Issue #854 MetaDataStorage class is made copyable/movable

core/indigo-core/molecule/metadata_storage.h

@@ -18,6 +18,9 @@
 #ifndef __metadata_storage__
 #define __metadata_storage__
 
+#include <memory>
+#include <vector>
+
 #include "base_cpp/ptr_array.h"
 
 namespace indigo
@@ -37,11 +40,10 @@ namespace indigo
     {
     public:
         DECL_ERROR;
-        void clone(const MetaDataStorage& other);
 
-        virtual ~MetaDataStorage()
-        {
-        }
+        using MetadataVector = std::vector<std::shared_ptr<MetaObject>>;
+
+        virtual ~MetaDataStorage() = default;
 
         void addMetaObject(MetaObject* pobj);
 
@@ -55,7 +57,7 @@ namespace indigo
 
         void resetReactionData();
 
-        const PtrArray<MetaObject>& metaData() const
+        const MetadataVector& metaData() const
         {
             return _meta_data;
         }
@@ -64,11 +66,11 @@ namespace indigo
         const MetaObject& getMetaObject(uint32_t meta_type, int index) const;
 
     protected:
-        PtrArray<MetaObject> _meta_data; // TODO: should be replaced with list of unique_ptr
-        Array<int> _plus_indexes;
-        Array<int> _arrow_indexes;
-        Array<int> _simple_object_indexes;
-        Array<int> _text_object_indexes;
+        MetadataVector _meta_data;
+        std::vector<int> _plus_indexes;
+        std::vector<int> _arrow_indexes;
+        std::vector<int> _simple_object_indexes;
+        std::vector<int> _text_object_indexes;
     };
 }
 #endif

core/indigo-core/molecule/src/base_molecule.cpp

@@ -636,7 +636,7 @@ void BaseMolecule::clone(BaseMolecule& other, Array<int>* mapping, Array<int>* i
 
     makeSubmolecule(other, *mapping, inv_mapping, skip_flags);
 
-    _meta.clone(other._meta);
+    _meta = other._meta;
 
     name.copy(other.name);
 }
@@ -667,7 +667,7 @@ void BaseMolecule::clone_KeepIndices(BaseMolecule& other, int skip_flags)
 
     _cloneGraph_KeepIndices(other);
 
-    _meta.clone(other._meta);
+    _meta = other._meta;
 
     _mergeWithSubmolecule_Sub(other, vertices, 0, mapping, edge_mapping, skip_flags);
 

core/indigo-core/molecule/src/metadata_storage.cpp

@@ -9,36 +9,27 @@ IMPL_ERROR(MetaDataStorage, "metadata storage");
 void MetaDataStorage::addMetaObject(MetaObject* pobj)
 {
     int index = _meta_data.size();
-    _meta_data.expand(index + 1);
-    _meta_data.set(index, pobj);
+    _meta_data.emplace_back(pobj);
 
     switch (pobj->_class_id)
     {
     case KETTextObject::CID:
-        _text_object_indexes.push() = index;
+        _text_object_indexes.push_back(index);
         break;
     case KETSimpleObject::CID:
-        _simple_object_indexes.push() = index;
+        _simple_object_indexes.push_back(index);
         break;
     case KETReactionPlus::CID:
-        _plus_indexes.push() = index;
+        _plus_indexes.push_back(index);
         break;
     case KETReactionArrow::CID:
-        _arrow_indexes.push() = index;
+        _arrow_indexes.push_back(index);
         break;
     default:
         break;
     }
 }
 
-void MetaDataStorage::clone(const MetaDataStorage& other)
-{
-    resetMetaData();
-    const auto& meta = other.metaData();
-    for (int i = 0; i < meta.size(); i++)
-        addMetaObject(meta[i]->clone());
-}
-
 const MetaObject& MetaDataStorage::getMetaObject(uint32_t meta_type, int index) const
 {
     switch (meta_type)
@@ -87,9 +78,30 @@ void MetaDataStorage::resetReactionData()
 {
     _plus_indexes.clear();
     _arrow_indexes.clear();
+
+    std::vector<int> indexes_to_remove;
     for (int i = _meta_data.size() - 1; i >= 0; i--)
     {
         if (_meta_data[i]->_class_id == KETReactionArrow::CID || _meta_data[i]->_class_id == KETReactionPlus::CID)
-            _meta_data.remove(i);
+        {
+            indexes_to_remove.push_back(i);
+        }
+    }
+
+    for (int i : indexes_to_remove)
+    {
+        _meta_data.erase(_meta_data.begin() + i);
+
+        for (int& toi : _text_object_indexes)
+        {
+            if (toi > i)
+                --toi;
+        }
+
+        for (int& soi : _simple_object_indexes)
+        {
+            if (soi > i)
+                --soi;
+        }
     }
 }

core/indigo-core/molecule/src/molecule_json_saver.cpp

@@ -1059,14 +1059,14 @@ void MoleculeJsonSaver::saveMetaData(rapidjson::Writer<rapidjson::StringBuffer>&
         }
         break;
         case KETSimpleObject::CID: {
-            auto simple_obj = (KETSimpleObject*)pobj;
+            KETSimpleObject& simple_obj = (KETSimpleObject&)(*pobj);
             writer.StartObject();
             writer.Key("type");
             writer.String("simpleObject");
             writer.Key("data");
             writer.StartObject();
             writer.Key("mode");
-            switch (simple_obj->_mode)
+            switch (simple_obj._mode)
             {
             case KETSimpleObject::EKETEllipse:
                 writer.String("ellipse");
@@ -1081,7 +1081,7 @@ void MoleculeJsonSaver::saveMetaData(rapidjson::Writer<rapidjson::StringBuffer>&
             writer.Key("pos");
             writer.StartArray();
 
-            auto& coords = simple_obj->_coordinates;
+            auto& coords = simple_obj._coordinates;
 
             // point1
             writer.StartObject();
@@ -1112,22 +1112,22 @@ void MoleculeJsonSaver::saveMetaData(rapidjson::Writer<rapidjson::StringBuffer>&
             break;
         }
         case KETTextObject::CID: {
-            auto simple_obj = (KETTextObject*)pobj;
+            KETTextObject& simple_obj = (KETTextObject&)(*pobj);
             writer.StartObject();
             writer.Key("type");
             writer.String("text");
             writer.Key("data");
             writer.StartObject();
             writer.Key("content");
-            writer.String(simple_obj->_content.c_str());
+            writer.String(simple_obj._content.c_str());
             writer.Key("position");
             writer.StartObject();
             writer.Key("x");
-            writer.Double(simple_obj->_pos.x);
+            writer.Double(simple_obj._pos.x);
             writer.Key("y");
-            writer.Double(simple_obj->_pos.y);
+            writer.Double(simple_obj._pos.y);
             writer.Key("z");
-            writer.Double(simple_obj->_pos.z);
+            writer.Double(simple_obj._pos.z);
             writer.EndObject(); // end position
             writer.EndObject(); // end data
             writer.EndObject(); // end node

core/indigo-core/reaction/src/base_reaction.cpp

@@ -372,7 +372,7 @@ void BaseReaction::clone(BaseReaction& other, Array<int>* mol_mapping, ObjArray<
     }
 
     name.copy(other.name);
-    _meta.clone(other._meta);
+    _meta = other._meta;
 }
 
 void BaseReaction::_clone(BaseReaction& other, int index, int i, ObjArray<Array<int>>* mol_mappings)

core/indigo-core/reaction/src/reaction_json_loader.cpp

@@ -68,7 +68,7 @@ void ReactionJsonLoader::loadReaction(BaseReaction& rxn)
     else
         throw Error("unknown reaction type: %s", typeid(rxn).name());
 
-    rxn.meta().clone(_pmol->meta());
+    rxn.meta() = std::move(_pmol->meta());
     _pmol->meta().resetMetaData();
 
     int arrow_count = rxn.meta().getMetaCount(KETReactionArrow::CID);

core/indigo-core/reaction/src/reaction_json_saver.cpp

@@ -66,7 +66,7 @@ void ReactionJsonSaver::saveReactionWithMetaData(BaseReaction& rxn, BaseMolecule
     for (int i = rxn.begin(); i != rxn.end(); i = rxn.next(i))
         merged.mergeWithMolecule(rxn.getBaseMolecule(i), 0, 0);
 
-    merged.meta().clone(rxn.meta());
+    merged.meta() = rxn.meta();
 
     StringBuffer s;
     Writer<StringBuffer> writer(s);