One more example

cacatodo.txt

@@ -1,4 +1,7 @@
 (caca)TODO
+> Option and example for serialising objects
+> Example of writing stuff to file and plot is with an Rscript
+> Modify hamburger menu in DOCs for small screens
 > Push data to graphs rather then completely reload it (not sure dygraphs allows for this, but could check)
 > FBA testing
 > Implement d3.js visualization like histograms / phylogenetic trees. 

dist/cacatoo.js

@@ -330,9 +330,9 @@ class Gridmodel {
     constructor(name, config, rng) {
         this.name = name;
         this.time = 0;
-        this.grid = MakeGrid(config.ncol, config.nrow);       // Initialises an (empty) grid
         this.nc = config.ncol || 200;
         this.nr = config.nrow || 200;
+        this.grid = MakeGrid(this.nc, this.nr);       // Initialises an (empty) grid
         this.wrap = config.wrap || [true, true];
         this.rng = rng;
         this.random = () => { return this.rng.genrand_real1()};
@@ -361,6 +361,14 @@ class Gridmodel {
         this.canvases = {};              // Object containing all Canvases belonging to this model (HTML usage only)
     }
 
+    /** Replaces current grid with an empty grid */
+    clearGrid()
+    {
+        this.grid = MakeGrid(this.nc,this.nr);
+
+    }
+
+
     /** Initiate a dictionary with colour arrays [R,G,B] used by Graph and Canvas classes
     *   @param {statecols} object - given object can be in two forms
     *                             | either {state:colour} tuple (e.g. 'alive':'white', see gol.html) 
@@ -818,30 +826,30 @@ class Gridmodel {
      *  @param {int} row position (row) for the focal gridpoint
      *  @param {Array} range from which to sample (1-8 is Moore8, 0-4 is Neu5, etc.)
      */
-    randomMoore(grid, col, row,range) {
+    randomNeighbour(grid, col, row,range) {
         let rand = this.rng.genrand_int(range[0], range[1]);
         let i = this.moore[rand][0];
         let j = this.moore[rand][1];
         let neigh = grid.getGridpoint(col + i, row + j);
-        while (neigh == undefined) neigh = this.randomMoore(grid, col, row,range);
+        while (neigh == undefined) neigh = this.randomNeighbour(grid, col, row,range);
         return neigh
     }
 
     /** randomMoore for range 1-8 (see randomMoore) */     
-    randomMoore8(model, col, row) { return this.randomMoore(model, col, row, [1,8]) }
-    randomNeighbour8(model, col, row) { return this.randomMoore(model, col, row, [1,8]) }
+    randomMoore8(model, col, row) { return this.randomNeighbour(model, col, row, [1,8]) }
+    randomNeighbour8(model, col, row) { return this.randomNeighbour(model, col, row, [1,8]) }
 
     /** randomMoore for range 0-8 (see randomMoore) */ 
-    randomMoore9(model, col, row) { return this.randomMoore(model, col, row, [0,8]) }
-    randomNeighbour9(model, col, row) { return this.randomMoore(model, col, row, [0,8]) }
+    randomMoore9(model, col, row) { return this.randomNeighbour(model, col, row, [0,8]) }
+    randomNeighbour9(model, col, row) { return this.randomNeighbour(model, col, row, [0,8]) }
 
     /** randomMoore for range 1-4 (see randomMoore) */ 
-    randomNeumann4(model, col, row) { return this.randomMoore(model, col, row, [1,4]) }
-    randomNeighbour4(model, col, row) { return this.randomMoore(model, col, row, [1,4]) }
+    randomNeumann4(model, col, row) { return this.randomNeighbour(model, col, row, [1,4]) }
+    randomNeighbour4(model, col, row) { return this.randomNeighbour(model, col, row, [1,4]) }
 
     /** randomMoore for range 0-4 (see randomMoore) */ 
-    randomNeumann5(model, col, row) { return this.randomMoore(model, col, row, [0,4]) }
-    randomNeighbour5(model, col, row) { return this.randomMoore(model, col, row, [0,4]) }
+    randomNeumann5(model, col, row) { return this.randomNeighbour(model, col, row, [0,4]) }
+    randomNeighbour5(model, col, row) { return this.randomNeighbour(model, col, row, [0,4]) }
 
 
     /** Diffuse continuous states on the grid. 
@@ -1774,19 +1782,19 @@ class Simulation {
     *  and sets options accordingly.  
     *  @param {dictionary} config A dictionary (object) with all the necessary settings to setup a Cacatoo simulation. 
     */
-    constructor(config) {
-        this.config = config;
+    constructor(config) {        
+        if(config == undefined) config = {};
+        this.config = config;                
         this.rng = new MersenneTwister(config.seed || 53);
 
-        this.sleep = config.sleep || 0;
-        this.maxtime = config.maxtime || 1000000;
-        this.ncol = config.ncol || 100;
-        this.nrow = config.nrow || 100;
-
-        this.scale = config.scale || 2;
-        this.maxtime = config.maxtime || 1000000;
-        this.graph_interval = config.graph_interval || 10;
-        this.graph_update = config.graph_update || 50;
+        this.sleep = config.sleep = config.sleep || 0;
+        this.maxtime = config.maxtime = config.maxtime || 1000000;
+        this.ncol = config.ncol = config.ncol || 100;
+        this.nrow = config.nrow = config.nrow || 100;  
+        this.scale = config.scale = config.scale || 2;
+
+        this.graph_interval = config.graph_interval = config.graph_interval || 10;
+        this.graph_update = config.graph_update= config.graph_update || 50;
         this.fps = config.fps * 1.4 || 60;
         // Three arrays for all the grids ('CAs'), canvases ('displays'), and graphs 
         this.gridmodels = [];            // All gridmodels in this simulation
@@ -1797,9 +1805,7 @@ class Simulation {
         this.printcursor = true;
         this.fpsmeter = false;
         if(config.fpsmeter == true) this.fpsmeter = true;
-        if(config.printcursor == false) this.printcursor = false;
-
-
+        if(config.printcursor == false) this.printcursor = false;        
     }
 
     /**
@@ -2231,7 +2237,6 @@ class Simulation {
 
      }
 
-
     /**
      *  addButton adds a HTML button which can be linked to a function by the user. 
      *  @param {string} text Text displayed on the button

docs/adding_ui_elements.html

@@ -18,6 +18,7 @@
     <!-- --------------------- START MENU. Couldnt get it to load dynamically, so this needs to be replaced in every HTML file upon changing --------------------- -->
     <header class="header" id="btnNav"><buton class="header__button" id="btnNav" type="button"><i class="material-icons">menu</i></buton></header>
 
+
     <nav class="nav"><div class="nav__links">            
             <a href="#" class="nav__head"><i id="btnNavclose" class="material-icons" style="cursor:pointer"> menu </i> Cacatoo </a>
             <a href="index.html"  id="nav__link" class="nav__link">Home</a>

docs/jsdocs/Canvas.html

@@ -238,7 +238,7 @@ <h5>Parameters:</h5>
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="cacatoo.js.html">cacatoo.js</a>, <a href="cacatoo.js.html#line1337">line 1337</a>
+        <a href="cacatoo.js.html">cacatoo.js</a>, <a href="cacatoo.js.html#line1345">line 1345</a>
     </li></ul></dd>
 
 
@@ -346,7 +346,7 @@ <h4 class="name" id="displaygrid"><span class="type-signature"></span>displaygri
 
     <dt class="tag-source">Source:</dt>
     <dd class="tag-source"><ul class="dummy"><li>
-        <a href="cacatoo.js.html">cacatoo.js</a>, <a href="cacatoo.js.html#line1383">line 1383</a>
+        <a href="cacatoo.js.html">cacatoo.js</a>, <a href="cacatoo.js.html#line1391">line 1391</a>
     </li></ul></dd>
 
 
@@ -398,7 +398,7 @@ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="Canvas.ht
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 3.6.7</a> on Thu Jan 06 2022 09:56:10 GMT+0100 (Central European Standard Time)
+    Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 3.6.7</a> on Tue Jan 18 2022 15:01:00 GMT+0100 (Central European Standard Time)
 </footer>
 
 <script> prettyPrint(); </script>

docs/jsdocs/Graph.html

@@ -535,7 +535,7 @@ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="Canvas.ht
 <br class="clear">
 
 <footer>
-    Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 3.6.7</a> on Thu Jan 06 2022 09:56:10 GMT+0100 (Central European Standard Time)
+    Documentation generated by <a href="https://github.com/jsdoc/jsdoc">JSDoc 3.6.7</a> on Tue Jan 18 2022 15:01:00 GMT+0100 (Central European Standard Time)
 </footer>
 
 <script> prettyPrint(); </script>