fixed species tracking bug

src/Organism/Anatomy.js

@@ -61,7 +61,7 @@ class Anatomy {
                 break;
             }
         }
-        this.checkTypeChange(cell.state);
+        this.checkTypeChange();
         return true;
     }
 
@@ -93,9 +93,7 @@ class Anatomy {
     }
 
     getNeighborsOfCell(col, row) {
-
         var neighbors = [];
-
         for (var x = -1; x <= 1; x++) {
             for (var y = -1; y <= 1; y++) {
 
@@ -107,6 +105,19 @@ class Anatomy {
 
         return neighbors;
     }
+
+    isEqual(anatomy) { // currently unused helper func. inefficient, avoid usage in prod.
+        if (this.cells.length !== anatomy.cells.length) return false;
+        for (let i in this.cells) {
+            let my_cell = this.cells[i];
+            let their_cell = anatomy.cells[i];
+            if (my_cell.loc_col !== their_cell.loc_col ||
+                my_cell.loc_row !== their_cell.loc_row ||
+                my_cell.state !== their_cell.state)
+                return false;
+        }
+        return true;
+    }
 }
 
 module.exports = Anatomy;

src/Organism/Organism.js

@@ -118,19 +118,21 @@ class Organism {
             }
         }
         Math.max(this.food_collected -= this.foodNeeded(), 0);
-
     }
 
     mutate() {
-        let mutated = false;
+        let added = false;
+        let changed = false;
+        let removed = false;
         if (this.calcRandomChance(Hyperparams.addProb)) {
+            // console.log('add')
             let branch = this.anatomy.getRandomCell();
             let state = CellStates.getRandomLivingType();//branch.state;
             let growth_direction = Neighbors.all[Math.floor(Math.random() * Neighbors.all.length)]
             let c = branch.loc_col+growth_direction[0];
             let r = branch.loc_row+growth_direction[1];
             if (this.anatomy.canAddCellAt(c, r)){
-                mutated = true;
+                added = true;
                 this.anatomy.addRandomizedCell(state, c, r);
             }
         }
@@ -138,15 +140,15 @@ class Organism {
             let cell = this.anatomy.getRandomCell();
             let state = CellStates.getRandomLivingType();
             this.anatomy.replaceCell(state, cell.loc_col, cell.loc_row);
-            mutated = true;
+            changed = true;
         }
         if (this.calcRandomChance(Hyperparams.removeProb)){
             if(this.anatomy.cells.length > 1) {
                 let cell = this.anatomy.getRandomCell();
-                mutated = this.anatomy.removeCell(cell.loc_col, cell.loc_row);
+                removed = this.anatomy.removeCell(cell.loc_col, cell.loc_row);
             }
         }
-        return mutated;
+        return added || changed || removed;
     }
 
     calcRandomChance(prob) {

src/Stats/FossilRecord.js

@@ -18,7 +18,6 @@ const FossilRecord = {
     },
 
     addSpecies: function(org, ancestor) {
-        // console.log("Adding Species")
         var new_species = new Species(org.anatomy, ancestor, this.env.total_ticks);
         this.extant_species.push(new_species);
         org.species = new_species;
@@ -26,7 +25,6 @@ const FossilRecord = {
     },
 
     addSpeciesObj: function(species) {
-        // console.log("Adding Species")
         this.extant_species.push(species);
         return species;
     },
@@ -38,6 +36,9 @@ const FossilRecord = {
             var s = this.extant_species[i];
             if (s == species) {
                 this.extant_species.splice(i, 1);
+                species.ancestor = undefined; // garbage collect dead species
+                // if (species.ancestor)
+                //     species.ancestor.ancestor = undefined;
                 if (species.cumulative_pop < this.min_pop) {
                     return false;
                 }

src/Stats/Species.js

@@ -1,9 +1,15 @@
 const CellStates = require("../Organism/Cell/CellStates");
+let FossilRecord = undefined; // workaround to a circular dependency problem
+const getFossilRecord = () => {
+    if (!FossilRecord)
+        FossilRecord = require("./FossilRecord");
+    return FossilRecord;
+}
 
 class Species {
     constructor(anatomy, ancestor, start_tick) {
         this.anatomy = anatomy;
-        // this.ancestor = ancestor; // garbage collect ancestors to avoid memory problems
+        this.ancestor = ancestor; // eventually need to garbage collect ancestors to avoid memory problems
         this.population = 1;
         this.cumulative_pop = 1;
         this.start_tick = start_tick;
@@ -33,8 +39,7 @@ class Species {
         this.population--;
         if (this.population <= 0) {
             this.extinct = true;
-            const FossilRecord = require("./FossilRecord");
-            FossilRecord.fossilize(this);
+            getFossilRecord().fossilize(this);
         }
     }