Template:Clade converter/doc
| This is a documentation subpage for Template:Clade converter. It contains usage information, categories and other content that is not part of the original template page. |
| This template uses Lua: |
Contents
Newick Converter
Convert simple Newick strings to the clade structure. This is a tool to aid contruction 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
- Modified Newick string:
((lion,jaguar,leopard),((siberian,javan,bengal)tiger,snow leopard))panthera
Output of clade template structure:{{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
- Modified Newick string:
(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
Output of clade template structure:{{clade |label1=Prionailurus ott570215 |1={{clade |1=Prionailurus planiceps ott86166 |label2= |2={{clade |label1= |1={{clade |label1=Prionailurus bengalensis ott280108 |1={{clade |1=Prionailurus bengalensis chinensis ott198595 |2=Prionailurus bengalensis euptilurus ott547362 |3=Prionailurus bengalensis bengalensis ott5557509 |4=Prionailurus bengalensis rabori ott7067613 }} |2=Prionailurus iriomotensis ott418475 }} |2=Prionailurus viverrinus ott862641 }} |3=Prionailurus rubiginosus ott507541 }} }}
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.
Principle
The following illustrates the code and the desired output:
| List code | Wanted clade code | Output | ||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|list1= @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
}}
}} |
|
Example
Calling the {{Clade converter}} template with the following code
{{Clade converter
|indent=3
|list=
@A
@@A1
@@A2
@B
@C
@@C1
@@C2
@@@C2a
@@@C2b
@@@@C2b1
@@@@C2b2
@@C3
@D
@@D1
@@D2
}}
- produces the following output:
{{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 }} }}