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Merge pull request #17 from sys-bio/add-features-fix-bugs
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Add features/ Fix bugs
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@adelhpour
adelhpour authored Dec 3, 2024
2 parents 49968b9 + 56d0dda commit 1dd539e
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Showing 47 changed files with 4,947 additions and 1,658 deletions.
72 changes: 36 additions & 36 deletions docs/api_reference/c_api_index.rst
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24 changes: 12 additions & 12 deletions docs/api_reference/cpp_api_index.rst
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Expand Up @@ -55,19 +55,19 @@ SBMLDocument Functions

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumCompartments(SBMLDocument* document)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthCompartmentId(SBMLDocument* document, unsigned int index)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getCompartmentId(SBMLDocument* document, unsigned int index)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getCompartment(SBMLDocument* document, const std::string& id)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumSpecies(SBMLDocument* document)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthSpeciesId(SBMLDocument* document, unsigned int index)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getSpeciesId(SBMLDocument* document, unsigned int index)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getSpecies(SBMLDocument* document, const std::string& id)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumReactions(SBMLDocument* document)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthReactionId(SBMLDocument* document, unsigned int index)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getReactionId(SBMLDocument* document, unsigned int index)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getReaction(SBMLDocument* document, const std::string& id)

Expand All @@ -79,11 +79,11 @@ SBMLDocument Functions

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumModifiers(SBMLDocument* document, const std::string& reactionId)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthReactantId(SBMLDocument* document, const std::string& reactionId, unsigned int index)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getReactantId(SBMLDocument* document, const std::string& reactionId, unsigned int index)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthProductId(SBMLDocument* document, const std::string& reactionId, unsigned int index)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getProductId(SBMLDocument* document, const std::string& reactionId, unsigned int index)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthModifierId(SBMLDocument* document, const std::string& reactionId, unsigned int index)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getModifierId(SBMLDocument* document, const std::string& reactionId, unsigned int index)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getSpeciesReference(SBMLDocument* document, const std::string& reactionId, const std::string& speciesId)

Expand Down Expand Up @@ -798,11 +798,11 @@ Render Functions

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumGlobalColorDefinitions(SBMLDocument* document, unsigned int renderIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthGlobalColorDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int colorIndex = 0)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getGlobalColorDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int colorIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumLocalColorDefinitions(SBMLDocument* document, unsigned int renderIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthLocalColorDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int colorIndex = 0)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getLocalColorDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int colorIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getColorDefinition(SBMLDocument* document, const std::string& sid)

Expand All @@ -826,9 +826,9 @@ Render Functions

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumLocalGradientDefinitions(SBMLDocument* document, unsigned int renderIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthGlobalGradientDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int gradientIndex = 0)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getGlobalGradientDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int gradientIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthLocalGradientDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int gradientIndex = 0)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getLocalGradientDefinitionId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int gradientIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getGradientDefinition(SBMLDocument* document, const std::string& sid)

Expand Down Expand Up @@ -1092,9 +1092,9 @@ Render Functions

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNumLocalLineEndings(SBMLDocument* document, unsigned int renderIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthGlobalLineEndingId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int lineEndingIndex = 0)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getGlobalLineEndingId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int lineEndingIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getNthLocalLineEndingId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int lineEndingIndex = 0)
.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getLocalLineEndingId(SBMLDocument* document, unsigned int renderIndex = 0, unsigned int lineEndingIndex = 0)

.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getLineEnding(SBMLDocument* document, const std::string& sid)

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4 changes: 2 additions & 2 deletions src/CMakeLists.txt
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Expand Up @@ -27,7 +27,7 @@ set(SOURCES
features/alias_elements/libsbmlnetwork_alias_element.cpp
features/alias_elements/libsbmlnetwork_alias_species.cpp
features/alias_elements/libsbmlnetwork_alias_reaction.cpp
features/hide_elements/libsbmlnetwork_hide_species.cpp
features/hide_elements/libsbmlnetwork_hide_elements.cpp
features/align_elements/libsbmlnetwork_align_element.cpp
features/align_elements/libsbmlnetwork_align_species.cpp
features/fix_elements/libsbmlnetwork_fix_element_position.cpp
Expand Down Expand Up @@ -63,7 +63,7 @@ set(HEADERS
features/alias_elements/libsbmlnetwork_alias_element.h
features/alias_elements/libsbmlnetwork_alias_species.h
features/alias_elements/libsbmlnetwork_alias_reaction.h
features/hide_elements/libsbmlnetwork_hide_species.h
features/hide_elements/libsbmlnetwork_hide_elements.h
features/align_elements/libsbmlnetwork_align_element.h
features/align_elements/libsbmlnetwork_align_species.h
features/fix_elements/libsbmlnetwork_fix_element_position.h
Expand Down
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