload pop mx1 aload pop mtx currentmatrix aload pop
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mx3 aload pop ps pm restore/ps xdf mx3 astore pop}bdf
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/bn{/pm save def mx3 setmatrix newpath 0 0 moveto ct dup 39 get 0 exch getinterval cvx exec mtx astore setmatrix mx1 astore pop mx2 astore pop 3a
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astore pop 2t astore pop/pnsh xdf/pnsv xdf gw
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/sfl fg 5 get 0 ne def array astore exch setdash setlinejoin setlinecap
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setlinewidth 4colors{setcmykcolor}{setrgbcolor}ifelse moveto}bdf
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/fc{save vmstatus exch sub 50000 lt
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{(%%[|0|]%%)=print flush}if pop restore}bdf
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/tc{32768 div add 3 1 roll 32768 div add 2t astore pop}bdf
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/3a [0 0 0] def
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/2t 2 array def
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/tp{3a astore pop}bdf
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/tt{mx2 currentmatrix pop currentpoint 2 copy 2t aload pop qa 2 copy translate 3a aload pop exch dup 0 eq
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{pop}{1 eq{-1 1}{1 -1}ifelse scale}ifelse rotate pop neg exch neg exch translate moveto}bdf
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/te{mx2 setmatrix}bdf
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/th{3 -1 roll div 3 1 roll exch div 2 copy mx1 scale pop scale/sfl true def}bdf
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/tu{1 1 mx1 itransform scale/sfl false def}bdf
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/ts{1 1 mx1 transform scale/sfl true def}bdf
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/fz{/ps xdf}bdf
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/dv{dup 0 ne{div}{pop}ifelse}bdf
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/pop4{pop pop pop pop}bdf
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/it{sfl{mx1 itransform}if}bdf
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/gm{exch it moveto}bdf/rm{it rmoveto}bdf
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/lm{currentpoint sfl{mx1 transform}if exch pop sub 0 exch it rmoveto}bdf
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/fm{statusdict/manualfeed known}bdf
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/se{statusdict exch/manualfeed exch put}bdf
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/mf{dup/ma exch def 0 gt{fm se/t1 5 st ok ma 1 gt and{/t2 0 st/t3 0 st
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statusdict/manualfeedtimeout 3600 put
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}if}if}bdf
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/jn{/statusdict where exch pop{statusdict exch /jobname exch put}if}bdf
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/pen{pnm mul/pnsh xdf pnm mul/pnsv xdf pnsh setlinewidth}bdf
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/min{2 copy gt{exch}if pop}bdf
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/max{2 copy lt{exch}if pop}bdf
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/dh{fg 6 1 put array astore dup {1 pxs div mul exch}forall astore exch pop exch pop exch setdash}bdf
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/ih[currentdash]def
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/rh{fg 6 0 put ih aload pop setdash}bdf
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/dl{gsave nlw pys div setlinewidth 0 setgray}bdf
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/dlin{exch currentpoint currentlinewidth 2 div dup
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translate newpath moveto lineto currentpoint stroke grestore moveto}bdf
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/lin{fg 6 get 0 ne{exch lineto currentpoint 0 doop moveto}
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{exch currentpoint/pnlv xdf/pnlh xdf gsave newpath/@1 xdf/@2 xdf fp{pnlh @2 lt{pnlv @1 ge
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{pnlh pnlv moveto @2 @1 lineto pnsh 0 rlineto
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0 pnsv rlineto pnlh pnsh add pnlv pnsv add lineto pnsh neg 0 rlineto}
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{pnlh pnlv moveto pnsh 0 rlineto @2 pnsh add @1 lineto 0 pnsv rlineto
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pnsh neg 0 rlineto pnlh pnlv pnsv add lineto}ifelse}{pnlv @1 gt
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{@2 @1 moveto pnsh 0 rlineto pnlh pnsh add pnlv lineto 0 pnsv rlineto
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pnsh neg 0 rlineto @2 @1 pnsv add lineto}{pnlh pnlv moveto pnsh 0 rlineto
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0 pnsv rlineto @2 pnsh add @1 pnsv add lineto pnsh neg 0 rlineto
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0 pnsv neg rlineto}ifelse}ifelse
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closepath fill}if @2 @1 grestore moveto}ifelse}bdf
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/gw{/pnm fg 3 get fg 4 get div def}bdf
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/lw{fg exch 4 exch put fg exch 3 exch put gw pnsv pnsh pen}bdf
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/barc{/@1 xdf/@2 xdf/@3 xdf/@4 xdf/@5 xdf
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/@6 xdf/@7 xdf/@8 xdf gsave
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@5 @7 add 2 div @6 @8 add 2 div translate newpath 0 0 moveto
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@5 @7 sub @6 @8 sub mtx currentmatrix pop scale @1{newpath}if
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0 0 0.5 @4 @3 arc @4 @3 sub abs 360 ge{closepath}if
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mtx setmatrix @2 doop grestore}bdf
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/ar{dup 0 eq barc}bdf
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/ov{0 exch 360 exch true barc}bdf
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/rc{/@t xdf currentpoint 6 2 roll newpath 4 copy 4 2 roll exch moveto
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6 -1 roll lineto lineto lineto closepath @t doop moveto}bdf
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/mup{dup pnsh 2 div le exch pnsv 2 div le or}bdf
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/rr{/@1 xdf 2. div/@2 xdf 2. div/@3 xdf
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/@4 xdf/@5 xdf/@6 xdf/@7 xdf
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@7 @5 eq @6 @4 eq @2 mup or or{@7 @6 @5 @4 @1 rc}
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{@4 @6 sub 2. div dup @2 lt{/@2 xdf}{pop}ifelse
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@5 @7 sub 2. div dup @2 lt{/@2 xdf}{pop}ifelse
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@1 0 eq{/@2 @2 pnsh 2 div 2 copy gt{sub def}{0 pop4}ifelse}if
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currentpoint newpath
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@4 @6 add 2. div @7 moveto
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@4 @7 @4 @5 @2 arcto pop4
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@4 @5 @6 @5 @2 arcto pop4
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@6 @5 @6 @7 @2 arcto pop4
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@6 @7 @4 @7 @2 arcto pop4
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closepath @1 doop moveto}ifelse}bdf
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/pr{gsave newpath/pl{exch moveto/pl{exch lineto}def}def}bdf
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/pl{exch lineto}bdf
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/ep{dup 0 eq{{moveto}{exch lin}{}{(%%[|1|]%%)= flush}pathforall
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pop grestore}{doop grestore}ifelse currentpoint newpath moveto}bdf
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/gr{64. div setgray}bdf
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/savescreen{ns not{/ns true def systemdict/currentcolorscreen known{currentcolorscreen/pkspf xdf/pkrot xdf/pkfreq xdf/pyspf xdf/pyrot xdf/pyfreq xdf/pmspf xdf/pmrot xdf/pmfreq xdf
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/pcspf xdf/pcrot xdf/pcfreq xdf}{currentscreen/sspf xdf/srot xdf/sfreq xdf}ifelse}if}bdf
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/restorescreen{/ns false def systemdict/setcolorscreen known{pcfreq pcrot/pcspf load pmfreq pmrot/pmspf load pyfreq pyrot/pyspf load
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pkfreq pkrot/pkspf load setcolorscreen}{sfreq srot/sspf load setscreen}ifelse}bdf
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/pat{savescreen sa8
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copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sa8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}setscreen exch not{gr}{pop}ifelse}bdf
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/sg{restorescreen gr}bdf
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/cpat{savescreen 10 2 roll 7 -1 roll sa8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sa8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}8 -1 roll sb8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sb8
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exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}9 -1 roll sc8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sc8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}10 -1 roll sd8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sd8
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exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}psuedo1 dsc 4{4 -1 roll 1 exch 64 div sub}repeat setcmykcolor pop pop}bdf
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systemdict/setcolorscreen known{/psuedo1 lnop bdf/dsc/setcolorscreen load def}{/psuedo1{16{pop}repeat sa8 copy pop 9.375 pa por not{90 add}if{1 add 4 mul cvi sa8 exch get exch 1 add 4 mul cvi 7 sub bitshift 1 and}}bdf
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/bwsc{setscreen dup gr 0 exch 0 exch 64 exch 64 exch 64 exch}bdf/dsc/bwsc load def
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}ifelse
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systemdict/setcmykcolor known not{/setcmykcolor{1 sub 4 1 roll 3{3 index add neg dup 0 lt{pop 0}if 3 1 roll}repeat setrgbcolor pop}bdf}if
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/dc{transform round .5 sub exch round .5 sub exch itransform}bdf
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/sn{userdict/smooth4 known}bdf
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/x8{3 bitshift}bdf
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/x4{2 bitshift}bdf
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/d4{-2 bitshift}bdf
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/d8{-3 bitshift}bdf
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/rb{15 add -4 bitshift 1 bitshift}bdf
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/db{/@7 save def/@1 xdf/@2 xdf/@3 xdf/@4 xdf/@5 xdf/@6 @5 @3 4 add mul def
|
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dc translate scale/xdbit 1 1 idtransform abs/ydbit exch def abs def{0 0 1 ydbit add 1 10 rc clip}if
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@1 0 eq @1 4 eq or{currentrgbcolor 1 setgray ydbit 0 1 ydbit add 1 2 rc setrgbcolor}if
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@1 3 eq @1 7 eq or{1 setgray}{currentrgbcolor 2 index eq exch 2 index eq and exch pop{0 setgray}if}ifelse/@9 @1 0 eq @1 1 eq @1 3 eq or or dbinvertflag xor def/@13 @6 def
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@2 fBitStretch or{/@10 @4 x4 def/@11 @3 x4 def/@12 @10 rb def/@13 @12 @11 mul def/@15 1 1 dtransform abs/calcY 1 index def round cvi/@14 exch def
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abs/calcX 1 index def round cvi scaleby96 not{1 add}if def/@16 @15 rb def/@17 @16 @14 mul def}if
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sn @13 60000 lt and @2 fBitStretch or and{mtx currentmatrix dup 1 get exch 2 get 0. eq exch 0. eq and @17 60000 lt and fBitStretch and{@16 3 bitshift @14 @9 [calcX 0 0 calcY 0 0]{@17 string @13 string
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currentfile @6 string readhexstring pop 1 index @4 @3 @5 @12 @2 smooth4
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@10 @11 @12 dup string 5 index @15 @14 @16 dup string stretch}imagemask}{@12 x8 @11 @9 [@10 0 0 @11 0 0]{@13 string
|
|
currentfile @6 string readhexstring pop 1 index @4 @3 @5 @12 @2 smooth4}imagemask}ifelse}{@5 3 bitshift @3 4 add @9 [@4 0 0 @3 0 2]{currentfile @6 string readhexstring pop}imagemask}ifelse
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|
@7 restore}bdf
|
|
systemdict/setcmykcolor known{/psuedo lnop bdf/di/colorimage load def}{/routines[{.3 mul add 1}bind{.59 mul add 2}bind{.11 mul add round cvi str exch i exch put/i i 1 add def 0 0}bind]def
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/psuedo{/i 0 def 0 exch 0 exch{exch routines exch get exec}forall pop pop str}bdf/bwi{pop pop image}bdf/di/bwi load def}ifelse
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/cdb{/@7 save def/@1 xdf/@2 xdf/@3 xdf/@4 xdf/@5 xdf
|
|
systemdict/setcmykcolor known not{dc}if translate scale /@6 xdf
|
|
/@18 @5 dup 60000 ge{pop 60000}if string def @6 not{/str @18 0 @18 length 3 idiv getinterval def}if @4 @3 8 [@4 0 0 @3 0 0]@6{{currentfile @18 readhexstring pop}image}{{currentfile @18 readhexstring pop psuedo}false 3 di}ifelse @7 restore}bdf
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/wd 16 dict def
|
|
/mfont 14 dict def
|
|
/mdf{mfont wcheck not{/mfont 14 dict def}if mfont begin xdf end}bdf
|
|
/cf{{1 index/FID ne{def}{pop pop}ifelse}forall}bdf/rf{/@1 exch def/@2 exch def
|
|
FontDirectory @2 known{cleartomark pop}{findfont dup begin dup length @1 add dict begin
|
|
cf{/Encoding macvec def}{Encoding dup length array copy/Encoding exch def
|
|
counttomark 2 idiv{Encoding 3 1 roll put}repeat}ifelse
|
|
pop
|
|
exec currentdict end end @2 exch definefont pop}ifelse}bdf
|
|
/bmbc{exch begin wd begin
|
|
/cr xdf
|
|
save
|
|
CharTable cr 6 mul 6 getinterval{}forall
|
|
/bitheight xdf/bitwidth xdf
|
|
.96 div/width xdf
|
|
Gkernmax add/XOffset xdf Gdescent add/YOffset xdf/rowbytes xdf
|
|
rowbytes 255 eq{0 0 0 0 0 0 setcachedevice}
|
|
{Gnormsize dup scale
|
|
width 0 XOffset YOffset bitwidth XOffset add bitheight YOffset add
|
|
setcachedevice
|
|
rowbytes 0 ne{
|
|
XOffset YOffset translate newpath 0 0 moveto
|
|
bitwidth bitheight scale
|
|
sn{
|
|
/xSmt bitwidth x4 def
|
|
/ySmt bitheight x4 def
|
|
/rSmt xSmt rb def
|
|
rSmt x8 ySmt true
|
|
[xSmt 0 0 ySmt neg 0 ySmt]
|
|
{rSmt ySmt mul string CharData cr get
|
|
1 index bitwidth bitheight rowbytes rSmt tso smooth4}
|
|
}{rowbytes 3 bitshift bitheight 4 add true
|
|
[bitwidth 0 0 bitheight neg 0 bitheight 2 add]
|
|
{CharData cr get}
|
|
}ifelse
|
|
imagemask
|
|
}if
|
|
}ifelse
|
|
restore
|
|
end end
|
|
}bdf
|
|
/bb{.96 exch div/Gnormsize mdf 2 index
|
|
/Gkernmax mdf 1 index/Gdescent mdf
|
|
3 index div 4 1 roll
|
|
2 index div 1. 5 2 roll
|
|
exch div 4 1 roll
|
|
4 array astore/FontBBox mdf
|
|
}bdf
|
|
/cdf{mfont/CharData get 3 1 roll put}bdf
|
|
/bf{
|
|
mfont begin
|
|
/FontType 3 def
|
|
/FontMatrix [1 0 0 1 0 0] def
|
|
/Encoding macvec def
|
|
/MFontType 0 def
|
|
/BuildChar/bmbc load def
|
|
end
|
|
mfont definefont pop
|
|
}bdf
|
|
/wi LW 1 eq{{gsave 0 0 0 0 0 0 0 0 moveto lineto lineto lineto closepath clip stringwidth grestore}bind}{/stringwidth load}ifelse def
|
|
/aps{0 get 124 eq}bdf
|
|
/xc{s75 cvs dup}bdf
|
|
/xp{put cvn}bdf
|
|
/scs{xc 3 67 put dup 0 95 xp}bdf
|
|
/sos{xc 3 79 xp}bdf
|
|
/sbs{xc 1 66 xp}bdf
|
|
/sis{xc 2 73 xp}bdf
|
|
/sob{xc 2 79 xp}bdf
|
|
/sss{xc 4 83 xp}bdf
|
|
/dd{exch 1 index add 3 1 roll add exch}bdf
|
|
/smc{moveto dup show}bdf
|
|
/ndf2{udf{dup /FontType get 0 eq{/FDepVector get{dup /FontType get 0 eq{ndf2}{dup /df2 known{begin df2 0 null put end
|
|
}{pop}ifelse}ifelse}forall}{/df2 known{dup begin df2 0 null put end}if}ifelse}{pop}ifelse}bdf
|
|
/kwn{FontDirectory 1 index known{findfont dup ndf2 exch pop}}bdf
|
|
/gl{1 currentgray sub setgray}bdf
|
|
/newmm{dup /FontType get 0 eq{dup maxlength dict begin{1 index/FID ne 2 index/UniqueID ne and{def}{pop pop}ifelse}forall currentdict end
|
|
dup /FDepVector 2 copy get[exch 6 index exch 6 index exch{newmm 3 1 roll}forall pop pop] put dup
|
|
}{/mfont 10 dict def mfont begin/FontMatrix [1 0 0 1 0 0] def
|
|
/FontType 3 def/Encoding macvec def/df 1 index def/df2 1 array def/FontBBox [0 0 1 1] def/StyleCode 2 index def
|
|
/mbc{bcarray StyleCode get}def/BuildChar{exch begin wd begin/cr exch def/cs s1 dup 0 cr put def df /MFontType known not{
|
|
df2 0 get null eq{df dup length 2 add dict begin{1 index/FID ne 2 index/UniqueID ne and{def}{pop pop}ifelse}forall
|
|
/StrokeWidth nlw 1000 mul pys div ps div dup 12 lt{pop 12}if def/PaintType 2 def currentdict end
|
|
/q exch definefont df2 exch 0 exch put}if}if mbc exec end end}def end mfont}ifelse
|
|
3 index exch definefont exch pop}bdf
|
|
/mb{dup sbs kwn{0 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
|
|
/mo{dup sos kwn{2 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
|
|
/ms{dup sss kwn{4 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
|
|
/ou{dup sos kwn{mfont/df2 known{mfont begin df2 0 null put end}if 3 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
|
|
/su{dup sss kwn{mfont/df2 known{mfont begin df2 0 null put end}if 5 2 index findfont newmm exch pop exch pop exch pop}ifelse sfd}bdf
|
|
/ao{/fmv true def ou}bdf/as{/fmv true def su}bdf
|
|
/vo{/fmv false def ou}bdf/vs{/fmv false def su}bdf
|
|
/c{currentrgbcolor dup 4 1 roll eq 3 1 roll eq and/gray xdf}bdf
|
|
/bcarray[{/da .03 def df setfont gsave cs wi 1 index 0 ne{exch da add exch}if grestore setcharwidth
|
|
cs 0 0 smc da 0 smc da da smc 0 da moveto show}bind dup{/da 1 ps div def df setfont gsave cs wi 1 index 0 ne{exch da add exch}if grestore setcharwidth
|
|
cs 0 0 smc da 0 smc da da smc 0 da smc c gray{gl}{1 setgray}ifelse da 2. div dup moveto show}bind
|
|
{df setfont gsave cs wi grestore setcharwidth c gray{gl}{currentrgbcolor 1 setgray}ifelse cs 0 0 smc df2 0 get setfont
|
|
gray{gl}{4 1 roll setrgbcolor}ifelse 0 0 moveto show}bind
|
|
{/da 1 ps div def/ds .05 def/da2 da 2. div def df setfont gsave cs wi 1 index 0 ne{exch ds add da2 add exch}if grestore setcharwidth
|
|
cs ds da2 add .01 add 0 smc 0 ds da2 sub translate 0 0 smc da 0 smc da da smc 0 da smc c gray{gl}{1 setgray}ifelse da 2. div dup moveto show}bind
|
|
{/da .05 def df setfont gsave cs wi 1 index 0 ne{exch da add exch}if grestore setcharwidth c cs da .01 add 0 smc 0 da translate
|
|
gray{gl}{currentrgbcolor 1 setgray 4 -1 roll}ifelse 0 0 smc gray{gl}{4 1 roll setrgbcolor}ifelse df2 0 get setfont 0 0 moveto show}bind]def
|
|
/st{1000 mul usertime add dup 2147483647 gt{2147483647 sub}if def}bdf
|
|
/the{usertime sub dup 0 lt exch -2147483648 gt and}bdf
|
|
/6a 6 array def
|
|
/2a 2 array def
|
|
/3q 3 array def
|
|
/qs{3 -1 roll sub exch 3 -1 roll sub exch}bdf
|
|
/qa{3 -1 roll add exch 3 -1 roll add exch}bdf
|
|
/qm{3 -1 roll 1 index mul 3 1 roll mul}bdf
|
|
/qn{6a exch get mul}bdf
|
|
/qA .166667 def/qB .833333 def/qC .5 def
|
|
/qx{6a astore pop
|
|
qA 0 qn qB 2 qn add qA 1 qn qB 3 qn add
|
|
qB 2 qn qA 4 qn add qB 3 qn qA 5 qn add
|
|
qC 2 qn qC 4 qn add qC 3 qn qC 5 qn add}bdf
|
|
/qp{6 copy 12 -2 roll pop pop}bdf
|
|
/qc{exch qp qx curveto}bdf
|
|
/qi{{exch 4 copy 2a astore aload pop qa .5 qm newpath moveto}{exch 2 copy 6 -2 roll 2 qm qs 4 2 roll}ifelse}bdf
|
|
/qq{{qc 2a aload pop qx curveto}{exch 4 copy qs qa qx curveto}ifelse}bdf
|
|
/pt{currentpoint newpath moveto}bdf
|
|
/qf{/fillflag true def}bdf
|
|
/ec{dup 4 and 0 ne{closepath}if 1 and 0 ne{0 doop}if grestore currentpoint newpath moveto/fillflag false def}bdf
|
|
/eu{currentpoint fp{0 ep}{grestore newpath}ifelse moveto/fillflag false def}bdf
|
|
/bp{currentpoint newpath 2 copy moveto}bdf
|
|
/ef{gsave fillflag{gsave eofill grestore}if}bdf
|
|
/sm{0 exch{@1 eq{1 add}if}forall}bdf
|
|
/lshow{4 1 roll exch/@1 exch def{1 index wi pop sub 1 index sm dv 0 @1 4 -1 roll widthshow}{1 index wi pop sub
|
|
1 index dup sm 10 mul exch length 1 sub add dv dup 10. mul 0 @1 4 -1 roll 0 6 -1 roll awidthshow}ifelse}bdf
|
|
/setTxMode{sa 9 2 index put exch not{3 eq{1}{0}ifelse setgray}{pop}ifelse}bdf
|
|
/SwToSym{{}mark false/Symbol/|______Symbol 0 rf 0 sa 6 get 0 ne{pop 1}{sa 7 get 0 eq{pop 2}if}ifelse
|
|
sa 1 get 0 ne/|______Symbol
|
|
sa 4 get 0 ne{vs}{sa 3 get 0 ne{vo}{fnt}ifelse}ifelse}bdf
|
|
/mc{0 3 1 roll transform neg exch pop}bdf
|
|
/ul{dup 0 ne sa 2 get 0 ne and{gsave 0 0
|
|
/UnderlinePosition kif{mc}{ps -10 div}ifelse/UnderlineThickness kif{mc}{ps 15 div}ifelse
|
|
abs setlinewidth neg rmoveto
|
|
sa 4 get 0 ne{gsave currentlinewidth 2. div dup rmoveto currentpoint newpath moveto
|
|
2 copy rlineto stroke grestore}if
|
|
sa 3 get sa 4 get or 0 ne{gsave currentrgbcolor dup 4 1 roll eq 3 1 roll eq and{gl}{1 setgray}ifelse 2 copy rlineto stroke grestore rlineto strokepath nlw pys div setlinewidth}{rlineto}ifelse
|
|
stroke grestore}{pop}ifelse}bdf
|
|
/sgt{2 copy known{get true}{pop pop false}ifelse}bdf
|
|
/kif{currentfont dup/FontMatrix get exch/FontInfo sgt{true}{currentfont/df sgt
|
|
{dup/FontInfo sgt{3 1 roll/FontMatrix get mtx concatmatrix exch true}{pop pop pop false}
|
|
ifelse}{pop pop false}ifelse}ifelse{3 -1 roll sgt{exch true}{pop false}ifelse}{false}ifelse}bdf
|
|
/blank/Times-Roman findfont/CharStrings get/space get def
|
|
/macvec 256 array def
|
|
/NUL/SOH/STX/ETX/EOT/ENQ/ACK/BEL/BS/HT/LF/VT/FF/CR/SO/SI
|
|
/DLE/DC1/DC2/DC3/DC4/NAK/SYN/ETB/CAN/EM/SUB/ESC/FS/GS/RS/US
|
|
macvec 0 32 getinterval astore pop
|
|
macvec 32/Times-Roman findfont/Encoding get
|
|
32 96 getinterval putinterval macvec dup 39/quotesingle put 96/grave put
|
|
/Adieresis/Aring/Ccedilla/Eacute/Ntilde/Odieresis/Udieresis/aacute
|
|
/agrave/acircumflex/adieresis/atilde/aring/ccedilla/eacute/egrave
|
|
/ecircumflex/edieresis/iacute/igrave/icircumflex/idieresis/ntilde/oacute
|
|
/ograve/ocircumflex/odieresis/otilde/uacute/ugrave/ucircumflex/udieresis
|
|
/dagger/degree/cent/sterling/section/bullet/paragraph/germandbls
|
|
/registered/copyright/trademark/acute/dieresis/notequal/AE/Oslash
|
|
/infinity/plusminus/lessequal/greaterequal/yen/mu/partialdiff/summation
|
|
/product/pi/integral/ordfeminine/ordmasculine/Omega/ae/oslash
|
|
/questiondown/exclamdown/logicalnot/radical/florin/approxequal/Delta/guillemotleft
|
|
/guillemotright/ellipsis/blank/Agrave/Atilde/Otilde/OE/oe
|
|
/endash/emdash/quotedblleft/quotedblright/quoteleft/quoteright/divide/lozenge
|
|
/ydieresis/Ydieresis/fraction/currency/guilsinglleft/guilsinglright/fi/fl
|
|
/daggerdbl/periodcentered/quotesinglbase/quotedblbase/perthousand/Acircumflex/Ecircumflex/Aacute
|
|
/Edieresis/Egrave/Iacute/Icircumflex/Idieresis/Igrave/Oacute/Ocircumflex
|
|
/apple/Ograve/Uacute/Ucircumflex/Ugrave/dotlessi/circumflex/tilde
|
|
/macron/breve/dotaccent/ring/cedilla/hungarumlaut/ogonek/caron
|
|
macvec 128 128 getinterval astore pop
|
|
{}mark true/Courier/|______Courier 0 rf
|
|
{/Metrics 21 dict begin/zero 600 def/one 600 def/two 600 def/three 600 def/four 600 def/five 600 def/six 600 def/seven 600 def/eight 600 def
|
|
/nine 600 def/comma 600 def/period 600 def/dollar 600 def/numbersign 600 def/percent 600 def/plus 600 def/hyphen 600 def/E 600 def/parenleft 600 def/parenright 600 def/space 600 def
|
|
currentdict end def currentdict/UniqueID known{/UniqueID 16#800000 def}if/FontBBox FontBBox 4 array astore def}mark true/Helvetica/|______Seattle 1 rf
|
|
/oldsettransfer/settransfer load def
|
|
/concatprocs{/proc2 exch cvlit def/proc1 exch cvlit def/newproc proc1 length proc2 length add array def
|
|
newproc 0 proc1 putinterval newproc proc1 length proc2 putinterval newproc cvx}def
|
|
/settransfer{currenttransfer concatprocs oldsettransfer}def
|
|
/PaintBlack{{1 exch sub}settransfer gsave newpath clippath 1 setgray fill grestore}def
|
|
/od{(Rvd\001\001\000\000\177) fg copy pop txpose
|
|
1 0 mtx defaultmatrix dtransform exch atan/pa exch def
|
|
newpath clippath mark
|
|
{transform{itransform moveto}}{transform{itransform lineto}}
|
|
{6 -2 roll transform 6 -2 roll transform 6 -2 roll transform
|
|
{itransform 6 2 roll itransform 6 2 roll itransform 6 2 roll curveto}}
|
|
{{closepath}}pathforall newpath counttomark array astore/gc xdf pop ct 39 0 put
|
|
10 fz 0 fs 2 F/|______Courier fnt invertflag{PaintBlack}if
|
|
statusdict/processcolors known{statusdict begin processcolors end dup 4 eq{/4colors true def pop}{3 eq{/3colors true def}{/2color true def}ifelse}ifelse}{/2colors true def}ifelse}bdf
|
|
/cd{}bdf
|
|
/op{/sfl false def systemdict/currentcolorscreen known{dcfreq dcrot/dcspf load dmfreq dmrot/dmspf load dyfreq dyrot/dyspf load
|
|
dkfreq dkrot/dkspf load setcolorscreen}{freq rot/spf load setscreen}ifelse savescreen
|
|
/ns false def/pm save def}bdf
|
|
/cp{not{userdict/#copies 0 put}if ma 0 gt{{t1 the{exit}if}loop}if{copypage}{showpage}ifelse pm restore}bdf
|
|
/px{0 3 1 roll tp tt}bdf
|
|
/psb{/us save def}bdf
|
|
/pse{us restore}bdf
|
|
/ct 40 string def
|
|
/nc{currentpoint initclip newpath gc{dup type dup/arraytype eq exch/packedarraytype eq or{exec}if}
|
|
forall clip newpath moveto}def
|
|
/kp{ct 0 2 index length 2 index 39 2 index put getinterval copy cvx exec mx3 currentmatrix pop}bdf
|
|
/av 70 def
|
|
end
|
|
LW 1 eq userdict/a4small known not and{/a4small
|
|
[[300 72 div 0 0 -300 72 div -120 3381]
|
|
280 3255
|
|
{statusdict/jobstate (printing) put 0 setblink
|
|
margins
|
|
exch 196 add exch 304 add 8 div round cvi frametoroket
|
|
statusdict/jobstate (busy) put
|
|
1 setblink}
|
|
/framedevice load
|
|
60 45{dup mul exch dup mul add 1.0 exch sub}/setscreen load
|
|
{}/settransfer load/initgraphics load/erasepage load]cvx
|
|
statusdict begin bind end readonly def}if
|
|
md begin/bigs[lnop userdict/letter known{/letter load}{lnop}ifelse userdict/legal known{/legal load}{lnop}ifelse userdict/a4 known{/a4 load}{lnop}ifelse userdict/b5 known{/b5 load}{lnop}ifelse
|
|
lnop lnop lnop /tab load/a3Size load]def
|
|
/smalls[lnop userdict/lettersmall known{/lettersmall load}{userdict/note known{/note load}{lnop}ifelse}ifelse
|
|
userdict/legal known{/legal load}{lnop}ifelse userdict/a4small known{/a4small load}{lnop}ifelse
|
|
userdict/b5 known{/b5 load}{userdict/note known{/note load}{lnop}ifelse}ifelse lnop lnop lnop /tab load/a3Size load]def end
|
|
systemdict/currentpacking known{setpacking}if
|
|
/checkload{{currentfile eexec} {/junk save def/mystring 65000 string def
|
|
/endexec (%endeexec) def{currentfile mystring readline not{stop}if endexec eq{exit}if}loop junk restore}ifelse}bind def
|
|
ok userdict/stretch known not and checkload
|
|
373A767D4B7FD94FE5903B7014B1B8D3BED02632C855D56F458B118ACF3AF73FC4EF5E81F5749042B5F9CF1016D093B75F250B7D8280B2EACE05A37037F7BDF6E12226D7D4E2DF2C52FAFD5FD40FE72A0D3AC4BD485D8369D4C87636E920D1DAF222D92155A9CB1667E715F0B82799B37CC8F5B32B74B39CF494536DC39C7EF04A7BCB29E2CEC79073CADCCFB23B4AA1363F876F5121B618071B7B4EB1E5DE75FAA2368A3E5DB2B198623AFE92AE9484270FE7F57A850E88C0D3EEA156611C91D8E480D4370B025CCA6929A2BF40AD3D01B2CB7EE6DFB46E12A830542337F7819B67F9765210F76DB06F34DA5B13A11759305C582E16D2B854939F6D9121F2A4F285282F5DCD3D15896D121E3D6F5BE79E087451BB0ED233CDBEF090D3B4AC2DC34B97E70C61D95FB072B8C12D2ABD843520949A39DCF99E2C1AA8FBCD025E47E0A82A8D96E75BAF40F52AD402495BBD4DE0F356C8B14E764874E639C9F045A0D1908EC6456EB6C5B8A6F826192F767EF2C55A21C58F5F9CC1F59247B55F2387828C7FE89D5E7D8484D1BC86CB6673BDBE4FE17DD9BDE95224FE645136F41330BF155A4DDE1B0A32233BF471CE58FBC660DC7E641B0A0D30018454E2191C414A3011FF3FED1C0D88FE1FF9F75DCC456D097947226FBEC92509146D3A4CFFC0471B31C53222ED9DD88566F60F6C0D705AD79DACF53B070026F083ED28B5CF757AAA0A169F6F320A75E9D2ED50ABD939AF85B6346C2ADB25D168F10508E1516D194C635E6B187FADEA0829DBF0390C0F003F0265E215BC96CA3CC13D4A8E01570BE193CA75A620728CD275ACF1986EFFB3A13419FE55EA7C4467B7E7EEDC1FC29C9F8C46A557D2CCDB914EF7B93E7530D555DFC2398AFC68CAD991F062EF85BAA1884EC166C7C5DF8543666D8C41BE267D706BD1588F1F662F705CAE4D29DC38EF66BFAA89470D8A099B6F1B4587F7B024412276106FCD3EB5AE17A5D1DF1781992DC40EA0A992F706F701304CEA9D9073E7A74F1E687D81C3E5841D31CF86855BAAAD9B5D30317C75150A857C6B114735315CDD1AEF36C26BBB0645499406DEE2F24B3B1C72FEC97C7BA31AA2CDAB25418BB1DC4C7E4757F1D625087B0FD0300C03A65F2A72CE734925735277E034CDCF599129679F70CC8B66E03878851DB75041F275E1E5761F3EC753BE1359CA364A22047AE4886217F9259FE19FF5B116E8019B98B143114B313E8BEF87EC949D85C82E0812E6F50525E73890AF362CC8EE8A85F4197E6AC18638EF12E56A808D439AF1BFD363F140314BF4E534485C42F1856688CC35288E8D770120A420FB9F1FCF8AE8BD6D6156CC23E6C51119FE4DE1B68C9DF3487E9974BF9ED31F8D3CE93FF101867319F2FF492D5D398B4F09A66F2F55BCAB34B99173B7EE89039D00DD21A7B3A52E9F028F8301B5FC12D409412E064513BC579AAC498F577EA8ECD1FE3E42DC3CC320786C7B00194FEDF344402C33FC492D4BA86992B01683F440220FFE756BC88A94223D316078D69D33560E8EAB76B24CB7AA4320CF435593D76F624324ABE00B5587A4F283C725EA24567133F25F472B5E2E4474DDB5A16AC5F2DF32350395D3E3892FE361F4D5C9A610C654C9227614FBBAFF3356A90A2266E00F66234061075491571A65616211257F160000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
0000000000000000000000000000000000000000000000000000000000000000
|
|
cleartomark
|
|
%endeexec
|
|
|
|
ok userdict/smooth4 known not and checkload
|
|
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%!PS-Adobe-2.0
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%%Title: GDE2.0_small
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%%Creator: Microsoft Word
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%%CreationDate: Sunday, April 26, 1992
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%%Pages: (atend)
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%%PageBoundingBox: 30 31 582 761
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%%For: Genome1
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T T 0 0 730 552 -31 -30 761 582 100 72 72 1 F F F F T T T T psu
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(Genome1; document: GDE2.0_small)jn
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1.00982 0. 32 0.10098 0.(version 2.0)awidthshow
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1.01469 0.(.....................................................................)ashow
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1.01313 0.(.............................................................................)ashow
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1.01264 0.(................................................................................)ashow
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-0.00480 0.(The Genetic Data Environment is part of a growing set of programs for manipulating and analyzing)ashow
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-0.02925 0.("genetic" data. It differs in design from other analysis programs in that it is intended to be an expandable and)ashow
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0.30548 0. 32 0.03054 0.(customizable system, while still being easy to use.)awidthshow
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170 90 gm
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-0.03929 0.(There are a tremendous number of publicly available programs for sequence analysis. Many of these)ashow
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-0.02575 0.(programs have found their way into commercial packages which incorporate them into integrated, easy to use)ashow
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192 90 gm
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0.00381 0. 32 0.00038 0.(systems. The goal of the GDE is to minimize the amount of effort required to integrate sequence analysis)awidthshow
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0.02471 0. 32 0.00247 0.(functions into a common environment. The GDE takes care of the user interface issues, and allows the)awidthshow
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0.08422 0. 32 0.00842 0.(programmer to concentrate on the analysis itself. Existing programs can be tied into the GDE in a matter of)awidthshow
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0.05676 0. 32 0.00567 0.(hours \(or minutes\) as apposed to days or weeks. Programs may be written in any language, and still)awidthshow
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-0.01551 0.(seamlessly be incorporated into the GDE.)ashow
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258 90 gm
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0.15960 0. 32 0.01596 0.(These programs are, and will continue to be, available at no charge. It is the hope that this system will)awidthshow
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269 90 gm
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-0.00163 0.(grow in functionality as more and more people see the benefits of a modular analysis environment. Users)ashow
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280 90 gm
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-0.04074 0.(are encouraged to make modifications to the system, and forward all changes and additions to Steven Smith)ashow
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291 90 gm
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0.33660 0. 32 0.03366 0.(What's New for this Release)awidthshow
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2 F /|______Times-Roman fnt
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-0.02201 0.(There have been several changes made for this 2.0 release of GDE. The most notable changes involve new)ashow
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350 90 gm
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0.06668 0. 32 0.00666 0.(editing capabilities. For most functions, the user can either select the sequences by their name, or by)awidthshow
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361 90 gm
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-0.06840 0.(dragging over sections of the sequence text. See editing for more details. Other added features include a new)ashow
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-0.07867 0.(checking mode, reduced scale viewing for sequence assembly, improved cut/copy/paste, and many new)ashow
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383 90 gm
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0.08651 0. 32 0.00865 0.(external functions. There is also a new file format, GDE format, which retains more of the all of the)awidthshow
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394 90 gm
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0.05279 0. 32 0.00527 0.(available information about a sequence. This format \(unlike Genbank format in GDE1.0\) will not loose)awidthshow
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405 90 gm
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0.02593 0. 32 0.00259 0.(fields such as group numbers, etc.)awidthshow
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-0.01397 0.(There is one other change that should be noted. The old "flat" file format has changed. The format now)ashow
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438 90 gm
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(compresses leading gaps by allowing an offset number in parentheses after the name. GDE2.0 will still read)show
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449 90 gm
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0.15045 0. 32 0.01504 0.(old "flat" files, but will write them out in the new format. This might cause difficulties for some external)awidthshow
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460 90 gm
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0.17807 0. 32 0.01780 0.(functions written using this format. Because of the change, it is VERY important to keep the GDE1.0)awidthshow
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471 90 gm
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0.02624 0. 32 0.00262 0.(support programs separate from GDE2.0, as some are now incompatible. The original flatfile format can be)awidthshow
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482 90 gm
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-0.10980 0.(duplicated using ReadSeq/FastA format and sed.)ashow
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14 fz
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-0.02626 0.(System Requirements)ashow
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541 90 gm
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10 fz
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2 F /|______Times-Roman fnt
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0.16036 0. 32 0.01603 0.(GDE 2.0 currently runs on the Sun family of workstations. This includes the Sun3 and Sun4 \(Sparcstation\))awidthshow
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552 90 gm
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0.19104 0. 32 0.01910 0.(systems. It was written in XView, and runs on Suns using OpenWindows 2.0 or MIT's X Windows. It)awidthshow
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563 90 gm
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0.00488 0. 32 0.00048 0.(runs in both monochrome, and color, and can be run remotely on any system capable of running X Windows)awidthshow
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574 90 gm
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-0.00602 0.(Release 4. You should have at least 15 meg of free disk space available.)ashow
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596 90 gm
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0.14724 0. 32 0.01472 0.(We are also supporting a DECStation version of GDE. This is running under XView 3.0/X11R5. We)awidthshow
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607 90 gm
|
|
0.02227 0. 32 0.00222 0.(encourage interested people to port the programs to their favorite Unix platform. We hope to support the)awidthshow
|
|
618 90 gm
|
|
-0.00794 0.(SGI and Cray line of Supercomputers.)ashow
|
|
643 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.36575 0. 32 0.03657 0.(Note to Motif users)awidthshow
|
|
666 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.08575 0. 32 0.00857 0.(GDE2.0 can be run using different window managers. The most common alternative to olwm is the Motif)awidthshow
|
|
677 90 gm
|
|
0.12878 0. 32 0.01287 0.(window manager \(mwm\). The only problem in using another window manager is that the status line is not)awidthshow
|
|
688 90 gm
|
|
-0.04948 0.(displayed. We have added a "Message panel" as an option under "File->Properties" which displays all of the)ashow
|
|
699 90 gm
|
|
0.10406 0. 32 0.01040 0.(information contained on the status line.)awidthshow
|
|
F T cp
|
|
%%Page: ? 3
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 303 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(3)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03054 0.(People using other window managers may also prefer using xterm, and xedit as default terminals and file)ashow
|
|
92 90 gm
|
|
-0.02236 0.(editors. This can be accomplished by replacing all occurrences of 'shelltool' and 'textedit' with 'xterm -e' and)ashow
|
|
103 90 gm
|
|
0.10833 0. 32 0.01083 0.('xedit' in the $GDE_HELP_DIR/.GDEmenus file.)awidthshow
|
|
128 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.33935 0. 32 0.03393 0.(Installing the GDE)awidthshow
|
|
151 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03640 0.(Instructions for the source code release are included in the README.install file.)ashow
|
|
173 90 gm
|
|
-0.00282 0.(The binary installations consist of creating a GDE directory, such as /usr/local/GDE, and un-taring the)ashow
|
|
184 90 gm
|
|
0.15594 0. 32 0.01559 0.(installation tarfile into the directory. If you are installing the GDE for your own use, then you can simply)awidthshow
|
|
195 90 gm
|
|
0.01647 0. 32 0.00164 0.(make a GDE subdirectory. There is no need to be superuser \(root\) to do the installation in your own)awidthshow
|
|
206 90 gm
|
|
-0.02723 0.(directory. For example:)ashow
|
|
225 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
0.69610 0. 32 0.06961 0.(demo% )awidthshow
|
|
1 fs
|
|
{}mark T /Courier-Bold /|______Courier-Bold 0 rf
|
|
2 F /|______Courier-Bold fnt
|
|
1.28005 0. 32 0.12800 0.(mkdir /usr/local/GDE)awidthshow
|
|
233 90 gm
|
|
0 fs
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
0.79788 0. 32 0.07978 0.(demo% )awidthshow
|
|
1 fs
|
|
{}mark T /Courier-Bold /|______Courier-Bold 0 rf
|
|
2 F /|______Courier-Bold fnt
|
|
1.26770 0. 32 0.12677 0.(cp GDE2.0.tar /usr/local/GDE)awidthshow
|
|
241 90 gm
|
|
0 fs
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
0.55816 0. 32 0.05581 0.(demo% )awidthshow
|
|
1 fs
|
|
{}mark T /Courier-Bold /|______Courier-Bold 0 rf
|
|
2 F /|______Courier-Bold fnt
|
|
0.97320 0. 32 0.09732 0.(cd /usr/local/GDE)awidthshow
|
|
249 90 gm
|
|
0 fs
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
0.65994 0. 32 0.06599 0.(demo% )awidthshow
|
|
1 fs
|
|
{}mark T /Courier-Bold /|______Courier-Bold 0 rf
|
|
2 F /|______Courier-Bold fnt
|
|
0.85617 0. 32 0.08561 0.(tar -xf GDE2.0.tar)awidthshow
|
|
271 90 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00643 0.(After this, each new user will need to add two lines to their .cshrc file so that they can find the gde programs)ashow
|
|
282 90 gm
|
|
-0.07226 0.(and files.)ashow
|
|
301 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
0.50384 0. 32 0.05038 0.(demo% )awidthshow
|
|
1 fs
|
|
{}mark T /Courier-Bold /|______Courier-Bold 0 rf
|
|
2 F /|______Courier-Bold fnt
|
|
0.59280 0. 32 0.05928 0.(cat >> ~/.cshrc)awidthshow
|
|
309 90 gm
|
|
1.39968 0. 32 0.13996 0.(set path = \($path /usr/local/GDE/bin\))awidthshow
|
|
317 90 gm
|
|
2.04071 0. 32 0.20407 0.(setenv GDE_HELP_DIR /usr/local/GDE/help/)awidthshow
|
|
325 90 gm
|
|
0.60202 0.(^D)ashow
|
|
344 90 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.06118 0. 32 0.00611 0.(You may wish to make a copy of the .GDEmenus file from the help directory into your home directory.)awidthshow
|
|
355 90 gm
|
|
0.13107 0. 32 0.01310 0.(This is only necessary if you wish to modify your menus. Copy the demo files from /usr/local/GDE/demo)awidthshow
|
|
366 90 gm
|
|
-0.02130 0.(into your local directory, and you are now ready to use the GDE.)ashow
|
|
388 90 gm
|
|
-0.05734 0.(FastA and Blast need to have the properly formatted databases installed in the $GDE_HELP_DIR under the)ashow
|
|
399 90 gm
|
|
0.15838 0. 32 0.01583 0.(directories FASTA/PIR, FASTA/GENBANK, BLAST/pir BLAST/genbank. For FASTA, simply copy a)awidthshow
|
|
410 90 gm
|
|
-0.01397 0.(version of PIR and Genbank into the proper directory. Alternately, the PIR and GENBANK files can be)ashow
|
|
421 90 gm
|
|
0.08224 0. 32 0.00822 0.(symbolic links to copies of Genbank held elsewhere on your system.)awidthshow
|
|
443 90 gm
|
|
0.01754 0. 32 0.00175 0.(Blast installation involves converting PIR and GENBANK to a temporary FASTA format \(using pir2fasta)awidthshow
|
|
454 90 gm
|
|
-0.07652 0.(and gb2fasta\) and then using pressdb for nucleic acid, and setdb for amino acid to reformat the databases again)ashow
|
|
465 90 gm
|
|
0.23468 0. 32 0.02346 0.(into blast format. The .GDEmenus file is currently set up to search with blast using the following)awidthshow
|
|
476 90 gm
|
|
0.01464 0. 32 0.00146 0.(databases: pir, genpept, genupdate, and genbank. If you wish to divide these into subdivisions, then the)awidthshow
|
|
487 90 gm
|
|
-0.00154 0.(.GDEmenus file will have to be edited.)ashow
|
|
509 90 gm
|
|
0.18249 0. 32 0.01824 0.(The most up to date release of blast can be obtained via anonymous ftp to ncbi.nlm.nih.gov. The most)awidthshow
|
|
520 90 gm
|
|
-0.02844 0.(recent release of FASTA can be obtained via anonymous ftp to uvaarpa.virginia.edu.)ashow
|
|
545 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.21560 0. 32 0.02156 0.(Using the GDE)awidthshow
|
|
568 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.08346 0. 32 0.00834 0.(It is assumed that the user is familiar with the Unix, and OpenWindows/Xwindows environments. It is also)awidthshow
|
|
579 90 gm
|
|
-0.04437 0.(assumed that people running standard MIT X-Windows will be using the OpenLook window manager)ashow
|
|
590 90 gm
|
|
0.03479 0. 32 0.00347 0.(\(olwm\). Other window managers work with varied success. If you are not certain as to how your system is)awidthshow
|
|
601 90 gm
|
|
0.06744 0. 32 0.00674 0.(set up, please contact your systems administrator.)awidthshow
|
|
623 90 gm
|
|
-0.00114 0.(Once the window system has started, and a terminal window \(xterm, shelltool etc.\) you can start up the GDE)ashow
|
|
634 90 gm
|
|
0.61325 0. 32 0.06132 0.(by typing:)awidthshow
|
|
656 90 gm
|
|
1.45217 0. 32 0.14521 0.(demo% )awidthshow
|
|
1 fs
|
|
{}mark T /Times-Bold /|______Times-Bold 0 rf
|
|
2 F /|______Times-Bold fnt
|
|
1.81137 0. 32 0.18113 0.(gde tRNAs)awidthshow
|
|
678 90 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
2 F /|______Times-Roman fnt
|
|
-0.00747 0.(This should load the sample data set tRNAs into GDE, and the following window should appear:)ashow
|
|
F T cp
|
|
%%Page: ? 4
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 303 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(4)show
|
|
0 0 gm
|
|
(nc 72 90 269 544 6 rc)kp
|
|
64 gr
|
|
112 136 243 419 1 rc
|
|
0 gr
|
|
T 283 8.72726 136 112 98 778 24 T 1 db
|
|
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T 283 8 136 128.72726 98 778 22 T 1 db
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T 283 8 136 226.72726 98 778 22 T 1 db
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00C00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000C0000000000000000
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00C00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000C0000000000000000
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00C001E0000000000F00000000000000030000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000C0000000000000000
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T 283 9 136 234.78259 98 778 23 T 1 db
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82 245 gm
|
|
(nc 73 244 85 330 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
2 F /|______Times-Roman fnt
|
|
-0.11044 0.(Command menus)ashow
|
|
256 425 gm
|
|
(nc 247 424 259 474 6 rc)kp
|
|
-0.07157 0.(Scrollbars)ashow
|
|
247 144 gm
|
|
(nc 238 143 250 195 6 rc)kp
|
|
-0.13261 0.(Status line)ashow
|
|
184 92 gm
|
|
(nc 175 91 199 123 6 rc)kp
|
|
(Short)show
|
|
196 92 gm
|
|
-0.16336 0.(names)ashow
|
|
85 416 gm
|
|
(nc 76 415 100 464 6 rc)kp
|
|
-0.13940 0.(Sequence)ashow
|
|
97 416 gm
|
|
-0.24850 0.(alignment)ashow
|
|
(nc 72 90 269 544 6 rc)kp
|
|
pr
|
|
140 195 pl
|
|
129 186 pl
|
|
127 189 pl
|
|
126 192 pl
|
|
140 195 pl
|
|
0 gr
|
|
1 ep
|
|
94 172 gm
|
|
127 189 0 gr
|
|
lin
|
|
pr
|
|
157 361 pl
|
|
145 368 pl
|
|
147 371 pl
|
|
150 373 pl
|
|
157 361 pl
|
|
1 ep
|
|
103 415 gm
|
|
147 371 0 gr
|
|
lin
|
|
pr
|
|
184 397 pl
|
|
196 406 pl
|
|
197 403 pl
|
|
198 399 pl
|
|
184 397 pl
|
|
1 ep
|
|
247 424 gm
|
|
197 403 0 gr
|
|
lin
|
|
pr
|
|
229 325 pl
|
|
228 340 pl
|
|
232 339 pl
|
|
235 338 pl
|
|
229 325 pl
|
|
1 ep
|
|
247 424 gm
|
|
232 339 0 gr
|
|
lin
|
|
pr
|
|
166 136 pl
|
|
178 129 pl
|
|
176 126 pl
|
|
173 124 pl
|
|
166 136 pl
|
|
1 ep
|
|
184 118 gm
|
|
176 126 0 gr
|
|
lin
|
|
94 137 gm
|
|
(nc 85 136 97 170 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
(Cursor)show
|
|
265 218 gm
|
|
(nc 256 217 268 327 6 rc)kp
|
|
-0.10447 0.(Split screen drag point)ashow
|
|
(nc 72 90 269 544 6 rc)kp
|
|
pr
|
|
225 384 pl
|
|
235 373 pl
|
|
232 372 pl
|
|
228 370 pl
|
|
225 384 pl
|
|
0 gr
|
|
1 ep
|
|
256 325 gm
|
|
232 372 0 gr
|
|
lin
|
|
167 472 gm
|
|
(nc 158 471 170 543 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
-0.16412 0.(Scroll elevator)ashow
|
|
(nc 72 90 269 544 6 rc)kp
|
|
pr
|
|
148 397 pl
|
|
147 412 pl
|
|
151 411 pl
|
|
154 410 pl
|
|
148 397 pl
|
|
0 gr
|
|
1 ep
|
|
161 465 gm
|
|
151 411 0 gr
|
|
lin
|
|
pr
|
|
129 228 pl
|
|
115 229 pl
|
|
116 232 pl
|
|
117 236 pl
|
|
129 228 pl
|
|
1 ep
|
|
84 243 gm
|
|
116 232 0 gr
|
|
lin
|
|
131 460 gm
|
|
(nc 122 459 134 515 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
-0.13102 0.(Resize tabs)ashow
|
|
(nc 72 90 269 544 6 rc)kp
|
|
pr
|
|
119 401 pl
|
|
118 416 pl
|
|
122 415 pl
|
|
125 414 pl
|
|
119 401 pl
|
|
0 gr
|
|
1 ep
|
|
129 454 gm
|
|
122 415 0 gr
|
|
lin
|
|
pr
|
|
229 399 pl
|
|
215 404 pl
|
|
217 407 pl
|
|
220 410 pl
|
|
229 399 pl
|
|
1 ep
|
|
164 445 gm
|
|
217 407 0 gr
|
|
lin
|
|
153 454 gm
|
|
137 465 lin
|
|
300 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.08865 0. 32 0.00886 0.(This is the sequence alignment editor. It consists of a color alignment display, a set of command menus,)awidthshow
|
|
311 90 gm
|
|
0.00823 0. 32 0.00082 0.(horizontal and vertical scroll bars to navigate the alignment, a list of short sequence names \(usually the)awidthshow
|
|
322 90 gm
|
|
0.02410 0. 32 0.00241 0.(LOCUS of a Genbank entry\), and a status line. The cursor is located in the upper left corner.)awidthshow
|
|
355 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.07032 0.(Using the Mouse)ashow
|
|
378 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02319 0.(The mouse follow OpenLook standards for operation. The functions for each button are:)ashow
|
|
0 0 gm
|
|
(nc 391 90 498 329 6 rc)kp
|
|
64 gr
|
|
411 178 497 239 17.5 17.5 1 rr
|
|
0 gr
|
|
411.5 178.5 496.5 238.5 17.5 17.5 0 rr
|
|
64 gr
|
|
426 189 460 197 17.5 17.5 1 rr
|
|
0 gr
|
|
426.5 189.5 459.5 196.5 17.5 17.5 0 rr
|
|
64 gr
|
|
426 205 460 212 17.5 17.5 1 rr
|
|
0 gr
|
|
426.5 205.5 459.5 211.5 17.5 17.5 0 rr
|
|
64 gr
|
|
426 220 460 227 17.5 17.5 1 rr
|
|
0 gr
|
|
426.5 220.5 459.5 226.5 17.5 17.5 0 rr
|
|
142 315 107 239 th
|
|
441 92 gm
|
|
tu
|
|
(nc 434 91 443 153 6 rc)kp
|
|
ts
|
|
0 gr
|
|
T 1 setTxMode
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.24205 0.(Object selection)ashow
|
|
tu
|
|
ts
|
|
450 92 gm
|
|
tu
|
|
(nc 443 91 452 165 6 rc)kp
|
|
ts
|
|
-0.14672 0.(clicking & dragging)ashow
|
|
tu
|
|
ts
|
|
441 270 gm
|
|
tu
|
|
(nc 434 269 443 328 6 rc)kp
|
|
ts
|
|
-0.20312 0.(Menu selection)ashow
|
|
tu
|
|
ts
|
|
450 270 gm
|
|
tu
|
|
(nc 443 269 452 302 6 rc)kp
|
|
ts
|
|
-0.09335 0.(dragging)ashow
|
|
tu
|
|
441 151 gm
|
|
(nc 391 90 498 329 6 rc)kp
|
|
441 189 0 gr
|
|
lin
|
|
433 182 449 198 165 195 1 ar
|
|
441 265 gm
|
|
441 231 lin
|
|
433 224 449 239 345 375 1 ar
|
|
ts
|
|
399 186 gm
|
|
tu
|
|
(nc 392 186 401 237 6 rc)kp
|
|
ts
|
|
0 gr
|
|
T 1 setTxMode
|
|
-0.22036 0.(Object adjust)ashow
|
|
tu
|
|
403 208 gm
|
|
(nc 391 90 498 329 6 rc)kp
|
|
426 208 0 gr
|
|
lin
|
|
418 201 434 217 255 285 1 ar
|
|
518 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.01296 0. 32 0.00129 0.(The left mouse button is used for placing the cursor, selecting sequences by their short)awidthshow
|
|
529 90 gm
|
|
0.16891 0. 32 0.01689 0.(names, scrolling/paging, performing split screens, and resizing. The right button is used for pop up menus,)awidthshow
|
|
540 90 gm
|
|
-0.01223 0.(and scrollbar menus. The middle button is used for extending a text selection.)ashow
|
|
562 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.11749 0.(Cursor Movement)ashow
|
|
585 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
(The cursor can be moved using the arrow keys, or by clicking the mouse within a sequence. The cursors)show
|
|
596 90 gm
|
|
0.14465 0. 32 0.01446 0.(position is displayed on the status line in both sequence position and alignment column number. The right)awidthshow
|
|
607 90 gm
|
|
0.06561 0. 32 0.00656 0.(hand side of the status line shows the left and right column positions of the currently active display.)awidthshow
|
|
629 90 gm
|
|
0.07385 0. 32 0.00738 0.(Scrolling is controlled by the scrollbar elevator. By clicking \(left mouse button\) on one of the elevator)awidthshow
|
|
640 90 gm
|
|
-0.03851 0.(arrows, the screen will scroll one character in that direction. By dragging the elevator center, the screen can)ashow
|
|
651 90 gm
|
|
-0.00059 0.(be moved directly to any location. By clicking directly to one side of the elevator, the screen will scroll one)ashow
|
|
662 90 gm
|
|
0.07583 0. 32 0.00758 0.(full screen in that direction. And by clicking on the scrollbar anchor, the elevator will move to that anchor.)awidthshow
|
|
673 90 gm
|
|
0.20538 0. 32 0.02053 0.(Scrollbars also have menus associated with them giving other scroll options. Use the right mouse button to)awidthshow
|
|
684 90 gm
|
|
(activate the menu.)show
|
|
F T cp
|
|
%%Page: ? 5
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 303 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(5)show
|
|
92 90 gm
|
|
-0.12741 0.(Selecting Sequences)ashow
|
|
115 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.05250 0.(Sequence selection is necessary before most functions can be performed. Selecting sequences is)ashow
|
|
126 90 gm
|
|
-0.03315 0.(accomplished by clicking or dragging \(left button\) over the short name associated with the sequence\(s\). The)ashow
|
|
137 90 gm
|
|
-0.01461 0.(name of the sequence should become highlighted on the release of the mouse button. By holding down the)ashow
|
|
148 90 gm
|
|
0.13977 0. 32 0.01397 0.(shift key, you can toggle the selection on or off for any set of sequences. By clicking just to the right of)awidthshow
|
|
159 90 gm
|
|
-0.00563 0.(any sequence short name, you will deselect all of them.)ashow
|
|
181 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.20321 0.(Selecting Text)ashow
|
|
204 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00436 0.(Selecting text is accomplished in much the same way as selecting entire sequences. In the editing window,)ashow
|
|
215 90 gm
|
|
0.04013 0. 32 0.00401 0.(you can drag the mouse pointer over a rectangular region the select a block of text. By using the shift key)awidthshow
|
|
226 90 gm
|
|
-0.01466 0.(\(or the middle mouse button\) you can adjust the selection to include other sequences, or other columns of)ashow
|
|
237 90 gm
|
|
-0.01264 0.(text. If groups are enabled, GDE will automatically select all sequences in a group if any one sequence in a)ashow
|
|
248 90 gm
|
|
-0.07606 0.(group is selected \(See Sequence Editing\).)ashow
|
|
270 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.12741 0.(Sequence Protection)ashow
|
|
293 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.05520 0.(All sequences can be individually protected against accidental modification. This is accomplished by)ashow
|
|
304 90 gm
|
|
-0.01127 0.(selecting the set of sequences that you are interested in editing, and choosing the "Set protections" menu)ashow
|
|
315 90 gm
|
|
0.03738 0. 32 0.00373 0.(item under the File menu. Your choices are:)awidthshow
|
|
337 90 gm
|
|
-0.03042 0.(Unambiguous modification)ashow
|
|
337 306 gm
|
|
-0.13563 0.(Changing/adding/deleting regular characters)ashow
|
|
348 90 gm
|
|
-0.02313 0.(Ambiguous changes)ashow
|
|
348 306 gm
|
|
0.28198 0. 32 0.02819 0.(Changing ambiguous codes \('N', 'X'...\))awidthshow
|
|
359 90 gm
|
|
-0.01168 0.(Alignment modifications)ashow
|
|
359 306 gm
|
|
0.23391 0. 32 0.02339 0.(Changing alignment gaps \('-', '~'\))awidthshow
|
|
381 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.15385 0.(Sequence Editing)ashow
|
|
404 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.04483 0.(Sequences can be edited by simply typing to insert, and using the delete or backspace key to delete characters.)ashow
|
|
415 90 gm
|
|
0.05371 0. 32 0.00537 0.(Sequences must have the proper protections set to allow the type of modifications that you are attempting.)awidthshow
|
|
426 90 gm
|
|
0.06790 0. 32 0.00679 0.(The default protection level only allows modification to the alignment, but not to the sequences themselves.)awidthshow
|
|
437 90 gm
|
|
-0.00852 0.(The Sun function keys, cut, copy and paste are used to edit selected text. Text selections work in rectangular)ashow
|
|
448 90 gm
|
|
(\(possibly disjointed\) regions. You can cut or copy a block of sequence text, and paste it to a new cursor)show
|
|
459 90 gm
|
|
0.10787 0. 32 0.01078 0.(location using these three keys.)awidthshow
|
|
F T cp
|
|
%%Page: ? 6
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 303 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(6)show
|
|
92 90 gm
|
|
-0.11007 0.(Repeat Counts)ashow
|
|
115 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02497 0.(By typing a numeric value before an editing function you can insert, delete or move a number of characters at)ashow
|
|
126 90 gm
|
|
-0.00587 0.(a time. The current repeat count is displayed on the status line, and can be cleared by clicking the left mouse)ashow
|
|
137 90 gm
|
|
0.08789 0. 32 0.00878 0.(button in the alignment window. In order to insert twenty gaps into a sequence, one would type "20-". In)awidthshow
|
|
148 90 gm
|
|
-0.02253 0.(order to move down five sequences, one would type "5)ashow
|
|
{}mark F /Symbol /|______Symbol 0 rf
|
|
7 fz
|
|
2 F /|______Symbol fnt
|
|
(\257)show
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02194 0.(". This works with all sequence types, however the)ashow
|
|
159 90 gm
|
|
-0.01254 0.(meta \(diamond\) key must be held down when the cursor is in a text or mask sequence. This is because)ashow
|
|
170 90 gm
|
|
-0.07215 0.(numbers are valid characters in these sequences, and would otherwise be confused with repeat counts.)ashow
|
|
192 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.11955 0.(Split Screen)ashow
|
|
215 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.11734 0. 32 0.01173 0.(Split screen editing allows the viewing one region while editing another. This is very useful for aligning)awidthshow
|
|
226 90 gm
|
|
-0.03680 0.("downstream" regions by editing "upstream".)ashow
|
|
248 90 gm
|
|
0.14480 0. 32 0.01448 0.(The alignment window can be split horizontally into two or more windows into the alignment. These)awidthshow
|
|
259 90 gm
|
|
-0.03460 0.(windows scroll independently of each other both horizontally and vertically. The short names displayed to)ashow
|
|
270 90 gm
|
|
-0.01350 0.(the left of the alignment correspond to the window that was last scrolled or edited. Care should be taken in)ashow
|
|
281 90 gm
|
|
-0.04472 0.(any modifications done in this mode so that edits are performed on the correct sequence. To avoid confusion)ashow
|
|
292 90 gm
|
|
0.00595 0. 32 0.00059 0.(during split screen operations, the vertical scroll bars may be locked so that all windows scroll together.)awidthshow
|
|
0 0 gm
|
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(nc 294 162 447 412 6 rc)kp
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006201088922000000000000000000000000000019200489122448608244840C10306080048A01C024801224489121820912103040C1820012244840C10206122601C0060000
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00620108900200000000000000000000000000001A000810204080908408041210489080081201C02800204081020242102010484122420020408041210209204201C0060000
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00620108900200000000000000000000000000001A000810204080908408041210489080081201C02800204081020242102010484122420020408041210209204201C0060000
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0062010F100400000000000000000000000000001A000810204080908408041210489080081201C02800204081020242102010484122420020408041210209204201C0060000
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00620109110800000000000000000000000000001A200811224481F88408843F10FDF880089201C028802044891207E2102210FC43F7E20022448043F1021FA04201C0060000
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00620108911000000000000000000000000000001A200811224481088408842110850880089201C02880204489120422102210844214220022448042110210A04201C0060000
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006201088920000000000000000000000000000019200409122441088204842110850880048A01C02480102448910422081210844214220012244042110210902201C0060000
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00620108873E000000000000000000000000000018E003870E1C390881C3842110850880038601C023800E1C3870E422070E1084421422000E1C38421102108E1E01C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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00620FEF071C000000000000000000000000000018E003870E1C3067F183877F1C3077FFE38601C023800E1C3870C19FC60E1DFC70C1DFFF8E1C03F8C1C3070E1A01C0060000
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006201088922000000000000000000000000000019200489122430608184890824309081048A01C0248012244890C1820612242090C2420412240040C24309121A01C0060000
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00620108900200000000000000000000000000001A000810204048908248100840490081081201C02800204081012242092040210124020420400041240490202601C0060000
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00620108900200000000000000000000000000001A000810204048908248100840490081081201C02800204081012242092040210124020420400041240490202601C0060000
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0062010F100C00000000000000000000000000001A000810204048908248100840490081081201C02800204081012242092040210124020420400041240490202601C0060000
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00620109110200000000000000000000000000001A2008112244FDF887E8900840FD1081089201C0288020448913F7E21FA2402103F4420422440043F44FD1207E01C0060000
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00620108910200000000000000000000000000001A200811224485088428900840851081089201C0288020448912142210A240210214420422440042144851204201C0060000
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006201088922000000000000000000000000000019200409122485088424880820849081048A01C02480102448921422109220208212420412240042124849104201C0060000
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00620108871C000000000000000000000000000018E003870E1C8508842387081C847081038601C023800E1C38721422108E1C207211C2040E1C004211C8470E4201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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00620FEF1108000000000000000000000000000018E1DFC70E1DFC67F183877F1C3077FFE38601C023877F1C3877F19FC60E1DFC70C1DFFF8E1C03F8C1C3070E1E01C0060000
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006201089118000000000000000000000000000019224209122420608184890824309081048A01C024890824489081820612242090C2420412240040C24309122601C0060000
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00620108912800000000000000000000000000001A040210204020908248100840490081081201C02810084081008242092040210124020420400041240490204201C0060000
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T 248 15 163 385.90908 70 554 33 T 1 db
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006200000000000000000000000000000000000018000000000000000000000000000000000201C02000000000000000000000000000000000000000000000000201C0060000
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00620FEF1108000000000000000000000000000018E1DFC70E1DFC67F183877F1C3077FFE38601C023877F1C3877F19FC60E1DFC70C1DFFF8E1C03F8C1C3070E1E01C0060000
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006201089118000000000000000000000000000019224209122420608184890824309081048A01C024890824489081820612242090C2420412240040C24309122601C0060000
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00620108912800000000000000000000000000001A040210204020908248100840490081081201C02810084081008242092040210124020420400041240490204201C0060000
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00620108910800000000000000000000000000001A040210204020908248100840490081081201C02810084081008242092040210124020420400041240490204201C0060000
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0062010F1F0800000000000000000000000000001A040210204020908248100840490081081201C02810084081008242092040210124020420400041240490204201C0060000
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00620109110800000000000000000000000000001A244211224021F887E8900840FD1081089201C028910844890087E21FA2402103F4420422440043F44FD1204201C0060000
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00620108910800000000000000000000000000001A244211224021088428900840851081089201C0289108448900842210A240210214420422440042144851204201C0060000
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006201089108000000000000000000000000000019224209122021088424880820849081048A0000248908244880842210922020821242041224004212484910220000060000
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006201089108000000000000000000000000000018E1C2070E1C2108842387081C847081038600002387081C38708422108E1C207211C2040E1C004211C8470E1E0000060000
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00620000000000000000000000000000000000001800000000000000000000000000000000020002200000000000000000000000000000000000000000000000020002060000
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00600000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000060000
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T 248 15 163 400.88232 70 554 34 T 1 db
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00600000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000060000
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00600000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000060000
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00600000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000060000
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00600000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000060000
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48 gr
|
|
391.5 255.5 446.5 314.5 90 180 0 ar
|
|
391.5 255.5 446.5 314.5 0 90 0 ar
|
|
0 0 2 9 9 2 dh
|
|
419 314 gm
|
|
425 321 lin
|
|
rh
|
|
psb
|
|
pse
|
|
0 0 2 9 9 2 dh
|
|
419 314 gm
|
|
425 307 lin
|
|
rh
|
|
psb
|
|
pse
|
|
0 0 pen
|
|
400 238 gm
|
|
400 238 lin
|
|
nc ct 39 0 put
|
|
pr
|
|
409 256 pl
|
|
400 238 pl
|
|
418 247 pl
|
|
409 256 pl
|
|
1 ep
|
|
1 1 pen
|
|
409 256 gm
|
|
bp
|
|
400 238 T qi
|
|
400 238 qc
|
|
418 247 qc
|
|
418 247 qc
|
|
409 256 qc
|
|
409 256 48 gr
|
|
T qq
|
|
qf
|
|
qf
|
|
ef
|
|
15 ec
|
|
(nc 294 162 447 412 6 rc)kp
|
|
2 2 pen
|
|
408 246 gm
|
|
417 255 lin
|
|
0 0 pen
|
|
401 306 gm
|
|
401 306 lin
|
|
nc ct 39 0 put
|
|
pr
|
|
410 324 pl
|
|
401 306 pl
|
|
419 315 pl
|
|
410 324 pl
|
|
0 gr
|
|
1 ep
|
|
1 1 pen
|
|
410 324 gm
|
|
bp
|
|
401 306 T qi
|
|
401 306 qc
|
|
419 315 qc
|
|
419 315 qc
|
|
410 324 qc
|
|
410 324 0 gr
|
|
T qq
|
|
qf
|
|
qf
|
|
ef
|
|
15 ec
|
|
(nc 294 162 447 412 6 rc)kp
|
|
2 2 pen
|
|
409 314 gm
|
|
418 323 lin
|
|
1 1 pen
|
|
467 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
2 F /|______Times-Roman fnt
|
|
0.05432 0. 32 0.00543 0.(In order to split a window into two views, grab \(left button\) the left or right anchor \(small rectangle\) at)awidthshow
|
|
478 90 gm
|
|
-0.02000 0.(either end of the horizontal scrollbar and drag to the middle of the window. This should split the window)ashow
|
|
489 90 gm
|
|
0.21789 0. 32 0.02178 0.(into two views. To join two views, place the mouse pointer on the horizontal scroll bar use the menu \(right)awidthshow
|
|
500 90 gm
|
|
0.61981 0. 32 0.06198 0.(button\) .)awidthshow
|
|
522 90 gm
|
|
(The views are NOT two copies of the alignment. Changes in one window are reflected in the other. Users)show
|
|
533 90 gm
|
|
0.00976 0. 32 0.00097 0.(should not be confused by this fact.)awidthshow
|
|
555 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06040 0.(Sequence Grouping)ashow
|
|
578 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00846 0.(Sequences can be grouped for editing functions. This is very helpful when trying to adjust several sub)ashow
|
|
589 90 gm
|
|
-0.00823 0.(alignments. When grouped, all sequences within a group will be affected by editing in any member of the)ashow
|
|
600 90 gm
|
|
0.07675 0. 32 0.00767 0.(group. All sequences within a group must have protections set to allow modification before any one will be)awidthshow
|
|
611 90 gm
|
|
-0.20011 0.(modified.)ashow
|
|
633 90 gm
|
|
-0.03013 0.(In order to group sequences, select the names of the sequences that should fall within a group, and select)ashow
|
|
644 90 gm
|
|
-0.02406 0.(Group under the Edit menu. A number will be placed at the left of the sequence representing its assigned)ashow
|
|
655 90 gm
|
|
-0.04641 0.(group number. To any sequence or sequences, the user selects those sequences and uses the Ungroup)ashow
|
|
666 90 gm
|
|
-0.06661 0.(command under the Edit menu.)ashow
|
|
688 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.11912 0.(Special keys)ashow
|
|
F T cp
|
|
%%Page: ? 7
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 303 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(7)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.01528 0.(There are also a few special function keys used in the GDE. Some functions have meta key equivalences so)ashow
|
|
92 90 gm
|
|
-0.01637 0.(that they can be called from the keyboard, instead of by the menu system. The "meta" key is a standard)ashow
|
|
103 90 gm
|
|
-0.05270 0.(property of X windows, and may be remapped to a different key symbol for different keyboards. For)ashow
|
|
114 90 gm
|
|
0.11459 0. 32 0.01145 0.(example, meta on Sun workstations is represented with a )awidthshow
|
|
{}mark F /Symbol /|______Symbol 0 rf
|
|
9 fz
|
|
2 F /|______Symbol fnt
|
|
(\340)show
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.11154 0. 32 0.01115 0.(, where on a Macintosh running MacX it might)awidthshow
|
|
125 90 gm
|
|
0.13610 0. 32 0.01361 0.(be the "apple" key. The operation of the key is the same as the control or shift key, it is held down while)awidthshow
|
|
136 90 gm
|
|
-0.04826 0.(pressing the second key in the sequence.)ashow
|
|
158 90 gm
|
|
0.07690 0. 32 0.00769 0.(Cut text, copy text and paste text are mapped to the Openlook equivalent keys \(L10, L6, and L8 on Sun)awidthshow
|
|
169 90 gm
|
|
-0.03259 0.(keyboards\). Other meta keys are defined in the .GDEmenus file, and may be changed to suit your)ashow
|
|
180 90 gm
|
|
-0.23315 0.(preferences.)ashow
|
|
205 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.01499 0.(Data Types)ashow
|
|
228 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.01342 0. 32 0.00134 0.(The GDE supports several data types. The data types supported in 2.0 are DNA, RNA, protein \(single letter)awidthshow
|
|
239 90 gm
|
|
-0.08953 0.(codes\), mask sequence, and text.)ashow
|
|
261 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.16458 0.(DNA and RNA)ashow
|
|
284 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06896 0.(Nucleic acid sequences are tightly type cast, and can contain any IUPAC code \(ACGTUM RSVWYHKDBN\))ashow
|
|
295 90 gm
|
|
0.00411 0. 32 0.00041 0.(as well as two alignment gap characters \('~' and '-'\). Some keys are remapped to fit IUPAC codes. For)awidthshow
|
|
306 90 gm
|
|
0.00274 0. 32 0.00027 0.(example, 'X' is mapped to 'N'. All nonstandard characters get mapped to the alignment gap '-'. Upper and)awidthshow
|
|
317 90 gm
|
|
-0.06726 0.(lower case are both supported, and the T/U characters are mapped based on whether you are working with)ashow
|
|
328 90 gm
|
|
-0.01962 0.(DNA or RNA. The color coding for DNA and RNA is identical. The color for ambiguous characters, and)ashow
|
|
339 90 gm
|
|
0.16555 0. 32 0.01655 0.(for alignment gaps is grey.)awidthshow
|
|
361 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.20167 0.(Amino Acid Sequence)ashow
|
|
384 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.04162 0.(Amino acid sequences are loosely type cast, and can contain any valid ASCII character. The results of)ashow
|
|
395 90 gm
|
|
-0.09436 0.(analysis on nonstandard characters is not guaranteed. The color for nonstandard amino acid characters, and for)ashow
|
|
406 90 gm
|
|
0.24002 0. 32 0.02400 0.(alignment gaps is grey.)awidthshow
|
|
428 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.16378 0.(Text Sequence)ashow
|
|
451 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03298 0.(Any valid ASCII printable character can be entered into a text sequence. Care should be taken with using)ashow
|
|
462 90 gm
|
|
-0.00344 0.(space characters, as these will only be saved properly in Genbank format, and not in flat file format. The)ashow
|
|
473 90 gm
|
|
-0.04928 0.(characters @#% and " should be avoided as well, as these can confuse the reading of flat files if saved in that)ashow
|
|
484 90 gm
|
|
-0.02505 0.(format.)ashow
|
|
506 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.13627 0.(Mask Sequence)ashow
|
|
529 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03303 0.(Mask sequence is identical to text sequence with the following exceptions. Mask sequence can have the)ashow
|
|
540 90 gm
|
|
0.06149 0. 32 0.00614 0.(ability \(function dependent\) of masking out positions in an alignment for analysis. If a mask sequence is)awidthshow
|
|
551 90 gm
|
|
0.01480 0. 32 0.00148 0.(selected along with some other sequence\(s\) for an analysis function that permits masking, then all columns)awidthshow
|
|
562 90 gm
|
|
0.06927 0. 32 0.00692 0.(that contain a '0' in the mask sequence will be ignored by the function. The mask itself would not be passed)awidthshow
|
|
573 90 gm
|
|
0.22354 0. 32 0.02235 0.(to the analysis function either. Some functions allow masking, some do not. Refer to the instruction page)awidthshow
|
|
584 90 gm
|
|
-0.00167 0.(for each function to see whether or not it supports sequence masking.)ashow
|
|
606 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06585 0.(Color Masks)ashow
|
|
629 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.01022 0. 32 0.00102 0.(Color masks give color to a sequence on a position by position basis. Individual sequences can have color)awidthshow
|
|
640 90 gm
|
|
-0.01266 0.(masks attached to them, or one color mask can be used for an entire alignment. Color masks are generated)ashow
|
|
651 90 gm
|
|
-0.00192 0.(externally by some analysis functions, and are then passed back to the GDE. The file format for a colormask)ashow
|
|
662 90 gm
|
|
-0.07350 0.(is described in Appendix A.)ashow
|
|
698 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.15777 0. 32 0.01577 0.(Menu Functions: File menu)awidthshow
|
|
F T cp
|
|
%%Page: ? 8
|
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op
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31 30 xl
|
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1 1 pen
|
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753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 303 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(8)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00126 0.(The GDE has several built-in menu functions under the File and Edit menus. These functions are unique in)ashow
|
|
92 90 gm
|
|
-0.02758 0.(that they are part of the primary display editor, and are not described in the .GDEmenus file.)ashow
|
|
126 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.33511 0.(Open...)ashow
|
|
138 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.19515 0. 32 0.01951 0.(Selecting this will bring up the open file dialog box. Users can scroll through a list of files in the current)awidthshow
|
|
149 90 gm
|
|
-0.07145 0.(directory, move up and down the directory tree, and open any individual data file. The sequence data in that)ashow
|
|
160 90 gm
|
|
-0.02137 0.(file is loaded into the current editing window below any existing sequences. The open command will open)ashow
|
|
171 90 gm
|
|
-0.01487 0.(any Genbank formatted file, or a GDE flat file.)ashow
|
|
193 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
1.41235 0. 32 0.14123 0.(Save as...)awidthshow
|
|
205 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.07537 0. 32 0.00753 0.(This function will save the entire alignment to a specified file in either Genbank or flat file format. The file)awidthshow
|
|
216 90 gm
|
|
-0.00964 0.(will be saved in the local directory unless a relative or absolute path is specified.)ashow
|
|
249 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.19628 0.(Properties...)ashow
|
|
261 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.02334 0. 32 0.00233 0.(Properties controls the display settings. Those settings include character size, color type, and insert)awidthshow
|
|
272 90 gm
|
|
-0.07415 0.(direction. The screen can also be inverted, vertical scroll lock and keyboard clicks \(tactile feedback\) can be)ashow
|
|
283 90 gm
|
|
0.11657 0. 32 0.01165 0.(turned on or off. Vertical scrollbar lock will cause all split views to scroll together in the vertical)awidthshow
|
|
294 90 gm
|
|
-0.11550 0.(direction.)ashow
|
|
0 0 gm
|
|
(nc 296 234 431 370 6 rc)kp
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64 gr
|
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297 235 430 369 1 rc
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0 gr
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T 134 33.87997 235 297 40 305 77 T 1 db
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473 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.15495 0.(Protections...)ashow
|
|
485 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.01272 0.(This will display, and then set the default protections for all selected sequences. If two or more of the)ashow
|
|
496 90 gm
|
|
-0.02812 0.(sequences differ in their current protection settings, a warning message will appear in the protection dialog)ashow
|
|
507 90 gm
|
|
-0.00859 0.(box. The protections currently available are alignment gap protection, ambiguous character protection,)ashow
|
|
518 90 gm
|
|
-0.02893 0.(unambiguous character protection, and translation protection.)ashow
|
|
0 0 gm
|
|
(nc 520 270 600 352 6 rc)kp
|
|
64 gr
|
|
521 271 599 351 1 rc
|
|
0 gr
|
|
T 80 39.75726 271 521 28 210 105 T 1 db
|
|
00000000000000000000000000000000000000000000000000000000
|
|
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|
|
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|
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|
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|
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|
|
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|
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C40110C40800122489908000000000000220400000000000030880000000000008910000000000000622004000000000000000000000000000000000000000000000000000201C006000
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C40111240800204289908000000000000220400E000000000508000E000000000091003C000000000A2200F800000000000000000000000000000000000000000000000000201C006000
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C40111260800204289508000000000000220801100000000010800100000000000910044000000001222004000000000000000000000000000000000000000000000000000201C006000
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C401E1238F002042895080000000000001C1000100000000010F002000000000030E004400000000221E004000000000000000000000000000000000000000000000000000201C006000
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C40113F0C800204289308000000000000221000F00000000010880200000000000910044000000003F02004000000000000000000000000000000000000000000000000000201C006000
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T 255 11 163 216.87997 74 579 25 T 1 db
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C40111240800204289908000000000000220400E000000000508000E000000000091003C000000000A2200F800000000000000000000000000000000000000000000000000201C006000
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C40111260800204289508000000000000220801100000000010800100000000000910044000000001222004000000000000000000000000000000000000000000000000000201C006000
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C401E1238F002042895080000000000001C1000100000000010F002000000000030E004400000000221E004000000000000000000000000000000000000000000000000000201C006000
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C40113F0C800204289308000000000000221000F00000000010880200000000000910044000000003F02004000000000000000000000000000000000000000000000000000201C006000
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C4011210480020428930800000000000022200110000000001088020000000000091004C000000000202004000000000000000000000000000000000000000000000000000201C006000
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C40112104800102489108000000000000222001100000000010880100000000008910034000000000222004000000000000000000000000000000000000000000000000000201C006000
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T 255 11 163 227.87997 74 579 25 T 1 db
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T 255 12 163 238.92306 74 579 26 T 1 db
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|
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285 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.53985 0. 32 0.05398 0.( Edit menu)awidthshow
|
|
308 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.29429 0.(Select All)ashow
|
|
320 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03724 0.(Selects all sequences. This is helpful when you have several dozen sequences.)ashow
|
|
342 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.19332 0. 32 0.01933 0.(Select by name...)awidthshow
|
|
354 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02021 0.(Select all sequences containing a given string in their short names field. No wild cards are allowed, and only)ashow
|
|
365 90 gm
|
|
-0.01213 0.(selecting is allowed, not de-selecting. The search is started when the Return key is pressed, and multiple)ashow
|
|
376 90 gm
|
|
-0.06175 0.(searches can be accumulated. Press Done when finished.)ashow
|
|
398 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.08575 0.(Cut/Copy/Paste sequences)ashow
|
|
410 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.05426 0.(Cut copy and paste are primarily useful for reordering sequences, and for making duplicate copies of a given)ashow
|
|
421 90 gm
|
|
0.07507 0. 32 0.00750 0.(sequence. They do not pass information to other programs. This capability will be implemented in a later)awidthshow
|
|
432 90 gm
|
|
-0.04278 0.(release. Cut and copy will place the selected sequences on an internal clipboard. They can then be pasted)ashow
|
|
443 90 gm
|
|
-0.06423 0.(back into the top of editing window \(default\) or under the last selected sequence.)ashow
|
|
465 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.02943 0.(Group/Ungroup)ashow
|
|
477 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00544 0.(Assign a group number to the selected sequences. Edit operations in any one sequence within the group will)ashow
|
|
488 90 gm
|
|
0.00320 0. 32 0.00032 0.(be propagated to all within the group. Sequence protections from one group are also imposed upon all other)awidthshow
|
|
499 90 gm
|
|
0.07339 0. 32 0.00733 0.(sequence in the given group. If a given operation is illegal in one sequence in a group \(i.e. alignment)awidthshow
|
|
510 90 gm
|
|
0.06820 0. 32 0.00682 0.(modification\) then it will not work in any of the sequences in that group. Ungroup will remove the selected)awidthshow
|
|
521 90 gm
|
|
-0.05171 0.(sequences from a given group.)ashow
|
|
543 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(Compress)show
|
|
555 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.01747 0.(Compress will remove gap characters from the selected sequences. The user has the option of removing all)ashow
|
|
566 90 gm
|
|
0.34576 0. 32 0.03457 0.(gaps, or simply all columns containing nothing but gaps. This is useful for minimizing the length of a)awidthshow
|
|
577 90 gm
|
|
0.05169 0.(subalignment.)ashow
|
|
599 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.10784 0.(Reverse Sequence)ashow
|
|
611 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06991 0.(Reverses the selected sequences. Alignment gaps are reversed as well. The selected sequences will remain)ashow
|
|
622 90 gm
|
|
-0.13101 0.(aligned after reversal.)ashow
|
|
647 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.04180 0. 32 0.00418 0.( DNA/RNA menu)awidthshow
|
|
671 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.16490 0.(Complement Sequence)ashow
|
|
683 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.20431 0. 32 0.02043 0.(Converts DNA/RNA into its complement strand \(keeping full IUPAC ambiguity\). This function has no)awidthshow
|
|
694 90 gm
|
|
-0.01968 0.(effect on text, protein, or mask sequence. Note that this function does not produce the reverse strand of DNA)ashow
|
|
705 90 gm
|
|
-0.02952 0.(but merely converts A<->T and G<->C. If the reverse strand is needed, remember to Complement and)ashow
|
|
716 90 gm
|
|
-0.09683 0.(Reverse the sequence \(Edit menu\).)ashow
|
|
F T cp
|
|
%%Page: ? 10
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(10)show
|
|
107 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.68984 0. 32 0.06898 0.(External Functions)awidthshow
|
|
130 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02468 0.(See appendix C for a full description of functions supported in GDE 2.0 All external functions are described)ashow
|
|
141 90 gm
|
|
0.00610 0. 32 0.00061 0.(in the configuration file .GDEmenus. Here is a brief description of some of the basic functions included.)awidthshow
|
|
163 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.16563 0.(File menu)ashow
|
|
186 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.07015 0.(New Sequence <meta n>)ashow
|
|
186 198 gm
|
|
-0.05102 0.(Create a new sequence. Prompts for sequence type, and short name.)ashow
|
|
208 90 gm
|
|
-0.03674 0.(Import foreign format)ashow
|
|
219 90 gm
|
|
-0.03681 0.(Export foreign format)ashow
|
|
219 198 gm
|
|
-0.08541 0.(Load and save sequences using Readseq by Don Gilbert \(see Appendix C\).)ashow
|
|
241 90 gm
|
|
-0.01116 0.(Save Selection)ashow
|
|
241 198 gm
|
|
-0.08074 0.(Save the currently selected sequences in a specified file.)ashow
|
|
263 90 gm
|
|
0.35308 0. 32 0.03530 0.(Print Selection)awidthshow
|
|
263 198 gm
|
|
0.01174 0. 32 0.00117 0.(Print the selected sequences to the chosen printer. This function supports)awidthshow
|
|
274 198 gm
|
|
0.04150 0. 32 0.00415 0.(the Unix command enscript as well as lpr. The .GDEmenus file may need to)awidthshow
|
|
285 198 gm
|
|
-0.00283 0.(be modified to add the names of local printers to the printer list.)ashow
|
|
307 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.20724 0.(Edit menu)ashow
|
|
330 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.25080 0.(sort...)ashow
|
|
330 198 gm
|
|
-0.06867 0.(Sort the selected sequences by a primary and secondary key. Pass the new order)ashow
|
|
341 198 gm
|
|
-0.00726 0.(to a new GDE window.)ashow
|
|
363 90 gm
|
|
-0.14492 0.(Extract)ashow
|
|
363 198 gm
|
|
-0.07679 0.(Extract the selected sequences into a new window.)ashow
|
|
385 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.24058 0.(DNA/RNA Menu)ashow
|
|
397 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.14962 0.(Translate)ashow
|
|
397 198 gm
|
|
-0.05361 0.(Translate the selected sequences from DNA/RNA to Amino acid. The user can)ashow
|
|
408 198 gm
|
|
-0.07470 0.(specify the desired reading frame, and the minimum open reading frame \(stop)ashow
|
|
419 198 gm
|
|
-0.00601 0.(codon to stop codon\) to translate. The user can also choose between single)ashow
|
|
430 198 gm
|
|
-0.09318 0.(letter code and triple letter codes.)ashow
|
|
452 90 gm
|
|
0.55633 0. 32 0.05563 0.(Dot plot)awidthshow
|
|
452 198 gm
|
|
-0.02882 0.(Display a dotplot identity matrix for the selected sequence\(s\). If only one)ashow
|
|
463 198 gm
|
|
(sequence is selected, then the dotplot is a self comparison. If two or more)show
|
|
474 198 gm
|
|
-0.10966 0.(sequences are selected, then the first two sequences are compared.)ashow
|
|
496 90 gm
|
|
0.63247 0. 32 0.06324 0.(Clustal Align)awidthshow
|
|
496 198 gm
|
|
0.04074 0. 32 0.00407 0.(Align the selected sequences using the clustalv algorithm by Des Higgins.)awidthshow
|
|
507 198 gm
|
|
-0.07983 0.(\(See Appendix C\))ashow
|
|
529 90 gm
|
|
0.29251 0. 32 0.02925 0.(Find All <meta f>)awidthshow
|
|
529 198 gm
|
|
-0.04464 0.(Search and highlight the selected sequences for a given substring. A specified)ashow
|
|
540 198 gm
|
|
-0.02334 0.(percent of mismatching can also be allowed.)ashow
|
|
562 90 gm
|
|
0.15136 0. 32 0.01513 0.(Variable Positions)awidthshow
|
|
562 198 gm
|
|
-0.06744 0.(The selected sequences are scored column by column for conservation. The)ashow
|
|
573 198 gm
|
|
0.02929 0. 32 0.00292 0.(result is returned as a grey scale alignment color mask. This can be useful)awidthshow
|
|
584 198 gm
|
|
0.41549 0. 32 0.04154 0.(in selecting PCR primers.)awidthshow
|
|
606 90 gm
|
|
-0.09349 0.(Sequence Consensus)ashow
|
|
606 198 gm
|
|
-0.02246 0.(Return the consensus for the selected sequences. This can either be a majority)ashow
|
|
617 198 gm
|
|
0.17730 0. 32 0.01773 0.(consensus, or an ambiguity consensus using IUPAC coding.)awidthshow
|
|
639 90 gm
|
|
-0.01284 0.(Distance Matrix )ashow
|
|
639 198 gm
|
|
-0.07553 0.(Calculate a distance matrix for the selected sequences. \(See Appendix C\))ashow
|
|
661 90 gm
|
|
(MFOLD)show
|
|
661 198 gm
|
|
-0.01577 0.(Fold the selected sequences using MFOLD by Michael Zuker. The resulting)ashow
|
|
672 198 gm
|
|
-0.08619 0.(structure is returned as a nested bracket \('[]'\) representation of the secondary)ashow
|
|
683 198 gm
|
|
-0.05360 0.(structure.\(See appendix C.\))ashow
|
|
705 90 gm
|
|
-0.13284 0.(Draw Secondary Structure)ashow
|
|
705 198 gm
|
|
-0.07971 0.(Draw the selected sequence using the proposed secondary structure. Both the)ashow
|
|
716 198 gm
|
|
-0.11421 0.(secondary structure prediction, and the RNA sequence should be selected before)ashow
|
|
F T cp
|
|
%%Page: ? 11
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(11)show
|
|
81 198 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.08117 0. 32 0.00811 0.(calling this function. The drawing program is LoopTool. \(See Appendix C\))awidthshow
|
|
103 90 gm
|
|
0.39718 0. 32 0.03971 0.(Highlight Helix)awidthshow
|
|
103 198 gm
|
|
-0.02478 0.(Show all violations to a proposed RNA secondary structure. The secondary)ashow
|
|
114 198 gm
|
|
-0.06376 0.(structure represented must be selected, as well as the aligned sequences to be)ashow
|
|
125 198 gm
|
|
-0.06709 0.(tested. The selected sequences will then be colored according to whether or not)ashow
|
|
136 198 gm
|
|
-0.02209 0.(they support the proposed 2)ashow
|
|
currentfont SwToSym
|
|
-0.02209 0.(\260)ashow
|
|
setfont
|
|
-0.02209 0.( structure. Standard Watson/Crick paring will be)ashow
|
|
147 198 gm
|
|
(colored dark blue, G-U paring will be colored light blue, mismatches will be)show
|
|
158 198 gm
|
|
-0.03656 0.(colored gold, and pairng to gaps will be red.)ashow
|
|
180 90 gm
|
|
-0.09217 0.(Blastn/BlastX)ashow
|
|
180 198 gm
|
|
-0.06690 0.(Search the selected sequence \(select only one\) against a given database with the)ashow
|
|
191 198 gm
|
|
0.21972 0. 32 0.02197 0.(BLAST searching tool written by Altschul, Gish, Miller, Myers, and Lipman.)awidthshow
|
|
202 198 gm
|
|
-0.05590 0.(Blastn searches DNA against DNA databases, blastx searches DNA against AA)ashow
|
|
213 198 gm
|
|
-0.04621 0.(databases by translating the sequence in all six reading frames. \(See Appendix C\))ashow
|
|
235 90 gm
|
|
0.02897 0.(FastA)ashow
|
|
235 198 gm
|
|
-0.06472 0.(Search the selected sequence \(select only one\) against a given database using the)ashow
|
|
246 198 gm
|
|
0.02075 0. 32 0.00207 0.(FASTA similarity search program written by Pearson and Lipman. \(See)awidthshow
|
|
257 198 gm
|
|
-0.09335 0.(Appendix C\))ashow
|
|
279 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.15008 0.(Protein Menu)ashow
|
|
313 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.63247 0. 32 0.06324 0.(Clustal Align)awidthshow
|
|
313 198 gm
|
|
-0.02090 0.(Align the selected amino acid sequences using the clustal algorithm. \(See)ashow
|
|
324 198 gm
|
|
-0.09335 0.(Appendix C\))ashow
|
|
346 90 gm
|
|
0.21408 0. 32 0.02140 0.(Blastp, Tblastn, Blast3)awidthshow
|
|
346 198 gm
|
|
-0.06690 0.(Search the selected sequence \(select only one\) against a given database with the)ashow
|
|
357 198 gm
|
|
0.21972 0. 32 0.02197 0.(BLAST searching tool written by Altschul, Gish, Miller, Myers, and Lipman.)awidthshow
|
|
368 198 gm
|
|
-0.04742 0.(Blastp searches AA against AA databases, tblastn searches AA against DNA)ashow
|
|
379 198 gm
|
|
-0.03672 0.(databases by translating the database in all six reading frames. Blast3 finds)ashow
|
|
390 198 gm
|
|
0.00274 0. 32 0.00027 0.(three way alignments that are could not be found with only pairwise comparisons.)awidthshow
|
|
401 198 gm
|
|
-0.07983 0.(\(See Appendix C\))ashow
|
|
423 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.20037 0.(Sequence Management Menu)ashow
|
|
446 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.07385 0. 32 0.00738 0.(Assemble contigs)awidthshow
|
|
446 198 gm
|
|
0.02410 0. 32 0.00241 0.(Assemble the selected sequences into contigs using the program CAP \(Contig)awidthshow
|
|
457 198 gm
|
|
-0.03036 0.(Assemble Program\) written by Xiaoqiu Huang. The resulting sequences are)ashow
|
|
468 198 gm
|
|
-0.03370 0.(returned to the current GDE window, and they are grouped into contigs. The)ashow
|
|
479 198 gm
|
|
-0.05517 0.(user can then sort the sequences by group, and offset to produce an ordered list of)ashow
|
|
490 198 gm
|
|
0.02960 0. 32 0.00296 0.(the contigs. \(See Appendix C\))awidthshow
|
|
512 90 gm
|
|
-0.02136 0.(Strategy view)ashow
|
|
512 198 gm
|
|
0.03570 0. 32 0.00357 0.(Pass out the selected sequences to StratView. This program will display contigs)awidthshow
|
|
523 198 gm
|
|
-0.01431 0.(in a greatly reduced line drawing. This is very useful for large contigs.)ashow
|
|
545 90 gm
|
|
0.32684 0. 32 0.03268 0.(Restriction sites)awidthshow
|
|
545 198 gm
|
|
-0.06761 0.(Search the selected sequences for the restriction enzymes specified in the given)ashow
|
|
556 198 gm
|
|
-0.01243 0.(enzyme file. The restriction sites are then colored by enzyme.)ashow
|
|
578 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.07624 0.(Phylogeny menu)ashow
|
|
602 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.07130 0.(DeSoete Tree fit)ashow
|
|
602 198 gm
|
|
-0.00927 0.(Calculate a phylogenetic tree using a least squares fitting algorithm on a distance)ashow
|
|
613 198 gm
|
|
-0.06059 0.(matrix calculated from the selected sequences. The results can then be passed on)ashow
|
|
624 198 gm
|
|
-0.01338 0.(to treetool for display and manipulation. \(See Appendix C\))ashow
|
|
646 90 gm
|
|
0.99151 0. 32 0.09915 0.(Phylip 3.4)awidthshow
|
|
646 198 gm
|
|
0.10299 0. 32 0.01029 0.(Pass the selected data to on of the treeing programs in Phylip, written by)awidthshow
|
|
657 198 gm
|
|
0.16418 0. 32 0.01641 0.(Joe Felsenstein. The chosen phylip program is started in it's own window,)awidthshow
|
|
668 198 gm
|
|
-0.12712 0.(with the selected sequences already loaded. \(See Appendix C\))ashow
|
|
F T cp
|
|
%%Page: ? 12
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(12)show
|
|
106 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.70434 0. 32 0.07043 0.(Citation of work)awidthshow
|
|
129 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.03417 0. 32 0.00341 0.(We ask that any published work using any of the external functions in GDE cite the appropriate authors.)awidthshow
|
|
140 90 gm
|
|
-0.08705 0.(Please see Appendix C for references.)ashow
|
|
187 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.42251 0. 32 0.04225 0.(Bug reports/extensions)awidthshow
|
|
210 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03602 0.(Any bug reports, RFE's \(request for enhancement\), and useful extensions to the GDE should be forwarded by)ashow
|
|
221 90 gm
|
|
0.06652 0. 32 0.00665 0.(electronic mail to:)awidthshow
|
|
243 90 gm
|
|
-0.12284 0.(smith@nucleus.harvard.edu)ashow
|
|
265 90 gm
|
|
-0.01402 0.(Please include as much detail as possible in bug reports so that the bug can be reproduced.)ashow
|
|
276 90 gm
|
|
-0.16358 0.(Correspondence should be addressed to:)ashow
|
|
298 90 gm
|
|
0.66253 0. 32 0.06625 0.(Steven Smith)awidthshow
|
|
309 90 gm
|
|
0.03417 0. 32 0.00341 0.(Director of Computation)awidthshow
|
|
320 90 gm
|
|
-0.16851 0.(Harvard Genome Laboratory)ashow
|
|
331 90 gm
|
|
0.55831 0. 32 0.05583 0.(16. Divinity Ave.)awidthshow
|
|
342 90 gm
|
|
-0.04499 0.(Cambridge, MA)ashow
|
|
342 162 gm
|
|
(02138)show
|
|
433 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06921 0.(Acknowledgments)ashow
|
|
456 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.01979 0.(I would like to thank the following people for their input and assistance and code used in the development of)ashow
|
|
467 90 gm
|
|
(the GDE:)show
|
|
489 90 gm
|
|
0.10726 0. 32 0.01072 0.(Carl Woese, Gary Olsen and Mike Maciukenas at University of Illinois Dept of Microbiology, Ross)awidthshow
|
|
500 90 gm
|
|
-0.02450 0.(Overbeek at Argonne National Laboratories,Walter Gilbert, Patrick Gillevet, Chunwei Wang and Susan)ashow
|
|
511 90 gm
|
|
0.02166 0. 32 0.00216 0.(Russo at the Harvard Genome Laboratory. I would also like to personally thank the following people for)awidthshow
|
|
522 90 gm
|
|
0.02990 0. 32 0.00299 0.(their permission to include their software with this release of GDE.)awidthshow
|
|
544 90 gm
|
|
0.14419 0. 32 0.01441 0.(Des Higgins)awidthshow
|
|
555 90 gm
|
|
-0.04928 0.(David Lipman and the group at NCBI)ashow
|
|
566 90 gm
|
|
0.03280 0. 32 0.00328 0.(William Pearson)awidthshow
|
|
577 90 gm
|
|
(Don Gilbert)show
|
|
588 90 gm
|
|
-0.11433 0.(Xiaoqui Huang)ashow
|
|
599 90 gm
|
|
0.07690 0. 32 0.00769 0.(Joe Felsenstein)awidthshow
|
|
610 90 gm
|
|
-0.09466 0.(Michael Zuker)ashow
|
|
621 90 gm
|
|
-0.13116 0.(Geert DeSoete)ashow
|
|
632 90 gm
|
|
-0.01974 0.(Michael Maciukenas and the group at the Ribosomal Database Project)ashow
|
|
654 90 gm
|
|
0.10925 0. 32 0.01092 0.(It is only by the generosity of these people that GDE has been successful.)awidthshow
|
|
F T cp
|
|
%%Page: ? 13
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(13)show
|
|
95 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.57128 0. 32 0.05712 0.(Appendix A, File Formats)awidthshow
|
|
122 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03565 0.(The currently supported file formats include GDE data files, Genbank formatted files \(with type extensions\),)ashow
|
|
133 90 gm
|
|
-0.01033 0.(a generic flat file format, and a color mask file.)ashow
|
|
155 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.18190 0.(GDE format)ashow
|
|
167 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02778 0.(GDE format is a tagged field format used for storing all available information about a sequence. The format)ashow
|
|
178 90 gm
|
|
-0.03959 0.(matches very closely the GDE internal structures for sequence data. The format consists of text records)ashow
|
|
189 90 gm
|
|
-0.08013 0.(starting and ending with braces \('{}'\). Between the open and close braces are several tagged field lines)ashow
|
|
200 90 gm
|
|
-0.04377 0.(specifying different pieces of information about a given sequence. The tag values can be wrapped with)ashow
|
|
211 90 gm
|
|
-0.05966 0.(double quote characters \('""'\) as needed. If quotes are not used, the first whitespace delimited string is taken)ashow
|
|
222 90 gm
|
|
-0.03451 0.(as the value. The allowable fields are:)ashow
|
|
244 90 gm
|
|
({)show
|
|
255 90 gm
|
|
-0.21841 0.(name)ashow
|
|
255 162 gm
|
|
-0.09494 0.("Short name for sequence")ashow
|
|
266 90 gm
|
|
-0.06198 0.(longname)ashow
|
|
266 162 gm
|
|
-0.11402 0.("Long \(more descriptive\) name for sequence")ashow
|
|
277 90 gm
|
|
-0.35173 0.(sequence-ID)ashow
|
|
277 162 gm
|
|
-0.09922 0.("Unique ID number")ashow
|
|
288 90 gm
|
|
-0.26521 0.(creation-date)ashow
|
|
288 162 gm
|
|
0.12008 0. 32 0.01200 0.("mm/dd/yy hh:mm:ss")awidthshow
|
|
299 90 gm
|
|
-0.19244 0.(direction)ashow
|
|
299 162 gm
|
|
-0.19648 0.([-1|1])ashow
|
|
310 90 gm
|
|
-0.28077 0.(strandedness)ashow
|
|
310 162 gm
|
|
-0.16368 0.([1|2])ashow
|
|
321 90 gm
|
|
-0.07225 0.(type)ashow
|
|
321 162 gm
|
|
-0.07638 0.([DNA|RNA||PROTEIN|TEXT|MASK])ashow
|
|
332 90 gm
|
|
-0.15226 0.(offset)ashow
|
|
332 162 gm
|
|
-0.03222 0.(\(-999999,999999\))ashow
|
|
343 90 gm
|
|
-0.17175 0.(group-ID)ashow
|
|
343 162 gm
|
|
-0.02587 0.(\(0,999\))ashow
|
|
354 90 gm
|
|
-0.29151 0.(creator)ashow
|
|
354 162 gm
|
|
-0.02342 0.("Author's name")ashow
|
|
365 90 gm
|
|
-0.31198 0.(descrip)ashow
|
|
365 162 gm
|
|
-0.12005 0.("Verbose description")ashow
|
|
376 90 gm
|
|
-0.01441 0.(comments)ashow
|
|
376 162 gm
|
|
-0.01306 0.("Lines of comments that can be fairly arbitrary)ashow
|
|
387 90 gm
|
|
-0.03907 0.(text about a sequence. Return characters are allowed, but no internal)ashow
|
|
398 90 gm
|
|
-0.05203 0.(double quotes or brace characters. Remember to close with a double)ashow
|
|
409 90 gm
|
|
-0.25929 0.(quote")ashow
|
|
420 90 gm
|
|
-0.37757 0.(sequence)ashow
|
|
420 162 gm
|
|
-0.11505 0.("gctagctagctagctagctcttagctgtagtcgtagctgatgctagct)ashow
|
|
431 90 gm
|
|
-0.13807 0.(gatgctagctagctagctagctgatcgatgctagctgatcgtagctgacg)ashow
|
|
442 90 gm
|
|
-0.09281 0.(gactgatgctagctagctagctagctgtctagtgtcgtagtgcttattgc")ashow
|
|
453 90 gm
|
|
(})show
|
|
475 90 gm
|
|
-0.03117 0.(Any fields that are not specified are assumed to be the default values. Offsets can be negative as well as)ashow
|
|
486 90 gm
|
|
-0.00729 0.(positive. Genbank entries written out in this format will have all \("\) converted to \('\), and all \({}\) converted)ashow
|
|
497 90 gm
|
|
-0.03678 0.(to \([]\) to avoid confusion in the parser. Leading and trailing gaps are removed prior to writing each sequence.)ashow
|
|
508 90 gm
|
|
-0.00801 0.(This format is deliberately verbose in order to be simple to duplicate.)ashow
|
|
552 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.11645 0.(Genbank format:)ashow
|
|
564 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06373 0.(GDE can read a concatenated list of Genbank entries, and extract certain fields from such files. The default)ashow
|
|
575 90 gm
|
|
(method for storing nucleic acid, amino acid, masking sequences or text is in Genbank format. The following)show
|
|
586 90 gm
|
|
-0.19308 0.(fields are recognized:)ashow
|
|
608 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.23880 0.(LOCUS:)ashow
|
|
608 162 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.04878 0.(Short name for this sequence \(Maximum of 32 characters\))ashow
|
|
0 -3 rm
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
(\240)show
|
|
619 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
-0.21890 0.(DEFINITION:)ashow
|
|
619 162 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06732 0.(Definition of sequence \(Maximum of 80 characters\))ashow
|
|
630 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.22387 0.(ORGANISM:)ashow
|
|
630 198 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
(Full name of organism \(Maximum of 80 characters\))show
|
|
641 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.22743 0.(AUTHORS:)ashow
|
|
641 198 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.04580 0.(Authors of this sequence \(Maximum of 80 characters\))ashow
|
|
652 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.22111 0.(ACCESSION:)ashow
|
|
652 162 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06069 0.(ID Number for this sequence \(Maximum of 80 characters\))ashow
|
|
663 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.23217 0.(ORIGIN:)ashow
|
|
663 162 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.16001 0.(Beginning of sequence data)ashow
|
|
0 -3 rm
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
(\240)show
|
|
-4096 -4096 gm
|
|
-4095 -4095 0 gr
|
|
lin
|
|
6 25 lw
|
|
691 90 gm
|
|
691 233 lin
|
|
25 6 lw
|
|
1 1 lw
|
|
704 90 gm
|
|
0 gr
|
|
T 1 setTxMode
|
|
9 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.03189 0.(\240 Required field)ashow
|
|
F T cp
|
|
%%Page: ? 14
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(14)show
|
|
81 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.39801 0.(//)ashow
|
|
81 198 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.22740 0.(End of sequence data)ashow
|
|
0 -3 rm
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
(\240)show
|
|
103 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.01617 0. 32 0.00161 0.(All other lines are retained as comments. The LOCUS line also specifies what type of sequence follows.)awidthshow
|
|
114 90 gm
|
|
0.31143 0. 32 0.03114 0.(The form of this line is:)awidthshow
|
|
133 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(LOCUS )ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.26533 0.(name)ashow
|
|
133 198 gm
|
|
-0.19900 0.(size)ashow
|
|
0 fs
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
-0.29850 0.( bp)ashow
|
|
133 234 gm
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.26533 0.(type)ashow
|
|
133 270 gm
|
|
-0.26533 0.(date)ashow
|
|
155 90 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.23757 0. 32 0.02375 0.(where )awidthshow
|
|
2 fs
|
|
{}mark T /Times-Italic /|______Times-Italic 0 rf
|
|
2 F /|______Times-Italic fnt
|
|
0.07641 0.(name)ashow
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
2 F /|______Times-Roman fnt
|
|
0.19012 0. 32 0.01901 0.( is the Genbank Locus name, )awidthshow
|
|
2 fs
|
|
{}mark T /Times-Italic /|______Times-Italic 0 rf
|
|
2 F /|______Times-Italic fnt
|
|
0.16464 0. 32 0.01646 0.(size )awidthshow
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
2 F /|______Times-Roman fnt
|
|
0.17791 0. 32 0.01779 0.(is total base count, )awidthshow
|
|
2 fs
|
|
{}mark T /Times-Italic /|______Times-Italic 0 rf
|
|
2 F /|______Times-Italic fnt
|
|
0.05877 0.(type)ashow
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
2 F /|______Times-Roman fnt
|
|
0.21957 0. 32 0.02195 0.( is one of DNA, RNA, PROTEIN,)awidthshow
|
|
166 90 gm
|
|
-0.03018 0.(MASK, or TEXT and )ashow
|
|
2 fs
|
|
{}mark T /Times-Italic /|______Times-Italic 0 rf
|
|
2 F /|______Times-Italic fnt
|
|
-0.02607 0.(date)ashow
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
2 F /|______Times-Roman fnt
|
|
-0.02537 0.( is of the form dd-MON-yyyy. In this way, the standard Genbank format is)ashow
|
|
177 90 gm
|
|
-0.06455 0.(extended to store all text, mask and protein data. The Genbank character set has also been extended in order)ashow
|
|
188 90 gm
|
|
-0.04171 0.(to support these other data types. Valid characters are:)ashow
|
|
210 90 gm
|
|
-0.04614 0.(DNA/RNA:)ashow
|
|
210 198 gm
|
|
-0.00355 0.(Full IUPAC coding as well as '-' and '~' characters for alignment)ashow
|
|
221 198 gm
|
|
-0.10925 0.(gaps)ashow
|
|
232 90 gm
|
|
0.04852 0.(Protein:)ashow
|
|
232 198 gm
|
|
-0.01260 0.(All valid single letter codes plus '-' and '~'. Other ASCII characters)ashow
|
|
243 198 gm
|
|
-0.04739 0.(may be inserted, however external functions may be confused by)ashow
|
|
254 198 gm
|
|
-0.12287 0.(such characters.)ashow
|
|
265 90 gm
|
|
(Mask:)show
|
|
265 198 gm
|
|
0.01281 0. 32 0.00128 0.(All legal printable ASCII characters. If used as a selection mask, all)awidthshow
|
|
276 198 gm
|
|
0.12207 0. 32 0.01220 0.(columns containing a '0' will be removed from any analysis.)awidthshow
|
|
287 90 gm
|
|
-0.02584 0.(Text:)ashow
|
|
287 198 gm
|
|
-0.05348 0.(All valid ASCII characters.)ashow
|
|
309 90 gm
|
|
0.05142 0. 32 0.00514 0.(Here is a valid Genbank entry for two E.coli tRNA's:)awidthshow
|
|
328 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.20202 0.(LOCUS ECOTRNT4 76 bp RNA 28-JAN-1991)ashow
|
|
336 90 gm
|
|
-0.20275 0.(DEFINITION E. coli \(T4 infected\) vulnerable tRNA \(A\).)ashow
|
|
344 90 gm
|
|
-0.20637 0.( ORGANISM Escherichia coli)ashow
|
|
352 90 gm
|
|
-0.20315 0.( AUTHORS Amitsur,M., Levitz,R. and Kaufmann,G.)ashow
|
|
360 90 gm
|
|
-0.20362 0.(FEATURES From To/Span Description)ashow
|
|
368 90 gm
|
|
-0.20298 0.( tRNA 1 76 vulnerable tRNA\(A\))ashow
|
|
376 90 gm
|
|
-0.21559 0.(BASE COUNT ?)ashow
|
|
384 90 gm
|
|
-0.23880 0.(ORIGIN)ashow
|
|
392 90 gm
|
|
-0.20169 0.( 1 GGGUCGUUAG CUCAGUUGGU AGAGCAGUUG ACUUUUAAUC AAUUGGNCGC AGGUUCGAAU)ashow
|
|
400 90 gm
|
|
-0.20666 0.( 61 CCUGCACGAC CCACCA)ashow
|
|
408 90 gm
|
|
-0.39801 0.(//)ashow
|
|
416 90 gm
|
|
-0.20202 0.(LOCUS ECOTRQ1 75 bp RNA 28-JAN-1991)ashow
|
|
424 90 gm
|
|
-0.20587 0.(DEFINITION E.coli Gln-tRNA-1.)ashow
|
|
432 90 gm
|
|
-0.20637 0.( ORGANISM Escherichia coli)ashow
|
|
440 90 gm
|
|
-0.20503 0.( AUTHORS Yaniv,M. and Folk,W.R.)ashow
|
|
448 90 gm
|
|
-0.20166 0.(SOURCE -REFERENCE [1] JOURNAL J. Biol. Chem. 250, 3243-3253 \(1975\))ashow
|
|
456 90 gm
|
|
-0.20362 0.(FEATURES From To/Span Description)ashow
|
|
464 90 gm
|
|
-0.20269 0.( tRNA 1 75 Gln-tRNA-1 \(NAR: 0510\))ashow
|
|
472 90 gm
|
|
-0.20231 0.( refnumbr 1 1 sequence not numbered in [1])ashow
|
|
480 90 gm
|
|
-0.21559 0.(BASE COUNT ?)ashow
|
|
488 90 gm
|
|
-0.23880 0.(ORIGIN)ashow
|
|
496 90 gm
|
|
-0.20169 0.( 1 UGGGGUAUCG CCAAGCGGUA AGGCACCGGU UUUUGAUACC GGCAUUCCCU GGUUCGAAUC)ashow
|
|
504 90 gm
|
|
-0.20697 0.( 61 CAGGUACCCC AGCCA)ashow
|
|
512 90 gm
|
|
-0.39801 0.(//)ashow
|
|
545 90 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.18539 0.(Flat file format:)ashow
|
|
557 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.11169 0. 32 0.01116 0.(This is a simplified format for importing sequence data, and passing it out to analysis functions. Very little)awidthshow
|
|
568 90 gm
|
|
0.02944 0. 32 0.00294 0.(information is actually retained in this format, and should be used carefully so as not to lose attribute)awidthshow
|
|
579 90 gm
|
|
0.03372 0. 32 0.00337 0.(information. It is defined as follow:)awidthshow
|
|
598 90 gm
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
7 fz
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.20729 0.(type_character short_name)ashow
|
|
606 90 gm
|
|
-0.21559 0.(sequence_data)ashow
|
|
614 90 gm
|
|
-0.21559 0.(sequence_data)ashow
|
|
622 90 gm
|
|
-0.21559 0.(sequence_data)ashow
|
|
630 90 gm
|
|
-0.29850 0.(...)ashow
|
|
652 90 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02508 0.(The type character is # for DNA/RNA, % for protein sequence, @ for mask sequence, and " for text. The)ashow
|
|
663 90 gm
|
|
0.07781 0. 32 0.00778 0.(short name is the same as the LOCUS line in Genbank. This is followed by lines of sequence, each ending)awidthshow
|
|
674 90 gm
|
|
-0.03877 0.(with a return character.These lines are read until the next type character is encountered, or until the end of the)ashow
|
|
685 90 gm
|
|
-0.01963 0.(file is reached. Care should be taken in using this format with text as space characters are stripped)ashow
|
|
-4096 -4096 gm
|
|
-4095 -4095 0 gr
|
|
lin
|
|
6 25 lw
|
|
703 90 gm
|
|
703 233 lin
|
|
25 6 lw
|
|
1 1 lw
|
|
F T cp
|
|
%%Page: ? 15
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(15)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.03921 0. 32 0.00392 0.(automatically. As of release 2.0, flat file format allows for an optional offset to be specified in parentheses)awidthshow
|
|
92 90 gm
|
|
-0.07716 0.(after the sequence name. An offset represents how many leading gap characters should be placed before the)ashow
|
|
103 90 gm
|
|
0.07568 0. 32 0.00756 0.(start of a sequence. If this offset does not exist, then it is defined to be 0.)awidthshow
|
|
125 90 gm
|
|
0.13809 0. 32 0.01380 0.(Here is a sample flat file for two Ecoli tRNA's:)awidthshow
|
|
144 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.22387 0.(#ECOTRNT4)ashow
|
|
152 90 gm
|
|
-0.20237 0.(GGGUCGUUAGCUCAGUUGGUAGAGCAGUUGACUUUUAAUCAAUUGGNCGCAGGUUCGAAU)ashow
|
|
160 90 gm
|
|
-0.21226 0.(CCUGCACGACCCACCA)ashow
|
|
168 90 gm
|
|
-0.22743 0.(#ECOTRQ1)ashow
|
|
176 90 gm
|
|
-0.20237 0.(UGGGGUAUCGCCAAGCGGUAAGGCACCGGUUUUUGAUACCGGCAUUCCCUGGUUCGAAUC)ashow
|
|
184 90 gm
|
|
-0.21322 0.(CAGGUACCCCAGCCA)ashow
|
|
217 90 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.09919 0.(Color mask:)ashow
|
|
229 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.10299 0. 32 0.01029 0.(The format for a color mask has been kept simple to make implementation of color functions easy. The)awidthshow
|
|
240 90 gm
|
|
0.05355 0. 32 0.00535 0.(format optionally defines which sequence to color, whether or not to color alignment gaps in the existing)awidthshow
|
|
251 90 gm
|
|
0.04089 0. 32 0.00408 0.(sequence, and how long the following mask will be. It is then followed by a list of decimal color codes)awidthshow
|
|
262 90 gm
|
|
-0.01760 0.(\(range 0 to 15\) for each position in the sequence. There are four keywords used in the color mask file.)ashow
|
|
273 90 gm
|
|
-0.12745 0.(Those keywords are:)ashow
|
|
295 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(name:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.22111 0.(short name)ashow
|
|
295 234 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.09985 0.(If short name matches a currently loaded sequence,)ashow
|
|
306 234 gm
|
|
0.16754 0. 32 0.01675 0.(then impose this color mask on that sequence. If this)awidthshow
|
|
317 234 gm
|
|
0.04577 0. 32 0.00457 0.(line is omitted, then color all sequences this color, and the color)awidthshow
|
|
328 234 gm
|
|
0.10223 0. 32 0.01022 0.(mask is expected to start at the leftmost column on the screen.)awidthshow
|
|
350 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(length:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.23880 0.(length)ashow
|
|
350 234 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.40191 0. 32 0.04019 0.(The following list in length long)awidthshow
|
|
372 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.23217 0.(nodash:)ashow
|
|
372 234 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.00579 0. 32 0.00057 0.(Skip over dash characters when imposing this color mask)awidthshow
|
|
383 234 gm
|
|
-0.03414 0.(on the named sequence. This allows an unaligned color)ashow
|
|
394 234 gm
|
|
-0.09637 0.(mask to be placed over aligned sequence.)ashow
|
|
416 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.23880 0.(start:)ashow
|
|
416 234 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.02685 0. 32 0.00268 0.(Begin reading the color mask on the next line.)awidthshow
|
|
438 90 gm
|
|
0.04302 0. 32 0.00430 0.(Here is a sample color mask file:)awidthshow
|
|
457 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.21070 0.(name:test_sequence)ashow
|
|
465 90 gm
|
|
-0.22387 0.(length:10)ashow
|
|
473 90 gm
|
|
-0.23217 0.(nodash:)ashow
|
|
481 90 gm
|
|
-0.23880 0.(start:)ashow
|
|
489 90 gm
|
|
(3)show
|
|
497 90 gm
|
|
(3)show
|
|
505 90 gm
|
|
(3)show
|
|
513 90 gm
|
|
(6)show
|
|
521 90 gm
|
|
(5)show
|
|
529 90 gm
|
|
(3)show
|
|
537 90 gm
|
|
(3)show
|
|
545 90 gm
|
|
(3)show
|
|
553 90 gm
|
|
(2)show
|
|
561 90 gm
|
|
(7)show
|
|
580 90 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00993 0.(The colors in the default color lookup table are:)ashow
|
|
591 90 gm
|
|
(0)show
|
|
591 126 gm
|
|
-0.10839 0.(White)ashow
|
|
591 270 gm
|
|
(8)show
|
|
591 306 gm
|
|
-0.33126 0.(Black)ashow
|
|
602 90 gm
|
|
(1)show
|
|
602 126 gm
|
|
-0.08668 0.(Yellow)ashow
|
|
602 234 gm
|
|
(9)show
|
|
602 270 gm
|
|
-0.09704 0.(Grey 1)ashow
|
|
613 90 gm
|
|
(2)show
|
|
613 126 gm
|
|
(Violet)show
|
|
613 270 gm
|
|
(10)show
|
|
613 306 gm
|
|
-0.09704 0.(Grey 2)ashow
|
|
624 90 gm
|
|
(3)show
|
|
624 126 gm
|
|
-0.55415 0.(Red)ashow
|
|
624 270 gm
|
|
(11)show
|
|
624 306 gm
|
|
-0.09704 0.(Grey 3)ashow
|
|
635 90 gm
|
|
(4)show
|
|
635 126 gm
|
|
-0.55255 0.(Aqua)ashow
|
|
635 270 gm
|
|
(12)show
|
|
635 306 gm
|
|
-0.09704 0.(Grey 4)ashow
|
|
646 90 gm
|
|
(5)show
|
|
646 126 gm
|
|
-0.11416 0.(Lime Green)ashow
|
|
646 270 gm
|
|
(13)show
|
|
646 306 gm
|
|
-0.09704 0.(Grey 5)ashow
|
|
657 90 gm
|
|
(6)show
|
|
657 126 gm
|
|
-0.29557 0.(Blue)ashow
|
|
657 270 gm
|
|
(14)show
|
|
657 306 gm
|
|
-0.09704 0.(Grey 6)ashow
|
|
668 90 gm
|
|
(7)show
|
|
668 126 gm
|
|
-0.02070 0.(Purple)ashow
|
|
668 270 gm
|
|
(15)show
|
|
668 306 gm
|
|
-0.10839 0.(White)ashow
|
|
F T cp
|
|
%%Page: ? 16
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(16)show
|
|
84 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.21636 0. 32 0.02163 0.(Appendix B, Adding Functions)awidthshow
|
|
107 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.04040 0.(The GDE uses a menu description language to define what external programs it can call, and what parameters)ashow
|
|
118 90 gm
|
|
0.08483 0. 32 0.00848 0.(and data to pass to each function. This language allows users to customize their own environment to suite)awidthshow
|
|
129 90 gm
|
|
-0.14483 0.(individual needs.)ashow
|
|
151 90 gm
|
|
-0.02262 0.(The following is how the GDE handles external programs when selected from a menu:)ashow
|
|
0 0 gm
|
|
(nc 164 126 255 369 6 rc)kp
|
|
64 gr
|
|
164 211 202 277 14.5 14.5 4 rr
|
|
0 gr
|
|
164.5 211.5 201.5 276.5 14.5 14.5 0 rr
|
|
64 gr
|
|
164 126 202 192 14.5 14.5 4 rr
|
|
0 gr
|
|
164.5 126.5 201.5 191.5 14.5 14.5 0 rr
|
|
64 gr
|
|
164 300 202 366 14.5 14.5 4 rr
|
|
0 gr
|
|
164.5 300.5 201.5 365.5 14.5 14.5 0 rr
|
|
183 192 gm
|
|
(nc 164 126 255 208 6 rc)kp
|
|
183 211 lin
|
|
(nc 164 126 255 369 6 rc)kp
|
|
177 205 190 218 165 195 4 ar
|
|
183 277 gm
|
|
(nc 164 126 255 296 6 rc)kp
|
|
183 300 lin
|
|
(nc 164 126 255 369 6 rc)kp
|
|
177 293 190 307 165 195 4 ar
|
|
145 385 91 243 th
|
|
177 133 gm
|
|
0 gr
|
|
T 1 setTxMode
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.17835 0.(Display dialog)ashow
|
|
185 133 gm
|
|
-0.07539 0.(box presenting)ashow
|
|
192 133 gm
|
|
0.30838 0. 32 0.03083 0.(user options.)awidthshow
|
|
177 215 gm
|
|
-0.19335 0.(Write out selected)ashow
|
|
185 215 gm
|
|
-0.13066 0.(data \(if any\) to)ashow
|
|
192 215 gm
|
|
-0.06405 0.(temporary files.)ashow
|
|
177 303 gm
|
|
-0.20286 0.(Call external )ashow
|
|
185 303 gm
|
|
(function, passing)show
|
|
192 303 gm
|
|
-0.10202 0.(parameters and data.)ashow
|
|
tu
|
|
64 gr
|
|
214 300 255 366 4 rc
|
|
0 gr
|
|
214.5 300.5 254.5 365.5 0 rc
|
|
202 331 gm
|
|
(nc 164 126 211 369 6 rc)kp
|
|
214 331 lin
|
|
(nc 164 126 255 369 6 rc)kp
|
|
208 325 221 338 255 285 4 ar
|
|
ts
|
|
224 307 gm
|
|
0 gr
|
|
T 1 setTxMode
|
|
-0.15270 0.(External program)ashow
|
|
232 307 gm
|
|
0.09719 0. 32 0.00971 0.(runs analysis, and)awidthshow
|
|
239 307 gm
|
|
-0.06079 0.(writes results to)ashow
|
|
247 307 gm
|
|
-0.06405 0.(temporary files.)ashow
|
|
tu
|
|
64 gr
|
|
217 211 255 277 14.5 14.5 4 rr
|
|
0 gr
|
|
217.5 211.5 254.5 276.5 14.5 14.5 0 rr
|
|
236 300 gm
|
|
(nc 164 281 255 369 6 rc)kp
|
|
236 277 lin
|
|
(nc 164 126 255 369 6 rc)kp
|
|
230 271 243 284 345 375 4 ar
|
|
ts
|
|
227 218 gm
|
|
0 gr
|
|
T 1 setTxMode
|
|
-0.08067 0.(GDE reads results)ashow
|
|
235 218 gm
|
|
-0.11495 0.(of temporary files)ashow
|
|
242 218 gm
|
|
0.20019 0. 32 0.02001 0.(\(if any\).)awidthshow
|
|
tu
|
|
64 gr
|
|
217 126 255 192 14.5 14.5 4 rr
|
|
0 gr
|
|
217.5 126.5 254.5 191.5 14.5 14.5 0 rr
|
|
236 211 gm
|
|
(nc 164 195 255 369 6 rc)kp
|
|
236 192 lin
|
|
(nc 164 126 255 369 6 rc)kp
|
|
230 186 243 199 345 375 4 ar
|
|
ts
|
|
227 133 gm
|
|
0 gr
|
|
T 1 setTxMode
|
|
-0.13632 0.(GDE cleans up)ashow
|
|
235 133 gm
|
|
-0.06405 0.(temporary files,)ashow
|
|
242 133 gm
|
|
-0.04287 0.(and displays new)ashow
|
|
250 133 gm
|
|
(data.)show
|
|
tu
|
|
275 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.03387 0. 32 0.00338 0.(Each step in this process is described in a file .GDEmenus in the user's current or home)awidthshow
|
|
286 90 gm
|
|
-0.17651 0.(directory.)ashow
|
|
308 90 gm
|
|
-0.02418 0.(The language used in this file describes three phases to an external function call. The first phase describes)ashow
|
|
319 90 gm
|
|
0.12283 0. 32 0.01228 0.(the menu item as it will appear, and the Unix command line that is actually run when it is selected. The)awidthshow
|
|
330 90 gm
|
|
-0.06280 0.(second phase describes how to prompt for the parameters needed by the function. The third phase describes)ashow
|
|
341 90 gm
|
|
-0.05538 0.(what data needs to be passed as input to the external function, and what data \(if any\) needs to be read back)ashow
|
|
352 90 gm
|
|
0.58975 0. 32 0.05897 0.(from its output.)awidthshow
|
|
374 90 gm
|
|
-0.01350 0.(The form of the language is a simple keyword/value list delimited by the colon \(:\) character. The language)ashow
|
|
385 90 gm
|
|
0.13610 0. 32 0.01361 0.(retains old values until new ones are set. For example, setting the menu name is done once for all items in)awidthshow
|
|
396 90 gm
|
|
0.02822 0. 32 0.00282 0.(that menu, and is only reset when the next menu is reached.)awidthshow
|
|
418 90 gm
|
|
-0.09211 0.(The keywords for phase one are:)ashow
|
|
440 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(menu:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.22387 0.(menu name)ashow
|
|
440 306 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06471 0.(Name of current menu)ashow
|
|
451 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(item:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.22387 0.(item name)ashow
|
|
451 306 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02093 0.(Name of current menu item)ashow
|
|
462 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(itemmeta:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.22743 0.(meta_key)ashow
|
|
462 306 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.12283 0.(Meta key equivalence \(quick keys\))ashow
|
|
473 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(itemhelp:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.22387 0.(help_file)ashow
|
|
473 306 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.15548 0. 32 0.01554 0.(Help file \(either full path, or in)awidthshow
|
|
484 306 gm
|
|
-0.09056 0.(GDE_HELP_DIR\))ashow
|
|
492 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(itemmethod:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21710 0.(Unix command)ashow
|
|
514 90 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.14251 0. 32 0.01425 0.(The item method command is a bit more involved, it is the Unix command that will actually run the)awidthshow
|
|
525 90 gm
|
|
0.02655 0. 32 0.00265 0.(external program intended. It is one line long, and can be up to 256 characters in length. It can have)awidthshow
|
|
536 90 gm
|
|
-0.02996 0.(embedded variable names \(starting with a '$'\) that will be replaced with appropriate values later on. It can)ashow
|
|
547 90 gm
|
|
-0.00277 0.(consist of multiple Unix commands separated by semi-colons \(;\), and may contain shell scripts and)ashow
|
|
558 90 gm
|
|
0.00350 0. 32 0.00035 0.(background processes as well as simple command names. Examples will be given later.)awidthshow
|
|
580 90 gm
|
|
-0.07740 0.(The keywords for phase two are:)ashow
|
|
602 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(arg:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.20848 0.(argument_variable_name)ashow
|
|
602 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.07934 0. 32 0.00793 0.(Name of this variable. It will appear)awidthshow
|
|
613 342 gm
|
|
0.09628 0. 32 0.00962 0.(in the itemmethod: line with a dollar)awidthshow
|
|
624 342 gm
|
|
0.35354 0. 32 0.03535 0.(sign \($\) in front of it.)awidthshow
|
|
635 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(argtype:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.20503 0.(slider,chooser,choice_menu or text)ashow
|
|
635 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02027 0.(The type of graphic object)ashow
|
|
646 342 gm
|
|
-0.00474 0.(representing this argument.)ashow
|
|
668 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(arglabel:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21144 0.(descriptive label)ashow
|
|
668 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.07995 0. 32 0.00799 0.(A short description of what this)awidthshow
|
|
679 342 gm
|
|
-0.09936 0.(argument represents)ashow
|
|
701 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(argmin:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.20805 0.(minimum_value \(integer\))ashow
|
|
701 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.11270 0.(Used for sliders.)ashow
|
|
723 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(argmax:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.20805 0.(maximum_value \(integer\))ashow
|
|
723 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.11270 0.(Used for sliders.)ashow
|
|
F T cp
|
|
%%Page: ? 17
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(17)show
|
|
92 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(argvalue:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.20805 0.(default_value \(integer\))ashow
|
|
92 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00714 0.(It is the numeric value associated with)ashow
|
|
103 342 gm
|
|
-0.05737 0.(sliders or the default choice in)ashow
|
|
114 342 gm
|
|
-0.06477 0.(choosers and choice_menus \(the first)ashow
|
|
125 342 gm
|
|
0.10726 0. 32 0.01072 0.(choice is 0, the second is 1 etc.\))awidthshow
|
|
147 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(argtext:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21559 0.(default value)ashow
|
|
147 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.07046 0.(Used for text fields.)ashow
|
|
169 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(argchoice:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.19900 0.(displayed value)ashow
|
|
0 fs
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21710 0.(passed value)ashow
|
|
169 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.15618 0.(Used for choosers and)ashow
|
|
180 342 gm
|
|
0.10101 0. 32 0.01010 0.(choice_menus. The first value is)awidthshow
|
|
191 342 gm
|
|
-0.12577 0.(displayed on screen, and the second)ashow
|
|
202 342 gm
|
|
-0.00753 0.(value is passed to the itemmethod)ashow
|
|
213 342 gm
|
|
0.12620 0.(line.)ashow
|
|
235 90 gm
|
|
-0.06112 0.(The keywords for phase three are as follows:)ashow
|
|
257 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(in:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.19900 0.(input_file)ashow
|
|
0 fs
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
2 F /|______Courier fnt
|
|
( )show
|
|
257 342 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.07873 0. 32 0.00787 0.(GDE will replace this name with a)awidthshow
|
|
268 342 gm
|
|
-0.12794 0.(randomly generated temporary file)ashow
|
|
279 342 gm
|
|
(name. It will then write the selected)show
|
|
290 342 gm
|
|
0.24902 0. 32 0.02490 0.(data out to this file.)awidthshow
|
|
312 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(informat:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21890 0.(file_format)ashow
|
|
312 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.14724 0. 32 0.01472 0.(Write data to this file for input to)awidthshow
|
|
323 342 gm
|
|
0.33538 0. 32 0.03353 0.(this function. Currently support)awidthshow
|
|
334 342 gm
|
|
-0.05738 0.(values are Genbank, and flat.)ashow
|
|
345 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.23217 0.(inmask:)ashow
|
|
345 342 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.05563 0.(This data can be controlled by a)ashow
|
|
356 342 gm
|
|
0.14770 0. 32 0.01477 0.(selection mask.)awidthshow
|
|
378 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.23217 0.(insave:)ashow
|
|
378 342 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.08697 0. 32 0.00869 0.(Do not remove this file after running)awidthshow
|
|
389 342 gm
|
|
0.19424 0. 32 0.01942 0.(the external function. This is useful)awidthshow
|
|
400 342 gm
|
|
0.01831 0. 32 0.00183 0.(for functions put in the background.)awidthshow
|
|
422 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(out:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21890 0.(output_file)ashow
|
|
422 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.07873 0. 32 0.00787 0.(GDE will replace this name with a)awidthshow
|
|
433 342 gm
|
|
-0.12794 0.(randomly generated temporary file)ashow
|
|
444 342 gm
|
|
0.21469 0. 32 0.02146 0.(name. It is up to the external function)awidthshow
|
|
455 342 gm
|
|
0.36849 0. 32 0.03684 0.(to fill this file with any results that)awidthshow
|
|
466 342 gm
|
|
0.03570 0. 32 0.00357 0.(might be read back into the GDE.)awidthshow
|
|
488 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.19900 0.(outformat:)ashow
|
|
2 fs
|
|
{}mark T /Courier-Oblique /|______Courier-Oblique 0 rf
|
|
2 F /|______Courier-Oblique fnt
|
|
-0.21890 0.(file_format)ashow
|
|
488 342 gm
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.18402 0. 32 0.01840 0.(The data in the output file will be in)awidthshow
|
|
499 342 gm
|
|
0.29846 0. 32 0.02984 0.(this format. Currently support)awidthshow
|
|
510 342 gm
|
|
-0.05863 0.(values are colormask, Genbank, and)ashow
|
|
521 342 gm
|
|
0.04431 0.(flat.)ashow
|
|
543 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.22743 0.(outsave:)ashow
|
|
543 342 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.01464 0.(Do not remove this file after reading.)ashow
|
|
554 342 gm
|
|
0.03158 0. 32 0.00315 0.(This is useful for background tasks.)awidthshow
|
|
576 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.21559 0.(outoverwrite:)ashow
|
|
576 342 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06021 0.(Overwrite existing sequences in the current)ashow
|
|
587 342 gm
|
|
-0.00816 0.(GDE window. Currently supported with)ashow
|
|
598 342 gm
|
|
-0.03097 0.("gde" format only.)ashow
|
|
642 90 gm
|
|
0.11749 0. 32 0.01174 0.(Here is a sample dialog box, and it's entry in the .GDEmenus file:)awidthshow
|
|
F T cp
|
|
%%Page: ? 18
|
|
op
|
|
31 30 xl
|
|
1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(18)show
|
|
454 408 241 216 th
|
|
147 170 gm
|
|
tu
|
|
(nc 143 169 312 327 6 rc)kp
|
|
ts
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
8.33332 fz
|
|
2 F /|______Courier fnt
|
|
( )show
|
|
165 170 gm
|
|
(menu:Test function)show
|
|
177 170 gm
|
|
(item:All capitals)show
|
|
182 170 gm
|
|
(itemmethod:\(tr '[a-z]' '[A-Z]' < INPUT_FILE > )show
|
|
188 170 gm
|
|
(INPUT_FILE.tmp ; mv INPUT_FILE.tmp $SAVE_FILE_NAME ; gde )show
|
|
194 170 gm
|
|
($SAVE_FILE_NAME -Wx $SIZE ; rm INPUT_FILE\) &)show
|
|
206 170 gm
|
|
(arg:SAVE_FILE_NAME)show
|
|
212 170 gm
|
|
(argtype:text)show
|
|
217 170 gm
|
|
(arglabel:Save converted data as?)show
|
|
223 170 gm
|
|
(argtext:CAPS)show
|
|
235 170 gm
|
|
(arg:SIZE)show
|
|
241 170 gm
|
|
(arglabel:Text size?)show
|
|
247 170 gm
|
|
(argtype:chooser)show
|
|
252 170 gm
|
|
(argvalue:1)show
|
|
258 170 gm
|
|
(argchoice:Small:small)show
|
|
264 170 gm
|
|
(argchoice:Medium:medium)show
|
|
270 170 gm
|
|
(argchoice:Large:large)show
|
|
276 170 gm
|
|
(argchoice:Extra Large:extra_large)show
|
|
288 170 gm
|
|
(in:INPUT_FILE)show
|
|
293 170 gm
|
|
(informat:flat)show
|
|
299 170 gm
|
|
(insave:)show
|
|
tu
|
|
305 170 gm
|
|
(nc 72 162 313 378 6 rc)kp
|
|
64 gr
|
|
73 166 142 355 1 rc
|
|
0 gr
|
|
73.5 166.5 141.5 354.5 0 rc
|
|
64 gr
|
|
79 174 89 193 12.5 12.5 1 rr
|
|
0 gr
|
|
79.5 174.5 88.5 192.5 12.5 12.5 0 rr
|
|
64 gr
|
|
77 172 137 352 1 rc
|
|
0 gr
|
|
T 180 31.07141 172 77 44 341 58 T 1 db
|
|
0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
|
|
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|
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|
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|
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|
|
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|
|
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|
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|
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|
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|
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|
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|
|
00C00006000000002600004000000880300C6000200000000002000000000804000800004000000001000000
|
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|
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|
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00C331A6038186331800003844408880300AA222222222200002012112200807850880404024224401000000
|
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00C3F0C601E18E3F1800000C44478880300923E22222222000020F2113E00804020883C041E4227C01000000
|
|
00C3016600718C30000000044448888030092202222222200002112132000804050884404224264001000000
|
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00C31336003198311800000444488880300822226226222000021120D22008040888844042241A4401000000
|
|
00C1E33383E19F1E1800007844474880300821C1A21A22200003CEA011C00807C88683A079D4023801000000
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
|
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|
|
0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
|
|
64 gr
|
|
77 172 137 352 1 rc
|
|
0 gr
|
|
T 180 31.07141 172 77 44 341 58 T 1 db
|
|
0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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T 180 30 172 108.05261 44 341 57 T 1 db
|
|
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|
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|
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|
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|
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|
|
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|
|
00C00006000000002600004000000880300C6000200000000002000000000804000800004000000001000000
|
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00C33336030183330C00006066488880300AA2222222332000021131122008040888C4404226224401000000
|
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00C331A6038186331800003844408880300AA222222222200002012112200807850880404024224401000000
|
|
00C3F0C601E18E3F1800000C44478880300923E22222222000020F2113E00804020883C041E4227C01000000
|
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00C3016600718C30000000044448888030092202222222200002112132000804050884404224264001000000
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00C31336003198311800000444488880300822226226222000021120D22008040888844042241A4401000000
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|
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|
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|
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|
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|
|
119 301 gm
|
|
119 274 lin
|
|
119 240 gm
|
|
119 214 lin
|
|
130 241 gm
|
|
130 276 lin
|
|
119 301 gm
|
|
119 345 lin
|
|
130 215 gm
|
|
119 215 lin
|
|
78.5 173.5 88.5 192.5 12.5 12.5 0 rr
|
|
78.5 197.5 88.5 228.5 12.5 12.5 0 rr
|
|
119 275 gm
|
|
130 275 lin
|
|
130 241 lin
|
|
200.5 163.5 224.5 263.5 13.5 13.5 0 rr
|
|
pr
|
|
100 268 pl
|
|
98 275 pl
|
|
100 275 pl
|
|
102 275 pl
|
|
100 268 pl
|
|
1 ep
|
|
100 377 gm
|
|
100 275 0 gr
|
|
lin
|
|
229.5 163.5 276.5 263.5 13.5 13.5 0 rr
|
|
0 0 pen
|
|
248 325 gm
|
|
248 325 lin
|
|
nc ct 39 0 put
|
|
1 1 pen
|
|
248 263 gm
|
|
bp
|
|
248 325 F qi
|
|
248 325 qc
|
|
248 363 qc
|
|
248 363 qc
|
|
124 363 qc
|
|
124 363 F qq
|
|
ef
|
|
9 ec
|
|
(nc 72 162 313 378 6 rc)kp
|
|
248 363 gm
|
|
pr
|
|
124 349 pl
|
|
122 356 pl
|
|
124 356 pl
|
|
126 356 pl
|
|
124 349 pl
|
|
1 ep
|
|
124 363 gm
|
|
124 356 0 gr
|
|
lin
|
|
100 377 gm
|
|
215 377 lin
|
|
215 263 gm
|
|
215 377 lin
|
|
322 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.02491 0.(Using the default parameters given in the dialog box, the executed Unix command line would be:)ashow
|
|
341 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.20088 0.(\(tr '[a-z]' '[A-Z]' < .gde_001 >.gde_001.tmp ; mv .gde_001.tmp CAPS ; gde CAPS -Wx medium ; rm .gde_001 \) &)ashow
|
|
363 90 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.06463 0.(where )ashow
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.06048 0.(.gde_001)ashow
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.05946 0.( is the name of the temporary file generated by the GDE which contains the selected sequences)ashow
|
|
374 90 gm
|
|
0.09124 0. 32 0.00912 0.(in flat file format. Since the GDE runs this command in the background \('&' at the end\) it is necessary to)awidthshow
|
|
385 90 gm
|
|
(specify the )show
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
(insave: )show
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.00428 0.(line, and to remove all temporary files manually. There is no output file specific because)ashow
|
|
396 90 gm
|
|
-0.02909 0.(the data is not loaded back into the current GDE window, but rather a new GDE window is opened on the)ashow
|
|
407 90 gm
|
|
-0.01303 0.(file. A simpler command that reloads the data after conversion might be:)ashow
|
|
426 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.21559 0.(item:All caps)ashow
|
|
434 90 gm
|
|
-0.20352 0.(itemmethod:tr '[a-z]' '[A-Z]' <INPUT > OUTPUT)ashow
|
|
450 90 gm
|
|
-0.22743 0.(in:INPUT)ashow
|
|
458 90 gm
|
|
-0.21559 0.(informat:flat)ashow
|
|
474 90 gm
|
|
-0.22111 0.(out:OUTPUT)ashow
|
|
482 90 gm
|
|
-0.21430 0.(outformat:flat)ashow
|
|
501 90 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.06103 0. 32 0.00610 0.(In this example, no arguments are specified, and so no dialog box will appear. The command is not run in)awidthshow
|
|
512 90 gm
|
|
-0.03242 0.(the background, so the GDE can clean up after itself automatically. The converted sequence is automatically)ashow
|
|
523 90 gm
|
|
-0.07383 0.(loaded back into the current GDE window.)ashow
|
|
545 90 gm
|
|
0.02014 0. 32 0.00201 0.(In general, the easiest type of program to integrate into the GDE is a program completely driven from a)awidthshow
|
|
556 90 gm
|
|
-0.00051 0.(Unix command line. Interactive programs can be tied in \(MFOLD for example\), however shell scripts must)ashow
|
|
567 90 gm
|
|
-0.01737 0.(be used to drive the parameter entry for these programs. Programs of the form:)ashow
|
|
586 90 gm
|
|
{}mark T /Courier /|______Courier 0 rf
|
|
7 fz
|
|
2 F /|______Courier fnt
|
|
-0.20149 0.(program_name -a1 argument1 -a2 arguement2 -f inputfile -er errorfile > outputfile)ashow
|
|
608 90 gm
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.06240 0. 32 0.00624 0.(can be specified in the .GDEmenus file directly. As this is the general form of most one Unix commands,)awidthshow
|
|
619 90 gm
|
|
0.06774 0. 32 0.00677 0.(these tend to be simpler to implement under the GDE.)awidthshow
|
|
641 90 gm
|
|
0.07995 0. 32 0.00799 0.(As functions grow in complexity, they may begin to need a user interface of their own. In these cases, the)awidthshow
|
|
652 90 gm
|
|
-0.01388 0.(command line calling arguments are still necessary in order to allow the GDE to hand them the appropriate)ashow
|
|
663 90 gm
|
|
-0.02767 0.(data, and possible retrieve results after some external manipulation.)ashow
|
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F T cp
|
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op
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31 30 xl
|
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1 1 pen
|
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753 90 gm
|
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(nc 31 30 761 582 6 rc)kp
|
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0 gr
|
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T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
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7 fz
|
|
2 F /|______Times-Roman fnt
|
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(19)show
|
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84 90 gm
|
|
14 fz
|
|
2 F /|______Times-Roman fnt
|
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0.49774 0. 32 0.04977 0.(Appendix C, External functions)awidthshow
|
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107 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.08163 0. 32 0.00816 0.(ClustalV - Cluster multiple sequence alignment)awidthshow
|
|
129 90 gm
|
|
0.30380 0. 32 0.03038 0.(Author: Des Higgins.)awidthshow
|
|
151 90 gm
|
|
-0.25508 0.(Reference:)ashow
|
|
151 162 gm
|
|
0.14328 0. 32 0.01432 0.(Higgins,D.G. Bleasby,A.J. and Fuchs,R. \(1991\) CLUSTAL V: improved software)awidthshow
|
|
162 162 gm
|
|
0.13442 0. 32 0.01344 0.(for multiple sequence alignment. ms. submitted to CABIOS)awidthshow
|
|
183 90 gm
|
|
-0.11924 0.(Parameters:)ashow
|
|
194 162 gm
|
|
-0.07839 0.(k-tuple pairwise search)ashow
|
|
194 270 gm
|
|
-0.07196 0.(Word size for pairwise comparisons)ashow
|
|
205 162 gm
|
|
-0.14807 0.(Window size)ashow
|
|
205 270 gm
|
|
0.07278 0. 32 0.00727 0.(Smaller values give faster alignments,)awidthshow
|
|
216 270 gm
|
|
-0.03422 0.(larger values are more sensitive.)ashow
|
|
227 162 gm
|
|
-0.05999 0.(Transitions weighted)ashow
|
|
227 270 gm
|
|
0.19729 0. 32 0.01972 0.(Can weight transitions twice as high as)awidthshow
|
|
238 270 gm
|
|
-0.01446 0.(transversions \(DNA only\).)ashow
|
|
249 162 gm
|
|
-0.04051 0.(Fixed gap penalty)ashow
|
|
249 270 gm
|
|
0.06027 0. 32 0.00602 0.(Gap insertion penalty, lower value, more gaps)awidthshow
|
|
260 162 gm
|
|
0.20385 0. 32 0.02038 0.(Floating gap penalty)awidthshow
|
|
260 270 gm
|
|
0.02777 0. 32 0.00277 0.(Gap extension penalty, lower value, longer gaps)awidthshow
|
|
304 90 gm
|
|
0.11117 0.(Comments:)ashow
|
|
315 162 gm
|
|
-0.01083 0.(ClustalV is a directed multiple sequence alignment algorithm that)ashow
|
|
326 162 gm
|
|
0.06652 0. 32 0.00665 0.(aligns a set of sequences based on their level of similarity. It first)awidthshow
|
|
337 162 gm
|
|
0.05584 0. 32 0.00558 0.(uses a Lipman Peasron pairwise similarity scoring to find "clusters")awidthshow
|
|
348 162 gm
|
|
-0.06562 0.(of similar sequences, and pre-aligns those sequences. It then adds)ashow
|
|
359 162 gm
|
|
0.03463 0. 32 0.00346 0.(other sequences to the alignment in the order of their similarity so as)awidthshow
|
|
370 162 gm
|
|
-0.02696 0.(to produce the cleanest alignment.)ashow
|
|
392 162 gm
|
|
0.09170 0. 32 0.00917 0.(Warning: ClustalV only uses unambiguous character codes. It will also)awidthshow
|
|
403 162 gm
|
|
0.04348 0. 32 0.00434 0.(convert all sequences to upper case in the process of aligning. Clustal)awidthshow
|
|
414 162 gm
|
|
0.04180 0. 32 0.00418 0.(does not pass back comments, author etc. Be sure to keep copies of your)awidthshow
|
|
425 162 gm
|
|
0.15106 0. 32 0.01510 0.(sequences if you do not wish to lose this information.)awidthshow
|
|
F T cp
|
|
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31 30 xl
|
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1 1 pen
|
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753 90 gm
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(nc 31 30 761 582 6 rc)kp
|
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0 gr
|
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T 1 setTxMode
|
|
0 fs
|
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{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
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(20)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
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-0.08074 0.(MFOLD - RNA secondary prediction)ashow
|
|
103 90 gm
|
|
-0.03694 0.(Author: Michael Zuker)ashow
|
|
125 90 gm
|
|
-0.17959 0.(Reference: )ashow
|
|
125 162 gm
|
|
0.13900 0. 32 0.01390 0.(M. Zuker)awidthshow
|
|
136 162 gm
|
|
0.27359 0. 32 0.02735 0.(On Finding All Suboptimal Foldings of an RNA Molecule.)awidthshow
|
|
147 162 gm
|
|
0.16525 0. 32 0.01652 0.(Science, 244, 48-52, \(1989\))awidthshow
|
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169 162 gm
|
|
0.12847 0. 32 0.01284 0.(J. A. Jaeger, D. H. Turner and M. Zuker)awidthshow
|
|
180 162 gm
|
|
-0.06132 0.(Improved Predictions of Secondary Structures for RNA.)ashow
|
|
191 162 gm
|
|
0.25482 0. 32 0.02548 0.(Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, \(1989\))awidthshow
|
|
213 162 gm
|
|
0.12847 0. 32 0.01284 0.(J. A. Jaeger, D. H. Turner and M. Zuker)awidthshow
|
|
224 162 gm
|
|
-0.01690 0.(Predicting Optimal and Suboptimal Secondary Structure for RNA.)ashow
|
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235 162 gm
|
|
0.13473 0. 32 0.01347 0.(in "Molecular Evolution: Computer Analysis of Protein and)awidthshow
|
|
246 162 gm
|
|
(Nucleic Acid Sequences", R. F. Doolittle ed.)show
|
|
257 162 gm
|
|
0.18035 0. 32 0.01803 0.(Methods in Enzymology, 183, 281-306 \(1989\))awidthshow
|
|
279 90 gm
|
|
-0.11924 0.(Parameters:)ashow
|
|
290 162 gm
|
|
-0.11352 0.(Linear/circular RNA fold)ashow
|
|
301 162 gm
|
|
0.25527 0. 32 0.02552 0.(ct File to save results)awidthshow
|
|
323 90 gm
|
|
0.11117 0.(Comments:)ashow
|
|
334 162 gm
|
|
0.06652 0. 32 0.00665 0.(MFOLD passes it's output to a program Zuk_to_gen that translates the secondary)awidthshow
|
|
345 162 gm
|
|
-0.01971 0.(structure prediction to a nested bracket \([]\) notation. This notation can then be used)ashow
|
|
356 162 gm
|
|
-0.00996 0.(in the Highlight Helix, and Draw Secondary structure \(LoopTool\) functions.)ashow
|
|
378 162 gm
|
|
-0.01683 0.(MFOLD currently does not support much in the way of additional parameters.)ashow
|
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389 162 gm
|
|
-0.04089 0.(We hope to have all additional parameters available soon.)ashow
|
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F T cp
|
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(nc 31 30 761 582 6 rc)kp
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0 gr
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T 1 setTxMode
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0 fs
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{}mark T /Times-Roman /|______Times-Roman 0 rf
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7 fz
|
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2 F /|______Times-Roman fnt
|
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(21)show
|
|
92 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
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-0.01799 0.(Blast - Basic Local Alignment Search Tool)ashow
|
|
114 90 gm
|
|
-0.25508 0.(Reference:)ashow
|
|
125 162 gm
|
|
0.16143 0. 32 0.01614 0.(Karlin, Samuel and Stephen F. Altschul \(1990\). Methods for)awidthshow
|
|
136 162 gm
|
|
-0.04147 0.(assessing the statistical significance of molecular sequence)ashow
|
|
147 162 gm
|
|
-0.01135 0.(features by using general scoring schemes, Proc. Natl. Acad.)ashow
|
|
158 162 gm
|
|
0.51742 0. 32 0.05174 0.(Sci. USA 87:2264-2268.)awidthshow
|
|
180 90 gm
|
|
0.46295 0. 32 0.04629 0.( )awidthshow
|
|
180 162 gm
|
|
0.27801 0. 32 0.02780 0.(Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W.)awidthshow
|
|
191 90 gm
|
|
0.46295 0. 32 0.04629 0.( )awidthshow
|
|
191 162 gm
|
|
0.10040 0. 32 0.01004 0.(Myers, and David J. Lipman \(1990\). Basic local alignment)awidthshow
|
|
202 90 gm
|
|
0.46295 0. 32 0.04629 0.( )awidthshow
|
|
202 162 gm
|
|
0.45684 0. 32 0.04568 0.(search tool, J. Mol. Biol. 215:403-410.)awidthshow
|
|
224 90 gm
|
|
0.46875 0. 32 0.04687 0.( )awidthshow
|
|
224 162 gm
|
|
0.40649 0. 32 0.04064 0.(Altschul, Stephen F. \(1991\). Amino acid substitution)awidthshow
|
|
235 90 gm
|
|
0.46875 0. 32 0.04687 0.( )awidthshow
|
|
235 162 gm
|
|
0.10742 0. 32 0.01074 0.(matrices from an information theoretic perspective. J. Mol.)awidthshow
|
|
246 90 gm
|
|
0.46295 0. 32 0.04629 0.( )awidthshow
|
|
246 162 gm
|
|
0.43884 0. 32 0.04388 0.(Biol. 219:555-565.)awidthshow
|
|
290 90 gm
|
|
-0.11924 0.(Parameters:)ashow
|
|
301 162 gm
|
|
-0.13816 0.(Which Database)ashow
|
|
301 270 gm
|
|
-0.09788 0.(Which nucleic or amino acid database)ashow
|
|
312 270 gm
|
|
-0.03448 0.(to search.)ashow
|
|
334 162 gm
|
|
-0.18505 0.(Word Size)ashow
|
|
334 270 gm
|
|
0.17608 0. 32 0.01760 0.(Length of initial hit. after locating a match of)awidthshow
|
|
345 270 gm
|
|
0.27908 0. 32 0.02790 0.(this length, alignment extension is attempted.)awidthshow
|
|
356 126 gm
|
|
-0.11082 0.(Blastn)ashow
|
|
367 162 gm
|
|
-0.11381 0.(Match score)ashow
|
|
367 270 gm
|
|
-0.03680 0.(Score for matches in secondary alignment extension)ashow
|
|
378 162 gm
|
|
-0.04492 0.(Mismatch score)ashow
|
|
378 270 gm
|
|
-0.02404 0.(Score for mismatches in secondary alignment extension)ashow
|
|
400 126 gm
|
|
0.49514 0. 32 0.04951 0.(Blastx, tblastn, blastp, blast3)awidthshow
|
|
411 162 gm
|
|
0.69580 0. 32 0.06958 0.(Substitution Matrix)awidthshow
|
|
411 270 gm
|
|
0.38192 0. 32 0.03819 0.(PAM120 or PAM250)awidthshow
|
|
444 126 gm
|
|
0.11117 0.(Comments:)ashow
|
|
444 198 gm
|
|
-0.01263 0.(The report is loaded into a text editor. This should be saved as a new file)ashow
|
|
455 198 gm
|
|
-0.01432 0.(as the default file is removed after execution. The latest version of blast can)ashow
|
|
466 198 gm
|
|
0.30914 0. 32 0.03091 0.(be obtained via anonymous ftp to ncbi.nlm.nih.gov.)awidthshow
|
|
F T cp
|
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753 90 gm
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T 1 setTxMode
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0 fs
|
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{}mark T /Times-Roman /|______Times-Roman 0 rf
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7 fz
|
|
2 F /|______Times-Roman fnt
|
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(22)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.14083 0. 32 0.01408 0.(FastA - Similarity search)awidthshow
|
|
103 126 gm
|
|
-0.25508 0.(Reference:)ashow
|
|
114 162 gm
|
|
0.31677 0. 32 0.03167 0.(W. R. Pearson and D. J. Lipman \(1988\),)awidthshow
|
|
125 162 gm
|
|
-0.00869 0.("Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448)ashow
|
|
147 162 gm
|
|
0.01358 0. 32 0.00135 0.(W. R. Pearson \(1990\) "Rapid and Sensitive Sequence)awidthshow
|
|
158 162 gm
|
|
0.26550 0. 32 0.02655 0.(Comparison with FASTP and FASTA" Methods in Enzymology 183:63-98)awidthshow
|
|
180 126 gm
|
|
-0.11924 0.(Parameters:)ashow
|
|
191 162 gm
|
|
-0.23434 0.(Database)ashow
|
|
191 306 gm
|
|
-0.12551 0.(Which database to search)ashow
|
|
202 162 gm
|
|
0.05493 0. 32 0.00549 0.(Number of alignments to report)awidthshow
|
|
213 162 gm
|
|
(SMATRIX)show
|
|
213 306 gm
|
|
0.26260 0. 32 0.02626 0.(Which similarity matrix to use)awidthshow
|
|
246 126 gm
|
|
0.11117 0.(Comments:)ashow
|
|
257 90 gm
|
|
0.47622 0. 32 0.04762 0.( )awidthshow
|
|
257 162 gm
|
|
-0.05303 0.(The FastA package includes several additional programs for pairwise alignment.)ashow
|
|
268 162 gm
|
|
-0.00224 0.(We have only included a bare bones link to FastA. We hope to include a more)ashow
|
|
279 162 gm
|
|
-0.00607 0.(complete setup for the actual 2.0 release.)ashow
|
|
F T cp
|
|
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753 90 gm
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|
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0 fs
|
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{}mark T /Times-Roman /|______Times-Roman 0 rf
|
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7 fz
|
|
2 F /|______Times-Roman fnt
|
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
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(23)show
|
|
81 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.38360 0. 32 0.03836 0.(Assemble Contigs - CAP Contig Assembly Program)awidthshow
|
|
103 126 gm
|
|
-0.04878 0.(Author - Xiaoqiu Huang)ashow
|
|
114 162 gm
|
|
-0.03823 0.(Department of Computer Science)ashow
|
|
125 162 gm
|
|
-0.02279 0.(Michigan Technological University)ashow
|
|
136 162 gm
|
|
0.34759 0. 32 0.03475 0.(Houghton, MI 49931)awidthshow
|
|
147 162 gm
|
|
-0.01989 0.(E-mail: huang@cs.mtu.edu)ashow
|
|
169 162 gm
|
|
0.31494 0. 32 0.03149 0.(Minor modifications for I/O by S. Smith)awidthshow
|
|
191 126 gm
|
|
-0.23449 0.(Reference -)ashow
|
|
202 162 gm
|
|
0.05538 0. 32 0.00553 0.("A Contig Assembly Program Based on Sensitive Detection of)awidthshow
|
|
213 90 gm
|
|
( )show
|
|
213 162 gm
|
|
0.00946 0. 32 0.00094 0.(Fragment Overlaps" \(submitted to Genomics, 1991\))awidthshow
|
|
235 126 gm
|
|
-0.11924 0.(Parameters:)ashow
|
|
246 162 gm
|
|
0.21423 0. 32 0.02142 0.(Minimum overlap)awidthshow
|
|
246 306 gm
|
|
-0.11988 0.(Number of bases required for overlap)ashow
|
|
257 162 gm
|
|
-0.01672 0.(Percent match within overlap)ashow
|
|
257 306 gm
|
|
-0.10456 0.(Percentage match required in the overlap)ashow
|
|
268 306 gm
|
|
-0.07734 0.(region before merge is alowwed.)ashow
|
|
290 126 gm
|
|
0.11117 0.(Comments:)ashow
|
|
312 162 gm
|
|
-0.06814 0.(CAP returns the aligned sequences to the current editor window. The sequences are)ashow
|
|
323 162 gm
|
|
0.00427 0. 32 0.00042 0.(placed into contigs by setting the groupid. Cap does not change the order of the)awidthshow
|
|
334 162 gm
|
|
-0.05079 0.(sequences, and so the results should be sorted by group and offset \(see sort under the)ashow
|
|
345 162 gm
|
|
-0.02096 0.(Edit menu\).)ashow
|
|
F T cp
|
|
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|
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31 30 xl
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1 1 pen
|
|
753 90 gm
|
|
(nc 31 30 761 582 6 rc)kp
|
|
0 gr
|
|
T 1 setTxMode
|
|
0 fs
|
|
{}mark T /Times-Roman /|______Times-Roman 0 rf
|
|
7 fz
|
|
2 F /|______Times-Roman fnt
|
|
0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
|
753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
|
(24)show
|
|
92 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
|
-0.10661 0.(Lsadt - Least squares additive tree analysis)ashow
|
|
114 90 gm
|
|
0.18157 0. 32 0.01815 0.(Author: Geert De Soete, 'C' implementation by Mike Maciukenas University of Illinois)awidthshow
|
|
136 90 gm
|
|
-0.00590 0.(Reference:LSADT, 1983 Psychometrika, 1984 Quality and Quantity)ashow
|
|
158 90 gm
|
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-0.11924 0.(Parameters:)ashow
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169 162 gm
|
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-0.02085 0.(Distance correction to use in distance matrix calculations \(see count below\).)ashow
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180 162 gm
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-0.03211 0.(What should be used for initial parameters estimates)ashow
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191 162 gm
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-0.12921 0.(Random number seed)ashow
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202 162 gm
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-0.05371 0.(Display method \(See TreeTool below\))ashow
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224 90 gm
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0.11117 0.(Comments:)ashow
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235 162 gm
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-0.02113 0.(The program has been rewritten in 'C' and will be included with the rRNA Database)ashow
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246 162 gm
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0.03906 0. 32 0.00390 0.(phylogenetic package being written at the University of Illinois Department of)awidthshow
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257 162 gm
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0.04248 0.(Microbiology.)ashow
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279 162 gm
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-0.01466 0.(Count is a short program to calculate a distance matrix from a sequence)ashow
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290 162 gm
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-0.01652 0.(alignment \(see below\).)ashow
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334 90 gm
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-0.00831 0.(Count - Distance matrix calculator)ashow
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356 90 gm
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0.45852 0. 32 0.04585 0.(Author: Steven Smith)awidthshow
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378 90 gm
|
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-0.11924 0.(Parameters:)ashow
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389 162 gm
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-0.07836 0.(Correction method)ashow
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389 306 gm
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-0.01190 0.(Currently Jukes-Cantor or none)ashow
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400 162 gm
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-0.17300 0.(Include dashed columns)ashow
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411 162 gm
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-0.04403 0.(Match upper case to lower)ashow
|
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444 90 gm
|
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0.11117 0.(Comments:)ashow
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455 162 gm
|
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-0.02917 0.(Passes back a distance matrix in a format readable by LSADT.)ashow
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510 90 gm
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-0.06629 0.(Treetool - Tree drawing/manipulation)ashow
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532 90 gm
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-0.01724 0.(Author:)ashow
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532 126 gm
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0.06912 0. 32 0.00691 0.(Michael Maciukenas, University of Illinois)awidthshow
|
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554 90 gm
|
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0.11117 0.(Comments:)ashow
|
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565 162 gm
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-0.08711 0.(See included documentation for TreeTool usage.)ashow
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F T cp
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
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753 300 gm
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12 fz
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2 F /|______Times-Roman fnt
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81 90 gm
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10 fz
|
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2 F /|______Times-Roman fnt
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0.08056 0. 32 0.00805 0.(Phylip - Complete phylogenetic analysis package \(3.4\))awidthshow
|
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103 90 gm
|
|
0.13824 0. 32 0.01382 0.(Author: Joe Felsenstein)awidthshow
|
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125 90 gm
|
|
-0.25508 0.(Reference:)ashow
|
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125 162 gm
|
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0.12664 0. 32 0.01266 0.(Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package \(Version 3.2\).)awidthshow
|
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136 162 gm
|
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0.18722 0. 32 0.01872 0.(Cladistics 5: 164-166)awidthshow
|
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169 90 gm
|
|
0.11117 0.(Comments:)ashow
|
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180 162 gm
|
|
0.13565 0. 32 0.01356 0.(Phylip is a very complete set of programs for phylogenetic analysis. GDE)awidthshow
|
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191 162 gm
|
|
-0.00163 0.(simply formats selected data \(obeying any selection mask\) to Phylip, and runs)ashow
|
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202 162 gm
|
|
0.06301 0. 32 0.00630 0.(the chosen program. Although all programs from Phylip are included, only)awidthshow
|
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213 162 gm
|
|
0.11154 0. 32 0.01115 0.(the programs pertaining to DNA/AA analysis are tied in to the menu system.)awidthshow
|
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224 162 gm
|
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-0.06831 0.(The complete set of documentation is included, and can be viewed directly from)ashow
|
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235 162 gm
|
|
-0.00129 0.(GDE. It is strongly suggested that user read the documentation before attempting to)ashow
|
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246 162 gm
|
|
(interpret results.)show
|
|
268 162 gm
|
|
-0.02252 0.(The full source code for Phylip can be obtained from genetics.washington.edu using)ashow
|
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279 162 gm
|
|
0.34255 0. 32 0.03425 0.(anonymous ftp.)awidthshow
|
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F T cp
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{}mark T /Times-Roman /|______Times-Roman 0 rf
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7 fz
|
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2 F /|______Times-Roman fnt
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0.34057 0. 32 0.03405 0.(GDE2.0 rev1)awidthshow
|
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753 300 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
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|
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92 90 gm
|
|
-0.10993 0.(Copyright Notice)ashow
|
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115 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
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-0.01510 0.(The Genetic Data Environment \(GDE\) software and documentation are not in the public domain. Portions)ashow
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126 90 gm
|
|
-0.04327 0.(of this code are owned and copyrighted by the The Board of Trustees of the University of Illinois and by)ashow
|
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137 90 gm
|
|
-0.03067 0.(Steven Smith at the Harvard Genome Laboratory. This release of the GDE program and documentation)ashow
|
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148 90 gm
|
|
-0.00248 0.(may not be sold, or incorporated into a commercial product, in whole or in part without the expressed)ashow
|
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159 90 gm
|
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0.24673 0. 32 0.02467 0.(written consent of the University of Illinois and of its author, Steven Smith.)awidthshow
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181 90 gm
|
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-0.01826 0.(All interested parties may redistribute the GDE as long as all copies are accompanied by this)ashow
|
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192 90 gm
|
|
0.05432 0. 32 0.00543 0.(documentation, and all copyright notices remain intact. Parties interested in redistribution must do so on a)awidthshow
|
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203 90 gm
|
|
-0.03430 0.(non-profit basis, charging only for cost of media. Modifications to the GDE core editor should be forwarded)ashow
|
|
214 90 gm
|
|
0.04577 0. 32 0.00457 0.(to the author Steven Smith at the address given below for inclusion into future releases. External programs)awidthshow
|
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225 90 gm
|
|
-0.02499 0.(used by the GDE are copyright by, and are the property of their respective authors unless otherwise stated.)ashow
|
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258 90 gm
|
|
0.02899 0. 32 0.00289 0.(While all attempts have been made to insure the integrity of these programs:)awidthshow
|
|
280 90 gm
|
|
12 fz
|
|
2 F /|______Times-Roman fnt
|
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-0.29307 0.(Disclaimer)ashow
|
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303 90 gm
|
|
10 fz
|
|
2 F /|______Times-Roman fnt
|
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(THE UNIVERSITY OF ILLINOIS, HARVARD UNIVERSITY AND THE AUTHOR, STEVEN SMITH)show
|
|
314 90 gm
|
|
0.21240 0. 32 0.02124 0.(GIVE NO WARRANTIES, EXPRESSED OR IMPLIED FOR THE SOFTWARE AND)awidthshow
|
|
325 90 gm
|
|
-0.03628 0.(DOCUMENTATION PROVIDED, INCLUDING, BUT NOT LIMITED TO WARRANTY OF)ashow
|
|
336 90 gm
|
|
0.20996 0. 32 0.02099 0.(MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE. User)awidthshow
|
|
347 90 gm
|
|
-0.06015 0.(understands the software is a research tool for which no warranties as to capabilities or accuracy are made,)ashow
|
|
358 90 gm
|
|
-0.01759 0.(and user accepts the software "as is." User assumes the entire risk as to the results and performance of the)ashow
|
|
369 90 gm
|
|
-0.05845 0.(software and documentation. The above parties cannot be held liable for any direct, indirect, consequential)ashow
|
|
380 90 gm
|
|
-0.00201 0.(or incidental damages with respect to any claim by user or any third party on account of, or arising from the)ashow
|
|
391 90 gm
|
|
-0.05157 0.(use of software and associated materials. This disclaimer covers both the GDE core editor and all external)ashow
|
|
402 90 gm
|
|
-0.01464 0.(programs used by the GDE.)ashow
|
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F T cp
|
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%%Trailer
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cd
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end
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%%Pages: 26 0
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%%EOF
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