Merge pull request #6 from sys-bio/fix-bugs-and-add-new-features

fix-bugs-and-add-new-features

src/autolayout/libsbmlnetwork_autolayout.cpp

@@ -28,7 +28,7 @@ void locateGlyphs(Model *model, Layout *layout, const bool &useNameAsTextLabel)
     autoLayoutAlgorithm->setWidth(layout);
     autoLayoutAlgorithm->setHeight(layout);
     autoLayoutAlgorithm->apply();
-    updateCompartmentExtents(model, layout);
+    updateCompartmentsExtents(model, layout);
     updateLayoutDimensions(layout);
     delete autoLayoutAlgorithm;
     if (!adjustLayoutDimensions(layout)) {
@@ -57,7 +57,7 @@ void locateReactions(Model *model, Layout *layout, const bool &useNameAsTextLabe
     autoLayoutAlgorithm->setWidth(layout);
     autoLayoutAlgorithm->setHeight(layout);
     autoLayoutAlgorithm->apply();
-    updateCompartmentExtents(model, layout);
+    updateCompartmentsExtents(model, layout);
     updateLayoutDimensions(layout);
     delete autoLayoutAlgorithm;
 }
@@ -189,22 +189,27 @@ initializeCompartmentGlyphExtents(BoundingBox *compartmentGlyphBoundingBox, Boun
     compartmentGlyphBoundingBox->setHeight(speciesGlyphBoundingBox->height() + 2 * padding);
 }
 
-void updateCompartmentExtents(Model *model, Layout *layout) {
-    updateCompartmentExtentsUsingItsElementsExtents(model, layout);
-    updateCompartmentExtentsUsingItsPresetAttributes(layout);
+void updateCompartmentsExtents(Model *model, Layout *layout) {
+    updateCompartmentsExtentsUsingTheirElementsExtents(model, layout);
+    updateCompartmentsExtentsUsingTheirPresetAttributes(layout);
 }
 
-void updateCompartmentExtentsUsingItsElementsExtents(Model *model, Layout *layout) {
+void updateCompartmentsExtentsUsingTheirElementsExtents(Model *model, Layout *layout) {
+    std::vector<std::string> extentsInitializedCompartmentGlyphIds;
     for (int i = 0; i < layout->getNumSpeciesGlyphs(); i++) {
         Compartment *compartment = findSpeciesGlyphCompartment(model, layout->getSpeciesGlyph(i));
         if (compartment) {
             std::vector < CompartmentGlyph * > compartmentGlyphs = getAssociatedCompartmentGlyphsWithCompartmentId(
                     layout, compartment->getId());
             for (int j = 0; j < compartmentGlyphs.size(); j++) {
                 CompartmentGlyph *compartmentGlyph = compartmentGlyphs.at(j);
-                if (i == 0)
+                if (std::find(extentsInitializedCompartmentGlyphIds.begin(),
+                              extentsInitializedCompartmentGlyphIds.end(), compartmentGlyph->getId()) ==
+                    extentsInitializedCompartmentGlyphIds.end()) {
                     initializeCompartmentGlyphExtents(compartmentGlyph->getBoundingBox(),
                                                       layout->getSpeciesGlyph(i)->getBoundingBox());
+                    extentsInitializedCompartmentGlyphIds.push_back(compartmentGlyph->getId());
+                }
                 updateCompartmentExtentsUsingItsElementsExtents(compartmentGlyph->getBoundingBox(),
                                          layout->getSpeciesGlyph(i)->getBoundingBox());
             }
@@ -280,7 +285,7 @@ void updateCompartmentExtentsUsingItsElementsExtents(BoundingBox *compartmentGly
     }
 }
 
-void updateCompartmentExtentsUsingItsPresetAttributes(Layout *layout) {
+void updateCompartmentsExtentsUsingTheirPresetAttributes(Layout *layout) {
     for (int i = 0; i < layout->getNumCompartmentGlyphs(); i++) {
         CompartmentGlyph *compartmentGlyph = layout->getCompartmentGlyph(i);
         if (LIBSBMLNETWORK_CPP_NAMESPACE::getUserData(compartmentGlyph, "locked") == "true") {
@@ -324,7 +329,7 @@ const bool adjustLayoutDimensions(Layout *layout) {
     double widthGap = desiredWidth - layout->getDimensions()->width();
     double desiredHeight = getLayoutDimensionsDesiredHeight(layout);
     double heightGap = desiredHeight - layout->getDimensions()->height();
-    if (widthGap < 0.1 * desiredWidth && heightGap < 0.1 * desiredHeight) {
+    if (widthGap <= 0.1 * desiredWidth && heightGap <= 0.1 * desiredHeight) {
         setLayoutDimensionsDesiredWidth(layout, layout->getDimensions()->width());
         setLayoutDimensionsDesiredHeight(layout, layout->getDimensions()->height());
         return true;

src/autolayout/libsbmlnetwork_autolayout.h

@@ -50,15 +50,15 @@ void setSpeciesGlyphDimensions(Model *model, SpeciesGlyph* speciesGlyph);
 
 void initializeCompartmentGlyphExtents(BoundingBox* compartmentGlyphBoundingBox, BoundingBox* speciesGlyphBoundingBox);
 
-void updateCompartmentExtents(Model *model, Layout *layout);
+void updateCompartmentsExtents(Model *model, Layout *layout);
 
-void updateCompartmentExtentsUsingItsElementsExtents(Model *model, Layout *layout);
+void updateCompartmentsExtentsUsingTheirElementsExtents(Model *model, Layout *layout);
 
 void updateCompartmentExtentsUsingItsElementsExtents(BoundingBox* compartmentGlyphBoundingBox, BoundingBox* speciesGlyphBoundingBox);
 
 void updateCompartmentExtentsUsingItsElementsExtents(BoundingBox* compartmentGlyphBoundingBox, Curve* reactionCurve);
 
-void updateCompartmentExtentsUsingItsPresetAttributes(Layout *layout);
+void updateCompartmentsExtentsUsingTheirPresetAttributes(Layout *layout);
 
 void updateLayoutDimensions(Layout* layout);
 

src/bindings/python/ctypes/libsbmlnetwork.py.cmake

@@ -490,29 +490,44 @@ class LibSBMLNetwork:
         """
         return lib.c_api_makeSpeciesGlyphVisible(self.sbml_object, str(species_id).encode(), str(reaction_id).encode(), visible, reaction_glyph_index, layout_index)
 
-    def makeSpeciesGlyphsVisible(self, species_ids=None, visible=True, layout_index=0):
+    def makeSpeciesGlyphsVisible(self, species=None, visible=True, layout_index=0):
         """
         Makes the SpeciesGlyphs of Species with the given species_ids in the Layout object with the given index in the given SBMLDocument visible or invisible
 
         :Parameters:
 
-            - species_ids (list of strings): a list of strings that determines the ids of the Species
+            - species = (list of lists or list of strings, optional): a list (default: None) that determines the list of Species. The list contains:
+                - a list of lists where each list includes:
+                    - 'id' (str): the ID of the Species
+                    - 'reaction_id' (str): the ID of the Reaction
+                    - 'reaction_glyph_index' (int, optional): the index (default: 0) of the ReactionGlyph in the given SBMLDocument
             - visible = (boolean, optional): a boolean (default: True) that determines whether to make the SpeciesGlyphs visible or invisible
             - layout_index (int, optional): an integer (default: 0) that determines the index of the Layout object in the given SBMLDocument
 
         :Returns:
 
             true on success and false if the SpeciesGlyphs could not be hidden
         """
-        species_ids_ptr = None
-        species_ids_len = 0
-        if species_ids is not None:
-            species_ids_len = len(species_ids)
-            species_ids_ptr = (ctypes.c_char_p * len(species_ids))()
-            for i in range(len(species_ids)):
-                species_ids_ptr[i] = ctypes.c_char_p(species_ids[i].encode())
+        species_ptr = None
+        if species is not None:
+            species_ptr = (ctypes.POINTER(ctypes.c_char_p) * len(species))()
+            for i in range(len(species)):
+                a_species_ptr = (ctypes.c_char_p * 3)()
+                if isinstance(species[i], list):
+                    if len(species[i]) == 3:
+                        print(species[i])
+                        a_species_ptr[0] = ctypes.c_char_p(str(species[i][0]).encode())
+                        a_species_ptr[1] = ctypes.c_char_p(str(species[i][1]).encode())
+                        a_species_ptr[2] = ctypes.c_char_p(str(species[i][2]).encode())
+                    elif len(species[i]) == 2:
+                        a_species_ptr[0] = ctypes.c_char_p(str(species[i][0]).encode())
+                        a_species_ptr[1] = ctypes.c_char_p(str(species[i][1]).encode())
+                        a_species_ptr[2] = ctypes.c_char_p(str(0).encode())
+                else:
+                    raise Exception("The species parameter should be a list of lists with species id, reaction id, and reaction glyph index or a list of lists with species id and reaction id.")
+                species_ptr[i] = a_species_ptr
 
-        return lib.c_api_makeSpeciesGlyphsVisible(self.sbml_object, species_ids_ptr, species_ids_len, visible, layout_index)
+        return lib.c_api_makeSpeciesGlyphsVisible(self.sbml_object, species_ptr, len(species_ptr), visible, layout_index)
 
     def getCanvasWidth(self, layout_index=0):
         """
@@ -9145,6 +9160,42 @@ class LibSBMLNetwork:
         """
         return lib.c_api_removeGeometricShape(self.sbml_object, str(id).encode(), geometric_shape_index, graphical_object_index, layout_index)
 
+    def getGeometricShapeId(self, id, geometric_shape_index=0, graphical_object_index=0, layout_index=0):
+        """
+        Returns the id of the GeometricShape object with the given index associated with the model entity with the given id in the given SBMLDocument
+
+        :Parameters:
+
+            - id (string): a string that determines the id of the model entity
+            - geometric_shape_index (int, optional): an integer (default: 0) that determines the index of the GeometricShape object associated with the model entity with the given id in the given SBMLDocument
+            - graphical_object_index (int, optional): an integer (default: 0) that determines the index of the GraphicalObject in the given SBMLDocument
+            - layout_index (int, optional): an integer (default: 0) that determines the index of the Layout object in the given SBMLDocument
+
+        :Returns:
+
+            a string that determines the id of the GeometricShape object associated with the model entity with the given id in the given SBMLDocument
+        """
+        lib.c_api_getGeometricShapeId.restype = ctypes.c_char_p
+        return ctypes.c_char_p(lib.c_api_getGeometricShapeId(self.sbml_object, str(id).encode(), geometric_shape_index, graphical_object_index, layout_index)).value.decode()
+
+    def setGeometricShapeId(self, id, geometric_shape_id, geometric_shape_index=0, graphical_object_index=0, layout_index=0):
+        """
+        Sets the id of the GeometricShape object with the given index associated with the model entity with the given id in the given SBMLDocument
+
+        :Parameters:
+
+            - id (string): a string that determines the id of the model entity
+            - geometric_shape_id (string): a string that determines the id of the GeometricShape object to be added to the model entity
+            - geometric_shape_index (int, optional): an integer (default: 0) that determines the index of the GeometricShape object associated with the model entity with the given id in the given SBMLDocument
+            - graphical_object_index (int, optional): an integer (default: 0) that determines the index of the GraphicalObject in the given SBMLDocument
+            - layout_index (int, optional): an integer (default: 0) that determines the index of the Layout object in the given SBMLDocument
+
+        :Returns:
+
+                true on success and false if the id of the GeometricShape object could not be set
+            """
+        return lib.c_api_setGeometricShapeId(self.sbml_object, str(id).encode(), str(geometric_shape_id).encode(), geometric_shape_index, graphical_object_index, layout_index)
+
     def getGeometricShapeType(self, id, geometric_shape_index=0, graphical_object_index=0, layout_index=0):
         """
         Returns the type of the GeometricShape object with the given index associated with the model entity with the given id in the given SBMLDocument

src/c_api/libsbmlnetwork_c_api.cpp

@@ -138,12 +138,19 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
         return makeSpeciesGlyphVisible(document, layoutIndex, speciesId, reactionId, reactionGlyphIndex, visible);
     }
 
-    int c_api_makeSpeciesGlyphsVisible(SBMLDocument* document, const char** speciesIds, const int speciesIdsSize, const bool visible, int layoutIndex) {
-        std::set<std::string> speciesIdsSet = std::set<std::string>();
-        for (int i = 0; i < speciesIdsSize; i++)
-            speciesIdsSet.insert(speciesIds[i]);
+    int c_api_makeSpeciesGlyphsVisible(SBMLDocument* document, const char ***species, const int speciesSize, const bool visible, int layoutIndex) {
+        std::set<std::tuple<std::string, std::string, int> > speciesSet = std::set<std::tuple<std::string, std::string, int> >();
+        if (species) {
+            for (int i = 0; i < speciesSize; i++) {
+                const char **aSpecies = species[i];
+                const char *speciesId = aSpecies[0];
+                const char *reactionId = aSpecies[1];
+                int reactionGlyphIndex = atoi(aSpecies[2]);
+                speciesSet.insert(std::make_tuple(speciesId, reactionId, reactionGlyphIndex));
+            }
+        }
 
-        return makeSpeciesGlyphsVisible(document, layoutIndex, speciesIdsSet, visible);
+        return makeSpeciesGlyphsVisible(document, layoutIndex, speciesSet, visible);
     }
 
     double c_api_getCanvasWidth(SBMLDocument* document, int layoutIndex) {
@@ -2422,6 +2429,14 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
         return setGeometricShapeType(document, getGraphicalObject(document, layoutIndex, id, graphicalObjectIndex), shape);
     }
 
+    const char* c_api_getGeometricShapeId(SBMLDocument* document, const char* id, int geometricShapeIndex, int graphicalObjectIndex, int layoutIndex) {
+        return strdup(getGeometricShapeId(document, getGraphicalObject(document, layoutIndex, id, graphicalObjectIndex), geometricShapeIndex).c_str());
+    }
+
+    int c_api_setGeometricShapeId(SBMLDocument* document, const char* id, const char* geometricShapeId, int geometricShapeIndex, int graphicalObjectIndex, int layoutIndex) {
+        return setGeometricShapeId(document, getGraphicalObject(document, layoutIndex, id, graphicalObjectIndex), geometricShapeIndex, geometricShapeId);
+    }
+
     const char* c_api_getCompartmentsGeometricShapeType(SBMLDocument* document) {
         return strdup(getCompartmentGeometricShapeType(document).c_str());
     }

src/c_api/libsbmlnetwork_c_api.h

@@ -163,12 +163,12 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
 
     /// @brief Hide the SpeciesGlyphs with the given species Ids in the Layout object with the given index in the ListOfLayouts of the SBML document.
     /// @param document a pointer to the SBMLDocument object.
-    /// @param speciesIds an array of strings containing the ids of the species to hide the SpeciesGlyphs for.
+    /// @param species an array of strings containing the ids of the species, ids of the reactions, and the indices of the reaction glyphs that the species are participants of.
     /// @param speciesIdsSize the size of speciesIds
     /// @param visible a boolean value to determine whether make SpeciesGlyph visible or invisible.
     /// @param layoutIndex the index number of the Layout to return.
     /// @return integer value indicating success/failure of the function.
-    LIBSBMLNETWORK_EXTERN int c_api_makeSpeciesGlyphsVisible(SBMLDocument* document, const char** speciesIds, const int speciesIdsSize, bool visible = true, int layoutIndex = 0);
+    LIBSBMLNETWORK_EXTERN int c_api_makeSpeciesGlyphsVisible(SBMLDocument* document, const char ***species, const int speciesSize, const bool visible, int layoutIndex);
 
     /// @brief Returns the value of the "width" attribute of the Dimensions object of the Layout object
     /// with the given index in the ListOfLayouts of the SBML document.
@@ -4765,6 +4765,25 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
     /// @return integer value indicating success/failure of the function.
     LIBSBMLNETWORK_EXTERN int c_api_setGeometricShapeType(SBMLDocument* document, const char* id, const char* shape, int graphicalObjectIndex = 0, int layoutIndex = 0);
 
+    /// @brief Returns the id of the geometric shape of the RenderGroup of the Style that matches this id of model entity associated with GraphicalObject.
+    /// @param document a pointer to the SBMLDocument object.
+    /// @param id the id of a model entity.
+    /// @param geometricShapeIndex an int representing the index of the Transformation2D to retrieve.
+    /// @param graphicalObjectIndex the index of the GraphicalObject to return.
+    /// @param layoutIndex the index number of the Layout to return.
+    /// @return the id of the geometric shape of the RenderGroup of the Style for this GraphicalObject, or @c "" if the object is @c NULL
+    LIBSBMLNETWORK_EXTERN const char* c_api_getGeometricShapesId(SBMLDocument* document, const char* id, int geometricShapeIndex = 0, int graphicalObjectIndex = 0, int layoutIndex = 0);
+
+    /// @brief Sets the id of the geometric shape of the RenderGroup of the Style that matches this id of model entity associated with GraphicalObject.
+    /// @param document a pointer to the SBMLDocument object.
+    /// @param id the id of a model entity.
+    /// @param geometricShapeId a string value indicating the id of the geometric shape to be set.
+    /// @param geometricShapeIndex an int representing the index of the Transformation2D to retrieve.
+    /// @param graphicalObjectIndex the index of the GraphicalObject to return.
+    /// @param layoutIndex the index number of the Layout to return.
+    /// @return integer value indicating success/failure of the function.
+    LIBSBMLNETWORK_EXTERN int c_api_setGeometricShapesId(SBMLDocument* document, const char* id, const char* geometricShapeId, int geometricShapeIndex = 0, int graphicalObjectIndex = 0, int layoutIndex = 0);
+
     /// @brief Sets the geometric shape as the single geometric shape of the RenderGroup of the Style of all SpeciesGlyph objects in this Layout object.
     /// @param document a pointer to the SBMLDocument object.
     /// @param shape a string value indicating the shape of the geometric shape to be set.

src/libsbmlnetwork_layout.cpp

@@ -1131,10 +1131,8 @@ Curve* getCurve(GraphicalObject* graphicalObject) {
 }
 
 int removeCurve(GraphicalObject* graphicalObject) {
-    if (isReactionGlyph(graphicalObject)) {
-        removeReactionGlyphCurve((ReactionGlyph *) graphicalObject);
-        return 0;
-    }
+    if (isReactionGlyph(graphicalObject))
+        return removeReactionGlyphCurve((ReactionGlyph*)graphicalObject);
 
     return -1;
 }