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Stoichiometry values are now handled #80

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merged 1 commit into from
Aug 29, 2024
Merged

Stoichiometry values are now handled #80

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29 changes: 20 additions & 9 deletions src/libsbmlnetwork_layout_helpers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -317,18 +317,22 @@ void setReactionGlyphCurve(ReactionGlyph* reactionGlyph) {
void setReactantGlyphs(Layout* layout, Reaction* reaction, ReactionGlyph* reactionGlyph) {
for (unsigned int i = 0; i < reaction->getNumReactants(); i++) {
SimpleSpeciesReference* speciesReference = reaction->getReactant(i);
SpeciesReferenceGlyph* speciesReferenceGlyph = createAssociatedSpeciesReferenceGlyph(layout, reaction, reactionGlyph, speciesReference);
speciesReferenceGlyph->setRole(SPECIES_ROLE_SUBSTRATE);
setSpeciesReferenceGlyphCurve(speciesReferenceGlyph);
for (unsigned int stoichiometryIndex = 0; stoichiometryIndex < getStoichiometryAsInteger(speciesReference); stoichiometryIndex++) {
SpeciesReferenceGlyph* speciesReferenceGlyph = createAssociatedSpeciesReferenceGlyph(layout, reaction, reactionGlyph, speciesReference, stoichiometryIndex);
speciesReferenceGlyph->setRole(SPECIES_ROLE_SUBSTRATE);
setSpeciesReferenceGlyphCurve(speciesReferenceGlyph);
}
}
}

void setProductGlyphs(Layout* layout, Reaction* reaction, ReactionGlyph* reactionGlyph) {
for (unsigned int i = 0; i < reaction->getNumProducts(); i++) {
SimpleSpeciesReference* speciesReference = reaction->getProduct(i);
SpeciesReferenceGlyph* speciesReferenceGlyph = createAssociatedSpeciesReferenceGlyph(layout, reaction, reactionGlyph, speciesReference);
speciesReferenceGlyph->setRole(SPECIES_ROLE_PRODUCT);
setSpeciesReferenceGlyphCurve(speciesReferenceGlyph);
for (unsigned int stoichiometryIndex = 0; stoichiometryIndex < getStoichiometryAsInteger(speciesReference); stoichiometryIndex++) {
SpeciesReferenceGlyph* speciesReferenceGlyph = createAssociatedSpeciesReferenceGlyph(layout, reaction, reactionGlyph, speciesReference, stoichiometryIndex);
speciesReferenceGlyph->setRole(SPECIES_ROLE_PRODUCT);
setSpeciesReferenceGlyphCurve(speciesReferenceGlyph);
}
}
}

Expand Down Expand Up @@ -504,14 +508,14 @@ CompartmentGlyph* getDefaultCompartmentGlyph(Layout* layout) {
return NULL;
}

SpeciesReferenceGlyph* createAssociatedSpeciesReferenceGlyph(Layout* layout, Reaction* reaction, ReactionGlyph* reactionGlyph, SimpleSpeciesReference* speciesReference) {
SpeciesReferenceGlyph* createAssociatedSpeciesReferenceGlyph(Layout* layout, Reaction* reaction, ReactionGlyph* reactionGlyph, SimpleSpeciesReference* speciesReference, unsigned int stoichiometryIndex) {
SpeciesReferenceGlyph* speciesReferenceGlyph = reactionGlyph->createSpeciesReferenceGlyph();
if (!speciesReference->getId().empty()) {
speciesReferenceGlyph->setId(speciesReference->getId() + "_Glyph_1");
speciesReferenceGlyph->setId(speciesReference->getId() + "_Glyph_1" + "_Stoichiometry_" + std::to_string(stoichiometryIndex + 1));
speciesReferenceGlyph->setSpeciesReferenceId(speciesReference->getId());
}
else
speciesReferenceGlyph->setId(speciesReference->getSpecies() + "_Glyph_1_" + reactionGlyph->getId() + "_SpeciesReference" + std::to_string(reactionGlyph->getNumSpeciesReferenceGlyphs()));
speciesReferenceGlyph->setId(speciesReference->getSpecies() + "_Glyph_1_" + reactionGlyph->getId() + "_SpeciesReference" + std::to_string(reactionGlyph->getNumSpeciesReferenceGlyphs()) + "_Stoichiometry_" + std::to_string(stoichiometryIndex + 1));
speciesReferenceGlyph->setSpeciesGlyphId(speciesReference->getSpecies() + "_Glyph_1");

return speciesReferenceGlyph;
Expand Down Expand Up @@ -810,6 +814,13 @@ const bool layoutContainsGlyphs(Layout* layout) {
(layout->getNumReactionGlyphs() > 0);
}

const int getStoichiometryAsInteger(SimpleSpeciesReference* speciesReference) {
if (dynamic_cast<SpeciesReference*>(speciesReference) && ((SpeciesReference*)speciesReference)->isSetStoichiometry())
return int(((SpeciesReference*)speciesReference)->getStoichiometry());
else
return 1;
}

void updateAssociatedTextGlyphsPositionX(Layout* layout, GraphicalObject* graphicalObject, const double& movedDistanceX) {
std::vector<TextGlyph*> textGlyphs = getAssociatedTextGlyphsWithGraphicalObject(layout, graphicalObject);
for (unsigned int i = 0; i < textGlyphs.size(); i++)
Expand Down
4 changes: 3 additions & 1 deletion src/libsbmlnetwork_layout_helpers.h
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ CompartmentGlyph* getCompartmentGlyphOfReactionGlyph(Model* model, Layout* layou

CompartmentGlyph* getDefaultCompartmentGlyph(Layout* layout);

SpeciesReferenceGlyph* createAssociatedSpeciesReferenceGlyph(Layout* layout, Reaction* reaction, ReactionGlyph* reactionGlyph, SimpleSpeciesReference* speciesReference);
SpeciesReferenceGlyph* createAssociatedSpeciesReferenceGlyph(Layout* layout, Reaction* reaction, ReactionGlyph* reactionGlyph, SimpleSpeciesReference* speciesReference, const unsigned int stoichiometryIndex = 0);

const int getNumSpeciesReferencesAssociatedWithSpecies(Reaction* reaction, const std::string& speciesId);

Expand Down Expand Up @@ -198,6 +198,8 @@ const std::string getTextGlyphUniqueId(Layout* layout, GraphicalObject* graphica

const bool layoutContainsGlyphs(Layout* layout);

const int getStoichiometryAsInteger(SimpleSpeciesReference* speciesReference);

void updateAssociatedTextGlyphsPositionX(Layout* layout, GraphicalObject* graphicalObject, const double& movedDistanceX);

void updateAssociatedTextGlyphsPositionY(Layout* layout, GraphicalObject* graphicalObject, const double& movedDistanceY);
Expand Down
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