Module:ImportProtein

local p = {}

function p.main (frame) Set up the initial frame parameters local debuglog="|}|}" local args=frame.args local parent=frame.getParent(frame) local pargs={} if parent then pargs=parent.args end local height=args.height or pargs.height or "50" local width=args.width or pargs.width or "600" local background=args.background or pargs.background or "#333333" local vtext=args.vtext or pargs.vtext or 25 -- characters of legend text to display vertically down from motifs local largeonlyregion=args.largeonlyregion or pargs.largeonlyregion or 20 local vtext=tonumber(vtext) -- no meaning except as a number local tableoutput=args.tableoutput or pargs.tableoutput or "collapsed" -- I've decided to use the table as the legend much of the time after all, I think. (previously defaulted to "nil" to suppress) if tableoutput=="no" then tableoutput=nil end local vwidth=args.vwidth or pargs.vwidth or 4 -- number of PIXELS to tag as not overwriteable with vertical text. local vclaim={} --- if vclaim[pixel] is true, that pixel is taken local vprotest='' --- list of positions not shown separated by spaces These parameters send text that needs to be processed into tables include is nil to include everything. If it exists then only what is in it is used. format is "I want only this" (any junk) "and this" etc. Note weakness - a stray quote would foul up the whole template. local include=args.include or pargs.include or "all" if include == "all" then include = nil end local tinclude={} if include then for i in mw.ustring.gmatch(include,%"(.-)%") do        tinclude[i]=1 end end replaceregion defines a section with too many features to note individually. Instead you group them with a new text. The format is xx..yy:"Use this text" local replaceregion=args.replaceregion or pargs.replaceregion or "" local treplaceregion={} treplaceregion.s={};treplaceregion.e={};treplaceregion.t={} for i,j,k in mw.ustring.gmatch(replaceregion,(%d+)%.%.(%d+):%"(.-)%") do         table.insert(treplaceregion.s,tonumber(i));table.insert(treplaceregion.e,tonumber(j));table.insert(treplaceregion.t,tostring(k)) end exclude "Forget about this" (junk between ignored). this prevents things from showing up even in the table and all motifs of this kind local exclude=args.exclude or pargs.exclude or "" -- for these empty arrays will be ignored later. local texclude={} for i in mw.ustring.gmatch(exclude,%"(.-)%") do     texclude[i]=1 end usenotes "This is a crummy motif name" (junk between ignored). Uses /note entries instead local usenotes=args.usenotes or pargs.usenotes or "" local tusenotes={} for i in mw.ustring.gmatch(usenotes,%"(.-)%") do     tusenotes[i]=1 end substitute "Don't like this wording":"That's what I want" (anything between these ignored) local substitute=args.substitute or pargs.substitute or "" local tsubstitute={} for i,j in mw.ustring.gmatch(substitute,%"(.-)%":%"(.-)%") do     tsubstitute[i]=j end toprow "Put this motif in the top row, no vertical annotation" If present, defines an upper part of the graphic to mark certain features by color only - most likely, helices and sheets and turns local toprowtext=args.toprow or pargs.toprow or "" local ttoprow={} local toprowheight=0 -- no height unless one exists local toprow -- boolean to mark if anything is actually on the top row for i in mw.ustring.gmatch(toprowtext,%"(.-)%") do     ttoprow[i]=1;toprow=true end if toprow then toprowheight=args.toprowheight or pargs.toprowheight or 10 end Check there is a protein sequence file and figure out where the CDS in it starts and ends local file=args.file or pargs.file if not(file) then return "error: use 'file=some cut-and-pasted NCBI protein sequence' to input a protein to be diagrammed" end local cdsstart, cdsend = mw.ustring.match(file,"Protein%s-(%d+)%.%.(%d+)") cdsstart=tonumber(cdsstart);cdsend=tonumber(cdsend) if ((cdsstart<1) or (cdsend<1)) then return error: the module expected a line "Protein: start amino acid..end amino acid" to define the CDS. end local cdswidth=cdsend-cdsstart Find and replace Site and Region to create unique separators so that every one of these sections can be individually processed in the main loop file = mw.ustring.gsub(file,"Site%s+","|##|S") -- there are no pipe characters in the input or it would have choked file = mw.ustring.gsub(file,"Region%s+","|##|R") file = mw.ustring.gsub(file,"$","|##|") --- close last feature at the EOF Load a set of colors to use for the different motifs. Any unicode separator changes them. No format expectations. local colorpage=mw.title.new("Template:ImportProtein/DefaultColors") local content local color={} if colorpage then content=colorpage.getContent(colorpage) if content then for x in mw.ustring.gmatch(content,"(%S+)") do             table.insert(color,x) end end end if #color<1 then color={"#000055","#000099","#0000CC","#0000FF","#550055","#550099","#5500CC","#5500FF","#990055","#990099","#9900CC","#9900FF","#CC0055","#CC0099","#CC00CC","#CC00FF","#FF0000","#FF0055","#FF0099","#FF00CC","#FF00FF","#005555","#005599","#0055CC","#0055FF","#55555","#555599","#5555CC","#5555FF","#995555","#995599","#9955CC","#9955FF","#CC5555","#CC5599","#CC55CC","#CC55FF","#FF5500","#FF5555","#FF5599","#FF55CC","#FF55FF"} end local claim={};local nextcolor=1 -- keeps track of the colors assigned to specific nkeys throughout the loop Begin the output and graphics files local output local tlegend="" -- legend for top row entries only, shown above table if tableoutput=="collapsed" then output={| class="wikitable collapsible collapsed" style="width:.. width .. px;" .. "\n" .. List of protein features .. "\n" .. |- else if tableoutput=="collapsible" then output={| class="wikitable collapsible" style="width:.. width .. px;" .. "\n" .. List of protein features .. "\n" .. |- else output={| class="wikitable" end end local graphics= MAIN LOOP this goes through features one by one and marks them down in "output" (legend/table) and "graphics" (protein box and vertical annotation) Note that this does NOT create an array of features to sort, but is purely once through. This means, for example, that there is no easy way to reposition adjacent motifs left and right to fit automatically. You could, of course, array the output and retroactively process it ... maybe even turn this into a sortable array of function tail calls??? (My head hurts) for feature, range in mw.ustring.gmatch(file,"#|(.-)|#") do      local t=mw.ustring.match(feature,"^(%a)") -- S or R placed in previous find/replace local s=mw.ustring.match(feature,"(%d+)") -- first number is the beginning of site or region local e=mw.ustring.match(feature,"^.%s-%d+%.%.(%d+)") or s -- second number in xx..yy range ; this needs updating! if s then decide on the name to be used for the motif and annotation local n,c if t=="R" then n=mw.ustring.match(feature,/region_name=%"(.-)%") end if t=="S" then n=mw.ustring.match(feature,/site_type=%"(.-)%") end n=tostring(n) if tusenotes[n] then n=mw.ustring.match(feature,/note=%"(.-)%") or n end n=tostring(n) n=mw.ustring.match(n,"^%s+(.+)%s+$") or n -- kill white space n=mw.ustring.gsub(n,"\n"," ") or n -- remove line feeds n=tostring(n) -- am I paranoid? if tsubstitute[n] then n=tostring(tsubstitute[n]) end n = mw.ustring.match(n,"(.+)%.") or n -- Don't need the ubiquitous final periods from the name (n) pull out an nkey that excludes parenthesized stuff each unique nkey can claim its own color to use from here on out local nkey=mw.ustring.match(n,"(.+)[%.;,%(%[]") or n         local newcolor=false; -- is this a new color (if so, then if it is toprow, then add to legend for those)          if claim[nkey] then c=claim[nkey] else c=color[nextcolor];claim[nkey]=c;nextcolor=nextcolor+1;newcolor=true end          local cstyle=style="color: .. c .. ;"            decide whether to show the motif, and crop it to the CDS          local showthismotif=true          s=tonumber(s);e=tonumber(e)          if scdsend then e=cdsend end          if s==cdsstart and e==cdsend then showthismotif=nil end          if include then if not (tinclude[n]) then showthismotif=nil end end -- if include is set, and n isn't in it, don't add to table or graphic          if exclude then if texclude[n] then showthismotif=nil end end -- if exclude is set and n is in it don't add if showthismotif then update the table output for the legend if tostring(t)=="R" then output = output .. "\n|" .. cstyle .. "region\n|" else output = output .. "\n|" .. cstyle .. "site\n|" end output = output .. cstyle .. tostring(s) .. "\n|" .. cstyle .. tostring(e) .. "\n|" .. cstyle .. n .. "\n|-" update the graphic display: first determine if the block is large to be displayed full height and annotated inside itself nkey=mw.ustring.sub(nkey,1,vtext) -- for graphics purposes, truncate the string (default 25 characters) local large local boxleft=math.floor(width*tonumber(s)/cdswidth) local boxwidth=math.floor(width*tonumber(e)/cdswidth)-boxleft if boxwidth>8*tonumber(mw.ustring.len(nkey)) then large=true else large=nil end then work out the horizontal or vertical display local vertical -- height substring of the drawn block local annot="" -- text contents of a large block if ttoprow[n] then vertical=tostring(toprowheight) if newcolor then tlegend=tlegend..  .. nkey .. "\n" end nkey="" else if large then vertical=tostring(height-toprowheight) if toprow then vertical=vertical .. "px;top:" .. tostring(toprowheight) end annot="'''" .. nkey .."'''" nkey="" -- no vertical text display else vertical=tostring(math.floor(height) - toprowheight - largeonlyregion) .. "px;top:" .. tostring(toprowheight + largeonlyregion) nkey=mw.ustring.gsub(nkey,"(.)","%1 ") -- verticalize the text end end local z=10000-1*boxwidth --- smaller elements in front of larger ones if not(large) then z=z+10000 end --- large elements reliably to the back -- draw graphics within the protein rectangle graphics = graphics ..  .. annot .. -- draw annotations vertically below it              -- don't do at all if no text (nkey=="", such as on the top row) if not (nkey=="") then -- first decide if in a replaceregion - if so, don't draw local toreplace;local ri=1 while treplaceregion.s[ri] do                  local rs=treplaceregion.s[ri] local re=treplaceregion.e[ri] if s>=rs and e<=re then toreplace=true;break end ri=ri+1 end if not toreplace and not large then --- center vt in the feature; then claim pixels one by one around it. --- Don't draw in a claimed pixel, but file a protest at bottom. local vt=math.floor(boxleft+boxwidth/2 - 2) -- vertical text's horizontal position if not vclaim[vt] then for i = vt-vwidth,vt+vwidth,1 do                         vclaim[i]=true end graphics = graphics ..  .. nkey .. else vprotest=vprotest .. s .. "-" .. e .. " "                  end -- (if not ttoprow[n]) end -- (if not vclaim) end -- (if not toreplace) end -- (if showthismotif) end -- (if s)  end -- for feature, range --- we're out of the loop - now draw annotations for the chosen replace regions based on user text local ri=1 while treplaceregion.s[ri] do        local rs=treplaceregion.s[ri] local re=treplaceregion.e[ri] local rt=mw.ustring.gsub(mw.ustring.sub(treplaceregion.t[ri],1,vtext),"(.)","%1 ") -- verticalize the text local boxleft=math.floor(width*tonumber(rs)/cdswidth) local boxwidth=math.floor(width*tonumber(re)/cdswidth)-boxleft local vt = math.floor(boxleft+boxwidth/2 -2) -- this formula should be synchronized with above, but defining constants seems silly. -- this ignores vclaim - it's a user input, therefore repositionable field graphics = graphics ..  .. rt .. ri=ri+1 end if not(tableoutput) then output = "" end if tlegend == "" then else tlegend =  .. Top row: .. tlegend .. end if vprotest == "" then else vprotest = "''Overlapping vertical annotations not shown above: " .. vprotest .. "''" end if debuglog == "|}|}" then debuglog="" else debuglog = debuglog .. "\n" end if vtext>2 then vtext=vtext-2 end -- make up for extra return required to start a table at the end there. local output = [=[{| style="width:]=]..width..px;" .. "\n|".. graphics .. .. mw.ustring.rep("\n",vtext) .. " " .. tlegend .. vprotest .. "\n" .. output .. "\n|}\n" .. debuglog .. "|}\n" return output

end

return p