Module:Clade
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This module is designed to be used with the clade template to draw phylogenetic trees or cladograms. The new template-module combination extends the feature available with the clade and cladex templates, while replicating the behaviour of the older templates written with the template language. This module is copied from the test version Module:Sandbox/Jts1882/CladeN, which was used with the template Template:CladeN to test the features during development.
Additionally, the module has the code for template {{clade newick converter}}, which is a basic utility to convert Newick strings into nested clade structures. This is not to be used in wikipedia articles, but is a tool to help construct cladograms for inclusion in articles.
The diagram below gives an overview of the features. See the template documentation for a more detailed description of how to use the templates.
Usage
{{#invoke:Clade|main|style={{{style}}}}}
Examples
Simple examples mimicking the clade template:
- User:Jts1882/sandbox/templates/Template:Passeroidea
- User:Jts1882/sandbox/templates/Template:Passerida
Example demonstrating more advanced features of cladeN:
Example demonstrating features available:
Subpages
--[[NOTE: this module contains functions for generating the table structure of the clade tree:
The main function is called by the template using the {{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
]]
require('Module:No globals')
local p = {}
local pargs = {} -- parent arguments
local lastNode=0
local nodeCount=0
local cladeCount=0
local leafCount=0
local templateStylesCount=0
local infoOutput
local reverseClade = false
--[[============================== main function ===========================
-- main function, which will generate the table structure of the tree
Test version:
Usage: {{#invoke:Module:Sandbox/Jts1882/CladeN|main|style={{{STYLE|}}} }}
Template:CladeN
Release version:
Usage: {{#invoke:Clade|main|style={{{STYLE|}}} }}
Template:Clade
]]
function p.main(frame)
local cladeString = ""
local maxChildren = 20 -- was 17 in the clade/cladex templates
local childNumber = 0
local childCount = 0 -- number of leaves in the clade (can use to set bottom of bracket in addTaxon()
local totalCount = 0
pargs = frame:getParent().args -- parent arguments
infoOutput = p.getCladeTreeInfo() -- get info about clade structure, e.g. lastNode (last |N= child number)
--[[ add the templatestyles tag conditionally to reduce expansion size (currently diabled)
when added to every clade table, it increases post‐expand include size significantly
e.g. the Neosuchia page (or test version) is increase by about 8% (672 bytes each)
if template styles added to all pages there are 133 stripmarkers
with cladeCount==1 condition, this is reduced to 34
however cladeCount==1 condition interfers with fix for additional line due to parser bug T18700
killing the strip markers also removes backlinks to references using citation templates
--]]
--cladeString =mw.text.killMarkers( cladeString ) -- also kills off strip markers using citation templates
--cladeString = mw.text.unstrip(cladeString)
--if cladeCount==1 then
local src = "Template:Clade/styles.css"
cladeString = cladeString .. p.templateStyle( frame, src ) .. '\n'
--end
local tableStyle = frame.args.style or ""
if tableStyle ~= "" then
tableStyle = ' style="' .. tableStyle .. '"' -- include style= in string to suppress empty style elements
end
reverseClade =frame.args.reverse or pargs.reverse or false -- a global
--ENFORCE GLOBAL FOR DEVELOPMENT
--reverseClade = true
local captionName = pargs['caption'] or ""
local captionStyle = pargs['captionstyle'] or ""
-- add an element to mimick nowiki WORKS BUT DISABLE FOR DEMO PURPOSES
--cladeString = '<p class="mw-empty-elt"></p>\n'
-- open table
-- (border-collapse causes problems (see talk) -- cladeString = cladeString .. '{| style="border-collapse:collapse;border-spacing:0;margin:0;' .. tableStyle .. '"'
-- (before CSS styling) -- cladeString = cladeString .. '{| style="border-spacing:0;margin:0;' .. tableStyle .. '"'
cladeString = cladeString .. '{|class="clade"' .. tableStyle
-- add caption
if captionName ~= "" then
cladeString = cladeString .. '\n|+ style="' .. captionStyle .. '"|' .. captionName
end
local moreNeeded = true
childNumber = 0
--lastNode = 0
--[[get child elements (add more rows for each child of node; each child is two rows)
the function addTaxon is called to add the rows for each child element;
each child add two rows: the first cell of each row contains the label or sublabel (below the line label), respectively;
the second cell spans both rows and contains the leaf name or a new clade structure
a third cell on the top row is sometimes added to contain a group to the right
]]
-- main loop
while childNumber < lastNode do -- use the last number determined in the preprocessing
childNumber = childNumber + 1 -- so we start with 1
local nodeLeaf = pargs[tostring(childNumber)] or "" -- get data from |N=
local nodeLabel = pargs['label'..tostring(childNumber)] or "" -- get data from |labelN=
local newickString = pargs['newick'..tostring(childNumber)] or "" -- get data from |labelN=
local listString = pargs['list'..tostring(childNumber)] or ""
if listString ~= "" then
cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, p.list(0, listString), nodeLabel, lastNode)
elseif newickString ~= "" then -- if using a newick string instead of a clade structure
newickString = p.processNewickString(newickString,childNumber)
if nodeLabel == "" then -- use labelN by default, otherwise use root name from Newick string
nodeLabel = p.getNewickOuterterm(newickString) -- need to use terminal part of newick string for label
end
cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, p.newick(0, newickString), nodeLabel, lastNode)
--lastNode=lastNode+1 -- there is a counting problem with the newickstring
elseif nodeLeaf ~= "" then -- if the node contains a leaf name or clade structue
--if reverseClade2 then
-- cladeString = cladeString .. '\n' .. p.addTaxonReverse(childNumber, nodeLeaf, nodeLabel, lastNode)
--else
cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode)
--end
end
end
local footerText = pargs['footer'] or ""
local footerStyle = pargs['footerstyle'] or ""
if footerText ~= "" then
cladeString = cladeString .. '\n|-style="' .. footerStyle .. '"\n|colspan="2"|<p>' .. footerText .. '</p>||'
-- 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><tr style="' .. footerStyle .. '"><td colspan="2"><p>' .. footerText .. '</p></td></tr></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|}'
cladeString = p.addSubTrees(cladeString) -- add subtrees
return cladeString
--return '<div style="width:auto;">\n' .. cladeString .. '</div>'
end
--[[ =============================function to add subtrees ========================================== ]]
function p.addSubTrees(cladeString)
--local pargs = mw.getCurrentFrame():getParent().args
local suffix = { [1]="A", [2]="B", [3]="C", [4]="D", [5]="E", [6]="F", [7]="G", [8]="H", [9]="I", [10]="J",
[11]="K", [12]="L", [13]="M", [14]="N", [15]="O", [16]="P", [17]="Q", [18]="R", [19]="S", [20]="T",
[21]="U", [22]="V", [23]="W", [24]="X", [25]="Y", [26]="Z"}
for i=1, 26, 1 do
local subclade = pargs['subclade'..suffix[i]]
local target = pargs['target'..suffix[i]] or "SUBCLADE_" .. suffix[i]
if subclade then
if string.find(cladeString, target) then
cladeString = string.gsub(cladeString,target,subclade)
end
end
end
return cladeString
end
--[[ -------------------------------------- p.addTaxon() ------------------------------------------
function to add child elements
adds wikitext for two rows of the table for each child node,
the first cell in each is used for the label and sublabel; the bottom border forms the horizonal branch of the bracket
the second cell is used for the leafname or a transcluded clade structure and spans both rows
note that the first and last child nodes need to be handled differently from the middle elements
the middle elements (|2, |3 ...) use a left border to create the vertical line of the bracket
the first child element doesn't use a left border for the first cell in the top row (as it is above the bracket)
the last child doesn't use a left border for the first cell in the second row (as it is below the bracket)
]]
function p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode)
--[[ get border formating parameters (i.e. color, thickness, state)
nodeParameters for whole bracket (unnumbered, i.e. color, thickness, state) apply to whole node bracket,
branchParameters apply to individual branches
the branch parameters have a number, e.g. |colorN, |thicknessN, |stateN
the node parameters have no number, e.g. |color, |thickness, |state
]]
local nodeColor = pargs['color'] or "" -- don't set default to allow green on black gadget
local nodeThickness = tonumber(pargs['thickness']) or 1
local nodeState = pargs['state'] or "solid"
-- get border formating parameters for branch (default to global nodeParameters)
local branchColor = pargs['color'..tostring(childNumber)] or nodeColor
local branchThickness = tonumber(pargs['thickness'..tostring(childNumber)]) or nodeThickness
local branchState = pargs['state'..tostring(childNumber)] or nodeState
if branchState == 'double' then
if branchThickness < 2 then branchThickness = 3 end -- need thick line for double
end
local branchStyle = pargs['style'..tostring(childNumber)] or ""
local branchLength = pargs['length'] or pargs['length'..tostring(childNumber)] or ""
-- the left border takes node parameters, the bottom border takes branch parameters
-- this has coding on the colours for green on black
local bottomBorder = tostring(branchThickness) ..'px ' .. branchState .. (branchColor~="" and ' ' .. branchColor or '')
local leftBorder = tostring(nodeThickness) ..'px ' .. nodeState .. (nodeColor~="" and ' ' .. nodeColor or '')
--The default border styles are in the CSS (styles.css)
-- the inline styling is applied when thickness, color or state are change
local useInlineStyle = false
-- use inline styling non-default color, line thickness or state have been set
if branchColor ~= "" or branchThickness ~= 1 or branchState ~= "solid" then
useInlineStyle = true
end
-- variables for right hand bar or bracket
--local barColor = ""
local barRight = pargs['bar'..tostring(childNumber)] or "0"
local barBottom = pargs['barend'..tostring(childNumber)] or "0"
local barTop = pargs['barbegin'..tostring(childNumber)] or "0"
local barLabel = pargs['barlabel'..tostring(childNumber)] or ""
local groupLabel = pargs['grouplabel'..tostring(childNumber)] or ""
local groupLabelStyle = pargs['grouplabelstyle'..tostring(childNumber)] or ""
local labelStyle = pargs['labelstyle'..tostring(childNumber)] or ""
local sublabelStyle = pargs['sublabelstyle'..tostring(childNumber)] or ""
--replace colours with format string; need right bar for all three options
if barRight ~= "0" then barRight = "2px solid " .. barRight end
if barTop ~= "0" then barRight = "2px solid " .. barTop end
if barBottom ~= "0" then barRight = "2px solid " .. barBottom end
if barTop ~= "0" then barTop = "2px solid " .. barTop end
if barBottom ~= "0" then barBottom = "2px solid " .. barBottom end
-- now construct wikitext
local cladeString = ''
local styleString = ''
local borderStyle = '' -- will be used if border color, thickness or state is to be changed
local classString = ''
local reverseClass = ''
local widthClass = ''
-- class to add if using reverse (rtl) cladogram;
if reverseClade then reverseClass = ' reverse' end
-- (1) wikitext for new row
--cladeString = cladeString .. '\n|-'
-- (2) now add cell with label
if useInlineStyle then
if childNumber == 1 then
borderStyle = 'border-left:none;border-right:none;border-bottom:' .. bottomBorder .. ';'
--borderStyle = 'border-bottom:' .. bottomBorder .. ';'
else -- for 2-17
if reverseClade then
borderStyle = 'border-left:none;border-right:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';'
else
borderStyle = 'border-left:' .. leftBorder .. ';border-bottom:' .. bottomBorder .. ';'
end
end
end
if useInlineStyle or branchStyle ~= '' or branchLength ~= "" or labelStyle ~= "" then
local branchLengthStyle = ""
if branchLength ~= "" then
if childNumber == 1 then
branchLengthStyle = 'width:' .. branchLength .. ';' -- add width to first element
end
--if childNumber > 1 then prefix = 'max-' end
branchLengthStyle = branchLengthStyle --= prefix .. 'width:' .. branchLength .. ';'
.. 'max-width:' .. branchLength ..';'
.. 'padding:0em;' -- remove padding to make calculation easier
-- following moved to styles.css
-- .. 'white-space:nowrap'
-- .. 'overflow:hidden;' -- clip labels longer than the max-width
-- .. 'text-overflow:clip;' -- ellipsis;'
widthClass = " clade-fixed-width"
end
styleString = 'style="' .. borderStyle .. branchLengthStyle .. branchStyle .. labelStyle .. '"'
end
if childNumber == 1 then
classString= 'class="clade-label first'.. widthClass .. '" ' -- add class "first" for top row
else
classString = 'class="clade-label' .. reverseClass .. widthClass .. '" ' -- add "reverse" class if ltr cladogram
end
-- wikitext for cell with label
local labelCellString = '\n|' .. classString .. styleString .. '|' .. p.addLabel(childNumber,nodeLabel) -- p.addLabel(nodeLabel)
--cladeString = cladeString .. labelCellString
---------------------------------------------------------------------------------
-- (3) add cell with leaf (which may be a table with transluded clade content)
if barRight ~= "0" then
if reverseClade then -- we want the bar on the left
styleString = ' style="border-left:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"'
else
styleString = ' style="border-right:' .. barRight .. ';border-bottom:' .. barBottom .. ';border-top:' .. barTop .. ';' .. branchStyle .. '"'
end
else
if (branchStyle ~= '') then
styleString = ' style="' .. branchStyle .. '"'
else
styleString = '' -- use defaults in styles.css
end
end
classString = 'class="clade-leaf' .. reverseClass .. '"'
--[[note: the \n causes plain leaf elements get wrapped in <p> with style="margin:0.4em 0 0.5em 0;"
this adds spacing to rows, but is set by defaults rather than the clade template
it also means there are two newlines when it is a clade structure (which might explain some past issues)
]]
local content = '\n' .. nodeLeaf -- the newline is not necessary, but keep for backward compatibility
-- test using image parameter
local image = pargs['image'..tostring(childNumber)] or ""
if image ~= "" then
--content = content .. image -- basic version
content = '\n{| class="clade" style="width:auto;"' --defaults to width:100% because of class "clade"
.. '\n| class="clade-leaf" ' .. '|\n' .. nodeLeaf
.. '\n| class="clade-leaf" ' .. '|\n' .. image
.. '\n|}'
-- note: the classes interfere with the node counter, so try simpler version with style
content = '\n{| style="width:100%;border-spacing:0;" ' --width:auto is "tight"; 100% needed for image alignment
.. '\n| style="border:0;padding:0;" ' .. '|\n' .. nodeLeaf
.. '\n| style="border:0;padding:0;" ' .. '|\n' .. image
.. '\n|}'
end
-- wikitext for leaf cell (note: nodeLeaf needs to be on newline if new wikitable)
-- but that is no longer the case (newline is now forced)
-- the newline wraps plain leaf terminals in <P> with vertical padding (see above)
--local leafCellString = '\n|rowspan=2 ' .. classString .. styleString .. ' |\n' .. content -- the new line causes <p> wrapping for plain leaf terminals
local leafCellString = '\n|rowspan=2 ' .. classString .. styleString .. ' |' .. content
--cladeString = cladeString .. leafCellString
-------------------------------------------
-- (4) stuff for right-hand bracket labels
classString='class="clade-bar' .. reverseClass .. '"'
local barLabelCellString = ''
if barRight ~= "0" and barLabel ~= "" then
barLabelCellString = '\n|rowspan=2 ' .. classString .. ' |' .. barLabel
else -- uncomment following line to see the cell structure
--barLabelCellString = '\n|rowspan=2 ' .. classString .. ' |' .. 'BL'
end
if groupLabel ~= "" then
barLabelCellString = barLabelCellString .. '\n|rowspan=2 ' .. classString .. ' style="'.. groupLabelStyle .. '" |' .. groupLabel
else -- uncomment following line to see the cell structure
--barLabelCellString = barLabelCellString .. '\n|rowspan=2 ' .. classString .. '" |' .. 'GL'
end
--cladeString = cladeString .. barLabelCellString
-------------------------------------------------------------------------------------
-- (5) add second row (only one cell needed for sublabel because of rowspan=2);
-- note: earlier versions applied branch style to row rather than cell
-- for consistency, it is applied to the sublabel cell as with the label cell
--cladeString = cladeString .. '\n|-'
-----------------------------------
-- (6) add cell containing sublabel
local subLabel = pargs['sublabel'..tostring(childNumber)] or "" -- request in addLabel
-- FOR TESTING: use subLabel for annotating the clade structues to use structure information (DEBUGGIING ONLY)
--if childNumber==lastNode then subLabel= infoOutput end
-- END TESTING
borderStyle = ''
styleString = ''
if useInlineStyle then
if childNumber==lastNode then -- if childNumber==lastNode we don't want left border, otherwise we do
borderStyle = 'border-right:none;border-left:none;'
else
if reverseClade then
borderStyle = 'border-left:none;border-right:' .. leftBorder .. ';'
else
borderStyle = 'border-right:none;border-left:' .. leftBorder .. ';'
end
end
end
if borderStyle ~= '' or branchStyle ~= '' or branchLength ~= '' or sublabelStyle ~= "" then
local branchLengthStyle = ""
if branchLength ~= "" then
if childNumber == 1 then
branchLengthStyle = 'width:' .. branchLength .. ';' -- add width to first element
end
--if childNumber > 1 then prefix = 'max-' end
branchLengthStyle = branchLengthStyle --= prefix .. 'width:' .. branchLength .. ';'
.. 'max-width:' .. branchLength ..';'
.. 'padding:0em;' -- remove padding to make calculation easier
end
styleString = 'style="' .. borderStyle .. branchLengthStyle .. branchStyle .. sublabelStyle .. '"'
--styleString = ' style="' .. borderStyle .. branchStyle .. sublabelStyle .. '"'
end
--local sublabel = p.addLabel(childNumber,subLabel)
if childNumber == lastNode then
classString = 'class="clade-slabel last' .. widthClass .. '" '
else
classString = 'class="clade-slabel' .. reverseClass .. widthClass .. '" '
end
local sublabelCellString = '\n|' .. classString .. styleString .. '|' .. p.addLabel(childNumber,subLabel)
--cladeString = cladeString .. sublabelCellString
-- constuct child element wikitext
if reverseClade then
cladeString = cladeString .. '\n|-'
cladeString = cladeString .. barLabelCellString
cladeString = cladeString .. leafCellString
cladeString = cladeString .. labelCellString
cladeString = cladeString .. '\n|-'
cladeString = cladeString .. sublabelCellString
else
cladeString = cladeString .. '\n|-'
cladeString = cladeString .. labelCellString
cladeString = cladeString .. leafCellString
cladeString = cladeString .. barLabelCellString
cladeString = cladeString .. '\n|-' -- add second row (only one cell needed for sublabel because of rowspan=2);
cladeString = cladeString .. sublabelCellString
end
return cladeString
end
--[[ adds text for label or sublabel to a cell
]]
function p.addLabel(childNumber,nodeLabel)
--local nodeLabel = mw.getCurrentFrame():getParent().args['label'..tostring(childNumber)] or ""
--local firstChars = string.sub(nodeLabel, 1,2) -- get first two characters; will be {{ if no parameter (for Old method?)
--if firstChars == "{{{" or nodeLabel == "" then
if nodeLabel == "" then
--return '<br/>' --' <br/>' -- remove space to reduce post-expand include size (the width=1.5em handles spacing)
--return '<br/>' -- 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 '<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
--TODO test following alternative
--if nodeLabel:find( "%b<>") then stylingElementDetected = true end
if stylingElementDetected == true then
return '<div style="display:inline;" class="nowrap">' .. nodeLabel .. '</div>'
else
local nowrapString = string.gsub(nodeLabel," ", " ") -- replace spaces with non-breaking space
if not nowrapString:find("UNIQ.-QINU") and not nowrapString:find("%[%[.-%]%]") then -- unless a strip marker
nowrapString = string.gsub(nowrapString,"-", "‑") -- replace hyphen with non-breaking hyphen (‑)
end
return nowrapString
end
end
end
--[[=================== Newick string handling function =============================
]]
function p.getNewickOuterterm(newickString)
return string.gsub(newickString, "%b()", "") -- delete parenthetic term
end
function p.newick(count,newickString)
local cladeString = ""
count = count+1
--start table
--cladeString = cladeString .. '{| style="border-collapse:collapse;border-spacing:0;border:0;margin:0;'
cladeString = cladeString .. '{| class="clade" '
local j,k
j,k = string.find(newickString, '%(.*%)') -- find location of outer parenthesised term
local innerTerm = string.sub(newickString, j+1, k-1) -- select content in parenthesis
local outerTerm = string.gsub(newickString, "%b()", "") -- delete parenthetic term
if outerTerm == 'panthera' then outerTerm = "x" end -- how is this set in local variable for inner nodes?
outerTerm = tostring(count)
-- need to remove commas in bracket terms before split, so temporarily replace commas between brackets
local innerTerm2 = string.gsub(innerTerm, "%b()", function (n)
return string.gsub(n, ",%s*", "XXX") -- also strip spaces after commas here
end)
--cladeString = cladeString .. '\n' .. p.addTaxon(1, innerTerm2, "")
-- this needs a lastNode variable
local s = p.strsplit(innerTerm2, ",")
--oldLastNode=lastNode
local lastNode=table.getn(s) -- number of child branches
local i=1
while s[i] do
local restoredString = string.gsub(s[i],"XXX", ",") -- convert back to commas
--restoredString = s[i]
local outerTerm = string.gsub(restoredString, "%b()", "")
if string.find(restoredString, '%(.*%)') then
--cladeString = cladeString .. '\n' .. p.addTaxon(i, restoredString, "x")
cladeString = cladeString .. '\n' .. p.addTaxon(i, p.newick(count,restoredString), outerTerm, lastNode)
-- p.addTaxon(2, p.newick(count,newickString2), "root")
else
cladeString = cladeString .. '\n' .. p.addTaxon(i, restoredString, "", lastNode) --count)
end
i=i+1
end
-- lastNode=oldLastNode
-- close table
--cladeString = cladeString .. '\n' .. '| style="border: 0; padding: 0; vertical-align: top;" | <br/> \n|}'
--cladeString = cladeString .. '\n| <br/> \n|}' -- is this legacy for extra sublabel?
cladeString = cladeString .. '\n|}'
return cladeString
end
-- emulate a standard split string function
-- why not use mw.text.split(s, sep)?
function p.strsplit(inputstr, sep)
if sep == nil then
sep = "%s"
end
local t={}
local i=1
for str in string.gmatch(inputstr, "([^"..sep.."]+)") do
t[i] = str
i = i + 1
end
return t
end
-- =================== experimental Newick to clade parser function =============================
--[[Function of convert Newick strings to clade format
Usage: {{#invoke:Module:Sandbox/Jts1882/CladeN|newickConverter|newickstring={{{NEWICK_STRING}}} }}
]]
function p.newickConverter(frame)
local newickString = frame.args['newickstring'] or pargs['newick']
--if newickString == '{{{newickstring}}}' then return newickString end
newickString = p.processNewickString(newickString,"") -- "childNumber")
-- show the Newick string
local cladeString = ''
local levelNumber = 1 -- for depth of iteration
local childNumber = 1 -- number of sister elements on node (always one for root)
-- converted the newick string to the clade structure
cladeString = cladeString .. '{{clade'
cladeString = cladeString .. p.newickParseLevel(newickString, levelNumber, childNumber)
cladeString = cladeString .. '\r}}'
local resultString = ''
local option = pargs['option'] or ''
if option == 'tree' then
--show the transcluded clade diagram
resultString = cladeString
else
-- show the Newick string
resultString = '<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 string
This function receives a Newick string, which has two components
1. the right hand term is a clade label: |labelN=labelname
2. the left hand term in parenthesis has common delimited child nodes, each of which can be
i. a taxon name which just needs: |N=leafname
ii. a Newick string which needs further processing through reiteration
]]
function p.newickParseLevel(newickString,levelNumber,childNumber)
local cladeString = ""
local indent = p.getIndent(levelNumber)
--levelNumber=levelNumber+1
local j=0
local k=0
j,k = string.find(newickString, '%(.*%)') -- find location of outer parenthesised term
local innerTerm = string.sub(newickString, j+1, k-1) -- select content in parenthesis
local outerTerm = string.gsub(newickString, "%b()", "") -- delete parenthetic term
cladeString = cladeString .. indent .. '|label'..childNumber..'=' .. outerTerm
cladeString = cladeString .. indent .. '|' .. childNumber..'=' .. '{{clade'
levelNumber=levelNumber+1
indent = p.getIndent(levelNumber)
-- protect commas in inner parentheses from split; temporarily replace commas between parentheses
local innerTerm2 = string.gsub(innerTerm, "%b()", function (n)
return string.gsub(n, ",%s*", "XXX") -- also strip spaces after commas here
end)
local s = p.strsplit(innerTerm2, ",")
local i=1
while s[i] do
local restoredString = string.gsub(s[i],"XXX", ",") -- convert back to commas
local outerTerm = string.gsub(restoredString, "%b()", "")
if string.find(restoredString, '%(.*%)') then
--cladeString = cladeString .. indent .. '|y' .. i .. '=' .. p.newickParseLevel(restoredString,levelNumber+1,i)
cladeString = cladeString .. p.newickParseLevel(restoredString,levelNumber,i)
else
cladeString = cladeString .. indent .. '|' .. i .. '=' .. restoredString --.. '(level=' .. levelNumber .. ')'
end
i=i+1
end
-- end -- end splitting of strings
cladeString = cladeString .. indent .. '}}'
return cladeString
end
function p.getIndent(levelNumber)
local indent = "\r"
local extraIndent = pargs['indent'] or mw.getCurrentFrame().args['indent'] or 0
while tonumber(extraIndent) > 0 do
indent = indent .. " " -- an extra indent to make aligining compound trees easier
extraIndent = extraIndent - 1
end
while levelNumber > 1 do
indent = indent .. " "
levelNumber = levelNumber-1
end
return indent
end
function p.newickstuff(newickString)
end
function p.processNewickString(newickString,childNumber)
local maxPatterns = 5
local i = 0
local pargs = pargs
local pattern = pargs['newick'..tostring(childNumber)..'-pattern'] -- unnumbered option for i=1
local replace = pargs['newick'..tostring(childNumber)..'-replace']
while i < maxPatterns do
i=i+1
pattern = pattern or pargs['newick'..tostring(childNumber)..'-pattern'..tostring(i)]
replace = replace or pargs['newick'..tostring(childNumber)..'-replace'..tostring(i)] or ""
if pattern then
newickString = string.gsub (newickString, pattern, replace)
end
pattern = nil; replace = nil
end
newickString = string.gsub (newickString, "_", " ") -- replace underscore with space
return newickString
end
------------------------------------------------------------------------------------------
function p.test2(target)
local target ="User:Jts1882/sandbox/templates/Template:Passeroidea"
local result = mw.getCurrentFrame():expandTemplate{ title = target, args = {['style'] = '' } }
return result
end
-------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------
--[[function getCladeTreeInfo()
this preprocessing loop gets information about the whole structure (number of nodes, leaves etc)
it makes a redundant calls to the templates through transclusion, but doen't affect the template depths;
it provides the global lastNode that is used to limit the main while loop
--]]
function p.getCladeTreeInfo()
-- enable proprocessing loop
local childNumber = 0
local childCount =0
local maxChildren =20
--info veriables (these are global for now)
nodeCount=0
cladeCount=0
leafCount=0
while childNumber < maxChildren do -- preprocessing loop
childNumber = childNumber + 1 -- so we start with 1
local nodeLeaf,data = pargs[tostring(childNumber)] or "" -- get data from |N=
local newickString = pargs['newick'..tostring(childNumber)] or "" -- get data from |labelN=
local listString = pargs['list'..tostring(childNumber)] or "" -- get data from |labelN=
if newickString ~= "" or nodeLeaf ~= "" or listString ~= "" then
--if nodeLeaf ~= "" then
childCount = childCount + 1 -- this counts child elements in this clade
--[[]
for i in string.gmatch(nodeLeaf, "||rowspan") do -- count number of rows started (transclusion)
nodeCount = nodeCount + 1
end
for i in string.gmatch(nodeLeaf, '{|class="clade"') do -- count number of tables started (transclusion)
cladeCount = cladeCount + 1
end
]]
-- count occurences of clade structure using number of classes used and add to counters
local _, nClades = string.gsub(nodeLeaf, 'class="clade"', "")
local _, nNodes = string.gsub(nodeLeaf, 'class="clade%-leaf"', "")
cladeCount = cladeCount + nClades
nodeCount = nodeCount + nNodes
lastNode = childNumber -- this gets the last node with a valid entry, even when missing numbers
end
end
--]]
-- nodes can be either terminal leaves or a clade structure (table)
-- note: should change class clade-leaf to clade-node to reflect this
nodeCount = nodeCount -- number of nodes (class clade-leaf) passed down by transduction
+ childCount + 1 -- plus one for current clade and one for each of its child element
cladeCount = cladeCount + 1 -- number of clade structure tables passed down by transduction (plus one for current clade)
leafCount = nodeCount-cladeCount -- number of terminal leaves (equals height of cladogram)
-- output for testing: number of clades / total nodes / terminal nodes (=leaves)
-- (internal nodes) (cladogram height)
infoOutput = '<small>[' .. cladeCount .. '/' .. nodeCount .. '/' .. leafCount .. ']</small>'
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 = "<pre>Hello</pre>"
--return string.sub(test,6,-7)
local o1 =frame:getParent():getArgument('code2')
return o1:expand()
--return string.sub(code,2,-1) -- strip marker \127'"`UNIQ--tagname-8 hex digits-QINU`"'\127
--return frame:preprocess(string.sub(code,3))
end
function p.firstToUpper(str)
return (str:gsub("^%l", string.upper))
end
--[[ function to generate cladogram from a wikitext-like list
- uses @ instead of * because we don't want wikitext processed and nowiki elements are passed as stripmarkers (?)
]]
function p.list(count,listString)
local cladeString = ""
--count = count+1
local list = mw.text.split(listString, "\n")
local i=1
local child=1
local lastNode=0--table.getn(list) -- number of child branches (potential)
cladeString = cladeString .. '{| class="clade" '
while list[i] do
list[i]=list[i]:gsub("^@", "") -- strip the first @
if not string.match( list[i], "^@", 1 ) then -- count children at this level (not beginning wiht @)
lastNode = lastNode+1
end
i=i+1
end
i=1
while list[i] do
--[[ pseudocode:
if next value begins with @ we have a subtree,
which must be recombined and past iteratively
else we have a simple leaf
]]
-- if the next value begins with @, we have a subtree which should be recombined
if list[i+1] and string.match( list[i+1], "^@", 1 ) then
local label=list[i]
i=i+1
local recombined = list[i]
while list[i+1] and string.match( list[i+1], "^@", 1 ) do
recombined = recombined .. "\n" .. list[i+1]
i=i+1
end
--cladeString = cladeString .. '\n' .. p.addTaxon(child, recombined, label, lastNode)
cladeString = cladeString .. '\n' .. p.addTaxon(child, p.list(count,recombined), label, lastNode)
else
cladeString = cladeString .. '\n' .. p.addTaxon(child, list[i], "", lastNode)
end
i=i+1
child=child+1
end
cladeString = cladeString .. '\n|}'
mw.addWarning("WARNING. This is a test feature only.")
return cladeString
end
-- =================== experimental Newick to clade parser function =============================
--[[Function of convert Newick strings to clade format
Usage: {{#invoke:Module:Sandbox/Jts1882/CladeN|newickConverter|newickstring={{{NEWICK_STRING}}} }}
]]
function p.cladeConverter(frame)
end
function p.listConverter(frame)
local listString = frame.args['list'] or pargs['list']
-- show the list string
local cladeString = ''
local levelNumber = 1 -- for depth of iteration
local childNumber = 1 -- number of sister elements on node (always one for root)
local indent = p.getIndent(levelNumber)
-- converted the newick string to the clade structure
cladeString = cladeString .. indent .. '{{clade'
cladeString = cladeString .. p.listParseLevel(listString, levelNumber, childNumber)
--cladeString = cladeString .. '\r}}'
local resultString = ''
local option = pargs['option'] or ''
if option == 'tree' then
--show the transcluded clade diagram
resultString = cladeString
else
-- show the Newick string
resultString = '<pre>'..listString..'</pre>'
-- show the converted clade structure
resultString = resultString .. '<pre>'.. cladeString ..'</pre>'
end
--resultString = frame:expandTemplate{ title = 'clade', frame:preprocess(cladeString) }
return resultString
end
function p.listParseLevel(listString,levelNumber,childNumber)
local cladeString = ""
local indent = p.getIndent(levelNumber)
levelNumber=levelNumber+1
local list = mw.text.split(listString, "\n")
local i=1
local child=1
local lastNode=0
while list[i] do
list[i]=list[i]:gsub("^@", "") -- strip the first @
if not string.match( list[i], "^@", 1 ) then -- count children at this level (not beginning wiht @)
lastNode = lastNode+1
end
i=i+1
end
i=1
while list[i] do
--[[ pseudocode:
if next value begins with @ we have a subtree,
which must be recombined and past iteratively
else we have a simple leaf
]]
-- if the next value begins with @, we have a subtree which should be recombined
if list[i+1] and string.match( list[i+1], "^@", 1 ) then
local label=list[i]
i=i+1
local recombined = list[i]
while list[i+1] and string.match( list[i+1], "^@", 1 ) do
recombined = recombined .. "\n" .. list[i+1]
i=i+1
end
cladeString = cladeString .. indent .. '|label' .. child ..'=' .. label
cladeString = cladeString .. indent .. '|' .. child ..'=' .. '{{clade'
.. p.listParseLevel(recombined,levelNumber,i)
else
cladeString = cladeString .. indent .. '|' .. child ..'=' .. list[i]
end
i=i+1
child=child+1
end
cladeString = cladeString .. indent .. '}}'
return cladeString
end
-- this must be at end
return p
