Module:Clade/converter - Revision history

Legoktm: Replace Module:No globals with require( "strict" )

2022-10-23T04:16:44Z

Replace Module:No globals with require( "strict" )

← Previous revision		Revision as of 04:16, 23 October 2022
Line 1:		Line 1:
	--require('~~Module:No globals~~') -- comment out until clade also uses noglobals		--require('strict') -- comment out until clade also uses noglobals

	local p = {}		local p = {}

Jts1882: use main entry function

2019-11-27T13:25:59Z

use main entry function

← Previous revision		Revision as of 13:25, 27 November 2019
Line 17:		Line 17:
	]]		]]
	function p.cladeConverter(frame)		function p.cladeConverter(frame)
			if frame.args['newickstring'] or pargs['newick'] or pargs['newickstring'] then

			return p.newickConverter(frame)
			elseif frame.args['list'] or pargs['list'] then
			return p.listConverter(frame)
			end
	end		end

Line 28:		Line 32:
	function p.newickConverter(frame)		function p.newickConverter(frame)

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

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

Jts1882: modify newick converter output with annotations

2019-11-27T13:02:29Z

modify newick converter output with annotations

← Previous revision		Revision as of 13:02, 27 November 2019
Line 52:		Line 52:
	else		else
	-- show the Newick string		-- show the Newick string
	resultString = '<~~pre~~>'~~..newickString..'</pre>'~~		resultString = '<div>Modified Newick string:'
			.. '<pre>'..newickString..'</pre>'
	-- show the converted clade structure		-- show the converted clade structure
	resultString = resultString .. '~~<pre>'..~~ ~~cladeString~~ ~~..'</pre>~~'		resultString = resultString .. 'Output of clade template structure:'
			.. '<pre>'.. cladeString ..'</pre></div>'
	end		end
	--resultString = frame:expandTemplate{ title = 'clade', frame:preprocess(cladeString) }		--resultString = frame:expandTemplate{ title = 'clade', frame:preprocess(cladeString) }
Line 158:		Line 160:
	resultString = cladeString		resultString = cladeString
	else		else
	-- show the ~~Newick~~ string		-- show the list string
	resultString = '<pre>'..listString..'</pre>'		--resultString = '<pre>'..listString..'</pre>'
	-- show the converted clade structure		-- show the converted clade structure
	resultString = resultString .. '<pre>'.. cladeString ..'</pre>'		resultString = resultString .. '<pre>'.. cladeString ..'</pre>'

Jts1882: call process newick from main module

2019-11-27T12:27:18Z

call process newick from main module

← Previous revision		Revision as of 12:27, 27 November 2019
Line 1:		Line 1:
			--require('Module:No globals') -- comment out until clade also uses noglobals

	local p = {}		local p = {}

Line 30:		Line 32:
	--if newickString == '{{{newickstring}}}' then return newickString end		--if newickString == '{{{newickstring}}}' then return newickString end

	newickString = p.processNewickString(newickString,"") -- "childNumber")		newickString = require('Module:Clade').processNewickString(newickString,"") -- "childNumber")


Line 90:		Line 92:
	end)		end)

	local s = p.strsplit(innerTerm2, ",")		--local s = p.strsplit(innerTerm2, ",")
			local s = mw.text.split(innerTerm2, ",")
	local i=1		local i=1
	while s[i] do		while s[i] do

Jts1882: parent args variable

2019-11-27T12:00:07Z

parent args variable

← Previous revision		Revision as of 12:00, 27 November 2019
Line 1:		Line 1:
	local p = {}		local p = {}

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

	--[[ =================== parser for conversion to clade structure =============================		--[[ =================== parser for conversion to clade structure =============================

Jts1882: move newick and list converter functions here

2019-11-27T11:56:48Z

move newick and list converter functions here

New page

local p = {}

--[[ =================== parser for conversion to clade structure =============================

Function p.newickConverter()
convert Newick strings to clade format
Usage: {{#invoke:Module:Sandbox/Jts1882/CladeN|newickConverter|newickstring={{{NEWICK_STRING}}} }}

Function p.listConverter()
convert wikitext-like lists to clade format
use @ instead of * in wikitext to avoid processing
Usage: {{#invoke:Module:Clade/converter|listConverter|list={{{LIST_STRING}}} }}
]]
function p.cladeConverter(frame)

end

--[[ =================== 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 mw.getCurrentFrame():getParent().args['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 = mw.getCurrentFrame():getParent().args['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

--[[ =================== experimental list to clade parser function =============================

Function of convert wikitext-like listss to clade format
- use @ instead of * in wikitext to avoid processing

Usage: {{#invoke:Module:Clade/converter|listConverter|list={{{LIST_STRING}}} }}
]]

function p.listConverter(frame)

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