#4 rename reset to resetAll, add new reset

js/copasi.d.ts

@@ -65,6 +65,7 @@ export interface ModelInfo {
 export default class COPASI {
     constructor(module: any);
     reset(): void;
+    resetAll(): void;
     readonly version: string;
     _vectorToArray(v: any): any[];
     loadExample(path: string) : ModelInfo;

js/copasi.js

@@ -42,6 +42,7 @@ class COPASI {
         this.destroy = Module.destroy;
         this.getValue = Module.getValue;
         this.setValue = Module.setValue;
+        this.resetAll = Module.resetAll;
 
         // init runtime
         this.initCps();

src/copasijs.cpp

@@ -784,6 +784,35 @@ std::string getModelInfo()
     return buildModelInfo().dump(2);
 }
 
+void _removeFixedElementsFromSet(CModelParameterGroup* group)
+{
+    if (!group)
+        return;
+
+    std::vector< CModelParameter * > toBeRemoved;
+    for (auto it = group->begin(); it != group->end(); ++it)
+    {
+        auto* p = *it;
+        if (p == NULL)
+            continue;
+
+        auto *pGroup = dynamic_cast<CModelParameterGroup*>(p);
+        if (pGroup)
+        {
+            _removeFixedElementsFromSet(pGroup);
+            continue;
+        }
+        if (p->getSimulationType() == CModelEntity::Status::FIXED)
+        {
+            toBeRemoved.push_back(p);
+        }
+    }
+
+    for (auto* p : toBeRemoved)
+    {
+        group->remove(p);
+    }
+}
 
 void loadCommon()
 {
@@ -793,6 +822,12 @@ void loadCommon()
     auto* newSet = new CModelParameterSet("_initial_state");
     sets.add(newSet, true);
     newSet->createFromModel();
+
+    // now create a second one with only the state variables
+    newSet = new CModelParameterSet("_initial_state_variables_only");
+    sets.add(newSet, true);
+    newSet->createFromModel();
+    _removeFixedElementsFromSet(newSet);
 }
 
 std::string loadFromFile(const std::string& modelFile)
@@ -874,6 +909,17 @@ std::string loadModel(const std::string& cpsCode)
 }
 
 void reset()
+{
+    if (pDataModel == NULL)
+        initCps();
+
+    auto* pModel = pDataModel->getModel();
+    auto& set = pModel->getModelParameterSets()["_initial_state_variables_only"];
+    set.updateModel();
+    pModel->applyInitialValues();
+}
+
+void resetAll()
 {
     if (pDataModel == NULL)
         initCps();
@@ -1336,6 +1382,7 @@ EMSCRIPTEN_BINDINGS(copasi_binding)
     emscripten::function("loadFromFile", &loadFromFile);
     emscripten::function("loadModel", &loadModel);
     emscripten::function("reset", &reset);
+    emscripten::function("resetAll", &resetAll);
     emscripten::function("simulate", &simulate);
     emscripten::function("simulateYaml", &simulateYaml);
     emscripten::function("simulateEx", &simulateEx);

src/copasijs.h

@@ -112,9 +112,16 @@ std::string loadModel(const std::string& modelString);
 
 /// @brief resets the model
 ///
+/// This function resets the models floating species and entities with 
+/// ODEs back to their initial values.
+void reset();
+
+/// @brief resets the model completely
+///
 /// This function resets the model to the state after loading
 /// the model. 
-void reset();
+void resetAll();
+
 
 /// @brief applies a yaml string to the model
 /// @param yaml the yaml string to apply

test/copasijs_test.cpp

@@ -196,6 +196,25 @@ TEST_CASE("Load SBML Model", "[copasijs][sbml]")
     REQUIRE(json["titles"][1] == "S1");
     REQUIRE(json["columns"][1][0] == 0);
 
+    setValue("J0_v0", 8);
+
+    // test difference between reset and restAll by changing the value of S1 and J0_v0
+    setValue("S1", 1);
+    setValue("J0_v0", 10);
+
+    reset();
+    // now S1 should be 0 and J0_v0 should be 10
+    REQUIRE(getValue("S1") == 0);
+    REQUIRE(getValue("J0_v0") == 10);
+
+    // now run resetAll
+    setValue("S1", 1);
+    setValue("J0_v0", 10);
+    resetAll();
+    // now S1 should be 0 and J0_v0 should be 8
+    REQUIRE(getValue("S1") == 0);
+    REQUIRE(getValue("J0_v0") == 8);
+
 }