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 ]]

local p = {}

--[[============================== 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 -- currently 17 in the clade/cladex templates local childNumber = 0 lastNode = 0 -- make this global for now local nodeCount = 0 -- total leafs plus new clade branches local leafCount = 0 -- just the terminal leaves local cladeCount = 0 -- new clade calls (each with a table) local childCount = 0 -- number of leaves in the clade (can use to set bottom of bracket in addTaxon	local totalCount = 0   infoOutput = p.getCladeTreeInfo -- get info about clade structure, e.g. lastNode (last |N= child number)

local tableStyle = frame.args.style or "" --if tableStyle == '' then tableStyle = "" end -- no longer needed as pipe added to template to suppress passing of {{{style}} when no value if tableStyle ~= "" then tableStyle = ' style="' .. tableStyle .. '"' -- include style= in string to suppress empty style elements end local reverseClade =frame.args.reverse or false local captionName =mw.getCurrentFrame:getParent.args['caption'] or "" local captionStyle = mw.getCurrentFrame:getParent.args['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 -- global nodeParameters (unnumber, i.e. color, thickness, state) apply to whole node bracket, --   but can be overrriden by branchParameters (numbered, e.g. color2, thickness2, state2) nodeColor = mw.getCurrentFrame:getParent.args['color'] or "" nodeThickness = tonumber(mw.getCurrentFrame:getParent.args['thickness']) or 1 nodeState = mw.getCurrentFrame:getParent.args['state'] or "solid" 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 = mw.getCurrentFrame:getParent.args[tostring(childNumber)] or "" -- get data from |N= local nodeLabel = mw.getCurrentFrame:getParent.args['label'..tostring(childNumber)] or "" -- get data from |labelN= local newickString = mw.getCurrentFrame:getParent.args['newick'..tostring(childNumber)] or "" -- get data from |labelN= if newickString ~= "" then -- if using a newick string instead of a clade structure 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 reverseClade 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 = mw.getCurrentFrame:getParent.args['footer'] or "" local footerStyle = mw.getCurrentFrame:getParent.args['footerstyle'] or ""

if footerText ~= "" then cladeString = cladeString .. '\n|-style="' .. footerStyle .. '"\n|colspan="2"| ' .. footerText .. ' ||'	end

-- close table (wikitext to close table) cladeString = cladeString .. '\n|}' return frame:extensionTag{ name='templatestyles', args = { src='Clade/styles.css'} } .. '\n' .. cladeString --return ' \n' .. 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 above the bracket)	     a complication is that the number of the last child node is not known;	     	as a result the cells will be added to the row on the next iteration or after the main loop finishes function p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode)

-- (1) get formating parameters for branch (default to global nodeParameters) --   - the branch parameters have a number, e.g. |colorN, |thicknessN, |stateN --   - the node parameters have no number, e.g. |color, |thickness, |state local branchThickness = tonumber(mw.getCurrentFrame:getParent.args['thickness'..tostring(childNumber)]) or nodeThickness local branchColor = mw.getCurrentFrame:getParent.args['color'..tostring(childNumber)] or nodeColor local branchStyle = mw.getCurrentFrame:getParent.args['style'..tostring(childNumber)] or "" local branchState = mw.getCurrentFrame:getParent.args['state'..tostring(childNumber)] or nodeState -- "solid" if branchState == 'double' then if branchThickness < 2 then branchThickness = 3 end end -- need thick line for double

-- the left border takes node parameters, the bottom border takes branch parameters local bottomBorder = tostring(branchThickness) ..'px ' .. branchState .. (branchColor~="" and ' ' .. branchColor or '') local leftBorder  =  tostring(nodeThickness)   ..'px ' .. nodeState .. (nodeColor~="" and ' ' .. nodeColor or '') -- The default border styles should be put in the CSS	    Then the inline styling would only be needed when thickness, color or state are changed	     Hence: 	         .clade-label {border-left:1px solid black;border-bottom:1px solid black;}	         .clade-slabel {border-left:1px solid black;}	         .clade-toplabel {border-bottom:1px solid black;}	         .clade-bottomsublabel {nothing}	     May be able to use td:first-child and td:last-child to handle top and bottom of bracket	     This would remove a large amount of inline styling and greatly reduce the transclusion size	     Need a flag to indicate when non-default styling is required	-- -- variables for right hand bar or bracket --local barColor = "" local barRight = mw.getCurrentFrame:getParent.args['bar'..tostring(childNumber)] or "0" local barBottom = mw.getCurrentFrame:getParent.args['barend'..tostring(childNumber)] or "0" local barTop   = mw.getCurrentFrame:getParent.args['barbegin'..tostring(childNumber)] or "0" local barLabel = mw.getCurrentFrame:getParent.args['barlabel'..tostring(childNumber)] or "" local groupLabel = mw.getCurrentFrame:getParent.args['grouplabel'..tostring(childNumber)] or "" local groupLabelStyle = mw.getCurrentFrame:getParent.args['labelstyle'..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 styleString = '' local cladeString = '' -- (1) wikitext for new row cladeString = cladeString .. '\n|-'

-- (2) now add cell with label styleString = '' if childNumber == 1 then -- the width gives minimum spacing when all labels are empty (was 1.5em) --(before CSS styling) -- styleString = ' style="width:1em;border:0;padding:0 0.2em;border-bottom:' .. bottomBorder .. ';vertical-align:bottom;text-align:center;' .. branchStyle .. '"' styleString = 'style="border-bottom:' .. bottomBorder .. ';' .. branchStyle .. '"' else -- for 2-17 --(before CSS styling) -- styleString = ' style="border:0;padding:0 0.2em;border-left:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';vertical-align:bottom;text-align:center;' .. branchStyle .. '"' styleString = 'style="border-left:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';' .. branchStyle .. '"' end -- add wikitext for cell with label cladeString = cladeString .. '\n|class="clade-label" ' .. styleString .. '|' .. p.addLabel(childNumber,nodeLabel) -- p.addLabel(nodeLabel)

-- (3) add cell with leaf (which may be a table with transluded clade content) --cladeString = cladeString .. '|| rowspan=2 style="border: 0; padding: 0; border-right: ' .. barRight .. ';border-bottom: ' .. barBottom .. ';border-top: ' .. barTop .. ';' .. branchStyle .. ' " | ' styleString = '' if barRight ~= "0"  then --(before CSS styling) -- styleString = 'style="border:0;padding:0;border-right:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"' styleString = ' style="border-right:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"' else --(before CSS styling) -- styleString = 'style="border:0;padding:0;' .. branchStyle .. '"' if (branchStyle ~= '') then styleString = ' style="' .. branchStyle .. '"' end end -- add wikitext for leaf cell (note: nodeLeaf needs to be on newline if new wikitable) cladeString = cladeString .. '\n|rowspan=2 class="clade-leaf"' .. styleString .. '|\n' .. nodeLeaf --cladeString = cladeString .. '\n' .. nodeLeaf -- needs to be on newline if new wikitable -- (4) stuff for right-hand brackets if barRight ~= "0"  then cladeString = cladeString .. ' '            -- add spaces between leaf text and bar if barLabel ~= "" then --cladeString = cladeString .. '' .. barLabel ..' ' cladeString = cladeString .. '\n| rowspan=2 class="clade-bar" |' .. barLabel end end -- note: it might be useful to add rowspan=2 to allow full range of positions if groupLabel ~= ""then --cladeString = cladeString .. '' .. groupLabel ..' ' cladeString = cladeString .. '\n| rowspan=2 class="clade-bar" style="'.. groupLabelStyle .. '" |' .. groupLabel end

-- (5) add second row (only one cell needed for sublabel because of rowspan=2); local branchStyleString = 'style="' .. branchStyle .. '" ' if branchStyle ==  then branchStyleString =  end -- avoid empty style elements cladeString = cladeString .. '\n|-' .. branchStyleString local subLabel = mw.getCurrentFrame:getParent.args['sublabel'..tostring(childNumber)] or "" -- request in addLabel -- FOR TESTING: use subLabel for annotating the clade structues to use structure information (DEBUGGIING ONLY) --subLabel= '(N=' .. infoOutput .. ')' -- END TESTING -- (6) add cell containing sublabel if childNumber~=lastNode then -- if childNumber==lastNode we don't want left border, otherwise we do styleString = ' style="border-left:' .. leftBorder ..';"' else --cladeString = cladeString .. '\n' .. '| style="border: 0; padding: 0; vertical-align: top;" | ' --(before CSS styling) -- styleString = 'style="border:0;vertical-align:top;text-align:center;"' styleString = '' end local sublabel = p.addLabel(childNumber,subLabel) local classString = '' -- class only needed if there is a label to display if sublabel ~= ' ' then classString = 'class="clade-slabel" ' end cladeString = cladeString .. '\n|' .. classString .. styleString .. '|' .. sublabel return cladeString end

- -- reverse version

function p.addTaxonReverse(childNumber, nodeLeaf, nodeLabel, lastNode)

-- (1) get formating parameters for branch (default to global nodeParameters) --   - the branch parameters have a number, e.g. |colorN, |thicknessN, |stateN --   - the node parameters have no number, e.g. |color, |thickness, |state local branchThickness = tonumber(mw.getCurrentFrame:getParent.args['thickness'..tostring(childNumber)]) or nodeThickness local branchColor = mw.getCurrentFrame:getParent.args['color'..tostring(childNumber)] or nodeColor local branchStyle = mw.getCurrentFrame:getParent.args['style'..tostring(childNumber)] or "" local branchState = mw.getCurrentFrame:getParent.args['state'..tostring(childNumber)] or nodeState -- "solid" if branchState == 'double' then if branchThickness < 2 then branchThickness = 3 end end -- need thick line for double

-- the left border takes node parameters, the bottom border takes branch parameters local bottomBorder = tostring(branchThickness) ..'px ' .. branchState .. (branchColor~="" and ' ' .. branchColor or '') local leftBorder  =  tostring(nodeThickness)   ..'px ' .. nodeState .. (nodeColor~="" and ' ' .. nodeColor or '') -- variables for right hand bar or bracket --local barColor = "" local barRight = mw.getCurrentFrame:getParent.args['bar'..tostring(childNumber)] or "0" local barBottom = mw.getCurrentFrame:getParent.args['barend'..tostring(childNumber)] or "0" local barTop   = mw.getCurrentFrame:getParent.args['barbegin'..tostring(childNumber)] or "0" local barLabel = mw.getCurrentFrame:getParent.args['barlabel'..tostring(childNumber)] or "" local groupLabel = mw.getCurrentFrame:getParent.args['grouplabel'..tostring(childNumber)] or "" local groupLabelStyle = mw.getCurrentFrame:getParent.args['labelstyle'..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 styleString = '' local cladeString = '' -- (1) wikitext for new row cladeString = cladeString .. '\n|-'

-- (4) stuff for right-hand brackets (or left hand brackets in reverse version)

-- note: it might be useful to add rowspan=2 to allow full range of positions if groupLabel ~= ""then cladeString = cladeString .. '\n|rowspan=2 class="clade-bar" style="'.. groupLabelStyle .. '" |' .. groupLabel end --rowspan=2 style="vertical-align:middle;" |' .. barLabel 		end	end    --

-- (3) add cell with leaf (which may be a table with transluded clade content) --cladeString = cladeString .. '|| rowspan=2 style="border: 0; padding: 0; border-right: ' .. barRight .. ';border-bottom: ' .. barBottom .. ';border-top: ' .. barTop .. ';' .. branchStyle .. ' " | ' styleString = '' if barRight ~= "0"  then --(before CSS styling) -- styleString = 'style="border:0;padding:0;border-right:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"' styleString = ' style="border-left:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"' else --(before CSS styling) -- styleString = 'style="border:0;padding:0;' .. branchStyle .. '"' if (branchStyle ~= '') then styleString = ' style="' .. branchStyle .. '"' end end -- add wikitext for leaf cell (note: nodeLeaf needs to be on newline if new wikitable) cladeString = cladeString .. '\n|rowspan=2 class="clade-leafR"' .. styleString .. '|\n' .. nodeLeaf --cladeString = cladeString .. '\n' .. nodeLeaf -- needs to be on newline if new wikitable

-- (2) now add cell with label styleString = '' if childNumber == 1 then -- the width gives minimum spacing when all labels are empty (was 1.5em) --(before CSS styling) -- styleString = ' style="width:1em;border:0;padding:0 0.2em;border-bottom:' .. bottomBorder .. ';vertical-align:bottom;text-align:center;' .. branchStyle .. '"' styleString = 'style="border-bottom:' .. bottomBorder .. ';' .. branchStyle .. '"' else -- for 2-17 --(before CSS styling) -- styleString = ' style="border:0;padding:0 0.2em;border-left:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';vertical-align:bottom;text-align:center;' .. branchStyle .. '"' styleString = 'style="border-right:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';' .. branchStyle .. '"' end -- add wikitext for cell with label cladeString = cladeString .. '\n|class="clade-label" ' .. styleString .. '|' .. p.addLabel(childNumber,nodeLabel) -- p.addLabel(nodeLabel)

-- (5) add second row (only one cell needed for sublabel because of rowspan=2) local branchStyleString = 'style="' .. branchStyle .. '" ' if branchStyle ==  then branchStyleString =  end -- avoid empty style elements cladeString = cladeString .. '\n|-' .. branchStyleString local subLabel = mw.getCurrentFrame:getParent.args['sublabel'..tostring(childNumber)] or "" -- request in addLabel -- FOR TESTING: use subLabel for annotating the clade structues to use structure information (DEBUGGIING ONLY) --subLabel= '(N=' .. infoOutput .. ')' -- END TESTING -- (6) add cell containing sublabel if childNumber~=lastNode then -- if childNumber==lastNode we don't want left border, otherwise we do styleString = ' style="border-right:' .. leftBorder ..';"' else --cladeString = cladeString .. '\n' .. '| style="border: 0; padding: 0; vertical-align: top;" | ' --(before CSS styling) -- styleString = 'style="border:0;vertical-align:top;text-align:center;"' styleString = '' end local sublabel = p.addLabel(childNumber,subLabel) local classString = '' -- class only needed if there is a label to display if sublabel ~= ' ' then classString = 'class="clade-slabel" ' end cladeString = cladeString .. '\n|' .. classString .. styleString .. '|' .. sublabel 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. <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 if stylingElementDetected == true then return ' ' .. nodeLabel .. ' '   	else local nowrapString = string.gsub(nodeLabel," ", " ") -- replace spaces with non-breaking space -- could replace hyphen with non-breaking hyphen (&#8209;) 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 = strsplit(innerTerm2, ",") --oldLastNode=lastNode local lastNode=table.getn(s) -- number of child branches local i=1 while s[i] do 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|}'	return cladeString end -- emulate a standard split string function function strsplit(inputstr, sep)         if sep == nil then                sep = "%s"        end        local t={} ; 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'] if newickString == '{{{newickstring}}}' then return newickString end

-- 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 = mw.getCurrentFrame:getParent.args['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 = strsplit(innerTerm2, ",") local i=1 while s[i] do 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 = mw.getCurrentFrame:getParent.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.test2(target) local target ="User:Jts1882/sandbox/templates/Template:Passeroidea" local result = mw.getCurrentFrame:expandTemplate{ title = target, args = {['style'] = '' } } return result end ---

function p.toggle(frame) if 1==2 then return 'some text' end --local toggleSymbol = 'toggle all' local toggleSymbol = mw.getCurrentFrame:getParent.args['button'] or ""

local toggleString = '<div class="'   local i=0    while 	i < 20 do  -- limit on number of toggle elements controlled by the trigger button    	i = i + 1 -- so we start with 1		local target = mw.getCurrentFrame:getParent.args['id'..tostring(i)] 	    -- add classes for the three elements of each target: expand symbol, collapse symbol and contents	    if target ~= nil then            toggleString = toggleString .. ' mw-customtoggle-myClade' .. target                 ..             ' mw-customtoggle-collapseSymbol' .. target                 ..             ' mw-customtoggle-expandSymbol' .. target         end    end toggleString = toggleString  ..  '">' .. toggleSymbol .. ' '

return toggleString end --- function p.hidden(frame) local id = mw.getCurrentFrame:getParent.args['id'] or "" local mode = mw.getCurrentFrame:getParent.args['mode'] or "right" local expandSymbol = mw.getCurrentFrame:getParent.args['expand-symbol'] or "&#8862;" local collapseSymbol = mw.getCurrentFrame:getParent.args['collapse-symbol'] or "&#8863;" local initialState = mw.getCurrentFrame:getParent.args['expanded'] -- default is content collapsed local contentState = " mw-collapsed" -- class to collapse content at start local collapseSymbolState = " mw-collapsed" local expandSymbolState = "" if initialState then contentState = "" collapseSymbolState = "" expandSymbolState = " mw-collapsed" end -- collapsible element containing the expand sympol and/or text local expandSymbolString = '' .. ' '               .. ' '                .. '' .. expandSymbol .. ' '               .. '   '    -- collapsible element containing the clade content local contentString = '' .. ' '               .. '' -- don't toggle on the content .. '\n' .. p.main(frame) -- important to start wikitext tables on new line .. '  '    -- collapsible element containing the collapse sympol and/or text local collapseSymbolString = '' .. '' .. ' '               .. '' .. collapseSymbol .. ' '                           .. '   '

local tableStyle = frame.args.style or "" if tableStyle == '' then tableStyle = "" end local cladeString = ' '

return cladeString 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 = mw.getCurrentFrame:getParent.args[tostring(childNumber)] or "" -- get data from |N= local newickString = mw.getCurrentFrame:getParent.args['newick'..tostring(childNumber)] or "" -- get data from |labelN= if newickString ~= "" or nodeLeaf ~= "" 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 tables and double span rows _, cladeCount = string.gsub(nodeLeaf, '{|class="clade"', "") _, nodeCount = string.gsub(nodeLeaf, "||rowspan", "") 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) nodeCount = nodeCount + childCount + 1-- number of double rows passed down by transduction plus current child elements (plus one for current clade) 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) infoOutput = nodeCount -- global return cladeCount end

-- this must be at end

return p