Modify 'makeSpeciesGlyphsVisible' function to receive a list of speci…

…es id, reaction id, and reaction glyph index as its input

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):
         """

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) {

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.

src/libsbmlnetwork_layout_helpers.cpp

@@ -655,17 +655,12 @@ int setSpeciesGlyphIndexInReactionGlyph(Layout* layout, const std::string specie
     return -1;
 }
 
-int makeSpeciesGlyphsVisible(Model* model, Layout* layout, std::set<std::string> speciesIds, bool visible) {
-    if (!speciesIds.size()) {
-        for (unsigned int i = 0; i < model->getNumSpecies(); i++)
-            speciesIds.insert(model->getSpecies(i)->getId());
+int makeSpeciesGlyphsVisible(Model* model, Layout* layout, std::set<std::tuple<std::string, std::string, int> > species, bool visible) {
+    for (std::set<std::tuple<std::string, std::string, int> >::const_iterator speciesIt = species.cbegin(); speciesIt != species.cend(); speciesIt++) {
+        if (makeSpeciesGlyphVisible(getReactionGlyph(layout, std::get<1>(*speciesIt), std::get<2>(*speciesIt)), std::get<0>(*speciesIt), visible))
+            return -1;
     }
 
-    if (!visible)
-        hideSpeciesGlyphs(layout, speciesIds);
-    else
-        unHideSpeciesGlyphs(layout, speciesIds);
-
     return 0;
 }
 
@@ -676,28 +671,6 @@ int makeSpeciesGlyphVisible(ReactionGlyph* reactionGlyph, const std::string spec
         return unHideSpeciesGlyph(reactionGlyph, speciesId);
 }
 
-int hideSpeciesGlyphs(Layout* layout, std::set<std::string> speciesIds) {
-    for (std::set<std::string>::const_iterator speciesIdsIt = speciesIds.cbegin(); speciesIdsIt != speciesIds.cend(); speciesIdsIt++) {
-        if (hideSpeciesGlyph(layout, *speciesIdsIt))
-            return -1;
-    }
-
-    return 0;
-}
-
-int unHideSpeciesGlyphs(Layout* layout, std::set<std::string> speciesIds) {
-    for (std::set<std::string>::const_iterator speciesIdsIt = speciesIds.cbegin(); speciesIdsIt != speciesIds.cend(); speciesIdsIt++) {
-        if (unHideSpeciesGlyph(layout, *speciesIdsIt))
-            return -1;
-        for (unsigned int i = 0; i < layout->getNumReactionGlyphs(); i++) {
-            ReactionGlyph* reactionGlyph = layout->getReactionGlyph(i);
-            makeSpeciesGlyphVisible(reactionGlyph, *speciesIdsIt, true);
-        }
-    }
-
-    return 0;
-}
-
 int hideSpeciesGlyph(SBase* sBase, const std::string speciesId) {
     if (sBase) {
         std::string hiddenSpeciesIds = getUserData(sBase, "hidden_species_ids");

src/libsbmlnetwork_layout_helpers.h

@@ -136,14 +136,10 @@ SpeciesGlyph* getSpeciesGlyph(Layout* layout, const std::string& speciesId, cons
 
 int setSpeciesGlyphIndexInReactionGlyph(Layout* layout, const std::string speciesId, ReactionGlyph* reactionGlyph, const unsigned int index);
 
-int makeSpeciesGlyphsVisible(Model* model, Layout* layout, std::set<std::string> speciesIds, bool visible = true);
+int makeSpeciesGlyphsVisible(Model* model, Layout* layout, std::set<std::tuple<std::string, std::string, int> > species, bool visible = true);
 
 int makeSpeciesGlyphVisible(ReactionGlyph* reactionGlyph, const std::string speciesId, bool visible = true);
 
-int hideSpeciesGlyphs(Layout* layout, std::set<std::string> speciesIds);
-
-int unHideSpeciesGlyphs(Layout* layout, std::set<std::string> speciesIds);
-
 int hideSpeciesGlyph(SBase* sBase, const std::string speciesId);
 
 int unHideSpeciesGlyph(SBase* sBase, const std::string speciesId);

src/libsbmlnetwork_sbmldocument_layout.cpp

@@ -190,19 +190,19 @@ int makeSpeciesGlyphVisible(SBMLDocument* document, unsigned int layoutIndex, co
     return -1;
 }
 
-int makeSpeciesGlyphsVisible(SBMLDocument* document, const std::set<std::string>& speciesIds, bool visible) {
+int makeSpeciesGlyphsVisible(SBMLDocument* document, const std::set<std::tuple<std::string, std::string, int> >& species, bool visible) {
     if (document && document->isSetModel()) {
-        if (!makeSpeciesGlyphsVisible(document->getModel(), getLayout(document), speciesIds, visible))
+        if (!makeSpeciesGlyphsVisible(document->getModel(), getLayout(document), species, visible))
             return setDefaultLayoutLocations(document, getLayout(document));
     }
 
 
     return -1;
 }
 
-int makeSpeciesGlyphsVisible(SBMLDocument* document, unsigned int layoutIndex, const std::set<std::string>& speciesIds, bool visible) {
+int makeSpeciesGlyphsVisible(SBMLDocument* document, unsigned int layoutIndex, const std::set<std::tuple<std::string, std::string, int> >& species, bool visible) {
     if (document && document->isSetModel()) {
-        if (!makeSpeciesGlyphsVisible(document->getModel(), getLayout(document, layoutIndex), speciesIds, visible))
+        if (!makeSpeciesGlyphsVisible(document->getModel(), getLayout(document, layoutIndex), species, visible))
             return setDefaultLayoutLocations(document, getLayout(document, layoutIndex));
     }
 

src/libsbmlnetwork_sbmldocument_layout.h

@@ -167,18 +167,18 @@ LIBSBMLNETWORK_EXTERN int makeSpeciesGlyphVisible(SBMLDocument* document, unsign
 
 /// @brief Makes the Species Glyph with the given species Id which is a participant of the reaction with the given Id and index in the first Layout object in the ListOfLayouts of the SBML document visible or invisible.
 /// @param document a pointer to the SBMLDocument object.
-/// @param speciesIds a set of the ids of the Species to hide/show.
+/// @param species a set of tuples of the ids of the Species, the id of the Reaction, and the index of the ReactionGlyph object to hide/show the SpeciesGlyph for.
 /// @param visible a boolean value to determine whether to make the SpeciesGlyph visible or invisible.
 /// @return integer value indicating success/failure of the function.
-LIBSBMLNETWORK_EXTERN int makeSpeciesGlyphsVisible(SBMLDocument* document, const std::set<std::string>& speciesIds, bool visible);
+LIBSBMLNETWORK_EXTERN int makeSpeciesGlyphsVisible(SBMLDocument* document, const std::set<std::tuple<std::string, std::string, int> >& species, bool visible);
 
 /// @brief Makes the Species Glyph with the given species Id which is a participant of the reaction with the given Id and index in the Layout object with the given index in the ListOfLayouts of the SBML document visible or invisible.
 /// @param document a pointer to the SBMLDocument object.
 /// @param layoutIndex the index number of the Layout to return.
-/// @param speciesIds a set of the ids of the Species to hide/show.
+/// @param species a set of tuples of the ids of the Species, the id of the Reaction, and the index of the ReactionGlyph object to hide/show the SpeciesGlyph for.
 /// @param visible a boolean value to determine whether to make the SpeciesGlyph visible or invisible.
 /// @return integer value indicating success/failure of the function.
-LIBSBMLNETWORK_EXTERN int makeSpeciesGlyphsVisible(SBMLDocument* document, unsigned int layoutIndex, const std::set<std::string>& speciesIds, bool visible);
+LIBSBMLNETWORK_EXTERN int makeSpeciesGlyphsVisible(SBMLDocument* document, unsigned int layoutIndex, const std::set<std::tuple<std::string, std::string, int> >& species, bool visible);
 
 /// @brief Returns the Dimensions object of the Layout object with the given index in the ListOfLayouts of the SBML document.
 /// @param document a pointer to the SBMLDocument object.