Prune top of phylogeny

emilydolson · Sep 26, 2018 · 5171c87 · 5171c87
1 parent 8f251d9
commit 5171c87
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Showing 2 changed files with 79 additions and 11 deletions.
diff --git a/source/Evolve/OEE.h b/source/Evolve/OEE.h
@@ -16,8 +16,8 @@ namespace emp {
         template <typename SKEL_TYPE>
         struct oee_data : public no_data {
 
-            SKEL_TYPE skeleton = NULL;
-            bool oee_calculated = false;
+            Ptr<SKEL_TYPE> skeleton = nullptr;
+            ~oee_data(){if(skeleton){skeleton.Delete();}}
         };
     };
 
@@ -36,6 +36,7 @@ namespace emp {
         };
 
         std::deque<emp::vector<snapshot_info_t>> snapshots;
+        std::deque<int> snapshot_times;
         Ptr<Systematics<ORG, ORG_INFO, DATA_STRUCT>> systematics_manager;
 
         std::map<SKEL_TYPE, int> prev_coal_set;
@@ -88,8 +89,11 @@ namespace emp {
         void SetResolution(int r) {resolution = r;}
         void SetGenerationInterval(int g) {generation_interval = g;}
 
-        void Update(size_t ud) {
-            if (Mod((int)ud, resolution) == 0) {
+        void Update(size_t gen, int ud = -1) {
+            if (Mod((int)gen, resolution) == 0) {
+                if (ud == -1) {
+                    ud = gen;
+                }
                 auto & sys_active = systematics_manager->GetActive();
 
                 emp::vector<snapshot_info_t> active(sys_active.size());
@@ -100,7 +104,10 @@ namespace emp {
                     i++;
                 }
                 snapshots.push_back(active);
+                snapshot_times.push_back(ud);
                 if ((int)snapshots.size() > generation_interval/resolution + 1) {
+                    systematics_manager->RemoveBefore(snapshot_times.front() - 1);
+                    snapshot_times.pop_front();
                     snapshots.pop_front();
                 }
                 CalcStats(ud);
@@ -162,7 +169,7 @@ namespace emp {
                 return res;
             }
 
-            std::set<Ptr<taxon_t>> extant_canopy_roots = systematics_manager->GetCanopyExtantRoots(ud-generation_interval);
+            std::set<Ptr<taxon_t>> extant_canopy_roots = systematics_manager->GetCanopyExtantRoots(snapshot_times.front());
             // std::cout << "exteant canpoy roots: ";
             // for (auto t : extant_canopy_roots) {
             //     std::cout << t->GetInfo() << " ";
@@ -171,14 +178,13 @@ namespace emp {
             for ( snapshot_info_t & t : snapshots.front()) {
                 if (Has(extant_canopy_roots, t.taxon)) {
                     // std::cout << t.taxon->GetInfo() << " Survived filter" << std::endl;
-                    if (!t.taxon->GetData().oee_calculated) {
-                        t.taxon->GetData().skeleton = skeleton_fun(t.taxon->GetInfo());
-                        t.taxon->GetData().oee_calculated = true;
+                    if (!t.taxon->GetData().skeleton) {
+                        t.taxon->GetData().skeleton.New(skeleton_fun(t.taxon->GetInfo()));
                     }
-                    if (Has(res, t.taxon->GetData().skeleton)) {
-                        res[t.taxon->GetData().skeleton] += t.count;
+                    if (Has(res, *(t.taxon->GetData().skeleton))) {
+                        res[*(t.taxon->GetData().skeleton)] += t.count;
                     } else {
-                        res[t.taxon->GetData().skeleton] = t.count;
+                        res[*(t.taxon->GetData().skeleton)] = t.count;
                     }
                 }
             }

diff --git a/source/Evolve/Systematics.h b/source/Evolve/Systematics.h
@@ -147,6 +147,7 @@ namespace emp {
 
     /// Retrieve a pointer to the parent Taxon.
     Ptr<this_t> GetParent() const { return parent; }
+    void NullifyParent() {parent = nullptr;}
 
     /// Get the number of living organisms currently associated with this Taxon.
     size_t GetNumOrgs() const { return num_orgs; }
@@ -993,7 +994,68 @@ namespace emp {
       return depth;
     }
 
+    void RemoveBefore(int ud) {
+
+      // @ELD: This would be such a nice way to do it
+      // but we can't because we need to notify offspring
+      // when there parents are un-tracked
+      // std::set<Ptr<taxon_t>> to_remove;
+      // for (Ptr<taxon_t> tax : ancestor_taxa) {
+      //   if (tax->GetDestructionTime() < ud) {
+      //     to_remove.insert(tax);
+      //   }
+      // }
+
+      // for (Ptr<taxon_t> tax : to_remove) {
+      //     ancestor_taxa.erase(tax);
+      //     tax.Delete();
+      // }
+
+      std::map<Ptr<taxon_t>, std::set<Ptr<taxon_t>>> to_remove;
 
+      for (Ptr<taxon_t> tax : active_taxa) {
+        Ptr<taxon_t> curr = tax;
+
+        while (curr && !CanRemove(curr->GetParent(), ud)) {
+          curr = curr->GetParent();           
+        }
+
+        if (curr) {
+          Ptr<taxon_t> next = curr->GetParent();
+          while (next) {
+            to_remove[next].insert(curr);
+            curr = next;
+            next = next->GetParent();
+          }
+        }
+      }
+      // std::cout << "About to remove " << to_remove.size() << " orgs" << std::endl;
+      for (std::pair<Ptr<taxon_t>, std::set<Ptr<taxon_t>>> el : to_remove) {
+        emp_assert(el.first->GetDestructionTime() < ud, el.first->GetDestructionTime(), ud);
+        if (el.first->GetNumOff() == el.second.size()) {
+          // Everything is account for
+          for (auto tax : el.second) {
+            tax->NullifyParent();
+          }
+          ancestor_taxa.erase(el.first);
+          el.first.Delete();
+        } 
+      }
+
+    }
+
+    bool CanRemove(Ptr<taxon_t> t, int ud) {
+      if (!t) {
+        return false;
+      }
+      while (t) {
+        if (t->GetNumOrgs() > 0 || t->GetDestructionTime() >= ud) {
+          return false;
+        }
+        t = t->GetParent();
+      }
+      return true;
+    }
 
     /// Request a pointer to the Most-Recent Common Ancestor for the population.
     Ptr<taxon_t> GetMRCA() const;