--[[NOTE: this module contains functions for generating the table structure of the clade tree:   The main function is called by the template using the  instruction; the three main functions are:         p.main(frame) - opens and closes table, loops through the children of node, main is invoked once and controls the rest, calling ...         p.addTaxon(childNumber, nodeLeaf) - the nuts and bolts; code dealing with each child node         p.addLabel(childNumber) - adds the label text                  now uses templatestyles ]] require('strict') local p = {} local pargs = {}  -- parent arguments local lastNode=0 local nodeCount=0 local cladeCount=0 local leafCount=0 local templateStylesCount=0 local infoOutput local reverseClade = false  --[[============================== main function  =========================== -- main function, which will generate the table structure of the tree  Test version: Usage:  Template:CladeN  Release version: Usage:  Template:Clade ]]  function p.main(frame)  	local cladeString = ""	 	local maxChildren = 20 -- was 17 in the clade/cladex templates 	local childNumber = 0 	local childCount = 0 -- number of leaves in the clade (can use to set bottom of bracket in addTaxon() 	local totalCount = 0 	 	pargs = frame:getParent().args -- parent arguments 	     infoOutput = p.getCladeTreeInfo() -- get info about clade structure, e.g. lastNode (last |N= child number)          --[[ add the templatestyles tag  conditionally to reduce expansion size (currently diabled)         when added to every clade table, it increases post‐expand include size significantly            e.g. the Neosuchia page (or test version) is increase by about 8% (672 bytes each)                 if template styles added to all pages there are 133 stripmarkers                  with cladeCount==1 condition, this is reduced to 34         however cladeCount==1 condition interfers with fix for additional line due to parser bug T18700         killing the strip markers also removes backlinks to references using citation templates      --]]     --cladeString =mw.text.killMarkers( cladeString ) -- also kills off strip markers using citation templates     --cladeString = mw.text.unstrip(cladeString)     --if cladeCount==1  then     cladeString = cladeString .. frame:extensionTag('templatestyles', ,     	{ src="টেমপ্লেট:ক্লেড/শৈলী.css" }) .. '\n'     --end	      	local tableStyle = frame.args.style or ""  	if tableStyle ~= "" then 		tableStyle = ' style="' .. tableStyle .. '"' -- include style= in string to suppress empty style elements 	end          reverseClade =frame.args.reverse or pargs.reverse or false -- a global     --ENFORCE GLOBAL FOR DEVELOPMENT     --reverseClade = true  	local captionName  = pargs['caption'] or "" 	local captionStyle = pargs['captionstyle'] or ""      -- add an element to mimick nowiki WORKS BUT DISABLE FOR DEMO PURPOSES     --cladeString = '\n'      	-- open table	 	-- (border-collapse causes problems (see talk) -- cladeString = cladeString .. '{| style="border-collapse:collapse;border-spacing:0;margin:0;' .. tableStyle .. '"'     -- (before CSS styling) -- cladeString = cladeString .. '{| style="border-spacing:0;margin:0;' .. tableStyle .. '"'     cladeString = cladeString .. '{|class="clade"' .. tableStyle      -- add caption 	if captionName ~= "" then 		cladeString = cladeString .. '\n|+ style="' .. captionStyle .. '"|' .. captionName 	end 	 	 	local moreNeeded = true 	childNumber = 0 	--lastNode = 0  	--[[get child elements (add more rows for each child of node; each child is two rows) 	    the function addTaxon is called to add the rows for each child element; 	    each child add two rows: the first cell of each row contains the label or sublabel (below the line label), respectively; 	    the second cell spans both rows and contains the leaf name or a new clade structure 	    a third cell on the top row is sometimes added to contain a group  to the right 	]] 	 	-- main loop 	while 	childNumber < lastNode do -- use the last number determined in the preprocessing  		childNumber = childNumber + 1 -- so we start with 1 		local nodeLeaf = pargs[tostring(childNumber)] or ""  -- get data from |N= 		local nodeLabel = pargs['label'..tostring(childNumber)] or ""  -- get data from |labelN= 		 		 		local newickString = pargs['newick'..tostring(childNumber)] or ""  -- get data from |labelN= 		local listString   = pargs['list'..tostring(childNumber)] or ""  		 		if listString ~= "" then 			cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, p.list(0, listString), nodeLabel, lastNode) 		elseif newickString ~= "" then -- if using a newick string instead of a clade structure 			newickString = p.processNewickString(newickString,childNumber) 			if nodeLabel == "" then -- use labelN by default, otherwise use root name from Newick string 				nodeLabel = p.getNewickOuterterm(newickString) -- need to use terminal part of newick string for label 			end 			cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, p.newick(0, newickString), nodeLabel, lastNode) 			--lastNode=lastNode+1 -- there is a counting problem with the newickstring 		elseif nodeLeaf ~= "" then -- if the node contains a leaf name or clade structue 			--if reverseClade2 then 			--	cladeString = cladeString .. '\n' .. p.addTaxonReverse(childNumber, nodeLeaf, nodeLabel, lastNode) 		    --else 				cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode) 			--end 		end 	end  	local footerText  = pargs['footer'] or "" 	local footerStyle = pargs['footerstyle'] or ""  	if footerText ~= "" then 	   cladeString = cladeString ..  '\n|-style="' .. footerStyle .. '"\n|colspan="2"|' .. footerText .. '||' 	   -- note the footer causes a problem with tr:last-child so need either 	   -- (1) use <tfoot> but it is not allowed or incompatable 	   --           cladeString = cladeString ..  '' .. footerText .. '' 	   -- (2) always add footer and use nth:last-child(2) but is this backwards compatible 	   -- (3) if footer= set the style inline for the last sublabel row (more a temp fix) 	   -- (4) set class for first and last element (DONE. Also works well with reverse class) 	end  	-- close table (wikitext to close table) 	cladeString = cladeString ..  '\n|}' 	 	cladeString = p.addSubTrees(cladeString) -- add subtrees 	 	return cladeString 	--return '\n' .. cladeString .. '' end  -- =============================function to add subtrees ==========================================   function p.addSubTrees(cladeString) 	 	--local pargs = mw.getCurrentFrame():getParent().args  	 	local suffix = { [1]="A", [2]="B", [3]="C", [4]="D", [5]="E", [6]="F", [7]="G", [8]="H", [9]="I", [10]="J",  		             [11]="K", [12]="L", [13]="M", [14]="N", [15]="O", [16]="P", [17]="Q", [18]="R", [19]="S", [20]="T",  		             [21]="U", [22]="V", [23]="W", [24]="X", [25]="Y", [26]="Z"} 	for i=1, 26, 1 do 		local subclade = pargs['subclade'..suffix[i]] 		local target = pargs['target'..suffix[i]] or "SUBCLADE_" .. suffix[i] 		if subclade  then  			if string.find(cladeString, target) then 				cladeString = string.gsub(cladeString,target,subclade) 			end 		end     end 	return cladeString end --[[ -------------------------------------- p.addTaxon() ------------------------------------------      function to add child elements      adds wikitext for two rows of the table for each child node,       	the first cell in each is used for the label and sublabel; the bottom border forms the horizonal branch of the bracket      	the second cell is used for the leafname or a transcluded clade structure and spans both rows      note that the first and last child nodes need to be handled differently from the middle elements 	     the middle elements (|2, |3 ...) use a left border to create the vertical line of the bracket 	     the first child element doesn't use a left border for the first cell in the top row (as it is above the bracket) 	     the last child doesn't use a left border for the first cell in the second row (as it is below the bracket) ]] function p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode)  	--[[ get border formating parameters (i.e. color, thickness, state)     		nodeParameters for whole bracket (unnumbered, i.e. color, thickness, state) apply to whole node bracket,  			branchParameters apply to individual branches 	    	the branch parameters have a number, e.g. |colorN, |thicknessN, |stateN 	    	the node parameters have no number, e.g. |color, |thickness, |state 	]]     local nodeColor = pargs['color'] or ""                 -- don't set default to allow green on black gadget 	local nodeThickness = tonumber(pargs['thickness']) or 1 	local nodeState = pargs['state'] or "solid" 	-- get border formating parameters for branch (default to global nodeParameters) 	local branchColor = pargs['color'..tostring(childNumber)] or nodeColor  	local branchThickness = tonumber(pargs['thickness'..tostring(childNumber)]) or nodeThickness 	local branchState = pargs['state'..tostring(childNumber)] or nodeState  	if branchState == 'double' then  		if branchThickness < 2 then branchThickness = 3 end -- need thick line for double 	end   	 	local branchStyle = pargs['style'..tostring(childNumber)] or "" 	local branchLength = pargs['length'] or pargs['length'..tostring(childNumber)] or ""      -- the left border takes node parameters, the bottom border takes branch parameters     -- this has coding on the colours for green on black    local bottomBorder =  tostring(branchThickness) ..'px ' .. branchState  .. (branchColor~="" and ' ' .. branchColor or )    local leftBorder   =  tostring(nodeThickness)   ..'px ' .. nodeState  .. (nodeColor~="" and ' ' .. nodeColor or ) 	 	--The default border styles are in the CSS (styles.css) 	--    the inline styling is applied when thickness, color or state are change 	 	local useInlineStyle = false 	-- use inline styling non-default color, line thickness or state have been set 	if branchColor ~= "" or branchThickness ~=  1 or branchState ~= "solid"  then 		useInlineStyle = true 	end 	 	 	-- variables for right hand bar or bracket 	--local barColor  = ""  	local barRight  = pargs['bar'..tostring(childNumber)] or "0" 	local barBottom = pargs['barend'..tostring(childNumber)] or "0" 	local barTop    = pargs['barbegin'..tostring(childNumber)] or "0" 	local barLabel  = pargs['barlabel'..tostring(childNumber)] or "" 	local groupLabel      = pargs['grouplabel'..tostring(childNumber)] or "" 	local groupLabelStyle = pargs['grouplabelstyle'..tostring(childNumber)] or "" 	local labelStyle      = pargs['labelstyle'..tostring(childNumber)] or "" 	local sublabelStyle   = pargs['sublabelstyle'..tostring(childNumber)] or ""  	--replace colours with format string; need right bar for all three options 	if barRight  ~= "0" then barRight  = "2px solid " .. barRight  end  	if barTop    ~= "0" then barRight  = "2px solid " .. barTop    end 	if barBottom ~= "0" then barRight  = "2px solid " .. barBottom end  	if barTop    ~= "0" then barTop    = "2px solid " .. barTop    end 	if barBottom ~= "0" then barBottom = "2px solid " .. barBottom end  	 	 	-- now construct wikitext  	local cladeString =  	local styleString =     local borderStyle =  -- will be used if border color, thickness or state is to be changed     local classString =     local reverseClass =      local widthClass =          -- class to add if using reverse (rtl) cladogram;      if reverseClade then reverseClass = ' reverse' end           -- (1) wikitext for new row     --cladeString = cladeString .. '\n|-'  	-- (2) now add cell with label      	if useInlineStyle then 		if childNumber == 1 then 	        borderStyle = 'border-left:none;border-right:none;border-bottom:' .. bottomBorder .. ';'  	        --borderStyle = 'border-bottom:' .. bottomBorder .. ';'  	 	else -- for 2-17 	 		if reverseClade then 	    		borderStyle  = 'border-left:none;border-right:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';'  	 	    else 	    		borderStyle  = 'border-left:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';'  	    	end 		end 	end 	    	if useInlineStyle or branchStyle ~=  or branchLength ~= "" or labelStyle ~= "" then    		local branchLengthStyle = ""    		if branchLength ~= "" then     			if childNumber == 1 then    				branchLengthStyle = 'width:' .. branchLength .. ';'  -- add width to first element    			end    			--if childNumber > 1 then prefix = 'max-' end    			branchLengthStyle = branchLengthStyle --= prefix  .. 'width:' .. branchLength .. ';'     										.. 'max-width:' .. branchLength ..';'    			                            .. 'padding:0em;'         -- remove padding to make calculation easier    						-- following moved to styles.css    						--				.. 'white-space:nowrap'    						--				.. 'overflow:hidden;'    -- clip labels longer than the max-width    						--				.. 'text-overflow:clip;' -- ellipsis;'    		    widthClass = " clade-fixed-width"    		end    		styleString = 'style="' .. borderStyle .. branchLengthStyle .. branchStyle .. labelStyle .. '"'     end	  	if childNumber == 1 then 		classString= 'class="clade-label first'.. widthClass .. '" '                  -- add class "first" for top row     else     	classString = 'class="clade-label' .. reverseClass .. widthClass .. '" ' -- add "reverse" class if ltr cladogram     end      --  wikitext for cell with label     local labelCellString = '\n|' .. classString .. styleString  .. '|' .. p.addLabel(childNumber,nodeLabel) -- p.addLabel(nodeLabel)          --cladeString = cladeString .. labelCellString  	--------------------------------------------------------------------------------- 	-- (3) add cell with leaf (which may be a table with transluded clade content)          if barRight  ~= "0"  then      	if reverseClade then -- we want the bar on the left     		styleString = ' style="border-left:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"'     	else     		styleString = ' style="border-right:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"'     	end     else     	if (branchStyle ~= ) then     		styleString = ' style="' .. branchStyle .. '"'         else         	styleString =  -- use defaults in styles.css         end     end         classString = 'class="clade-leaf' .. reverseClass .. '"'       --[[note: the \n causes plain leaf elements get wrapped in <p> with style="margin:0.4em 0 0.5em 0;"      	       this adds spacing to rows, but is set by defaults rather than the clade template     	       it also means there are two newlines when it is a clade structure (which might explain some past issues)     ]]     local content = '\n' .. nodeLeaf  -- the newline is not necessary, but keep for backward compatibility      -- test using image parameter     local image = pargs['image'..tostring(childNumber)] or ""        if image ~= "" then                                        	--content = content .. image -- basic version       	content = '\n{|class=clade style=width:auto'  --defaults to width:100% because of class "clade"     	       .. '\n|class=clade-leaf|\n' .. nodeLeaf      	       .. '\n|class=clade-leaf|\n' .. image      	       .. '\n|}'       	-- note: the classes interfere with the node counter, so try simpler version with style         content = '\n{|style=width:100%;border-spacing:0'  --width:auto is "tight"; 100% needed for image alignment     	       .. '\n|style=border:0;padding:0|\n' .. nodeLeaf      	       .. '\n|style=border:0;padding:0|\n' .. image      	       .. '\n|}'     end      -- wikitext for leaf cell (note: nodeLeaf needs to be on newline if new wikitable)     --                         but that is no longer the case (newline is now forced)     --                         the newline wraps plain leaf terminals in <P> with vertical padding (see above)      --local leafCellString = '\n|rowspan=2 ' .. classString  .. styleString .. ' |\n' .. content -- the new line causes <p> wrapping for plain leaf terminals     local leafCellString = '\n|rowspan=2 ' .. classString  .. styleString .. ' |' .. content         --cladeString = cladeString .. leafCellString           -------------------------------------------     -- (4) stuff for right-hand bracket labels    	classString='class="clade-bar' .. reverseClass .. '"'     	     local barLabelCellString = 	if barRight  ~= "0"  and barLabel ~= "" then  	   barLabelCellString = '\n|rowspan=2 ' .. classString .. ' |' .. barLabel 	else -- uncomment following line to see the cell structure 	   --barLabelCellString = '\n|rowspan=2 ' .. classString .. ' |' .. 'BL' 	end  	 	if groupLabel ~= "" then 		 		barLabelCellString = barLabelCellString .. '\n|rowspan=2 ' .. classString .. ' style="'.. groupLabelStyle .. '" |' .. groupLabel  	else -- uncomment following line to see the cell structure 	    --barLabelCellString = barLabelCellString .. '\n|rowspan=2 ' .. classString .. '" |' .. 'GL'     end 	     --cladeString = cladeString .. barLabelCellString      	------------------------------------------------------------------------------------- 	-- (5) add second row (only one cell needed for sublabel because of rowspan=2);  	--     note: earlier versions applied branch style to row rather than cell 	--           for consistency, it is applied to the sublabel cell as with the label cell 	 	--cladeString = cladeString .. '\n|-'  	 	----------------------------------- 	-- (6) add cell containing sublabel 	 	local subLabel = pargs['sublabel'..tostring(childNumber)] or ""  -- request in addLabel 	 	-- FOR TESTING: use subLabel for annotating the clade structues to use structure information (DEBUGGIING ONLY) 	--if childNumber==lastNode then subLabel= infoOutput end 	-- END TESTING 	 	borderStyle =  	styleString = 	if useInlineStyle then 		if childNumber==lastNode then 		-- if childNumber==lastNode we don't want left border, otherwise we do 			borderStyle = 'border-right:none;border-left:none;' 	    else 	 		if reverseClade then 	    		borderStyle  = 'border-left:none;border-right:' .. leftBorder .. ';'  	 	    else 	    		borderStyle  = 'border-right:none;border-left:' .. leftBorder .. ';'   	    	end 	    end      end     if borderStyle ~=  or  branchStyle ~=  or  branchLength ~=  or sublabelStyle ~= "" then             		local branchLengthStyle = ""    		if branchLength ~= "" then     			if childNumber == 1 then    				branchLengthStyle = 'width:' .. branchLength .. ';'  -- add width to first element    			end    			--if childNumber > 1 then prefix = 'max-' end    			branchLengthStyle = branchLengthStyle --= prefix  .. 'width:' .. branchLength .. ';'     										.. 'max-width:' .. branchLength ..';'    			                            .. 'padding:0em;'         -- remove padding to make calculation easier    		end    		styleString = 'style="' .. borderStyle .. branchLengthStyle .. branchStyle .. sublabelStyle .. '"'         --styleString = ' style="' .. borderStyle .. branchStyle .. sublabelStyle .. '"'     end      --local sublabel = p.addLabel(childNumber,subLabel)      if childNumber == lastNode then      	classString = 'class="clade-slabel last' .. widthClass .. '" '      else         classString = 'class="clade-slabel' .. reverseClass .. widthClass .. '" '     end     local sublabelCellString = '\n|' .. classString .. styleString .. '|' ..  p.addLabel(childNumber,subLabel)          --cladeString = cladeString .. sublabelCellString      -- constuct child element wikitext     if reverseClade then 	    cladeString = cladeString .. '\n|-' 	    cladeString = cladeString .. barLabelCellString 	    cladeString = cladeString .. leafCellString 	    cladeString = cladeString .. labelCellString 		cladeString = cladeString .. '\n|-'      		cladeString = cladeString .. sublabelCellString     else	 	    cladeString = cladeString .. '\n|-' 	    cladeString = cladeString .. labelCellString 	    cladeString = cladeString .. leafCellString 	    cladeString = cladeString .. barLabelCellString 		cladeString = cladeString .. '\n|-'     -- add second row (only one cell needed for sublabel because of rowspan=2); 		cladeString = cladeString .. sublabelCellString     end      	return cladeString end  --[[ adds text for label or sublabel to a cell ]] function p.addLabel(childNumber,nodeLabel) 	 	--local nodeLabel = mw.getCurrentFrame():getParent().args['label'..tostring(childNumber)] or ""  	--local firstChars = string.sub(nodeLabel, 1,2) -- get first two characters; will be {{ if no parameter (for Old method?) 	--if firstChars == "{{{" or nodeLabel == "" then 	if nodeLabel == "" then 		-- Has to be some content for layout, but can use CSS to add it instead. 		return 	else 		-- spaces can cause  wrapping and can break tree structure, hence use span with nowrap class 		--return '' .. nodeLabel .. '' 		 		-- a better method for template expansion size is to replace spaces with nonbreaking spaces 		-- however, there is a problem if labels have a styling element (e.g. <span style= ..., <span title= ...) 		local stylingElementDetected = false 		if string.find(nodeLabel, "span ") ~= nil  then  stylingElementDetected = true end 		if string.find(nodeLabel, " style") ~= nil then stylingElementDetected = true end  		--TODO test following alternative 		--if nodeLabel:find( "%b<>") then stylingElementDetected = true end  		 		if stylingElementDetected == true then  			return '' .. nodeLabel .. ''     	else	      		local nowrapString = string.gsub(nodeLabel, " ", " ")   -- replace spaces with non-breaking space 		    if not nowrapString:find("UNIQ.-QINU") and not nowrapString:find("%[%[.-%]%]") then                 -- unless a strip marker 			    nowrapString = string.gsub(nowrapString, "-", "‑") -- replace hyphen with non-breaking hyphen (‑)             end 			return nowrapString 		end 	end end  --[[=================== Newick string handling function ============================= ]] function p.getNewickOuterterm(newickString) 	return string.gsub(newickString, "%b()", "")   -- delete parenthetic term end  function p.newick(count,newickString) 	--start table 	--'{| style="border-collapse:collapse;border-spacing:0;border:0;margin:0;' 	local cladeString = '{|class=clade ' 	count = count + 1  	local j,k 	j,k = string.find(newickString, '%(.*%)')                 -- find location of outer parenthesised term 	local innerTerm = string.sub(newickString, j+1, k-1)      -- select content in parenthesis 	local outerTerm = string.gsub(newickString, "%b()", "")   -- delete parenthetic term 	if outerTerm == 'panthera' then outerTerm = "x" end     -- how is this set in local variable for inner nodes? 	 	outerTerm = tostring(count) 	 	-- need to remove commas in bracket terms before split, so temporarily replace commas between brackets     local innerTerm2 =  string.gsub(innerTerm, "%b()",  function (n)                                          	return string.gsub(n, ",%s*", "XXX")  -- also strip spaces after commas here                                             end) 	--cladeString = cladeString .. '\n' .. p.addTaxon(1, innerTerm2, "")      -- this needs a lastNode variable 	local s = p.strsplit(innerTerm2, ",") 	--oldLastNode=lastNode 	local lastNode=table.getn(s) -- number of child branches 	local i=1	 	while s[i] do	 		local restoredString = string.gsub(s[i],"XXX", ",")   -- convert back to commas 		--restoredString = s[i] 		local outerTerm = string.gsub(restoredString, "%b()", "") 		if string.find(restoredString, '%(.*%)') then 			--cladeString = cladeString .. '\n' .. p.addTaxon(i, restoredString, "x") 			cladeString = cladeString .. '\n' .. p.addTaxon(i, p.newick(count,restoredString), outerTerm, lastNode) 			-- p.addTaxon(2, p.newick(count,newickString2), "root") 		else 			cladeString = cladeString .. '\n' .. p.addTaxon(i, restoredString, "", lastNode) --count) 		end 		i=i+1 	end    -- lastNode=oldLastNode      	-- close table 	--cladeString = cladeString ..  '\n' .. '| style="border: 0; padding: 0; vertical-align: top;" |  \n|}' 	--cladeString = cladeString ..  '\n|  \n|}' -- is this legacy for extra sublabel? 	cladeString = cladeString ..  '\n|}' 	return cladeString end -- emulate a standard split string function -- why not use mw.text.split(s, sep)? function p.strsplit(inputstr, sep)          if sep == nil then                 sep = "%s"         end         local t={}          local i=1         for str in string.gmatch(inputstr, "([^"..sep.."]+)") do                 t[i] = str                 i = i + 1         end         return t end  -- =================== experimental Newick to clade parser function =============================  --[[Function of convert Newick strings to clade format  Usage:  ]] function p.newickConverter(frame) 	 	local newickString = frame.args['newickstring'] or frame.args['newick'] or pargs['newickstring'] or pargs['newick'] 	 	--if newickString == '' then return newickString  end      newickString = p.processNewickString(newickString,"") -- "childNumber")           	-- show the Newick string 	local cladeString =  	local levelNumber = 1           --  for depth of iteration 	local childNumber = 1           --  number of sister elements on node  (always one for root) 	 	--  converted the newick string to the clade structure 	cladeString = cladeString .. '{{clade' 	cladeString = cladeString .. p.newickParseLevel(newickString, levelNumber, childNumber)  	cladeString = cladeString .. '\r}}'    	local resultString =     local option = pargs['option'] or      if option == 'tree' then 	 	--show the transcluded clade diagram 		resultString =   cladeString    	     else     	-- show the Newick string 		resultString = ''..newickString..''	 	    -- show the converted clade structure 	    resultString = resultString .. ''.. cladeString ..''	     end     --resultString = frame:expandTemplate{ title = 'clade',  frame:preprocess(cladeString) }      return resultString end  --[[ Parse one level of Newick string      This function receives a Newick string, which has two components       1. the right hand term is a clade label: |labelN=labelname       2. the left hand term in parenthesis has common delimited child nodes, each of which can be            i.  a taxon name which just needs:  |N=leafname             ii. a Newick string which needs further processing through reiteration ]] function p.newickParseLevel(newickString,levelNumber,childNumber)       	local cladeString = "" 	local indent = p.getIndent(levelNumber)  	--levelNumber=levelNumber+1 	 	local j=0 	local k=0 	j,k = string.find(newickString, '%(.*%)')                 -- find location of outer parenthesised term 	local innerTerm = string.sub(newickString, j+1, k-1)      -- select content in parenthesis 	local outerTerm = string.gsub(newickString, "%b()", "")   -- delete parenthetic term  	cladeString = cladeString .. indent .. '|label'..childNumber..'='  .. outerTerm 	cladeString = cladeString .. indent .. '|' .. childNumber..'='  .. '{{clade'  	levelNumber=levelNumber+1 	indent = p.getIndent(levelNumber) 	 		-- protect commas in inner parentheses from split; temporarily replace commas between parentheses 	    local innerTerm2 =  string.gsub(innerTerm, "%b()",  function (n) 	                                         	return string.gsub(n, ",%s*", "XXX")  -- also strip spaces after commas here 	                                            end) 	 		local s = p.strsplit(innerTerm2, ",") 		local i=1	 		while s[i] do	 			local restoredString = string.gsub(s[i],"XXX", ",")   -- convert back to commas 	 			local outerTerm = string.gsub(restoredString, "%b()", "") 			if string.find(restoredString, '%(.*%)') then 				--cladeString = cladeString .. indent .. '|y' .. i .. '=' .. p.newickParseLevel(restoredString,levelNumber+1,i)  				cladeString = cladeString  .. p.newickParseLevel(restoredString,levelNumber,i)  			else 				cladeString = cladeString .. indent .. '|' .. i .. '=' .. restoredString --.. '(level=' .. levelNumber .. ')' 			end 			i=i+1 		end --    end -- end splitting of strings  	cladeString = cladeString .. indent .. '}}'       return cladeString end  function p.getIndent(levelNumber) 	local indent = "\r" 	local extraIndent = pargs['indent'] or mw.getCurrentFrame().args['indent'] or 0 	 	while tonumber(extraIndent) > 0 do 	    indent = indent .. " " -- an extra indent to make aligining compound trees easier 	    extraIndent = extraIndent - 1 	end 	 	while levelNumber > 1 do 		indent = indent .. "   " 		levelNumber = levelNumber-1 	end 	return indent end  function p.newickstuff(newickString)  	 end function p.processNewickString(newickString,childNumber) 	 	local maxPatterns = 5 	local i = 0 	local pargs = pargs 	local pattern = pargs['newick'..tostring(childNumber)..'-pattern'] -- unnumbered option for i=1     local replace = pargs['newick'..tostring(childNumber)..'-replace'] 	 	while i < maxPatterns do 		i=i+1 		pattern = pattern or pargs['newick'..tostring(childNumber)..'-pattern'..tostring(i)] 		replace = replace or pargs['newick'..tostring(childNumber)..'-replace'..tostring(i)] or "" 	 		if pattern then 			newickString = string.gsub (newickString, pattern, replace) 		end         pattern = nil; replace = nil 	end 	newickString = string.gsub (newickString, "_", " ") -- replace underscore with space 	return newickString end  function p.test2(target) 	local target ="User:Jts1882/sandbox/templates/Template:Passeroidea" 	local result = mw.getCurrentFrame():expandTemplate{ title = target, args = {['style'] =  } } 	return result end  --[[function getCladeTreeInfo() 	    this preprocessing loop gets information about the whole structure (number of nodes, leaves etc) 		it makes a redundant calls to the templates through transclusion, but doen't affect the template depths;  		it provides the global lastNode that is used to limit the main while loop --]] function p.getCladeTreeInfo()      -- enable proprocessing loop     local childNumber = 0     local childCount =0     local maxChildren =20          --info veriables (these are global for now)     nodeCount=0     cladeCount=0     leafCount=0      	while 	childNumber < maxChildren do -- preprocessing loop 		childNumber = childNumber + 1 -- so we start with 1 		local nodeLeaf,data = pargs[tostring(childNumber)] or ""  -- get data from |N=         local newickString = pargs['newick'..tostring(childNumber)] or ""  -- get data from |labelN=         local listString = pargs['list'..tostring(childNumber)] or ""  -- get data from |labelN= 		if newickString ~= "" or nodeLeaf ~= "" or listString ~= "" then 		--if nodeLeaf ~= "" then  			childCount = childCount + 1  -- this counts child elements in this clade  		    --[[] 		    for i in string.gmatch(nodeLeaf, "||rowspan") do -- count number of rows started (transclusion)    				nodeCount = nodeCount + 1      		end 		    for i in string.gmatch(nodeLeaf, '{|class="clade"') do -- count number of tables started (transclusion)    				cladeCount = cladeCount + 1      		end      		]]      		-- count occurences of clade structure using number of classes used and add to counters             local _, nClades = string.gsub(nodeLeaf, 'class="clade"', "")              local _, nNodes = string.gsub(nodeLeaf, 'class="clade%-leaf"', "")             cladeCount = cladeCount + nClades             nodeCount = nodeCount  + nNodes              			lastNode = childNumber -- this gets the last node with a valid entry, even when missing numbers 		end 	end --]]	     -- nodes can be either terminal leaves or a clade structure (table)     --    note: should change class clade-leaf to clade-node to reflect this     nodeCount = nodeCount            -- number of nodes (class clade-leaf) passed down by transduction                      + childCount + 1 --  plus one for current clade and one for each of its child element 	cladeCount = cladeCount + 1       -- number of clade structure tables passed down by transduction (plus one for current clade) 	leafCount = nodeCount-cladeCount   -- number of terminal leaves (equals height of cladogram) 	 	-- output for testing: number of clades / total nodes / terminal nodes (=leaves) 	--                     (internal nodes)                   (cladogram height) 	infoOutput = '[' .. cladeCount .. '/' .. nodeCount .. '/' .. leafCount .. ']' 	 	return infoOutput  	 end  function p.showClade(frame) 	--local code = frame.args.code or ""     local code = frame:getParent().args['code2'] or "" 	 	--return  code  	--return mw.text.unstrip(code) 	 	--local test = "Hello" 	--return string.sub(test,6,-7) 	 	local o1 =frame:getParent():getArgument('code2') 	return o1:expand() 	 	--return string.sub(code,2,-1)              -- strip marker  \127'"`UNIQ--tagname-8 hex digits-QINU`"'\127 	--return frame:preprocess(string.sub(code,3)) end  function p.firstToUpper(str)     return (str:gsub("^%l", string.upper)) end --[[ function to generate cladogram from a wikitext-like list          - uses @ instead of * because we don't want wikitext processed and nowiki elements are passed as stripmarkers (?) ]] function p.list(count,listString) 	 	local cladeString = "" 	--count = count+1     local i=1     local child=1 	local lastNode=0--table.getn(list) -- number of child branches (potential)     local listChar = "@"          if listString:find("UNIQ.-QINU") then -- if wrapped in nowiki        mw.addWarning("Stripping content in nowiki tags")        listString = mw.text.trim( mw.text.unstripNoWiki( listString ) )     end     if string.match( listString, "^*", 1 ) then        listChar = "*"     end              local list = mw.text.split(listString, "\n")      	cladeString = cladeString .. '{| class="clade" ' 	 	while list[i]  do 		list[i]=list[i]:gsub("^"..listChar, "")               -- strip the first @ or * 		list[i]=mw.text.trim(list[i])                -- trim  		 		if not string.match( list[i], "^"..listChar, 1 ) then -- count children at this level (not beginning wiht @/*) 			lastNode = lastNode+1   		end 		i=i+1 	end 	 	i=1 	while list[i]  do  	    --[[ pseudocode:  	         if next value begins with @ we have a subtree,  	        	which must be recombined and past iteratively 	         else we have a simple leaf 	    ]]  	    -- if the next value begins with @, we have a subtree which should be recombined 	    if list[i+1] and string.match( list[i+1], "^"..listChar, 1 )  then 	    	 	        local label=list[i]            	i=i+1 	    	local recombined = list[i] 	    	while list[i+1] and string.match( list[i+1], "^"..listChar, 1 ) do 	    		recombined = recombined .. "\n" .. list[i+1]  	    		i=i+1 	    	end 	    	--cladeString = cladeString .. '\n' .. p.addTaxon(child, recombined, label, lastNode)  	    	cladeString = cladeString .. '\n' .. p.addTaxon(child, p.list(count,recombined), label, lastNode)  	    else 	    	cladeString = cladeString .. '\n' .. p.addTaxon(child, list[i], "", lastNode) 	 	    end 		i=i+1 		child=child+1 	end  	cladeString = cladeString .. '\n|}' 	 	mw.addWarning("WARNING. This is a test feature only.") 	return cladeString   end -- =================== experimental wikitext list to clade parser function =============================  --[[Function of convert wikitext lists to clade format  Usage:  ]] function p.cladeConverter(frame) 	pargs = frame:getParent().args 	 	if  frame.args['list'] or pargs['list'] then  		return p.listConverter(frame)     elseif frame.args['newickstring'] or frame.args['newick'] or pargs['newickstring'] or pargs['newick'] then     	return p.newickConverter(frame) 	else 		local message = "Conversion needs wikitext list or newick string in parameters list or newick respectively" 		mw.addWarning(message) 		return message 	end end function p.listConverter(frame) 	 	local listString = frame.args['list'] or pargs['list']  	-- show the list string 	local cladeString =  	local levelNumber = 1           --  for depth of iteration 	local childNumber = 1           --  number of sister elements on node  (always one for root) 	local indent = p.getIndent(levelNumber) 	--  converted the newick string to the clade structure 	cladeString = cladeString .. indent .. '{{clade' 	cladeString = cladeString .. p.listParseLevel(listString, levelNumber, childNumber)  	--cladeString = cladeString .. '\r}}'    	local resultString =     local option = pargs['option'] or      if option == 'tree' then 	 	--show the transcluded clade diagram 		resultString =   cladeString    	     else     	-- show the wikitext list string 		resultString = ''..listString..''	 	    -- show the converted clade structure 	    resultString = resultString .. ''.. cladeString ..''	     end     --resultString = frame:expandTemplate{ title = 'clade',  frame:preprocess(cladeString) }      return resultString end  function p.listParseLevel(listString,levelNumber,childNumber)  	local cladeString = "" 	local indent = p.getIndent(levelNumber)     levelNumber=levelNumber+1          local nowiki = false     if listString:find("UNIQ.-QINU") then -- if wrapped in nowiki        mw.addWarning("Stripping content in nowiki tags")        listString = mw.text.trim( mw.text.unstripNoWiki( listString ) )        nowiki = true     end     local listChar = "@"     if string.match( listString, "^*", 1 ) then        listChar = "*"     end         local list = mw.text.split(listString, "\n")     local i=1     local child=1     local lastNode=0          while list[i]  do 		list[i]=list[i]:gsub("^"..listChar, "")               -- strip the first @ 		 		if not string.match( list[i], "^"..listChar, 1 ) then -- count children at this level (not beginning wiht @) 			lastNode = lastNode+1   		end 		i=i+1 	end     i=1  	while list[i]  do  	    --[[ pseudocode:  	         if next value begins with @ we have a subtree,  	        	which must be recombined and past iteratively 	         else we have a simple leaf 	    ]]  	    -- if the next value begins with @, we have a subtree which should be recombined 	    if list[i+1] and string.match( list[i+1], "^"..listChar, 1 )  then 	    	 	        local label=list[i]            	i=i+1 	    	local recombined = list[i] 	    	while list[i+1] and string.match( list[i+1], "^"..listChar, 1 ) do 	    		recombined = recombined .. "\n" .. list[i+1]  	    		i=i+1 	    	end 	    	cladeString = cladeString .. indent .. '|label' .. child ..'=' ..  label	 	    	cladeString = cladeString .. indent .. '|' .. child ..'=' ..  '{{clade' 	    	                          .. p.listParseLevel(recombined,levelNumber,i)   	    else 	    	cladeString = cladeString .. indent .. '|' .. child ..'=' ..  list[i]	 	    end 		i=i+1 		child=child+1 	end  	cladeString = cladeString .. indent .. '}}'   	 	if nowiki then 		return mw.getCurrentFrame():preprocess( ''.. cladeString .. '') --return wrapped in nowiki 	else 		return  cladeString 	end end  -- this must be at end return p