Module:Sandbox/Jts1882/CladeN: Difference between revisions

Revision as of 07:56, 26 December 2019

Latest revision as of 21:14, 23 October 2022

(20 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 - the nodeformating parameters have no number, (i.e.g. |color, |thickness, |state)

-- global nodeParameters for whole bracket (unnumberunnumbered, 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(mw.getCurrentFrame():getParent().argspargs['thickness']) or 1

local nodeState = mw.getCurrentFrame():getParent().argspargs['state'] or "solid"

-- get border formating parameters for branch (default to global nodeParameters)

local branchColor = mw.getCurrentFrame():getParent().argspargs['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

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

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

local branchLength = mw.getCurrentFrame():getParent().args['length'] or mw.getCurrentFrame():getParent().args['length'..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 -- need thick line for double

end

end -- need thick line for double

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

local branchLength = mw.getCurrentFrame():getParent().argspargs['length'] or mw.getCurrentFrame():getParent().argspargs['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 = mw.getCurrentFrame():getParent().argspargs['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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local branchLengthStyle = ""

if branchLength ~= "" then

if childNumber == 1 then

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

branchLengthStyle = 'width:' .. branchLength .. 'padding:0em;' -- removeadd paddingwidth to make calculationfirst easierelement

end

.. 'overflow-x:hidden;' -- clip labels longer than the width

--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-x: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 .. '"'

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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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it also means there are two newlines when it is a clade structure (which might explain some past issues)

]]

local content = '\n' .. nodeLeaf -- the newlinnewline 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 -- simplebasic version

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

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

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

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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 .. sublabelStyle .. '"'

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 422 ⟶ 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 534 ⟶ 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

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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 690 ⟶ 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

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function p.listConverter(frame)

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

-- show the list string

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local resultString = ''

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

if option == 'tree' then

--show the transcluded clade diagram