Módulo:Clade

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Módulo de suporte de clade

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--NOTE: this module contains functions for generating the table structure of the clade tree in two ways:
-- (1) the original method was generated by a number of function calls from the template using {{invoke}}
--        function p.openTable(frame) - creates wikitext code to open the HTML table
--        function p.node(frame)  - deals with the first node (|1,|label1) and creates wikitext for top row of the table
--        function p.nodeN(frame) - deals with a sister nodes (|2-17), adding a row each time it is called
--        function p.closeTable() - closes the HTML table
-- (2) the revised method is called by the template with one {{invoke}} instruction; it has three functions:
--        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 (for Method 2) ===========================
-- main function, which will
--[[Main function to generate the table structure of the tree

Usage: {{#invoke:Módulo:Testes/Jts1882/CladeN|main|style={{{STYLE}}} }}
Predefiição: Ussário:Jts1882/Testes/predefinições/CladeN
]]


function p.main(frame)

    local cladeString = ""    
    local maxChildren = 20 -- currently 17 in the clade/cladex templates
    local childNumber = 0
    local lastNode = 0
    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
    
    --[[Note: 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 would probably be better to store the transcluded nodes in a table (a job for later)
    ]]
--[[ disable proprocessing loop
    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=
 
        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, "{| cellspacing") do -- count number of tables started (transclusion)
                   cladeCount = cladeCount + 1
             end
           -- _, cladeCount = string.gsub(nodeLeaf, "{| cellspacing", "")
            --_, nodeCount = string.gsub(nodeLeaf, "|| rowspan", "")
            
            --totalCount = totalCount + nodeCount
            lastNode = childNumber
        --    if data ~= nil then totalCount = totalCount + tonumber(data) else totalCount = totalCount + 1 end
        end


        --cladeString = cladeString .. '\n' .. ' count= ' .. totalCount

    end
]]    
    nodeCount = nodeCount + childCount --(elements passed down by transduction plus current child elements)
    cladeCount = cladeCount + 1        --(elements passed down by transduction plus current clade)
    leafCount = nodeCount-cladeCount+1
    totalCount =leafCount-- cladeCount --nodeCount



    local testing = false
    --testing = true                  -- COMMENT OUT TO GET MODULE RUNNING WITHOUT THE TEST
    if testing then
        local dataString = p.test(1)
        cladeString = cladeString .. dataString
        return cladeString
    end

    local tableStyle = frame.args.style or ""
    local tableStyleString = ' style="' .. tableStyle .. '" '
    if tableStyle == '{{{style}}}' then tableStyleString = "" end
    
    local captionName =mw.getCurrentFrame():getParent().args['caption'] or ""
    local captionStyle = mw.getCurrentFrame():getParent().args['captionstyle'] or ""

    -- open table    
    --cladeString = cladeString .. '{| cellspacing=0 cellpadding=0 border=0 style="' .. tableStyle .. '"'
    cladeString = cladeString .. '{|cellspacing=0 cellpadding=0 ' .. tableStyleString
    --cladeString = cladeString .. '{| cellspacing=0 ' .. tableStyleString  -- NOTE: cellpadding supposedly not supported in HTML5

    -- 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 "black"
    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
    ]]
    
    while     childNumber < maxChildren do -- disable moreNeeded
                                            -- while childNumber < 17 and moreNeeded == true do
        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 = childNumber
        elseif nodeLeaf ~= "" then -- if the node contains a leaf name or clade structue
            cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, nodeLeaf, nodeLabel)
            lastNode = childNumber
        else
            moreNeeded = false -- no |N= so don't look for more
            -- Note: this changes the behaviour. If there is no |2, it won't look for |3 or |4, which clade does (is this desirable?)
            -- this has been disabled to allow consistent behaviour with clade/cladex (it will check to the limit set)
        end
    end

    --[[finish last row by adding cell with no left border
        note: the row was started in addTaxon(), but the cell not added as left border yet to be determined;
             here the cell is added to the last child node with no left border as it is below the bracket
             this will be moved to addTaxon() when the number of the last child is known
       ]]
   local subLabel = mw.getCurrentFrame():getParent().args['sublabel'..tostring(lastNode)] or ""  -- request in addLabel
    
    --use subLabel for annotating the clade structues to use structure information (DEBUGGIING ONLY)
    --subLabel= '(N=' .. totalCount .. ')'
    
    --cladeString = cladeString ..  '\n' .. '| style="border: 0; padding: 0; vertical-align: top;" | <br/> '
    cladeString = cladeString ..  '\n' .. '|style="border:0;vertical-align:top;text-align:center;"|' .. p.addLabel(lastNode-1,subLabel)

    --[[ footer description (add addition row spanning two columns at bottom of table)
        this is designed to provide the description below the whole clade structure (mimicking cladogram);
        however, it can also be used to add labels and spacing to the whole clade structre
    ]]
    local footerText  = mw.getCurrentFrame():getParent().args['footer'] or ""
    local footerStyle = mw.getCurrentFrame():getParent().args['footerstyle'] or ""

    if footerText ~= "" then
       --cladeString = cladeString ..  '<tr><td>Test <br/><br/><br/><br/><br/></td></tr>'
       cladeString = cladeString ..  '\n|-style="' .. footerStyle .. '"\n|colspan="2"|<p>' .. footerText .. '</p>||'
    end

    -- close table (wikitext to close table)
    cladeString = cladeString ..  '\n|}'
    
    return cladeString
end

--[[ 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 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)

    -- get leaf and labels
    --local nodeLeaf  = mw.getCurrentFrame():getParent().args[tostring(childNumber)] or ""    -- used passed variable to avoid redundancy
    --local nodeLabel = mw.getCurrentFrame():getParent().args['label'..tostring(childNumber)] or ""  -- request in addLabel
    
    -- 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 --"black"
    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    
   local leftBorder   =  tostring(nodeThickness)   ..'px ' .. nodeState  .. ' ' .. nodeColor
    
    -- 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 = ''

    --[[ first add cell to the spacing row (for 2-17); it completes the previous row
        why is this here rather than at the end of each row?
        To allow left border (here while extending bracket) or not (end of bracket)
    ]]
    if childNumber  ~= 1 then
          local subLabel = mw.getCurrentFrame():getParent().args['sublabel'..tostring(childNumber-1)] or ""  -- request in addLabel

        --styleString = ' style="border-left:' .. leftBorder ..';border-top:0;border-right:0;border-bottom:0;vertical-align:top;text-align:center;"'
        styleString = ' style="border:0;border-left:' .. leftBorder ..';vertical-align:top;text-align:center;"'
        --cladeString = cladeString .. '| ' .. styleString .. ' | <br/> ' -- for sublabel ' | y<br/> '
        cladeString = cladeString .. '|' .. styleString .. '|' ..  p.addLabel(childNumber-1,subLabel)
    end
   
   -- new row
   cladeString = cladeString .. '\n|-'

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

    -- add cell with leaf (which may be a table with transluded 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
        styleString = 'style="border:0;padding:0;border-right:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"'
    else
        styleString = 'style="border:0;padding:0;' .. branchStyle .. '"'
    end

    cladeString = cladeString .. '||rowspan=2 ' .. styleString .. '|'
    -- note: this is where leading spaces can be added to labels and leaves. This was commented out in the clade template. Most trees seem to have added spaces, to would need to check for existing spaces; however, cladex uses it
    -- or could use padding:0 0.2em in cell style as for labels
    cladeString = cladeString .. '\n' .. nodeLeaf
    
    -- stuff for right-hand bar-bracket
    if barRight  ~= "0"  then
        cladeString = cladeString .. '&nbsp;&nbsp;'            -- add spaces between leaf text and bar
        if barLabel ~= "" then
            -- cladeString = cladeString ..  '\n| ' .. barLabel end  -- experiment for labeling the bar
            cladeString = cladeString .. '<td style="vertical-align:middle;">' .. barLabel ..'</td>'
        end
    end
    if groupLabel ~= ""then
        --cladeString = cladeString .. '&nbsp;&nbsp;'            -- add spaces between leaf text and bar (could use padding)
        cladeString = cladeString .. '<td style="'.. groupLabelStyle .. '">' .. groupLabel ..'</td>'
    end     

    -- add row    (needed because of rowspan=2);
    -- note: the cell will be added on the next iteration of addTaxon (with left border) or after the main loop (without left border)
    local branchStyleString = 'style="' .. branchStyle .. '"  '
    if branchStyle == '' then branchStyleString = ''  end -- avoid empty style elements
    cladeString = cladeString .. '\n|-' .. branchStyleString
    
    -- TODO code to put whole row here instead of completing on next call to addTaxon() or after main loop

    
    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 nodeLabel ~= "{{{label1}}}" then
    if firstChars == "{{{" or nodeLabel == "" then
        return '<br/>' --'&nbsp;<br/>'  -- remove space to reduce post-expand include size (the width=1.5em handles spacing)
    else
        -- spaces can cause  wrapping and can break tree structure, hence use span with nowrap class
        --return '<span class="nowrap">' .. nodeLabel .. '</span>'
        
        -- 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 '<span class="nowrap">' .. nodeLabel .. '</span>'
        else    
            local nowrapString = string.gsub(nodeLabel," ", "&nbsp;") -- replace spaces with non-breaking space
            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 .. '{| cellspacing=0 cellpadding=0 border=0 '  
    
    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, "")

    local s = strsplit(innerTerm2, ",")
    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)
            -- p.addTaxon(2, p.newick(count,newickString2), "root")
        else
            cladeString = cladeString .. '\n' .. p.addTaxon(i, restoredString, "") --count)
        end
        i=i+1
    end

    -- close table
    cladeString = cladeString ..  '\n' .. '| style="border: 0; padding: 0; vertical-align: top;" | <br/> \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


-- Bits from Peter Coxhead's module
--    https://en.wikipedia.org/w/index.php?title=Module:Autotaxobox&action=edit

--[[
Utility function primarily intended for use in checking and debugging.
Returns number of levels in a taxonomic hierarchy, starting from
the supplied taxon as level 1.
Usage: {{#invoke:Autotaxobox|nLevels|TAXON}}
]]
function p.nLevels(frame)
    local currTaxon = frame.args[1]
    local i = 1
    local maxN = 2
    local searching = true
    while searching and i < maxN  do
        --local parent = frame:expandTemplate{ title = 'Template:Taxonomy/' .. currTaxon, args = {['machine code'] = 'parent' } }
        local parent = frame:expandTemplate{ title =  currTaxon, args = {['machine code'] = 'parent' } }
        if parent ~= '' then
            currTaxon = parent
            i = i + 1
        else
            searching = false
        end
    end
    if searching then return currTaxon --maxN .. '+'
    else return i
    end
end

--[[
Utility function primarily intended for use in checking and debugging.
Returns a comma separated list of a taxonomic hierarchy, starting from
the supplied taxon.
Usage: {{#invoke:Autotaxobox|listAll|TAXON}}
]]
function p.listAll(frame)
    local currTaxon = frame.args[1]
    local i = 1
    local searching = true
    local maxN = 100
    local lst = currTaxon
    while i < maxN and searching do
        local currCall = 'Template:Taxonomy/' .. currTaxon
        local parent = frame:expandTemplate{ title = currCall, args = {['machine code'] = 'parent' } }
        if parent ~= '' then
            currTaxon = parent
            lst = lst .. ', ' .. currTaxon
            i = i + 1
        else
            searching = false
        end
    end
    if searching then lst = lst .. '...' end
    return lst .. ' (' .. i .. ')'
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 = '<pre>'..newickString..'</pre>'    
        -- show the converted clade structure
        resultString = resultString .. '<pre>'.. cladeString ..'</pre>'    
    end
    --resultString = frame:expandTemplate{ title = 'clade',  frame:preprocess(cladeString) }

    return resultString
end

--[[ Parse one level of Newick sting
     This function recieves 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 = 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.test(dummy)
    local dataString = ""
    dataString =    "NEWCLADE:"
    
    local childNumber =0
    local lastNode = 0
    while     childNumber < 17 do -- disable moreNeeded
    
        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=
        if nodeLeaf ~= "" then
            dataString = dataString .. tostring(childNumber)

            local firstChars = string.sub(nodeLeaf, 1,2) -- get first two characters
            --if nodeLabel ~= "{{{label1}}}" then
            if firstChars == "{{"  then
                dataString = dataString .. 'XXX' .. nodeLeaf
            end
            dataString = dataString .. 'LEAF:' .. nodeLeaf
            
            lastNode = childNumber
        end
    end
    local numClades=0
    local numBranches=0
    -- _, count = string.gsub(dataString, "NEWCLADE", "NEXT")
   
    for i in string.gmatch(dataString, "NEWCLADE") do
           numClades = numClades + 1
     end
    dataString =   dataString .. '<br/>(numClades=' .. numClades .. ')'
    for i in string.gmatch(dataString, "LEAF") do
           numBranches = numBranches + 1
     end
    dataString =   dataString .. '<br/>(numClades=' .. numClades .. ')'
    dataString =   dataString .. '<br/>(numBranches=' .. numBranches .. ')'
    
    mw:log(numClades)
    
    --return 'numClades=' .. numClades .. '; numBranches=' .. numBranches
    return  dataString
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


-- this must be at end

return p