Module:Sandbox/Jts1882/CladeN
--[[NOTE: this module contains functions for generating the table structure of the clade tree:
The main function is called by the template using the Template:Invoke 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
]]
local p = {}
--[[============================== main function =========================== -- main function, which will generate the table structure of the tree
Test version: Usage: Script error: No such module "Module:Sandbox/Jts1882/CladeN". Template:CladeN
Release version: Usage: Script error: No such module "Clade". 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 (declaring here prevents lua error for nil value in template)
--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)
--[[ add the templatestyles tag
add to every clade table >> 137 times in Passeriformes test page
cladeCount==1 >> 43 insertions
nodeCount==2 >> 5 insertions (once for the style css, one link in each cladegram)
2 in Neosuchia (one for style css, one link for second cladogram)
this is because it counts "dummy" clades and outer clades with one leaf
cladeCount==1 AND nodeCount==2 >> 1 insertions
but none in Neosuchia
--]]
-- worked for wrong reasons if nodeCount==2 then
if cladeCount==1 then
local src = "Template:CladeN/styles.css"
cladeString = cladeString .. p.templateStyle( frame, src ) .. '\n'
end
local tableStyle = frame.args.style or "" --if tableStyle == '{{{style}}}' then tableStyle = "" end -- no longer needed as pipe added to template to suppress passing of {Template:Style when no value
if tableStyle ~= "" then tableStyle = ' style="' .. tableStyle .. '"' -- include style= in string to suppress empty style elements end
reverseClade =frame.args.reverse or false -- a global --ENFORCE GLOBAL FOR DEVELOPMENT --reverseClade = true
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 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 = 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 .. '
||'
-- note the footer causes a problem with tr:last-child so need either -- (1) use <tfoot> but it is not allowed or incompatable
-- cladeString = cladeString .. '<tfoot>
' .. footerText .. '
</tfoot>'
-- (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|}'
return cladeString
--return '
'
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 below the bracket) ]] function p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode)
-- get border 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 -- 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 = 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 cladeString =
local styleString =
local borderStyle = -- will be used if border color, thickness or state is to be changed local classString = local reverseClass = -- 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 ~= ) then styleString = 'style="' .. borderStyle .. branchStyle .. '"' end
if childNumber == 1 then classString= 'class="clade-label first" ' -- add class first for top row
else classString = 'class="clade-label' .. reverseClass .. '" ' -- 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
-- wikitext for leaf cell (note: nodeLeaf needs to be on newline if new wikitable)
classString = 'class="clade-leaf' .. reverseClass .. '"'
local leafCellString = '\n|rowspan=2 ' .. classString .. styleString .. ' |\n' .. nodeLeaf --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 -- groupLabelStyle = groupLabelStyle .. 'border-left:5px solid red;' 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 = 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) --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 ~= then
styleString = ' style="' .. borderStyle .. branchStyle .. '"'
end
--local sublabel = p.addLabel(childNumber,subLabel)
if childNumber == lastNode then
classString = 'class="clade-slabel last" '
else
classString = 'class="clade-slabel' .. reverseClass .. '" '
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
--[[ reverse version;
currently duplicates the code changing order of elements (bars, leaf, label, sublabel)
variables border-right
--]] 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
--[[ don't use bar label in the reverse version (probably best to get rid altogether)
if barRight ~= "0" then
cladeString = cladeString .. ' ' -- add spaces between leaf text and bar
if barLabel ~= "" then cladeString = cladeString .. '\n|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 ' ' -- (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 (‑) 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|}' -- is this legacy for extra sublabel?
cladeString = cladeString .. '\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: Script error: No such module "Module:Sandbox/Jts1882/CladeN". ]] 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
--[[ Parse one level of Newick string
This function receives a Newick string, which has two components
1. the right hand term is a clade label: |labelN=labelname
2. the left hand term in parenthesis has common delimited child nodes, each of which can be
i. a taxon name which just needs: |N=leafname
ii. a Newick string which needs further processing through reiteration
]] function p.newickParseLevel(newickString,levelNumber,childNumber)
local cladeString = ""
local indent = p.getIndent(levelNumber)
--levelNumber=levelNumber+1
local j=0 local k=0 j,k = string.find(newickString, '%(.*%)') -- find location of outer parenthesised term local innerTerm = string.sub(newickString, j+1, k-1) -- select content in parenthesis local outerTerm = string.gsub(newickString, "%b()", "") -- delete parenthetic term
cladeString = cladeString .. indent .. '|label'..childNumber..'=' .. outerTerm cladeString = cladeString .. indent .. '|' .. childNumber..'=' .. '{{clade'
levelNumber=levelNumber+1 indent = p.getIndent(levelNumber)
-- protect commas in inner parentheses from split; temporarily replace commas between parentheses local innerTerm2 = string.gsub(innerTerm, "%b()", function (n) return string.gsub(n, ",%s*", "XXX") -- also strip spaces after commas here end)
local s = 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 "⊞"
local collapseSymbol = mw.getCurrentFrame():getParent().args['collapse-symbol'] or "⊟"
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 = '' .. '
'
-- collapsible element containing the clade content
local contentString = '' .. '
.. '\n' .. p.main(frame) -- important to start wikitext tables on new line.. '
'
-- collapsible element containing the collapse sympol and/or text
local collapseSymbolString = '' .. '
.. ''
.. ''
local tableStyle = frame.args.style or ""
if tableStyle == '{{{style}}}' then tableStyle = "" end
local cladeString = '
' cladeString = cladeString .. expandSymbolString if mode == "left" then cladeString = cladeString .. collapseSymbolString end cladeString = cladeString .. contentString if mode == "right" then cladeString = cladeString .. collapseSymbolString end -- Note: if we want collapse string left and right it needs an extra element with a different id cladeString = 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 --[[] for i in string.gmatch(nodeLeaf, "||rowspan") do -- count number of rows started (transclusion)
nodeCount = nodeCount + 1
end
for i in string.gmatch(nodeLeaf, '{|class="clade"') do -- count number of tables started (transclusion)
cladeCount = cladeCount + 1
end
]]
-- count occurences of clade structure using number of classes used and add to counters
local _, nClades = string.gsub(nodeLeaf, 'class="clade"', "")
local _, nNodes = string.gsub(nodeLeaf, 'class="clade%-leaf"', "")
cladeCount = cladeCount + nClades
nodeCount = nodeCount + nNodes
lastNode = childNumber -- this gets the last node with a valid entry, even when missing numbers end end --]]
-- nodes can be either terminal leaves or a clade structure (table)
-- note: should change class clade-leaf to clade-node to reflect this
nodeCount = nodeCount -- number of nodes (class clade-leaf) passed down by transduction
+ childCount + 1 -- plus one for current clade and one for each of its child element
cladeCount = cladeCount + 1 -- number of clade structure tables passed down by transduction (plus one for current clade) leafCount = nodeCount-cladeCount -- number of terminal leaves (equals height of cladogram)
-- output for testing: number of clades / total nodes / terminal nodes (=leaves) -- (internal nodes) (cladogram height) infoOutput = '[' .. cladeCount .. '/' .. nodeCount .. '/' .. leafCount .. ']'
return infoOutput
end
--[[ 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.testTable(frame)
-- build HTML table local galleryTable = mw.html.create('table') galleryTable:addClass('wikitable') galleryTable:addClass('sortable') galleryTable:css('text-align', 'center')
galleryTable:tag('caption'):wikitext('Table created with mw.html')
local row = galleryTable:tag('tr')
row:tag('th'):wikitext('Header 1') row:tag('th'):wikitext('Header 2') row:tag('th'):wikitext('Header 3') --:attr('rowspan', 2)
row = galleryTable:tag('tr') row:tag('td'):css('text-align', 'left'):wikitext('A1') row:tag('td'):css('text-align', 'left'):wikitext('B1') row:tag('td'):css('text-align', 'left'):wikitext('C1')
local row2 = mw.html.create('tr') -- create an independent row element row2:tag('td'):css('text-align', 'left'):wikitext('A3') row2:tag('td'):css('text-align', 'left'):wikitext('B3') row2:tag('td'):css('text-align', 'left'):wikitext('C3')
row = galleryTable:tag('tr') row:tag('td'):css('text-align', 'left'):wikitext('A2') row:tag('td'):css('text-align', 'left'):wikitext('B2') row:tag('td'):css('text-align', 'left'):wikitext('C2')
galleryTable:node(row2) -- now add row2 as node
return tostring(galleryTable) end
function p.example(frame)
local params = mw.getCurrentFrame():getParent().args -- build HTML table local exampleTable = mw.html.create('table') exampleTable:addClass('wikitable') local align = params['align'] or 'center' if align == 'center' then exampleTable:css('margin-left', 'auto') exampleTable:css('margin-right','auto') elseif align == 'right' then exampleTable:css('float',align) end
local columns = {'description','code','output','comment'} --local headers = {'Description','Code','Output','Comment'}
-- create header row and add requested headers
local row = exampleTable:tag('tr')
local headerText
for k,v in pairs(columns) do
if params[v] then if params[v]~= then headerText=params[v] else headerText = firstToUpper(v) end row:tag('th'):wikitext(headerText) end
end
-- now deal with the data rows local i=0 while i<10 do i=i+1 local moreRows = false for k,v in pairs(columns) do if params[v..i] then moreRows = true end end if not moreRows then break end
row = exampleTable:tag('tr') for k,v in pairs(columns) do if params[v] then if params[v] then row:tag('td'):css('text-align', 'left'):wikitext(params[v..i]) else row:tag('td') end end end
end
return tostring(exampleTable) end function firstToUpper(str)
return (str:gsub("^%l", string.upper))
end
-- display a gallery of cladograms using floating div elements
function p.gallery(frame)
local params = mw.getCurrentFrame():getParent().args
local outerBorders = false if params['caption'] or params['footer'] then outerBorders = true end
-- the gallery container local gallery = mw.html.create('div'):addClass('clade-gallery'):css('float',params['align'])
-- main caption for gallery if there is one
if params['main-caption'] then gallery:tag('div'):wikitext(params['main-caption']):addClass('main-caption') end
-- a gallery of floating divs with content
local shading =
--if params['shading'] then shading = 'shading' end -- class for shading if params['shading'] then shading = 'wikitable' end -- class for shading
local vertical = -- defaults to horizontal if params['vertical'] then vertical = 'vertical' end -- class for vertical display
local sizeStyling = if params['width'] then sizeStyling = sizeStyling .. 'width:' .. params['width'] .. ';' end if params['height'] then sizeStyling = sizeStyling .. 'height:' .. params['height'] .. ';' end
local noborder =
if not params['main-borders'] then noborder = 'no-border' end
-- the gallery contents
local content = gallery:tag('div'):addClass('main-content'):addClass(noborder)
:css('height',params['height'])
local i=0
while i<15 do i=i+1 local caption = params['caption'..i] --or local header = params['header'..i] --or local footer = params['footer'..i] --or
-- for each gallery element containing a cladogram
if params['cladogram'..i] then
local cladogramTable = content:tag('table') :addClass(shading):addClass('gallery-element'):addClass(vertical) :css('width',params['width']) :css('height',params['height'])
if caption then
cladogramTable:tag('caption'):wikitext(caption):addClass('caption') end if header then local row = cladogramTable:tag('tr'):addClass('header') row:tag('th'):wikitext(header) end -- if params['cladogram'..i] already checked local row = cladogramTable:tag('tr') row:tag('td'):wikitext("\n" .. params['cladogram'..i]) :addClass('cladogram') --:css("padding", "20px") :css('width',params['cladogram-width']) :css('height',params['cladogram-height'])
if footer then local row = cladogramTable:tag('tr') row:tag('td'):wikitext(footer):addClass('footer'):addClass(shading) end
--[[DIV VERSION - different browsers behave differently -- the div containing each element in the gallery local div = content:tag('div'):addClass('gallery-element'):addClass(direction) :css('width',params['width']) :css('height',params['height'])
-- the caption, header, content and footer for each element if caption then div:tag('div'):wikitext(caption):addClass('caption'):addClass(shading) end
if header then div:tag('div'):wikitext(header):addClass('header'):addClass(shading) end
div:tag('div'):wikitext(params['cladogram'..i]):addClass('cladogram'):addClass(shading) :css('width',params['cladogram-width']) :css('height',params['cladogram-height'])
if footer then div:tag('div'):wikitext(footer):addClass('footer'):addClass(shading) end END DIV VERSION--]] else break end end
-- main footer if params['main-footer'] then gallery:tag('div'):wikitext(params['main-footer']):addClass('main-footer'):addClass(noborder) end -- TemplateStyles file local src = "Template:Clade gallery/styles.css"
return p.templateStyle( frame, src ) .. tostring(gallery) end
-- this must be at end return p
