From e26244717462733e8a0f3a1eb0dba4c3eb7ff762 Mon Sep 17 00:00:00 2001
From: Pascal Serrarens <pascal@passer.life>
Date: Tue, 17 Feb 2026 13:02:43 +0100
Subject: [PATCH] Fix array extension for clusters

---
 Cluster.cs         | 39 ++++++++++++++++++++++++++++++---------
 ClusterReceptor.cs | 33 +++++++++++----------------------
 2 files changed, 41 insertions(+), 31 deletions(-)

diff --git a/Cluster.cs b/Cluster.cs
index aaa6429..a2bc161 100644
--- a/Cluster.cs
+++ b/Cluster.cs
@@ -151,16 +151,27 @@ public class Cluster : Nucleus {
         return sortedOrder;
     }
 
-    public override Nucleus Clone(ClusterPrefab prefab) {
-        Neuron clone = new(prefab, this.name);
+    public override Nucleus Clone(ClusterPrefab parent) {
+        Cluster clone = new(this.prefab, parent);
 
         foreach (Synapse synapse in this.synapses) {
             Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
             clonedSynapse.weight = synapse.weight;
         }
-        // foreach (Nucleus receiver in this.receivers) {
-        //     clone.AddReceiver(receiver);
-        // }
+
+        foreach (Neuron output in this.outputs) {
+            foreach (Nucleus receiver in output.receivers) {
+                int ix = GetNucleusIndex(this.clusterNuclei.ToArray(), output);
+                if (ix < 0)
+                    continue;
+                
+                if (clone.clusterNuclei[ix] is not Neuron clonedOutput)
+                    continue;
+
+                clonedOutput.AddReceiver(receiver);
+            }
+        }
+
         return clone;
     }
 
@@ -172,9 +183,19 @@ public class Cluster : Nucleus {
         return clone;
     }
 
-    private int GetNucleusIndex(Nucleus[] nucleiArray, Nucleus nucleus) {
-        for (int i = 0; i < nucleiArray.Length; i++) {
-            if (nucleus == nucleiArray[i])
+    protected int GetNucleusIndex(Nucleus[] nuclei, Nucleus nucleus) {
+        for (int i = 0; i < nuclei.Length; i++) {
+            if (nucleus == nuclei[i])
+                return i;
+        }
+        return -1;
+    }
+
+    protected int GetNucleusIndex(List<Nucleus> nuclei, Nucleus nucleus) {
+        int i = 0;
+        foreach (Nucleus nucleiElement in nuclei) {
+        //for (int i = 0; i < nuclei.Length; i++) {
+            if (nucleus == nucleiElement)
                 return i;
         }
         return -1;
@@ -318,7 +339,7 @@ public class Cluster : Nucleus {
             return null;
         }
     }
-    private List<Neuron> _outputs = null;
+    protected List<Neuron> _outputs = null;
     public List<Neuron> outputs {
         get {
             if (this._outputs == null) {
diff --git a/ClusterReceptor.cs b/ClusterReceptor.cs
index e72cdd7..8e13779 100644
--- a/ClusterReceptor.cs
+++ b/ClusterReceptor.cs
@@ -32,9 +32,20 @@ public class ClusterReceptor : Cluster, IReceptor {
             Synapse clonedSynapse = clone.AddSynapse(synapse.nucleus);
             clonedSynapse.weight = synapse.weight;
         }
+
         // foreach (Nucleus receiver in this.receivers) {
         //     clone.AddReceiver(receiver);
         // }
+
+        this._outputs = null; // Make sure the output are regenerated
+        foreach (Neuron output in this.outputs) {
+            int ix = GetNucleusIndex(this.clusterNuclei, output);
+            if (ix < 0 || clone.clusterNuclei[ix] is not Neuron clonedOutput)
+                continue;
+
+            foreach (Nucleus receiver in output.receivers)
+                clonedOutput.AddReceiver(receiver);            
+        }
         return clone;
     }
 
@@ -45,28 +56,6 @@ public class ClusterReceptor : Cluster, IReceptor {
         set { _array = value; }
     }
 
-    #region Receivers
-
-    private List<Nucleus> _clusterReceivers = null;
-    // public override List<Nucleus> receivers {
-    //     get {
-    //         if (_clusterReceivers == null || _clusterReceivers.Count == 0) {
-    //             _clusterReceivers = new();
-    //             foreach (Nucleus output in this.clusterNuclei) {
-    //                 _clusterReceivers.AddRange(output.receivers);                    
-    //             }
-    //         }
-    //         return _clusterReceivers;
-    //     }
-    // }
-    // public override void AddReceiver(Nucleus receivingNucleus, float weight = 1) {
-    //     string nucleusName = this.
-    //     this.output.receivers.Add(receivingNucleus);
-    //     receivingNucleus.AddSynapse(this.output, weight);
-    // }
-
-    #endregion Receivers
-
     public override void UpdateStateIsolated() {
         float3 sum = this.bias;