extensions [ nw ]

; we have two different kinf of link breeds, one directed and one undirected, just
; to show what the different networks look like with directed vs. undirected links
directed-link-breed [ dirlinks dirlink ]


globals [
  highlighted-node                ; used for the "highlight mode" buttons to keep track of the currently highlighted node
  highlight-maximal-cliques-on    ; indicates highlight-maximal-cliques mode is active
  stop-highlight-maximal-cliques  ; indicates highlight-maximal-cliques mode needs to stop
]

to setup
  clear-all
  set-default-shape turtles "circle"
  
  create-turtles 10
  
ifelse community? [
  make-edge turtle 0 turtle 1
  make-edge turtle 0 turtle 2
  make-edge turtle 0 turtle 3
  make-edge turtle 0 turtle 4
  make-edge turtle 1 turtle 2
  make-edge turtle 1 turtle 3
  make-edge turtle 1 turtle 4
  make-edge turtle 2 turtle 3
  make-edge turtle 2 turtle 4
  make-edge turtle 3 turtle 4

  make-edge turtle 2 turtle 6
  make-edge turtle 3 turtle 5
  
  make-edge turtle 5 turtle 6
  make-edge turtle 5 turtle 7
  make-edge turtle 5 turtle 8
  make-edge turtle 5 turtle 9
  make-edge turtle 6 turtle 7
  make-edge turtle 6 turtle 8
  make-edge turtle 6 turtle 9
  make-edge turtle 7 turtle 8
  make-edge turtle 7 turtle 9
  make-edge turtle 8 turtle 9
  ]
  [
  while [count links < 22] [
    make-edge (one-of turtles) (one-of turtles)
  ]
  ]
end


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Layouts
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to redo-layout [ forever? ]
    let factor sqrt count turtles
    if factor = 0 [ set factor 1 ]
    repeat ifelse-value forever? [ 1 ] [ 50 ] [
      layout-spring turtles links (1 / factor) (14 / factor) (1.5 / factor)
      display
      if not forever? [ wait 0.005 ]
    ]
end


to spring-forever
  redo-layout true
end

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Clusterers
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Allows the user to mouse over and highlight all maximal cliques
to highlight-maximal-cliques
  if stop-highlight-maximal-cliques = true [
    ; we're asked to stop - do so
    set stop-highlight-maximal-cliques false
    set highlight-maximal-cliques-on false
    stop
  ]
  set highlight-maximal-cliques-on true ; we're on!

  if mouse-inside? [ 
    nw:set-context turtles links
    highlight-clusters nw:maximal-cliques
  ]
  display
end

;; Colorizes the biggest maximal clique in the graph, or a random one if there is more than one
to find-biggest-clique
  nw:set-context turtles links
  ;; color-clusters takes a list of lists (clusters) 
  ;; but we only have one, so we package it in a list
  color-clusters (nw:biggest-maximal-cliques)
end

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Highlighting and coloring of clusters
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Allows the user to mouse over different nodes and 
;; highlight all the clusters that this node is a part of
to highlight-clusters [ clusters ]
  ;; get the node with neighbors that is closest to the mouse
  let node min-one-of turtles [ distancexy mouse-xcor mouse-ycor ]
  if node != nobody and node != highlighted-node [
    set highlighted-node node
    ;; find all clusters the node is in and assign them different colors
    color-clusters filter [ member? node ? ] clusters
    ;; highlight target node
    ask node [ set color white ]
  ]
end

to color-clusters [ clusters ]
  ;; reset all colors
  ask turtles [ set color gray - 3 ]
  ask links [ set color gray - 3 ]
  let n length clusters
  let colors ifelse-value (n <= 12)
    [ n-of n remove gray remove white base-colors ] ;; choose base colors other than white and gray
    [ n-values n [ __approximate-hsb-old (random 255) (255) (100 + random 100) ] ] ; too many colors - pick random ones
  
    ;; loop through the clusters and colors zipped together
    (foreach clusters colors [      
      let cluster ?1
      let cluster-color ?2
      ask cluster [ ;; for each node in the cluster
       
          ;; give the node the color of its cluster
          set color cluster-color
          ;; colorize the links from the node to other nodes in the same cluster
          ;; link color is slightly darker...
          ask my-links [ if member? other-end cluster [ set color cluster-color - 1 ] ]
          ask my-in-dirlinks [ if member? other-end cluster [ set color cluster-color - 1 ] ]
          ask my-out-dirlinks [ if member? other-end cluster [ set color cluster-color - 1 ] ]
        
      ]
    ])
end


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Generators
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to generate [ generator-task ]
  ; we have a general "generate" procedure that basically just takes a task 
  ; parameter and run it, but takes care of calling layout and update stuff
  set-default-shape turtles "circle"
  run generator-task
  redo-layout false
  update-plots
end


;; connects the two turtles
to make-edge [node1 node2]
  ask node1 [
    ifelse (node1 = node2) 
    [
      show "error: self-loop attempted"
    ]
    [
      create-link-with node2 [ set color green ]
     ;; position the new node near its partner
      setxy ([xcor] of node2) ([ycor] of node2)
      rt random 360
      fd 8
     ]
  ]
end


;; Copyright 2012 Uri Wilensky.
;; See Info tab for full copyright and license.
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@#$#@#$#@
## WHAT IS IT?



## HOW IT WORKS

You generate either an Erdos-Renyi graph or a pre-specified graph with community structure. Then you find the maximal clique.

## HOW TO USE IT

Select whether of not you want COMMUNITY? structure. Then click on BIGGEST-MAXIMAL-CLIQUE. If there is more than one, you might click on this button a few times to highlight them all.



#### highlight bicomponents

Clicking on this button will put you in a mode where you use your mouse to highlight the different [bicomponent clusters](http://en.wikipedia.org/wiki/Biconnected_component) in the current network. A bicomponent (also known as a maximal biconnected subgraph) is a part of a network that cannot be disconnected by removing only one node (i.e. you need to remove at least two to disconnect it).

Note that one turtle can be a member of more than one bicomponent at once. If it is the case, all the bicomponents that the target turtle is part of will be highlighted when you move your mouse pointer near it, but they will be of different color.

#### highlight maximal cliques

Clicking on this button will put you in a mode where you use your mouse to highlight the different maximal cliques. Note that one turtle can be a member of more than one maximal clique at once. If it is the case, all the cliques that the target turtle is part of will be highlighted when you move your mouse pointer near it, but they will be of different color.

A [clique](http://en.wikipedia.org/wiki/Clique_%28graph_theory%29) is a subset of a network in which every node has a direct link to every other node. A maximal clique is a clique that is not, itself, contained in a bigger clique.

#### biggest maximal clique

This simply highlights the biggest of all the maximal cliques in the networks. If there are multiple cliques that are equally big (as is often the case), it simply highlights one at random.

## CREDITS AND REFERENCES

Copyright 2012 Uri Wilensky.

Modified by Lada Adamic 2012 from the NW Extension Demo.

![CC BY-NC-SA 3.0](http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png)

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License.  To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.

Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at uri@northwestern.edu.
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