Module:Clade and Module:Clade/sandbox: Difference between pages

The main function is called by the template using the {{invoke}} instruction; the three main functions are:

]]

require('strict')

local p = {}

local pargs = {} -- parent arguments

local totalCount = 0

if tableStyle ~= "" then

tableStyle = ' style="' .. tableStyle .. '"' -- include style= in string to suppress empty style elements

end

local captionName = pargs['caption'] or ""

local captionStyle = pargs['captionstyle'] or ""

-- open table

-- (border-collapse causes problems (see talk) -- cladeString = cladeString .. '{| style="border-collapse:collapse;border-spacing:0;margin:0;' .. tableStyle .. '"'

if captionName ~= "" then

cladeString = cladeString .. '\n|+ style="' .. captionStyle .. '"|' .. captionName

--[[get child elements (add more rows for each child of node; each child is two rows)

]]

--if reverseClade2 then

-- cladeString = cladeString .. '\n' .. p.addTaxonReverse(childNumber, nodeLeaf, nodeLabel, lastNode)

cladeString = cladeString .. '\n' .. p.addTaxon(childNumber, nodeLeaf, nodeLabel, lastNode)

--end

-- note the footer causes a problem with tr:last-child so need either

-- (1) use <tfoot> but it is not allowed or incompatable

-- (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)

cladeString = p.addSubTrees(cladeString) -- add subtrees

--return '<div style="width:auto;">\n' .. cladeString .. '</div>'

end

local suffix = { [1]="A", [2]="B", [3]="C", [4]="D", [5]="E", [6]="F", [7]="G", [8]="H", [9]="I", [10]="J",

local subclade = pargs['subclade'..suffix[i]]

local target = pargs['target'..suffix[i]] or "SUBCLADE_" .. suffix[i]

end

end

return cladeString

end

--[[ -------------------------------------- p.addTaxon() ------------------------------------------

]]

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

--[[ get border formating parameters (i.e. color, thickness, state)

branchParameters apply to individual branches

]]

local nodeThickness = tonumber(pargs['thickness']) or 1

local nodeState = pargs['state'] or "solid"

local branchLength = pargs['length'] or pargs['length'..tostring(childNumber)] or ""

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)

local useInlineStyle = false

local barRight = pargs['bar'..tostring(childNumber)] or "0"

local barBottom = pargs['barend'..tostring(childNumber)] or "0"

local barLabel = pargs['barlabel'..tostring(childNumber)] or ""

local groupLabelStyle = pargs['grouplabelstyle'..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 barBottom ~= "0" then barRight = "2px solid " .. barBottom end

if barBottom ~= "0" then barBottom = "2px solid " .. barBottom end

local cladeString = ''

local styleString = ''

-- (2) now add cell with label

if useInlineStyle then

if childNumber == 1 then

else -- for 2-17

if reverseClade then

end

end

branchLengthStyle = branchLengthStyle --= prefix .. 'width:' .. branchLength .. ';'

.. 'max-width:' .. branchLength ..';'

-- following moved to styles.css

-- .. 'white-space:nowrap'

-- .. 'text-overflow:clip;' -- ellipsis;'

end

styleString = 'style="' .. borderStyle .. branchLengthStyle .. branchStyle .. labelStyle .. '"'

if childNumber == 1 then

---------------------------------------------------------------------------------

-- (3) add cell with leaf (which may be a table with transluded clade content)

classString='class="clade-bar' .. reverseClass .. '"'

if barRight ~= "0" and barLabel ~= "" then

barLabelCellString = '\n|rowspan=2 ' .. classString .. ' |' .. barLabel

barLabelCellString = barLabelCellString .. '\n|rowspan=2 ' .. classString .. ' style="'.. groupLabelStyle .. '" |' .. groupLabel

else -- uncomment following line to see the cell structure

end

--cladeString = cladeString .. barLabelCellString

-------------------------------------------------------------------------------------

-- (5) add second row (only one cell needed for sublabel because of rowspan=2);

--cladeString = cladeString .. '\n|-'

if childNumber==lastNode then -- if childNumber==lastNode we don't want left border, otherwise we do

borderStyle = 'border-right:none;border-left:none;'

local branchLengthStyle = ""

if branchLength ~= "" then

branchLengthStyle = branchLengthStyle --= prefix .. 'width:' .. branchLength .. ';'

.. 'max-width:' .. branchLength ..';'

end

styleString = 'style="' .. borderStyle .. branchLengthStyle .. branchStyle .. sublabelStyle .. '"'

cladeString = cladeString .. sublabelCellString

cladeString = cladeString .. sublabelCellString

return cladeString

end

-- however, there is a problem if labels have a styling element (e.g. <span style= ..., <span title= ...)

local stylingElementDetected = false

--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>'

return nowrapString

end

local j,k

local outerTerm = string.gsub(newickString, "%b()", "") -- delete parenthetic term

outerTerm = tostring(count)

-- need to remove commas in bracket terms before split, so temporarily replace commas between brackets

--cladeString = cladeString .. '\n' .. p.addTaxon(1, innerTerm2, "")

local s = p.strsplit(innerTerm2, ",")

--oldLastNode=lastNode

local lastNode=table.getn(s) -- number of child branches

while s[i] do

local restoredString = string.gsub(s[i],"XXX", ",") -- convert back to commas

cladeString = cladeString .. '\n' .. p.addTaxon(i, restoredString, "", lastNode) --count)

end

end

-- lastNode=oldLastNode

-- close table

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

-- why not use mw.text.split(s, sep)?

function p.strsplit(inputstr, sep)

end

--if newickString == '{{{newickstring}}}' then return newickString end

-- show the Newick string

local cladeString = ''

-- converted the newick string to the clade structure

local resultString = ''

--show the transcluded clade diagram

resultString = '<pre>'..newickString..'</pre>'

end

--[[ Parse one level of Newick string

]]

function p.newickParseLevel(newickString,levelNumber,childNumber)

local cladeString = ""

local indent = p.getIndent(levelNumber)

local j=0

local k=0

local outerTerm = string.gsub(newickString, "%b()", "") -- delete parenthetic term

-- protect commas in inner parentheses from split; temporarily replace commas between parentheses

local s = p.strsplit(innerTerm2, ",")

while s[i] do

local restoredString = string.gsub(s[i],"XXX", ",") -- convert back to commas

cladeString = cladeString .. indent .. '|' .. i .. '=' .. restoredString --.. '(level=' .. levelNumber .. ')'

end

end

cladeString = cladeString .. indent .. '}}'

end

local extraIndent = pargs['indent'] or mw.getCurrentFrame().args['indent'] or 0

return indent

end

local i = 0

local pargs = pargs

while i < maxPatterns do

pattern = pattern or pargs['newick'..tostring(childNumber)..'-pattern'..tostring(i)]

replace = replace or pargs['newick'..tostring(childNumber)..'-replace'..tostring(i)] or ""

if pattern then

end

end

return newickString

end

--[[function getCladeTreeInfo()

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()

childNumber = childNumber + 1 -- so we start with 1

local nodeLeaf,data = pargs[tostring(childNumber)] or "" -- get data from |N=

if newickString ~= "" or nodeLeaf ~= "" or listString ~= "" then

--if nodeLeaf ~= "" then

childCount = childCount + 1 -- this counts child elements in this clade

nodeCount = nodeCount + 1

cladeCount = cladeCount + 1

lastNode = childNumber -- this gets the last node with a valid entry, even when missing numbers

end

end

--]]

leafCount = nodeCount-cladeCount -- number of terminal leaves (equals height of cladogram)

-- output for testing: number of clades / total nodes / terminal nodes (=leaves)

infoOutput = '<small>[' .. cladeCount .. '/' .. nodeCount .. '/' .. leafCount .. ']</small>'

function p.showClade(frame)

--local code = frame.args.code or ""

--return code

--return string.sub(test,6,-7)

return o1:expand()

--return frame:preprocess(string.sub(code,3))

end

function p.firstToUpper(str)

end

--[[ function to generate cladogram from a wikitext-like list

]]

function p.list(count,listString)

local cladeString = ""

--count = count+1

local lastNode=0--table.getn(list) -- number of child branches (potential)

cladeString = cladeString .. '{| class="clade" '

if not string.match( list[i], "^"..listChar, 1 ) then -- count children at this level (not beginning wiht @/*)

lastNode = lastNode+1

end

end

while list[i] do

end

]]

function p.cladeConverter(frame)

return p.listConverter(frame)

else

local message = "Conversion needs wikitext list or newick string in parameters ''list'' or ''newick'' respectively"

-- show the list string

local cladeString = ''

local indent = p.getIndent(levelNumber)

-- converted the newick string to the clade structure

local resultString = ''

--show the transcluded clade diagram

resultString = '<pre>'..listString..'</pre>'

end

local cladeString = ""

local indent = p.getIndent(levelNumber)

end

end

while list[i] do

child=child+1

end