Module:Sandbox/Jts1882/CladeN: Difference between revisions

Revision as of 10:20, 24 December 2019

Latest revision as of 21:14, 23 October 2022

(27 intermediate revisions by one other user not shown)

Line 8:

now uses templatestyles

]]

require('Module:No globalsstrict')

local p = {}

local pargs = {} -- parent arguments

Line 18:

local infoOutput

local reverseClade = false

local nodeColor

local nodeThickness

local nodeState

--[[============================== main function ===========================

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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 {{{style}} when no value

if tableStyle ~= "" then

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

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--reverseClade = true

local captionName =mw.getCurrentFrame():getParent().args pargs['caption'] or ""

local captionStyle = mw.getCurrentFrame():getParent().argspargs['captionstyle'] or ""

-- add an element to mimick nowiki WORKS BUT DISABLE FOR DEMO PURPOSES

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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

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

local nodeLeaf = mw.getCurrentFrame():getParent().argspargs[tostring(childNumber)] or "" -- get data from |N=

local nodeLabel = mw.getCurrentFrame():getParent().argspargs['label'..tostring(childNumber)] or "" -- get data from |labelN=

local newickString = mw.getCurrentFrame():getParent().argspargs['newick'..tostring(childNumber)] or "" -- get data from |labelN=

local listString = mw.getCurrentFrame():getParent().argspargs['list'..tostring(childNumber)] or ""

if listString ~= "" then

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end

local footerText = mw.getCurrentFrame():getParent().argspargs['footer'] or ""

local footerStyle = mw.getCurrentFrame():getParent().argspargs['footerstyle'] or ""

if footerText ~= "" then

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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",

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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

-- - the branch parameters have a number, e.g. |colorN, |thicknessN, |stateN

local branchThickness = tonumber(pargs['thickness'..tostring(childNumber)]) or nodeThickness

-- - the node parameters have no number, e.g. |color, |thickness, |state

local branchThicknessbranchState = tonumber(mw.getCurrentFrame():getParent().argspargs['thicknessstate'..tostring(childNumber)]) or nodeThicknessnodeState

if branchState == 'double' then

local branchColor = mw.getCurrentFrame():getParent().args['color'..tostring(childNumber)] or nodeColor

if branchThickness < 2 then branchThickness = 3 end -- need thick line for double

local branchStyle = mw.getCurrentFrame():getParent().args['style'..tostring(childNumber)] or ""

end

local branchLabelStyle = mw.getCurrentFrame():getParent().args['branch'..tostring(childNumber)] or ""

local branchState = mw.getCurrentFrame():getParent().args['state'..tostring(childNumber)] or nodeState -- "solid"

local branchStyle = pargs['style'..tostring(childNumber)] or ""

if branchState == 'double' then if branchThickness < 2 then branchThickness = 3 end end -- need thick line for double

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

-- the left border takes node parameters, the bottom border takes branch parameters

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-- variables for right hand bar or bracket

--local barColor = ""

local barRight = mw.getCurrentFrame():getParent().argspargs['bar'..tostring(childNumber)] or "0"

local barBottom = mw.getCurrentFrame():getParent().argspargs['barend'..tostring(childNumber)] or "0"

local barTop = mw.getCurrentFrame():getParent().argspargs['barbegin'..tostring(childNumber)] or "0"

local barLabel = mw.getCurrentFrame():getParent().argspargs['barlabel'..tostring(childNumber)] or ""

local groupLabel = mw.getCurrentFrame():getParent().argspargs['grouplabel'..tostring(childNumber)] or ""

local groupLabelStyle = mw.getCurrentFrame():getParent().argspargs['grouplabelstyle'..tostring(childNumber)] or ""

local labelStyle = mw.getCurrentFrame():getParent().argspargs['labelstyle'..tostring(childNumber)] or ""

local sublabelStyle = pargs['sublabelstyle'..tostring(childNumber)] or ""

--replace colours with format string; need right bar for all three options

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local classString = ''

local reverseClass = ''

local widthClass = ''

-- class to add if using reverse (rtl) cladogram;

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end

end

if useInlineStyle or (branchStyle ~= '') or (branchLabelStylebranchLength ~= '')"" or labelStyle ~= "" then

local branchLengthStyle = ""

styleString = 'style="' .. borderStyle .. branchStyle .. branchLabelStyle .. '"'

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;'

--if pargs['noclip'] then

if string.find(nodeLabel, '<div style="position:absolute;') then

branchLengthStyle = branchLengthStyle .. 'overflow:visible;'

end

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

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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

local content = nodeLeaf

if --content = content .. image ~=-- ""basic thenversion

content = '\n{| class="clade" style="width:auto;"' --defaults to width:100% because of class "clade"

content = content .. image -- simple version

.. '\n| class="clade-leaf" ' .. '|\n' .. nodeLeaf

--[[note: plain leaf elements get wrapped in <p>.. with'\n| styleclass="margin:0clade-leaf" ' ..4em 0'|\n' 0.5em. 0;"image

this adds spacing to rows, but is set by defaults rather than the clade template

]]

--content = '\n{| class="clade-image" style="border-collapse:separate;border-spacing:0;margin:0;" '

content = '\n{| class="clade" style="width:auto;" '

.. '\n| class="clade-leaf" style=background-color:#ddffdd;' .. '|' .. nodeLeaf

.. '\n| class="clade-leaf" style=background-color:#ffffdd;' .. '|' .. 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

content = '\n{| style="border-collapse:collapse;border-spacing:0;margin:0;" \n|' .. nodeLeaf .. '||' .. 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 paddingtpadding (see above)

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

--local leafCellString = '\n|rowspan=2 ' .. classString .. styleString .. ' |\n' .. content -- the new line causes <p> wrapping for plain leaf terminals

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-- (6) add cell containing sublabel

local subLabel = mw.getCurrentFrame():getParent().argspargs['sublabel'..tostring(childNumber)] or "" -- request in addLabel

-- FOR TESTING: use subLabel for annotating the clade structues to use structure information (DEBUGGIING ONLY)

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end

end

if borderStyle ~= '' or branchStyle ~= '' or branchLength ~= '' or sublabelStyle ~= "" then

local branchLengthStyle = ""

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

if branchLength ~= "" then

if childNumber == 1 then

--only set for label 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

--if pargs['noclip'] then

if string.find(subLabel, '<div style="position:absolute;') then

branchLengthStyle = branchLengthStyle .. 'overflow:visible;'

end

end

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

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

end

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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)

Line 415 ⟶ 454:

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/>' --'&nbsp;<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 '&#8239;' -- &nbsp; &thinsp; &#8239;(thin nbsp)

else

-- spaces can cause wrapping and can break tree structure, hence use span with nowrap class

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--TODO test following alternative

--if nodeLabel:find( "%b<>") then stylingElementDetected = true end

-- we know the no break is handled when using {{clade label}}

if string.find(nodeLabel, '<div style="position:absolute;') then stylingElementDetected = false end

if stylingElementDetected == true then

return '<span class="nowrap">' .. nodeLabel .. '</span>'

else

--local nowrapString = string.gsub(nodeLabel," ", "&nbsp;") -- replace spaces with non-breaking space

local nowrapString = nodeLabel -- spaces are now handled by CSS "white-space:nowrap;""

if not nowrapString:find("UNIQ.-QINU") then -- unless a strip marker

nowrapString = string.gsub(nowrapString,"-", "&#8209;") -- replace hyphen with non-breaking hyphen (&#8209;)

Line 527 ⟶ 566:

function p.newickConverter(frame)

local newickString = frame.args['newickstring'] or mw.getCurrentFrame():getParent().argspargs['newick']

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

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local resultString = ''

local option = mw.getCurrentFrame():getParent().argspargs['option'] or ''

if option == 'tree' then

--show the transcluded clade diagram

Line 635 ⟶ 674:

local maxPatterns = 5

local i = 0

local pargs = mw.getCurrentFrame():getParent().argspargs

local pattern = pargs['newick'..tostring(childNumber)..'-pattern'] -- unnumbered option for i=1

local replace = pargs['newick'..tostring(childNumber)..'-replace']

Line 683 ⟶ 722:

while childNumber < maxChildren do -- preprocessing loop

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

local nodeLeaf,data = mw.getCurrentFrame():getParent().argspargs[tostring(childNumber)] or "" -- get data from |N=

local newickString = mw.getCurrentFrame():getParent().argspargs['newick'..tostring(childNumber)] or "" -- get data from |labelN=

local listString = mw.getCurrentFrame():getParent().argspargs['list'..tostring(childNumber)] or "" -- get data from |labelN=

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

--if nodeLeaf ~= "" then

Line 819 ⟶ 858:

function p.listConverter(frame)

local listString = frame.args['list'] or mw.getCurrentFrame():getParent().argspargs['list']

-- show the list string

Line 832 ⟶ 871:

local resultString = ''

local option = mw.getCurrentFrame():getParent().argspargs['option'] or ''

if option == 'tree' then

--show the transcluded clade diagram