set layout features and update curves are extracted as features

sys-bio · Nov 20, 2024 · c371fe5 · c371fe5
1 parent b290301
commit c371fe5
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Showing 10 changed files with 604 additions and 523 deletions.
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -32,6 +32,8 @@ set(SOURCES
 		features/align_elements/libsbmlnetwork_align_species.cpp
 		features/fix_elements/libsbmlnetwork_fix_element_position.cpp
 		features/fix_elements/libsbmlnetwork_fix_element_dimensions.cpp
+		features/set_layout_features/libsbmlnetwork_set_layout_features.cpp
+		features/update_curves/libsbmlnetwork_update_curves.cpp
         c_api/libsbmlnetwork_c_api.cpp)
 
 ## headers
@@ -66,6 +68,8 @@ set(HEADERS
 		features/align_elements/libsbmlnetwork_align_species.h
 		features/fix_elements/libsbmlnetwork_fix_element_position.h
 		features/fix_elements/libsbmlnetwork_fix_element_dimensions.h
+		features/set_layout_features/libsbmlnetwork_set_layout_features.h
+		features/update_curves/libsbmlnetwork_update_curves.h
 		c_api/libsbmlnetwork_c_api.h)
 
 #### dependencies

diff --git a/src/features/alias_elements/libsbmlnetwork_alias_reaction.cpp b/src/features/alias_elements/libsbmlnetwork_alias_reaction.cpp
@@ -1,6 +1,7 @@
 #include "libsbmlnetwork_alias_reaction.h"
 #include "../../libsbmlnetwork_layout.h"
 #include "../../libsbmlnetwork_layout_helpers.h"
+#include "../../features/set_layout_features/libsbmlnetwork_set_layout_features.h"
 #include "../../features/alias_elements/libsbmlnetwork_alias_element.h"
 #include "../../features/alias_elements/libsbmlnetwork_alias_species.h"
 #include "../../features/defaults/libsbmlnetwork_defaults_layout.h"
@@ -19,7 +20,7 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
     ReactionGlyph* alias_element_createAliasReactionGlyph(Layout* layout, ReactionGlyph* reactionGlyph) {
         ReactionGlyph* aliasReactionGlyph = NULL;
         if (reactionGlyph) {
-            aliasReactionGlyph = createReactionGlyph(layout, reactionGlyph->getReactionId());
+            aliasReactionGlyph = set_layout_features_createReactionGlyph(layout, reactionGlyph->getReactionId());
             alias_element_setAliasGraphicalObjectPosition(aliasReactionGlyph, reactionGlyph, defaults_getAliasReactionGlyphPadding());
             alias_element_setAliasReactionGlyphTextGlyph(layout, aliasReactionGlyph, reactionGlyph);
         }
@@ -62,9 +63,9 @@ namespace LIBSBMLNETWORK_CPP_NAMESPACE {
     }
 
     SpeciesReferenceGlyph* alias_element_createAliasSpeciesReferenceGlyph(ReactionGlyph* reactionGlyph, SpeciesReferenceGlyph* referenceSpeciesReferenceGlyph, const std::string& speciesGlyphId, unsigned int stoichiometryIndex) {
-        SpeciesReferenceGlyph* aliasSpeciesReferenceGlyph = createSpeciesReferenceGlyph(reactionGlyph, speciesGlyphId, stoichiometryIndex);
+        SpeciesReferenceGlyph* aliasSpeciesReferenceGlyph = set_layout_features_createSpeciesReferenceGlyph(reactionGlyph, speciesGlyphId, stoichiometryIndex);
         aliasSpeciesReferenceGlyph->setRole(referenceSpeciesReferenceGlyph->getRole());
-        setSpeciesReferenceGlyphCurve(aliasSpeciesReferenceGlyph, referenceSpeciesReferenceGlyph);
+        set_layout_features_setSpeciesReferenceGlyphCurve(aliasSpeciesReferenceGlyph, referenceSpeciesReferenceGlyph);
         return aliasSpeciesReferenceGlyph;
     }
 

diff --git a/src/features/alias_elements/libsbmlnetwork_alias_species.cpp b/src/features/alias_elements/libsbmlnetwork_alias_species.cpp
@@ -1,6 +1,7 @@
 #include "libsbmlnetwork_alias_species.h"
 #include "../../libsbmlnetwork_layout.h"
 #include "../../libsbmlnetwork_layout_helpers.h"
+#include "../../features/set_layout_features/libsbmlnetwork_set_layout_features.h"
 #include "../../features/alias_elements/libsbmlnetwork_alias_element.h"
 #include "../../features/defaults/libsbmlnetwork_defaults_layout.h"
 
@@ -26,7 +27,7 @@ int alias_element_createAliasSpeciesGlyph(Layout* layout, const std::string spec
 SpeciesGlyph* alias_element_createAliasSpeciesGlyph(Layout* layout, SpeciesGlyph* speciesGlyph) {
     SpeciesGlyph* aliasSpeciesGlyph = NULL;
     if (speciesGlyph) {
-        aliasSpeciesGlyph = createSpeciesGlyph(layout, speciesGlyph->getSpeciesId());
+        aliasSpeciesGlyph = set_layout_features_createSpeciesGlyph(layout, speciesGlyph->getSpeciesId());
         alias_element_setAliasGraphicalObjectPosition(aliasSpeciesGlyph, speciesGlyph, defaults_getAliasSpeciesGlyphPadding());
         alias_element_setAliasSpeciesGlyphDimensions(aliasSpeciesGlyph, speciesGlyph);
         alias_element_setAliasSpeciesGlyphTextGlyph(layout, aliasSpeciesGlyph);
@@ -38,7 +39,7 @@ SpeciesGlyph* alias_element_createAliasSpeciesGlyph(Layout* layout, SpeciesGlyph
 SpeciesGlyph* alias_element_createAliasSpeciesGlyph(Layout* layout, const std::string& speciesId, std::vector<SpeciesReferenceGlyph*> speciesGlyphReferences) {
     SpeciesGlyph* aliasSpeciesGlyph = NULL;
     if (speciesGlyphReferences.size()) {
-        aliasSpeciesGlyph = createSpeciesGlyph(layout, speciesId);
+        aliasSpeciesGlyph = set_layout_features_createSpeciesGlyph(layout, speciesId);
         while (speciesGlyphReferences.size()) {
             SpeciesReferenceGlyph* speciesReferenceGlyph = speciesGlyphReferences.back();
             speciesReferenceGlyph->setId(getIdOfSpeciesReferenceGlyphConnectedToNewSpeciesGlyph(speciesReferenceGlyph->getId(), speciesReferenceGlyph->getSpeciesGlyphId(), aliasSpeciesGlyph->getId()));
@@ -53,7 +54,7 @@ SpeciesGlyph* alias_element_createAliasSpeciesGlyph(Layout* layout, const std::s
 const bool alias_element_canHaveAlias(Layout* layout, std::vector<SpeciesReferenceGlyph*> connectedSpeciesGlyphReferencesOfReactionGlyph) {
     if (connectedSpeciesGlyphReferencesOfReactionGlyph.size()) {
         SpeciesGlyph* speciesGlyph = layout->getSpeciesGlyph(connectedSpeciesGlyphReferencesOfReactionGlyph.at(0)->getSpeciesGlyphId());
-        std::vector<SpeciesReferenceGlyph*> connectedSpeciesGlyphReferencesOfSpeciesGlyph = getConnectedSpeciesGlyphReferences(layout, speciesGlyph);
+        std::vector<SpeciesReferenceGlyph*> connectedSpeciesGlyphReferencesOfSpeciesGlyph = set_layout_features_getConnectedSpeciesGlyphReferences(layout, speciesGlyph);
         if (connectedSpeciesGlyphReferencesOfSpeciesGlyph.size() > connectedSpeciesGlyphReferencesOfReactionGlyph.size())
             return true;
     }