Issue #854 MetaDataStorage class is made copyable/movable

core/indigo-core/molecule/metadata_storage.h

@@ -19,6 +19,8 @@
 #define __metadata_storage__
 
 #include <cstdint>
+#include <memory>
+#include <vector>
 
 #include "base_cpp/ptr_array.h"
 
@@ -42,9 +44,9 @@ namespace indigo
         void clone(const MetaDataStorage& other);
         void append(const MetaDataStorage& other);
 
-        virtual ~MetaDataStorage()
-        {
-        }
+        using MetadataVector = std::vector<std::shared_ptr<MetaObject>>;
+
+        virtual ~MetaDataStorage() = default;
 
         int addMetaObject(MetaObject* pobj);
 
@@ -59,7 +61,7 @@ namespace indigo
 
         void resetReactionData();
 
-        const PtrArray<MetaObject>& metaData() const
+        const MetadataVector& metaData() const
         {
             return _meta_data;
         }
@@ -71,11 +73,11 @@ namespace indigo
         int getMetaObjectIndex(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

@@ -649,7 +649,7 @@ 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);
 }
@@ -680,7 +680,7 @@ 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

@@ -9,22 +9,21 @@ IMPL_ERROR(MetaDataStorage, "metadata storage");
 int 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;
@@ -103,9 +102,30 @@ 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

@@ -1233,14 +1233,14 @@ void MoleculeJsonSaver::saveMetaData(JsonWriter& writer, MetaDataStorage& meta)
         }
         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");
@@ -1255,7 +1255,7 @@ void MoleculeJsonSaver::saveMetaData(JsonWriter& writer, MetaDataStorage& meta)
             writer.Key("pos");
             writer.StartArray();
 
-            auto& coords = simple_obj->_coordinates;
+            auto& coords = simple_obj._coordinates;
 
             // point1
             writer.StartObject();
@@ -1286,22 +1286,22 @@ void MoleculeJsonSaver::saveMetaData(JsonWriter& writer, MetaDataStorage& meta)
             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

@@ -388,7 +388,7 @@ 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

@@ -81,7 +81,7 @@ 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;
     JsonWriter writer(pretty_json);
     writer.Reset(s);

core/indigo-core/tests/tests/metadata_storage.cpp

@@ -0,0 +1,59 @@
+/****************************************************************************
+ * Copyright (C) from 2009 to Present EPAM Systems.
+ *
+ * This file is part of Indigo toolkit.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ***************************************************************************/
+
+#include <gtest/gtest.h>
+
+#include "common.h"
+#include "molecule/ket_commons.h"
+#include "molecule/metadata_storage.h"
+
+using namespace std;
+using namespace indigo;
+
+class IndigoCoreMetadataStorageTest : public IndigoCoreTest
+{
+};
+
+TEST_F(IndigoCoreMetadataStorageTest, reset_reaction_data)
+{
+    MetaDataStorage ms;
+
+    KETTextObject* to = new KETTextObject({}, "{ \"data\" : \"test\" }");
+    KETSimpleObject* so = new KETSimpleObject(10, std::make_pair(Vec2f{}, Vec2f{}));
+    KETReactionArrow* ra = new KETReactionArrow(15, {}, {});
+    KETReactionPlus* rp = new KETReactionPlus({20, 25});
+
+    ms.addMetaObject(ra);
+    ms.addMetaObject(rp);
+    ms.addMetaObject(to);
+    ms.addMetaObject(so);
+
+    ms.resetReactionData();
+
+    ASSERT_EQ(ms.metaData().size(), 2);
+
+    const KETTextObject& to2 = static_cast<const KETTextObject&>(ms.getMetaObject(KETTextObject::CID, 0));
+    ASSERT_EQ(to2._content, "{ \"data\" : \"test\" }");
+
+    const KETSimpleObject& so2 = static_cast<const KETSimpleObject&>(ms.getMetaObject(KETSimpleObject::CID, 0));
+    ASSERT_EQ(so2._mode, 10);
+
+    MetaDataStorage ms2(ms);
+
+    MetaDataStorage ms3(std::move(ms2));
+}