Modul:Clade/dok

To je dokumentacijska podstran za glavno stran Modul:Clade.
Namenjena je shranjevanju navodil, kategorizaciji in drugi vsebini, ki ni del glavne strani.

Predloga se uporablja na številnih straneh, zato bo vsaka njena sprememba takoj zelo opazna. Prosimo, da vse spremembe, ki jih želite uvesti, pred uvedbo preizkusite na podstraneh predloge (/peskovnik in /testniprimeri) ali na svojih lastnih podstraneh. Pred spreminjanjem te predloge se o želenih spremembah rajši pogovorite na pogovorni strani.

Ta modul je odvisen od zaščite strani. Je zelo viden modul, ki ga uporabljajo številne strani, ali pa je pogosto substituiran. Ker bi vandalizem ali napake vplivale na številne strani in bi lahko celo trivialno urejanje povzročilo veliko obremenitev strežnikov, je zaščiten pred urejanjem.

Ta modul uporablja TemplateStyles:

Predloga:Klad/styles.css

This module is designed to be used with the clade template to draw phylogenetic trees or cladograms. The new template-module combination extends the feature available with the clade and cladex templates, while replicating the behaviour of the older templates written with the template language. This module is copied from the test version en:Module:Sandbox/Jts1882/CladeN, which was used with the template Predloga:KladN to test the features during development.

Additionally, the module has the code for template {{clade newick converter}}, which is a basic utility to convert Newick strings into nested clade structures. This is not to be used in wikipedia articles, but is a tool to help construct cladograms for inclusion in articles.

The diagram below gives an overview of the features. See the template documentation for a more detailed description of how to use the templates.

Usage

{{#invoke:Clade|main|style={{{style}}}}}

Examples

Simple examples mimicking the clade template:

Example demonstrating more advanced features of cladeN:

en:User:Jts1882/sandbox/test/Felidae

Example demonstrating features available:

Predloga:Klad

Node structure

label1

leaf 1

label2

label A	leaf A

label B	leaf B

leaf 2 is a nested clade structure

label3

leaf 3

sublabel3

|label1=Node structure  |sublabel1=(brackets)
|style1=background-color:#ffdddd;
|1={{Klad
   |label1=label1  
   |1=leaf 1             
   |label2=label2
   |grouplabel2=&nbsp;leaf 3 is a nested clade structure 
   |2={{Klad |style=background-color:#ffaaaa;
      |label1=label A
      |1=leaf A
      |label2=label B
      |2=leaf B
      |bar1=purple |bar2=purple 
      }}
   |label3=label3 |sublabel3=sublabel3
   |3=leaf 3           
   }}

(brackets)

Leaf styling

thicknessN

	1 (default)

	2	line thickness

	3

colorN

	black (default)

	red

	blue

	#00ff00

stateN

	solid (default)

	dotted

	dashed	line styles

	none

	double

|label3=Leaf styling  |sublabel3=(branches)
|style3=background-color:#eeeeee;
|3={{Klad
   |label1=thicknessN
   |1={{Klad
      |1=1 (default) |thickness1=1 |barbegin1=blue 
      |2=2           |thickness2=2 |bar2=blue |barlabel2=&nbsp;line thickness
      |3=3           |thickness3=3 |barend3=blue 
      }}
   |label2=colorN
   |2={{Klad
      |1=black (default) |color1=black          
      |2=red             |color2=red    
      |3=blue            |color3=blue   
      |4=&nbsp;#00ff00   |color4=#00ff00   
      }}
   |label3=stateN
   |3={{Klad
      |1=solid (default) |state1=solid  |barbegin1=purple 
      |2=dotted          |state2=dotted |bar2=purple 
      |3=dashed          |state3=dashed |bar3=purple |barlabel3=&nbsp;line styles
      |4=none            |state4=none   |bar4=purple
      |5=double          |state5=double |barend5=purple 
      }}
   }}

(branches)

node styling

thickness

	I

	J

	K

color

	A

	B

	C

state

	X

	Y

	Z

|label4=node styling  |sublabel4=(brackets)
|style4=background-color:#ffffee;
|4={{Klad
   |label1=thickness
   |1={{Klad |thickness=3
      |1=I  
      |2=J          
      |3=K             
      }}
   |label2=color
   |2={{Klad |color=red 
      |1=A
      |2=B                
      |3=C             
      }}
   |label3=state
   |3={{Klad |state=dashed
      |1=X 
      |2=Y         
      |3=Z        
   }} }}

(brackets)

newick

string

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

subtree

panthera

	lion

	jaguar

	leopard

tiger

	siberian

	bengal

snow leopard

expanded Newick string

|label6=newick  
|style6=background-color:#ddffdd;
|6={{Klad
   |label1=string
   |1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera         
   |label2=subtree 
   |grouplabel2=&nbsp;expanded Newick string    
   |grouplabelstyle2=vertical-align: middle;
   |2={{Klad |style=background-color:#ccffcc;
      |newick1=((lion,jaguar,leopard),((siberian,bengal)tiger,snow leopard))panthera
      |1=Leaf1 (redundant if newick1 set)        
      }}
   }}

paraphyly example

	Geraniales

	Myrtales

clade

	Brassicales

	Malvales

label a paraphyletic group within a clade

|label7=paraphyly example&nbsp; |style7=background-color:#ffeeff;
|7={{Klad
   |1={{Klad
      |1=[[Geraniales]]          
      |2=[[Myrtales]]            
      }}
   |grouplabel2=&nbsp;label a paraphyletic group within a clade   
   |label2=clade
   |style2=background-color:#ffddff;
   |2={{Klad
      |1=[[Crossosomatales]]         |barbegin1=purple
      |2={{Klad
         |1=[[Picramniales]]         |bar1=purple
         |2={{Klad
            |1=[[Sapindales]]        |bar1=purple 
            |2={{Klad
               |1=[[Huerteales]]     |bar1=purple
               |2={{Klad
                  |1=[[Brassicales]] |barend1=purple
                  |2=[[Malvales]]    |style2=background-color:#ff99ff;
   }} }} }} }} }} }}

A cladogram illustrating clade features.

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