Merge pull request #11 from sys-bio/fix-bugs-and-add-new-features

fix-bugs-and-add-new-features
sys-bio · Nov 19, 2024 · 06fb807 · 06fb807
2 parents e49f7f0 + c0b7d5f
commit 06fb807
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Showing 13 changed files with 352 additions and 112 deletions.
diff --git a/src/autolayout/libsbmlnetwork_autolayout_node.cpp b/src/autolayout/libsbmlnetwork_autolayout_node.cpp
@@ -168,13 +168,17 @@ GraphicalObject* AutoLayoutCentroidNode::getGraphicalObject() {
 
 void AutoLayoutCentroidNode::updateDimensions() {
     std::string fixedWidth = LIBSBMLNETWORK_CPP_NAMESPACE::getUserData(getGraphicalObject(), "width");
-    if (fixedWidth.empty())
-        setWidth(std::max(calculateWidth(), getWidth()));
+    if (fixedWidth.empty()) {
+        if (!isSetCurve())
+            setWidth(std::max(calculateWidth(), getWidth()));
+    }
     else
         setWidth(std::stod(fixedWidth));
     std::string fixedHeight = LIBSBMLNETWORK_CPP_NAMESPACE::getUserData(getGraphicalObject(), "height");
-    if (fixedHeight.empty())
-        setHeight(std::max(calculateHeight(), getHeight()));
+    if (fixedHeight.empty()) {
+        if (!isSetCurve())
+            setHeight(std::max(calculateHeight(), getHeight()));
+    }
     else
         setHeight(std::stod(fixedHeight));
 }

diff --git a/src/bindings/python/ctypes/libsbmlnetwork.py.cmake b/src/bindings/python/ctypes/libsbmlnetwork.py.cmake
diff --git a/src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/sbmlnetwork.py b/src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/sbmlnetwork.py
@@ -16,12 +16,12 @@ def draw(self, file_name=""):
         :param file_name:
         """
         if file_name:
-            networkinfotranslator.import_sbml_export_figure(self.save(), file_name, self.use_name_as_text_label,
+            networkinfotranslator.import_sbml_export_figure(self, file_name, self.use_name_as_text_label,
                                                             self.display_compartments_text_label,
                                                             self.display_species_text_label,
                                                             self.display_reactions_text_label)
         else:
-            display(networkinfotranslator.import_sbml_export_pil_image(self.save(), self.use_name_as_text_label,
+            display(networkinfotranslator.import_sbml_export_pil_image(self, self.use_name_as_text_label,
                                                                        self.display_compartments_text_label,
                                                                        self.display_species_text_label,
                                                                        self.display_reactions_text_label))

diff --git a/src/c_api/libsbmlnetwork_c_api.cpp b/src/c_api/libsbmlnetwork_c_api.cpp
@@ -353,6 +353,14 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
         return strdup(getSpeciesReferenceSpeciesGlyphId(document, layoutIndex, reactionId, reactionGlyphIndex, speciesReferenceIndex).c_str());
     }
 
+    bool c_api_isSetSpeciesReferenceEmptySpeciesGlyph(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex, int speciesReferenceIndex, int layoutIndex) {
+        return isSetSpeciesReferenceEmptySpeciesGlyph(document, layoutIndex, reactionId, reactionGlyphIndex, speciesReferenceIndex);
+    }
+
+    const char* c_api_getSpeciesReferenceEmptySpeciesGlyphId(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex, int speciesReferenceIndex, int layoutIndex) {
+        return strdup(getSpeciesReferenceEmptySpeciesGlyphId(document, layoutIndex, reactionId, reactionGlyphIndex, speciesReferenceIndex).c_str());
+    }
+
     bool c_api_isSetSpeciesReferenceRole(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex, int speciesReferenceIndex, int layoutIndex) {
         return isSetSpeciesReferenceRole(document, layoutIndex, reactionId, reactionGlyphIndex, speciesReferenceIndex);
     }
@@ -533,76 +541,76 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
         return getPositionX(document, layoutIndex, id, graphicalObjectIndex);
     }
 
-    int c_api_setX(SBMLDocument* document, const char* id, const double x, const int graphicalObjectIndex, int layoutIndex) {
-        return setPositionX(document, layoutIndex, id, graphicalObjectIndex, x);
+    int c_api_setX(SBMLDocument* document, const char* id, const double x, const int graphicalObjectIndex, int layoutIndex, bool updateCurves) {
+        return setPositionX(document, layoutIndex, id, graphicalObjectIndex, x, updateCurves);
     }
 
     const double c_api_getY(SBMLDocument* document, const char* id, const int graphicalObjectIndex, int layoutIndex) {
         return getPositionY(document, layoutIndex, id, graphicalObjectIndex);
     }
 
-    int c_api_setY(SBMLDocument* document, const char* id, const double y, const int graphicalObjectIndex, int layoutIndex) {
-        return setPositionY(document, layoutIndex, id, graphicalObjectIndex, y);
+    int c_api_setY(SBMLDocument* document, const char* id, const double y, const int graphicalObjectIndex, int layoutIndex, bool updateCurves) {
+        return setPositionY(document, layoutIndex, id, graphicalObjectIndex, y, updateCurves);
     }
 
-    int c_api_setPosition(SBMLDocument* document, const char* id, const double x, const double y, const int graphicalObjectIndex, int layoutIndex) {
-        return setPosition(document, layoutIndex, id, graphicalObjectIndex, x, y);
+    int c_api_setPosition(SBMLDocument* document, const char* id, const double x, const double y, const int graphicalObjectIndex, int layoutIndex, bool updateCurves) {
+        return setPosition(document, layoutIndex, id, graphicalObjectIndex, x, y, updateCurves);
     }
 
     const double c_api_getWidth(SBMLDocument* document, const char* id, const int graphicalObjectIndex, int layoutIndex) {
         return getDimensionWidth(document, layoutIndex, id, graphicalObjectIndex);
     }
 
-    int c_api_setWidth(SBMLDocument* document, const char* id, const double width, const int graphicalObjectIndex, int layoutIndex) {
-        return setDimensionWidth(document, layoutIndex, id, graphicalObjectIndex, width);
+    int c_api_setWidth(SBMLDocument* document, const char* id, const double width, const int graphicalObjectIndex, int layoutIndex, bool updateCurves) {
+        return setDimensionWidth(document, layoutIndex, id, graphicalObjectIndex, width, updateCurves);
     }
 
-    int c_api_setCompartmentsWidth(SBMLDocument* document, const double width, int layoutIndex) {
-        return setCompartmentDimensionWidth(document, layoutIndex, width);
+    int c_api_setCompartmentsWidth(SBMLDocument* document, const double width, int layoutIndex, bool updateCurves) {
+        return setCompartmentDimensionWidth(document, layoutIndex, width, updateCurves);
     }
 
     const double c_api_getSpeciesWidth() {
         return getSpeciesDimensionWidth();
     }
 
-    int c_api_setSpeciesWidth(SBMLDocument* document, const double width, int layoutIndex) {
-        return setSpeciesDimensionWidth(document, layoutIndex, width);
+    int c_api_setSpeciesWidth(SBMLDocument* document, const double width, int layoutIndex, bool updateCurves) {
+        return setSpeciesDimensionWidth(document, layoutIndex, width, updateCurves);
     }
 
     const double c_api_getReactionsWidth() {
         return getReactionDimensionWidth();
     }
 
-    int c_api_setReactionsWidth(SBMLDocument* document, const double width, int layoutIndex) {
-        return setReactionDimensionWidth(document, layoutIndex, width);
+    int c_api_setReactionsWidth(SBMLDocument* document, const double width, int layoutIndex, bool updateCurves) {
+        return setReactionDimensionWidth(document, layoutIndex, width, updateCurves);
     }
 
     const double c_api_getHeight(SBMLDocument* document, const char* id, const int graphicalObjectIndex, int layoutIndex) {
         return getDimensionHeight(document, layoutIndex, id, graphicalObjectIndex);
     }
 
-    int c_api_setHeight(SBMLDocument* document, const char* id, const double height, const int graphicalObjectIndex, int layoutIndex) {
-        return setDimensionHeight(document, layoutIndex, id, graphicalObjectIndex, height);
+    int c_api_setHeight(SBMLDocument* document, const char* id, const double height, const int graphicalObjectIndex, int layoutIndex, bool updateCurves) {
+        return setDimensionHeight(document, layoutIndex, id, graphicalObjectIndex, height, updateCurves);
     }
 
-    int c_api_setCompartmentsHeight(SBMLDocument* document, const double height, int layoutIndex) {
-        return setCompartmentDimensionHeight(document, layoutIndex, height);
+    int c_api_setCompartmentsHeight(SBMLDocument* document, const double height, int layoutIndex, bool updateCurves) {
+        return setCompartmentDimensionHeight(document, layoutIndex, height, updateCurves);
     }
 
     const double c_api_getSpeciesHeight() {
         return getSpeciesDimensionHeight();
     }
 
-    int c_api_setSpeciesHeight(SBMLDocument* document, const double height, int layoutIndex) {
-        return setSpeciesDimensionHeight(document, layoutIndex, height);
+    int c_api_setSpeciesHeight(SBMLDocument* document, const double height, int layoutIndex, bool updateCurves) {
+        return setSpeciesDimensionHeight(document, layoutIndex, height, updateCurves);
     }
 
     const double c_api_getReactionsHeight() {
         return getReactionDimensionHeight();
     }
 
-    int c_api_setReactionsHeight(SBMLDocument* document, const double height, int layoutIndex) {
-        return setReactionDimensionHeight(document, layoutIndex, height);
+    int c_api_setReactionsHeight(SBMLDocument* document, const double height, int layoutIndex, bool updateCurves) {
+        return setReactionDimensionHeight(document, layoutIndex, height, updateCurves);
     }
 
     const double c_api_getTextX(SBMLDocument* document, const char* id, const int graphicalObjectIndex, const int textGlyphIndex, int layoutIndex) {