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Add features/ Fix bugs #17

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merged 10 commits into from
Dec 3, 2024
Merged

Add features/ Fix bugs #17

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2432691
- API functions to handle to work with the geometric shapes of line e…
adelhpour Nov 23, 2024
a8174d2
Hide elements feature is modified
adelhpour Nov 27, 2024
f1568d0
use_name_as_text_label is now stored in the Layout object user data a…
adelhpour Nov 27, 2024
e4cce28
Fix the issue with creating reaction alias glyphs
adelhpour Nov 27, 2024
1cf10db
Nth from the function names.
adelhpour Nov 27, 2024
883b6a1
The feature to set/get the id of each graphical object is added (now …
adelhpour Nov 28, 2024
a2c04cd
Fix the issue with padding while creating multiple alias reaction glyphs
adelhpour Nov 28, 2024
aebd51c
Minor bug fix to pass 'layoutIndex' to 'getReactionGlyph' functions.
adelhpour Nov 28, 2024
833f7f6
Add the api functions to add/remove additional graphical objects to t…
adelhpour Dec 2, 2024
56d0dda
replace function name 'getCompartmentId' in the tests with its new 'g…
adelhpour Dec 2, 2024
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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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Original file line number Diff line number Diff line change
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)

Expand Down
4 changes: 2 additions & 2 deletions src/CMakeLists.txt
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Original file line number Diff line number Diff line change
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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