Module:Clade

--[[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 local src = "Template:Clade/styles.css" cladeString = cladeString .. p.templateStyle( frame, src ) .. '\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 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 --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)

--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 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  with vertical padding (see above)

--local leafCellString = '\n|rowspan=2 ' .. classString .. styleString .. ' |\n' .. content -- the new line causes 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 --return ' ' --' ' -- remove space to reduce post-expand include size (the width=1.5em handles spacing) --return ' ' -- must return something; this is critical for clade structure return '&#8239;' --  &thinsp; &#8239;(thin nbsp) 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. ") 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,"-", "&#8209;") -- replace hyphen with non-breaking hyphen (&#8209;) 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) local cladeString = "" count = count+1 --start table --cladeString = cladeString .. '{| style="border-collapse:collapse;border-spacing:0;border:0;margin:0;'	cladeString = cladeString .. '{| class="clade" '	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: {{#invoke:Module:Sandbox/Jts1882/CladeN|newickConverter|newickstring={{{NEWICK_STRING}}} }} ]] function p.newickConverter(frame) local newickString = frame.args['newickstring'] or pargs['newick'] --if newickString == '{{{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

--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 --|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

-- code for placing TemplateStyles from the module    source: Anomie (CC-0)  https://phabricator.wikimedia.org/T200442

function p.templateStyle( frame, src ) return frame:extensionTag( 'templatestyles', '', { src = src } ); 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 list = mw.text.split(listString, "\n") local i=1 local child=1 local lastNode=0--table.getn(list) -- number of child branches (potential)

cladeString = cladeString .. '{| class="clade" ' while list[i] do		list[i]=list[i]:gsub("^@", "")               -- strip the first @ if not string.match( list[i], "^@", 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], "^@", 1 ) then local label=list[i] i=i+1 local recombined = list[i] while list[i+1] and string.match( list[i+1], "^@", 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 Newick to clade parser function =============================

--[[Function of convert Newick strings to clade format

Usage: {{#invoke:Module:Sandbox/Jts1882/CladeN|newickConverter|newickstring={{{NEWICK_STRING}}} }} ]] function p.cladeConverter(frame) 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 Newick 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 list = mw.text.split(listString, "\n") local i=1 local child=1 local lastNode=0 while list[i] do		list[i]=list[i]:gsub("^@", "")               -- strip the first @ if not string.match( list[i], "^@", 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], "^@", 1 ) then local label=list[i] i=i+1 local recombined = list[i] while list[i+1] and string.match( list[i+1], "^@", 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 .. '}}' 	return cladeString end

-- this must be at end return p