Andoza:Clade newick converter/doc

Wikitext list converter

Converts a list in wikitext marker to the clade structure. The list must be wrapped in <nowiki>...</nowiki> tags.

{{clade converter|list=<nowiki>
* ''Sitta''
** [[Sittelle superbe]] (''S. formosa'')
** 
*** 
**** [[Sittelle des rochers]] (''S. tephronota'')
**** [[Sittelle de Neumayer]] (''S. neumayer'')
***
**** 
***** [[Sittelle du Cachemire]] (''S. cashmirensis'')
***** '''Sittelle des Naga''' (''S. nagaensis'')
***** [[Sittelle torchepot]] (''S. europaea'')
**** [[Sittelle de l'Himalaya]] (''S. himalayensis'')
</nowiki>
}}

Alternatively invoke function directly:

{{#invoke:Clade|listConverter|list=
PUT LIST HERE
}}

produces

* ''Sitta''
** [[Sittelle superbe]] (''S. formosa'')
** 
*** 
**** [[Sittelle des rochers]] (''S. tephronota'')
**** [[Sittelle de Neumayer]] (''S. neumayer'')
***
**** 
***** [[Sittelle du Cachemire]] (''S. cashmirensis'')
***** '''Sittelle des Naga''' (''S. nagaensis'')
***** [[Sittelle torchepot]] (''S. europaea'')
**** [[Sittelle de l'Himalaya]] (''S. himalayensis'')

{{clade
|label1= ''Sitta''
|1={{clade
   |1= [[Sittelle superbe]] (''S. formosa'')
   |label2= 
   |2={{clade
      |label1= 
      |1={{clade
         |1= [[Sittelle des rochers]] (''S. tephronota'')
         |2= [[Sittelle de Neumayer]] (''S. neumayer'')
         }}
      |label2=
      |2={{clade
         |label1= 
         |1={{clade
            |1= [[Sittelle du Cachemire]] (''S. cashmirensis'')
            |2= '''Sittelle des Naga''' (''S. nagaensis'')
            |3= [[Sittelle torchepot]] (''S. europaea'')
            }}
         |2= [[Sittelle de l'Himalaya]] (''S. himalayensis'')
         }}
      }}
   }}
}}

Newick converter

Convert simple Newick strings to the clade structure. This is a tool to aid construction of cladograms using the {{clade}} template and not for use directly in the article namespace.

Parameters

• |newickstring= – the Newick format data to be converted
• |indent= – optionally set an indent, which will indent every line by N spaces. This can help alignment in the final cladogram.

Example

The following code

{{Template:Clade newick converter
|newickstring=((lion,jaguar,leopard),((siberian,javan,bengal)tiger,snow leopard))panthera
|indent=10
}}

produces the output below

((lion,jaguar,leopard),((siberian,javan,bengal)tiger,snow leopard))panthera

{{clade
          |label1=panthera
          |1={{clade
             |label1=
             |1={{clade
                |1=lion
                |2=jaguar
                |3=leopard
                }}
             |label2=
             |2={{clade
                |label1=tiger
                |1={{clade
                   |1=siberian
                   |2=javan
                   |3=bengal
                   }}
                |2=snow leopard
                }}
             }}
}}

Processing the Newick string

The Newick format data provided Open Tree of Life and other sources typically has extraneous encoding data. This extra information can be removed using the |newickN-pattern= and |newickN-replace= parameters which supply a Lua pattern (similar to Regex) and replacement. The following code uses Newick format data for the genus Prionailurus downloaded from using Open Tree of Life (source data):

{{clade newick converter
   |newickstring=(Prionailurus_planiceps_ott86166,(((Prionailurus_bengalensis_chinensis_ott198595,Prionailurus_bengalensis_euptilurus_ott547362,Prionailurus_bengalensis_bengalensis_ott5557509,Prionailurus_bengalensis_rabori_ott7067613)Prionailurus_bengalensis_ott280108,Prionailurus_iriomotensis_ott418475),Prionailurus_viverrinus_ott862641),Prionailurus_rubiginosus_ott507541)Prionailurus_ott570215
   |newick-pattern=([%a_]+)_(ott[%d]*)
   |newick-replace={{'}}{{'}}%1{{'}}{{'}}
   |newick-pattern2=(%a)(%l+)_
   |newick-replace2=%1._ 
}}

produces

(''P. planiceps'',(((''P. b. chinensis'',''P. b. euptilurus'',''P. b. bengalensis'',''P. b. rabori'')''P. bengalensis'',''P. iriomotensis''),''P. viverrinus''),''P. rubiginosus'')''Prionailurus''

{{clade
|label1=''Prionailurus''
|1={{clade
   |1=''P. planiceps''
   |label2=
   |2={{clade
      |label1=
      |1={{clade
         |label1=''P. bengalensis''
         |1={{clade
            |1=''P. b. chinensis''
            |2=''P. b. euptilurus''
            |3=''P. b. bengalensis''
            |4=''P. b. rabori''
            }}
         |2=''P. iriomotensis''
         }}
      |2=''P. viverrinus''
      }}
   |3=''P. rubiginosus''
   }}
}}

In this example there are two replacements. The first strips the _ott suffix and applies Wikitext markup. Note the Wikitext markup has to be handled with a template ({{'}}) The second abbreviates the genus name when not standalone. In addition, underscores are always replaced by spaces.

List Converter

Converts a Wikitext-like list to a clade structure. The list uses the symbol @ as the * would be processed as Wikitext.

Example

The following illustrates the code and the desired output:

Template call with pseudo-Wikitext list	Output of template as clade code	The cladogram that the code produces
{{Clade converter |indent=3 |list= @A @@A1 @@A2 @B @C @@C1 @@C2 @@@C2a @@@C2b @@@@C2b1 @@@@C2b2 @@C3 @D @@D1 @@D2 }}	@A @@A1 @@A2 @B @C @@C1 @@C2 @@@C2a @@@C2b @@@@C2b1 @@@@C2b2 @@C3 @D @@D1 @@D2 {{clade |label1=A |1={{clade |1=A1 |2=A2 }} |2=B |label3=C |3={{clade |1=C1 |label2=C2 |2={{clade |1=C2a |label2=C2b |2={{clade |1=C2b1 |2=C2b2 }} }} |3=C3 }} |label4=D |4={{clade |1=D1 |2=D2 }} }}	Andoza:CladeN