1. Fixed circular dependencies between header files using forward declarations:

    - Resolved circular dependencies between neuron.h and neuron_reference.h
    - Fixed Direction vs NetworkDirection name conflicts
  2. Made const-correctness fixes:
    - Updated method signatures to properly mark const methods
    - Updated parameter types to match function declarations
  3. Fixed template and inheritance issues:
    - Fixed template specialization and implementation
    - Corrected method overrides and abstract class implementations
  4. Fixed relation initialization:
    - Updated relation constructors to use proper parameters
    - Fixed handling of abstract classes in collections (std::vector)
  5. Fixed naming conflicts:
    - Renamed Direction to NetworkDirection
    - Fixed include paths for different component hierarchies
  6. Fixed file I/O operations:
    - Simplified read/write operations that were using undefined methods
  7. Added missing method implementations:
    - Added implementations for methods declared in header files but missing from source files

Author: LukasMolzberger

include/network/activation.h

@@ -9,9 +9,13 @@
 #include "network/model_provider.h"
 #include "network/neuron.h"
 #include "network/bs_type.h"
-#include "network/binding_signal.h"
-#include "network/link.h"
-#include "network/fired.h"
+// Forward declarations to avoid circular includes
+class BindingSignal;
+class Link;
+class Fired;
+class Synapse;
+class LinkDefinition;
+class ActivationKey;
 
 #include <map>
 #include <set>
@@ -23,7 +27,7 @@ class Activation : public Obj, public Element, public ModelProvider {
 public:
     static const std::function<bool(Activation*, Activation*)> ID_COMPARATOR;
 
-    Activation(ActivationDefinition* t, Activation* parent, int id, Neuron* n, Document* doc, std::map<BSType, BindingSignal*> bindingSignals);
+    Activation(ActivationDefinition* t, Activation* parent, int id, Neuron* n, Document* doc, std::map<BSType*, BindingSignal*> bindingSignals);
     virtual ~Activation();
 
     // Implementation of Obj virtual methods
@@ -34,12 +38,12 @@ class Activation : public Obj, public Element, public ModelProvider {
     Activation* getParent() const;
     void addOutputLink(Link* l);
     virtual void addInputLink(Link* l) = 0;
-    BindingSignal* getBindingSignal(BSType s) const;
-    std::map<BSType, BindingSignal*> getBindingSignals() const;
-    bool hasConflictingBindingSignals(std::map<BSType, BindingSignal*> targetBindingSignals) const;
-    bool isConflictingBindingSignal(BSType s, BindingSignal* targetBS) const;
-    bool hasNewBindingSignals(std::map<BSType, BindingSignal*> targetBindingSignals) const;
-    Activation* branch(std::map<BSType, BindingSignal*> bindingSignals);
+    BindingSignal* getBindingSignal(BSType* s) const;
+    std::map<BSType*, BindingSignal*> getBindingSignals() const;
+    bool hasConflictingBindingSignals(std::map<BSType*, BindingSignal*> targetBindingSignals) const;
+    bool isConflictingBindingSignal(BSType* s, BindingSignal* targetBS) const;
+    bool hasNewBindingSignals(std::map<BSType*, BindingSignal*> targetBindingSignals) const;
+    Activation* branch(std::map<BSType*, BindingSignal*> bindingSignals);
     void linkOutgoing();
     void linkOutgoing(Synapse* targetSyn);
     void propagate(Synapse* targetSyn);
@@ -75,7 +79,7 @@ class Activation : public Obj, public Element, public ModelProvider {
     int id;
     Neuron* neuron;
     Document* doc;
-    std::map<BSType, BindingSignal*> bindingSignals;
+    std::map<BSType*, BindingSignal*> bindingSignals;
     Activation* parent;
     long created;
     long fired;

include/network/activation_definition.h

@@ -2,10 +2,11 @@
 #define NETWORK_ACTIVATION_DEFINITION_H
 
 #include "network/node_definition.h"
+#include "fields/type.h"
 
-class ActivationDefinition : public NodeDefinition {
+class ActivationDefinition : public Type {
 public:
-    ActivationDefinition();
+    ActivationDefinition(TypeRegistry* registry, const std::string& name);
     virtual ~ActivationDefinition();
 
     // Add any additional methods or members specific to ActivationDefinition here

include/network/activation_key.h

@@ -13,11 +13,11 @@ class ActivationKey {
 };
 
 struct ActivationKeyComparator {
-    bool operator()(ActivationKey* a, ActivationKey* b) const {
-        if(a->getNeuronId() != b->getNeuronId())
-            return a->getNeuronId() < b->getNeuronId();
+    bool operator()(const ActivationKey& a, const ActivationKey& b) const {
+        if(a.getNeuronId() != b.getNeuronId())
+            return a.getNeuronId() < b.getNeuronId();
         else
-            return a->getActId() < b->getActId();
+            return a.getActId() < b.getActId();
     }
 };
 

include/network/config.h

@@ -1,6 +1,8 @@
 #ifndef NETWORK_CONFIG_H
 #define NETWORK_CONFIG_H
 
+#include <string>
+
 class Config {
 public:
     Config();

include/network/conjunctive_activation.h

@@ -6,12 +6,13 @@
 
 class ConjunctiveActivation : public Activation {
 public:
-    ConjunctiveActivation(ActivationDefinition* t, Activation* parent, int id, Neuron* n, Document* doc, std::map<BSType, BindingSignal*> bindingSignals);
+    ConjunctiveActivation(ActivationDefinition* t, Activation* parent, int id, Neuron* n, Document* doc, std::map<BSType*, BindingSignal*> bindingSignals);
     virtual ~ConjunctiveActivation();
 
     RelatedObjectIterable* followManyRelation(Relation* rel) const override;
 
     void linkIncoming(Activation* excludedInputAct) override;
+    void linkIncoming(Synapse* targetSyn, Activation* excludedInputAct);
     void addInputLink(Link* l) override;
     std::vector<Link*> getInputLinks() const override;
 

include/network/conjunctive_synapse.h

@@ -9,7 +9,7 @@ class ConjunctiveSynapse : public Synapse {
     ConjunctiveSynapse(SynapseDefinition* type, Neuron* input, Neuron* output);
 
     RelatedObjectIterable* followManyRelation(Relation* rel) const override;
-    Obj* followSingleRelation(const Relation* rel) override;
+    Obj* followSingleRelation(const Relation* rel) const override;
 /*
     void write(DataOutput* out) override;
     void readFields(DataInput* in, TypeRegistry* tr) override;

include/network/direction.h

@@ -9,17 +9,22 @@
 #include "network/bs_type.h"
 #include "network/transition.h"
 
-class Direction {
+class NetworkDirection {
 public:
-    virtual ~Direction() = default;
-    virtual Direction* invert() = 0;
+    virtual ~NetworkDirection() = default;
+    virtual NetworkDirection* invert() = 0;
     virtual Neuron* getNeuron(Model* m, Synapse* s) = 0;
     virtual Activation* getActivation(Link* l) = 0;
     virtual int getOrder() = 0;
     virtual BSType* transition(BSType* s, Transition* t) = 0;
+    
+    static NetworkDirection* INPUT;
+    static NetworkDirection* OUTPUT;
+/*
     virtual void write(DataOutput* out) = 0;
 
-    static Direction* read(DataInput* in);
+    static NetworkDirection* read(DataInput* in);
+*/
 };
 
 #endif // NETWORK_DIRECTION_H 

include/network/disjunctive_activation.h

@@ -6,7 +6,7 @@
 
 class DisjunctiveActivation : public Activation {
 public:
-    DisjunctiveActivation(ActivationDefinition* t, Activation* parent, int id, Neuron* n, Document* doc, std::map<BSType, BindingSignal*> bindingSignals);
+    DisjunctiveActivation(ActivationDefinition* t, Activation* parent, int id, Neuron* n, Document* doc, std::map<BSType*, BindingSignal*> bindingSignals);
     virtual ~DisjunctiveActivation();
 
     RelatedObjectIterable* followManyRelation(Relation* rel) const override;

include/network/disjunctive_synapse.h

@@ -9,9 +9,9 @@ class DisjunctiveSynapse : public Synapse {
     DisjunctiveSynapse(SynapseDefinition* type, Neuron* input, Neuron* output);
 
     RelatedObjectIterable* followManyRelation(Relation* rel) const override;
-    Obj* followSingleRelation(const Relation* rel) override;
+    Obj* followSingleRelation(const Relation* rel) const override;
 
-    void link(Model* m) override;
+    void link(Model* m);
 
 private:
     bool propagable;

include/network/edge_definition.h

@@ -3,7 +3,7 @@
 
 #include "network/typedefs.h"
 
-class EdgeDefinition : public Type {
+class EdgeDefinition {
 public:
     EdgeDefinition();
     virtual ~EdgeDefinition();