From 4990ae078a562ac50c69f85871464d276241c170 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Tue, 29 Apr 2025 14:03:28 -0700 Subject: [PATCH 1/3] Only call loadPlugins once in constructors. libsbml is leaking memory in the loadPlugins functions, and my working theory is that this is because some constructors call it multiple times: once in the base class, then again in the derived class. This change removes *all* calls of loadPlugins for all derived classes where the base class also calls loadPlugins. I'm not sure why we don't call loadPlugins in the SBase constructor directly, but changing that would be a fairly significant design change, so no need to try it now. I believe that we cannot do the same thing with 'connectToChild', because it becomes important when it's the derived class that overrides the base definition for it, and I *think* that a base class constructor would not call the derived class version. If I'm wrong, we can revisit, but it's also true that connectToChild doesn't leak memory, so it's not dangerous to call it multiple times. 'setElementNamespace' also only needs to be called once, but this is sort of incidental to the other cleanups. I have not yet tested whether this change actually fixes the leak--needed to check this in from my development machine so I could check it out on my valgrind-enabled machine. --- .../packages/distrib/sbml/DistribBase.cpp | 1 + .../packages/distrib/sbml/UncertParameter.cpp | 7 +- src/sbml/packages/distrib/sbml/UncertSpan.cpp | 8 +- .../packages/distrib/sbml/Uncertainty.cpp | 7 +- src/sbml/packages/fbc/sbml/FbcAnd.cpp | 12 +- src/sbml/packages/fbc/sbml/FbcOr.cpp | 12 +- src/sbml/packages/fbc/sbml/GeneProductRef.cpp | 11 +- src/sbml/packages/fbc/sbml/KeyValuePair.cpp | 8 +- .../packages/layout/sbml/CompartmentGlyph.cpp | 39 ++----- src/sbml/packages/layout/sbml/CubicBezier.cpp | 76 +++---------- .../packages/layout/sbml/GeneralGlyph.cpp | 43 ++----- .../packages/layout/sbml/ReactionGlyph.cpp | 43 ++----- .../packages/layout/sbml/ReferenceGlyph.cpp | 27 +---- .../packages/layout/sbml/SpeciesGlyph.cpp | 47 +++----- .../layout/sbml/SpeciesReferenceGlyph.cpp | 27 +---- src/sbml/packages/layout/sbml/TextGlyph.cpp | 45 +++----- src/sbml/packages/render/sbml/Ellipse.cpp | 105 ++++++++---------- .../render/sbml/GlobalRenderInformation.cpp | 21 ++-- src/sbml/packages/render/sbml/GlobalStyle.cpp | 25 +++-- .../packages/render/sbml/GradientBase.cpp | 12 +- .../render/sbml/GraphicalPrimitive1D.cpp | 32 +++--- .../render/sbml/GraphicalPrimitive2D.cpp | 26 +++-- src/sbml/packages/render/sbml/Image.cpp | 19 ++-- src/sbml/packages/render/sbml/LineEnding.cpp | 19 ++-- .../packages/render/sbml/LinearGradient.cpp | 21 ++-- .../render/sbml/LocalRenderInformation.cpp | 21 ++-- src/sbml/packages/render/sbml/LocalStyle.cpp | 25 +++-- src/sbml/packages/render/sbml/Polygon.cpp | 21 ++-- .../packages/render/sbml/RadialGradient.cpp | 21 ++-- src/sbml/packages/render/sbml/Rectangle.cpp | 51 ++++----- .../render/sbml/RenderCubicBezier.cpp | 27 ++--- src/sbml/packages/render/sbml/RenderCurve.cpp | 19 ++-- src/sbml/packages/render/sbml/RenderGroup.cpp | 19 ++-- .../render/sbml/RenderInformationBase.cpp | 12 +- src/sbml/packages/render/sbml/Text.cpp | 21 ++-- .../packages/render/sbml/Transformation2D.cpp | 31 +++--- 36 files changed, 397 insertions(+), 564 deletions(-) diff --git a/src/sbml/packages/distrib/sbml/DistribBase.cpp b/src/sbml/packages/distrib/sbml/DistribBase.cpp index 753f99a86d..d6436acbce 100644 --- a/src/sbml/packages/distrib/sbml/DistribBase.cpp +++ b/src/sbml/packages/distrib/sbml/DistribBase.cpp @@ -80,6 +80,7 @@ DistribBase::DistribBase(DistribPkgNamespaces *distribns) , mElementName("distribBase") { setElementNamespace(distribns->getURI()); + connectToChild(); loadPlugins(distribns); } diff --git a/src/sbml/packages/distrib/sbml/UncertParameter.cpp b/src/sbml/packages/distrib/sbml/UncertParameter.cpp index 9dc4b81c87..474b1f23a2 100644 --- a/src/sbml/packages/distrib/sbml/UncertParameter.cpp +++ b/src/sbml/packages/distrib/sbml/UncertParameter.cpp @@ -95,9 +95,12 @@ UncertParameter::UncertParameter(DistribPkgNamespaces *distribns) , mUncertParameters (new ListOfUncertParameters (distribns)) , mMath (NULL) { - setElementNamespace(distribns->getURI()); connectToChild(); - loadPlugins(distribns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/distrib/sbml/UncertSpan.cpp b/src/sbml/packages/distrib/sbml/UncertSpan.cpp index 99cdc00b5e..d63818660d 100644 --- a/src/sbml/packages/distrib/sbml/UncertSpan.cpp +++ b/src/sbml/packages/distrib/sbml/UncertSpan.cpp @@ -87,8 +87,12 @@ UncertSpan::UncertSpan(DistribPkgNamespaces *distribns) , mValueUpper (util_NaN()) , mIsSetValueUpper (false) { - setElementNamespace(distribns->getURI()); - loadPlugins(distribns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/distrib/sbml/Uncertainty.cpp b/src/sbml/packages/distrib/sbml/Uncertainty.cpp index f2c41bd9c9..35efafe6fb 100644 --- a/src/sbml/packages/distrib/sbml/Uncertainty.cpp +++ b/src/sbml/packages/distrib/sbml/Uncertainty.cpp @@ -80,9 +80,12 @@ Uncertainty::Uncertainty(DistribPkgNamespaces *distribns) : DistribBase(distribns) , mUncertParameters (distribns) { - setElementNamespace(distribns->getURI()); connectToChild(); - loadPlugins(distribns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/fbc/sbml/FbcAnd.cpp b/src/sbml/packages/fbc/sbml/FbcAnd.cpp index b6823c84a4..4a3810535c 100644 --- a/src/sbml/packages/fbc/sbml/FbcAnd.cpp +++ b/src/sbml/packages/fbc/sbml/FbcAnd.cpp @@ -80,14 +80,12 @@ FbcAnd::FbcAnd (FbcPkgNamespaces* fbcns) : FbcAssociation(fbcns) , mAssociations (fbcns) { - // set the element namespace of this object - setElementNamespace(fbcns->getURI()); - - // connect to child objects connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(fbcns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/fbc/sbml/FbcOr.cpp b/src/sbml/packages/fbc/sbml/FbcOr.cpp index 6c27cb888c..427331c96d 100644 --- a/src/sbml/packages/fbc/sbml/FbcOr.cpp +++ b/src/sbml/packages/fbc/sbml/FbcOr.cpp @@ -81,14 +81,12 @@ FbcOr::FbcOr (FbcPkgNamespaces* fbcns) : FbcAssociation(fbcns) , mAssociations (fbcns) { - // set the element namespace of this object - setElementNamespace(fbcns->getURI()); - - // connect to child objects connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(fbcns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/fbc/sbml/GeneProductRef.cpp b/src/sbml/packages/fbc/sbml/GeneProductRef.cpp index 0962d753a7..145d667926 100644 --- a/src/sbml/packages/fbc/sbml/GeneProductRef.cpp +++ b/src/sbml/packages/fbc/sbml/GeneProductRef.cpp @@ -77,11 +77,12 @@ GeneProductRef::GeneProductRef (FbcPkgNamespaces* fbcns) , mGeneProduct ("") // , mName ("") { - // set the element namespace of this object - setElementNamespace(fbcns->getURI()); - - // load package extensions bound with this object (if any) - loadPlugins(fbcns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/fbc/sbml/KeyValuePair.cpp b/src/sbml/packages/fbc/sbml/KeyValuePair.cpp index 38a6489afc..f8ee6c9c7b 100644 --- a/src/sbml/packages/fbc/sbml/KeyValuePair.cpp +++ b/src/sbml/packages/fbc/sbml/KeyValuePair.cpp @@ -76,8 +76,12 @@ KeyValuePair::KeyValuePair(FbcPkgNamespaces *fbcns) , mValue ("") , mUri ("") { - setElementNamespace(fbcns->getURI()); - loadPlugins(fbcns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } diff --git a/src/sbml/packages/layout/sbml/CompartmentGlyph.cpp b/src/sbml/packages/layout/sbml/CompartmentGlyph.cpp index 8191fad820..3147d5ef0b 100644 --- a/src/sbml/packages/layout/sbml/CompartmentGlyph.cpp +++ b/src/sbml/packages/layout/sbml/CompartmentGlyph.cpp @@ -76,8 +76,9 @@ CompartmentGlyph::CompartmentGlyph (unsigned int level, unsigned int version, un , mOrder(numeric_limits::quiet_NaN()) , mIsSetOrder(false) { + connectToChild(); // - // (NOTE) Developers don't have to invoke setSBMLNamespacesAndOwn function as follows (commentted line) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the function is properly invoked in the constructor of the // base class (GraphicalObject). // @@ -91,18 +92,12 @@ CompartmentGlyph::CompartmentGlyph(LayoutPkgNamespaces* layoutns) , mOrder(numeric_limits::quiet_NaN()) , mIsSetOrder(false) { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the // base class (GraphicalObject). // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) - // - loadPlugins(layoutns); } @@ -116,18 +111,12 @@ CompartmentGlyph::CompartmentGlyph (LayoutPkgNamespaces* layoutns, const std::st , mIsSetOrder(false) { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the // base class (GraphicalObject). // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) - // - loadPlugins(layoutns); } /* @@ -141,18 +130,12 @@ CompartmentGlyph::CompartmentGlyph (LayoutPkgNamespaces* layoutns, const std::st , mIsSetOrder(false) { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the // base class (GraphicalObject). // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) - // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/layout/sbml/CubicBezier.cpp b/src/sbml/packages/layout/sbml/CubicBezier.cpp index 3a281b0e73..a32dc4f424 100644 --- a/src/sbml/packages/layout/sbml/CubicBezier.cpp +++ b/src/sbml/packages/layout/sbml/CubicBezier.cpp @@ -101,19 +101,11 @@ CubicBezier::CubicBezier(LayoutPkgNamespaces* layoutns) this->mBasePoint2.setElementName("basePoint2"); connectToChild(); - - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -133,19 +125,11 @@ CubicBezier::CubicBezier (LayoutPkgNamespaces* layoutns, double x1, double y1, d this->mBasePoint2.setElementName("basePoint2"); connectToChild(); - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) - // - loadPlugins(layoutns); } @@ -166,19 +150,11 @@ CubicBezier::CubicBezier (LayoutPkgNamespaces* layoutns, double x1, double y1, d this->mBasePoint2.setElementName("basePoint2"); connectToChild(); - - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* @@ -245,19 +221,11 @@ CubicBezier::CubicBezier (LayoutPkgNamespaces* layoutns, const Point* start, con this->mBasePoint2.setElementName("basePoint2"); connectToChild(); - - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). // - - // setElementNamespace(layoutns->getURI()); - + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - // load package extensions bound with this object (if any) - // - loadPlugins(layoutns); } @@ -285,20 +253,12 @@ CubicBezier::CubicBezier (LayoutPkgNamespaces* layoutns, const Point* start, con this->mEndPoint=Point(layoutns); } - connectToChild(); - - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) - // - loadPlugins(layoutns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). + // } /* diff --git a/src/sbml/packages/layout/sbml/GeneralGlyph.cpp b/src/sbml/packages/layout/sbml/GeneralGlyph.cpp index f0887b309b..58f167ec28 100644 --- a/src/sbml/packages/layout/sbml/GeneralGlyph.cpp +++ b/src/sbml/packages/layout/sbml/GeneralGlyph.cpp @@ -119,21 +119,12 @@ GeneralGlyph::GeneralGlyph(LayoutPkgNamespaces* layoutns) , mCurveExplicitlySet ( false ) { mSubGlyphs.setElementName("listOfSubGlyphs"); - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - connectToChild(); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -150,20 +141,12 @@ GeneralGlyph::GeneralGlyph (LayoutPkgNamespaces* layoutns, const std::string& id { mSubGlyphs.setElementName("listOfSubGlyphs"); - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - connectToChild(); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -182,20 +165,12 @@ GeneralGlyph::GeneralGlyph (LayoutPkgNamespaces* layoutns, const std::string& id { mSubGlyphs.setElementName("listOfSubGlyphs"); - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - connectToChild(); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/layout/sbml/ReactionGlyph.cpp b/src/sbml/packages/layout/sbml/ReactionGlyph.cpp index 8754bfa326..07b34d9649 100644 --- a/src/sbml/packages/layout/sbml/ReactionGlyph.cpp +++ b/src/sbml/packages/layout/sbml/ReactionGlyph.cpp @@ -111,21 +111,12 @@ ReactionGlyph::ReactionGlyph(LayoutPkgNamespaces* layoutns) ,mCurve(layoutns) , mCurveExplicitlySet ( false ) { - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - connectToChild(); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -139,20 +130,12 @@ ReactionGlyph::ReactionGlyph (LayoutPkgNamespaces* layoutns, const std::string& ,mCurve(layoutns) ,mCurveExplicitlySet (false) { - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - connectToChild(); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -168,20 +151,12 @@ ReactionGlyph::ReactionGlyph (LayoutPkgNamespaces* layoutns, const std::string& ,mCurve(layoutns) , mCurveExplicitlySet (false) { - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - connectToChild(); - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/layout/sbml/ReferenceGlyph.cpp b/src/sbml/packages/layout/sbml/ReferenceGlyph.cpp index 1c64e70272..5425a75e7e 100644 --- a/src/sbml/packages/layout/sbml/ReferenceGlyph.cpp +++ b/src/sbml/packages/layout/sbml/ReferenceGlyph.cpp @@ -113,17 +113,10 @@ ReferenceGlyph::ReferenceGlyph(LayoutPkgNamespaces* layoutns) { connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* @@ -148,19 +141,11 @@ ReferenceGlyph::ReferenceGlyph , mCurveExplicitlySet (false) { connectToChild(); - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/layout/sbml/SpeciesGlyph.cpp b/src/sbml/packages/layout/sbml/SpeciesGlyph.cpp index 16189fd515..a28a59b4e3 100644 --- a/src/sbml/packages/layout/sbml/SpeciesGlyph.cpp +++ b/src/sbml/packages/layout/sbml/SpeciesGlyph.cpp @@ -68,13 +68,12 @@ SpeciesGlyph::SpeciesGlyph (unsigned int level, unsigned int version, unsigned i : GraphicalObject(level,version,pkgVersion) , mSpecies("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setSBMLNamespacesAndOwn function as follows (commentted line) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the function is properly invoked in the constructor of the // base class (GraphicalObject). // - - //setSBMLNamespacesAndOwn(new LayoutPkgNamespaces(level,version,pkgVersion)); } @@ -86,18 +85,12 @@ SpeciesGlyph::SpeciesGlyph (LayoutPkgNamespaces* layoutns) : GraphicalObject(layoutns) , mSpecies("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -108,18 +101,12 @@ SpeciesGlyph::SpeciesGlyph (LayoutPkgNamespaces* layoutns, const std::string& si : GraphicalObject(layoutns, sid ) ,mSpecies("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* @@ -131,18 +118,12 @@ SpeciesGlyph::SpeciesGlyph (LayoutPkgNamespaces* layoutns, const std::string& si : GraphicalObject( layoutns, sid ) ,mSpecies ( speciesId ) { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.cpp b/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.cpp index 903711a1cc..1d38588878 100644 --- a/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.cpp +++ b/src/sbml/packages/layout/sbml/SpeciesReferenceGlyph.cpp @@ -127,17 +127,10 @@ SpeciesReferenceGlyph::SpeciesReferenceGlyph(LayoutPkgNamespaces* layoutns) { connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* @@ -162,19 +155,11 @@ SpeciesReferenceGlyph::SpeciesReferenceGlyph ,mCurveExplicitlySet (false) { connectToChild(); - // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/layout/sbml/TextGlyph.cpp b/src/sbml/packages/layout/sbml/TextGlyph.cpp index 154ccb6f9c..c1fd8ce44f 100644 --- a/src/sbml/packages/layout/sbml/TextGlyph.cpp +++ b/src/sbml/packages/layout/sbml/TextGlyph.cpp @@ -76,8 +76,9 @@ TextGlyph::TextGlyph (unsigned int level, unsigned int version, unsigned int pkg ,mGraphicalObject("") ,mOriginOfText("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setSBMLNamespacesAndOwn function as follows (commentted line) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the function is properly invoked in the constructor of the // base class (GraphicalObject). // @@ -96,18 +97,12 @@ TextGlyph::TextGlyph (LayoutPkgNamespaces* layoutns) ,mGraphicalObject("") ,mOriginOfText("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } @@ -120,18 +115,12 @@ TextGlyph::TextGlyph (LayoutPkgNamespaces* layoutns, const std::string& id) ,mGraphicalObject("") ,mOriginOfText("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* @@ -145,18 +134,12 @@ TextGlyph::TextGlyph (LayoutPkgNamespaces* layoutns, const std::string& id, cons ,mGraphicalObject("") ,mOriginOfText("") { + connectToChild(); // - // (NOTE) Developers don't have to invoke setElementNamespace function as follows (commentted line) - // in this constuctor because the function is properly invoked in the constructor of the - // base class (LineSegment). - // - - // setElementNamespace(layoutns->getURI()); - - // - // load package extensions bound with this object (if any) + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GraphicalObject). // - loadPlugins(layoutns); } /* diff --git a/src/sbml/packages/render/sbml/Ellipse.cpp b/src/sbml/packages/render/sbml/Ellipse.cpp index 1e1e56fd8c..6211c6efb8 100644 --- a/src/sbml/packages/render/sbml/Ellipse.cpp +++ b/src/sbml/packages/render/sbml/Ellipse.cpp @@ -107,9 +107,12 @@ Ellipse::Ellipse(RenderPkgNamespaces *renderns) , mRatio (util_NaN()) , mIsSetRatio (false) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -169,14 +172,12 @@ Ellipse::Ellipse(const XMLNode& node, unsigned int l2version) std::cerr << "Warning. Ellipse::Ellipse(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(0.0,0.0); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -209,14 +210,12 @@ Ellipse::Ellipse(RenderPkgNamespaces* renderns, const RelAbsVector& cx,const Rel std::cerr << "Warning. Ellipse::Ellipse(const RelAbsVector& cx,const RelAbsVector& cy,const RelAbsVector& r) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(r,r); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -242,14 +241,12 @@ Ellipse::Ellipse(RenderPkgNamespaces* renderns, const RelAbsVector& cx,const Rel std::cerr << "Warning. Ellipse::Ellipse(const RelAbsVector& cx,const RelAbsVector& cy,const RelAbsVector& rx,const RelAbsVector& ry) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(rx,ry); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -283,14 +280,12 @@ Ellipse::Ellipse(RenderPkgNamespaces* renderns, const RelAbsVector& cx,const Rel std::cerr << "Warning. Ellipse::Ellipse(const RelAbsVector& cx,const RelAbsVector& cy,const RelAbsVector& cz,const RelAbsVector& rx,const RelAbsVector& ry) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(rx,ry); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -323,14 +318,12 @@ Ellipse::Ellipse(RenderPkgNamespaces* renderns, const std::string& id,const RelA std::cerr << "Warning. Ellipse::Ellipse(const std::string& id,const RelAbsVector& cx,const RelAbsVector& cy,const RelAbsVector& r) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(r,r); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -365,14 +358,12 @@ Ellipse::Ellipse(RenderPkgNamespaces* renderns, const std::string& id,const RelA std::cerr << "Warning. Ellipse::Ellipse(const std::string& id,const RelAbsVector& cx,const RelAbsVector& cy,const RelAbsVector& rx,const RelAbsVector& ry) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(rx,ry); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -407,14 +398,12 @@ Ellipse::Ellipse(RenderPkgNamespaces* renderns, const std::string& id,const RelA std::cerr << "Warning. Ellipse::Ellipse(const std::string& id,const RelAbsVector& cx,const RelAbsVector& cy,const RelAbsVector& cz,const RelAbsVector& rx,const RelAbsVector& ry) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setRadii(rx,ry); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/GlobalRenderInformation.cpp b/src/sbml/packages/render/sbml/GlobalRenderInformation.cpp index b36ee7f9c1..0eb6230d13 100644 --- a/src/sbml/packages/render/sbml/GlobalRenderInformation.cpp +++ b/src/sbml/packages/render/sbml/GlobalRenderInformation.cpp @@ -88,9 +88,12 @@ GlobalRenderInformation::GlobalRenderInformation(RenderPkgNamespaces *renderns) : RenderInformationBase(renderns) , mGlobalStyles (renderns) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (RenderInformationBase). + // } @@ -113,14 +116,12 @@ GlobalRenderInformation::GlobalRenderInformation(RenderPkgNamespaces* renderns, #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. GlobalRenderInformation::GlobalRenderInformation(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (RenderInformationBase). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/GlobalStyle.cpp b/src/sbml/packages/render/sbml/GlobalStyle.cpp index 1b97b7706a..877ba1790f 100644 --- a/src/sbml/packages/render/sbml/GlobalStyle.cpp +++ b/src/sbml/packages/render/sbml/GlobalStyle.cpp @@ -80,8 +80,12 @@ GlobalStyle::GlobalStyle(unsigned int level, GlobalStyle::GlobalStyle(RenderPkgNamespaces *renderns) : Style(renderns) { - setElementNamespace(renderns->getURI()); - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Style). + // } @@ -113,19 +117,18 @@ GlobalStyle::GlobalStyle(const XMLNode& node, unsigned int l2version) * constructors which take the SBML level and version or one that takes * an SBMLNamespaces object. */ -GlobalStyle::GlobalStyle(RenderPkgNamespaces* renderns, const std::string& id):Style(renderns,id) +GlobalStyle::GlobalStyle(RenderPkgNamespaces* renderns, const std::string& id) + :Style(renderns,id) { #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. GlobalStyle::GlobalStyle(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Style). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/GradientBase.cpp b/src/sbml/packages/render/sbml/GradientBase.cpp index e16e41423f..4bf94ee8ed 100644 --- a/src/sbml/packages/render/sbml/GradientBase.cpp +++ b/src/sbml/packages/render/sbml/GradientBase.cpp @@ -180,14 +180,14 @@ GradientBase::GradientBase(RenderPkgNamespaces* renderns, const std::string& id) setId(id); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); + // set the element namespace of this object + setElementNamespace(renderns->getURI()); - // connect child elements to this element. - connectToChild(); + // connect child elements to this element. + connectToChild(); - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // load package extensions bound with this object (if any) + loadPlugins(renderns); } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp b/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp index b95c047504..4507ebe3bd 100644 --- a/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp +++ b/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp @@ -95,18 +95,16 @@ GraphicalPrimitive1D::GraphicalPrimitive1D(unsigned int level, */ GraphicalPrimitive1D::GraphicalPrimitive1D(RenderPkgNamespaces *renderns) : Transformation2D(renderns) - , mStroke ("") - ,mStrokeWidth(std::numeric_limits::quiet_NaN()) - , mIsSetStrokeWidth (false) + , mStroke("") + , mStrokeWidth(std::numeric_limits::quiet_NaN()) + , mIsSetStrokeWidth(false) { - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -176,14 +174,12 @@ GraphicalPrimitive1D::GraphicalPrimitive1D(RenderPkgNamespaces* renderns, const #endif // DEPRECATION_WARNINGS setId(id); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp b/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp index 4dda496d6c..24cdc95767 100644 --- a/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp +++ b/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp @@ -96,8 +96,12 @@ GraphicalPrimitive2D::GraphicalPrimitive2D(RenderPkgNamespaces *renderns) , mFill ("") , mFillRule (FILL_RULE_UNSET) { - setElementNamespace(renderns->getURI()); - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -142,21 +146,19 @@ GraphicalPrimitive2D::GraphicalPrimitive2D(const XMLNode& node, unsigned int l2v * an SBMLNamespaces object. */ GraphicalPrimitive2D::GraphicalPrimitive2D(RenderPkgNamespaces* renderns, const std::string& id) - :GraphicalPrimitive1D(renderns, id) + : GraphicalPrimitive1D(renderns, id) , mFill("") - ,mFillRule(GraphicalPrimitive2D::UNSET) + , mFillRule(GraphicalPrimitive2D::UNSET) { #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. GraphicalPrimitive2D::GraphicalPrimitive2D(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/Image.cpp b/src/sbml/packages/render/sbml/Image.cpp index 424030076f..691964be2a 100644 --- a/src/sbml/packages/render/sbml/Image.cpp +++ b/src/sbml/packages/render/sbml/Image.cpp @@ -99,9 +99,12 @@ Image::Image(RenderPkgNamespaces *renderns) ,mHeight(RelAbsVector(0.0,0.0)) ,mHref("") { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ @@ -169,14 +172,12 @@ Image::Image(const XMLNode& node, unsigned int l2version):Transformation2D(node, #endif // DEPRECATION_WARNINGS setId(id); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/LineEnding.cpp b/src/sbml/packages/render/sbml/LineEnding.cpp index aa4f428095..c76c1e59b4 100644 --- a/src/sbml/packages/render/sbml/LineEnding.cpp +++ b/src/sbml/packages/render/sbml/LineEnding.cpp @@ -96,9 +96,12 @@ LineEnding::LineEnding(RenderPkgNamespaces *renderns) { mGroup = new RenderGroup(renderns); mBoundingBox = new BoundingBox(renderns->getLevel(), renderns->getVersion()); - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -188,14 +191,12 @@ LineEnding::LineEnding(RenderPkgNamespaces* renderns, const std::string& id) : #endif // DEPRECATION_WARNINGS setId(id); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/LinearGradient.cpp b/src/sbml/packages/render/sbml/LinearGradient.cpp index 95a48bf329..d908f15d18 100644 --- a/src/sbml/packages/render/sbml/LinearGradient.cpp +++ b/src/sbml/packages/render/sbml/LinearGradient.cpp @@ -98,9 +98,12 @@ LinearGradient::LinearGradient(RenderPkgNamespaces *renderns) ,mY2(RelAbsVector(0.0,100.0)) ,mZ2(RelAbsVector(0.0,100.0)) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GradientBase). + // } /** @cond doxygenLibsbmlInternal */ @@ -152,19 +155,17 @@ LinearGradient::LinearGradient(const XMLNode& node, unsigned int l2version):Grad ,mZ1(RelAbsVector(0.0,0.0)) ,mX2(RelAbsVector(0.0,100.0)) ,mY2(RelAbsVector(0.0,100.0)) - ,mZ2(RelAbsVector(0.0,100.0)) + ,mZ2(RelAbsVector(0.0,100.0)) { #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. LinearGradient::LinearGradient(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GradientBase). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/LocalRenderInformation.cpp b/src/sbml/packages/render/sbml/LocalRenderInformation.cpp index bb94475e8d..83f65b9714 100644 --- a/src/sbml/packages/render/sbml/LocalRenderInformation.cpp +++ b/src/sbml/packages/render/sbml/LocalRenderInformation.cpp @@ -92,9 +92,12 @@ LocalRenderInformation::LocalRenderInformation(RenderPkgNamespaces *renderns) : RenderInformationBase(renderns) , mLocalStyles (renderns) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (RenderInformationBase). + // } @@ -117,14 +120,12 @@ LocalRenderInformation::LocalRenderInformation(RenderPkgNamespaces* renderns, co #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. LocalRenderInformation::LocalRenderInformation(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (RenderInformationBase). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/LocalStyle.cpp b/src/sbml/packages/render/sbml/LocalStyle.cpp index 1d3bc5700f..c993aca44b 100644 --- a/src/sbml/packages/render/sbml/LocalStyle.cpp +++ b/src/sbml/packages/render/sbml/LocalStyle.cpp @@ -87,8 +87,12 @@ LocalStyle::LocalStyle(unsigned int level, LocalStyle::LocalStyle(RenderPkgNamespaces *renderns) : Style(renderns) { - setElementNamespace(renderns->getURI()); - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Style). + // } @@ -130,19 +134,18 @@ LocalStyle::LocalStyle(const XMLNode& node, unsigned int l2version):Style(node, * constructors which take the SBML level and version or one that takes * an SBMLNamespaces object. */ -LocalStyle::LocalStyle(RenderPkgNamespaces* renderns, const std::string& id):Style(renderns,id) +LocalStyle::LocalStyle(RenderPkgNamespaces* renderns, const std::string& id) + :Style(renderns,id) { #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. LocalStyle::LocalStyle(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Style). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/Polygon.cpp b/src/sbml/packages/render/sbml/Polygon.cpp index 35fbfd33f0..76d792f1da 100644 --- a/src/sbml/packages/render/sbml/Polygon.cpp +++ b/src/sbml/packages/render/sbml/Polygon.cpp @@ -94,9 +94,12 @@ Polygon::Polygon(RenderPkgNamespaces *renderns) : GraphicalPrimitive2D(renderns) , mRenderPoints (renderns) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -264,14 +267,12 @@ Polygon::Polygon(RenderPkgNamespaces* renderns, const std::string& id) #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. Polygon::Polygon(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/RadialGradient.cpp b/src/sbml/packages/render/sbml/RadialGradient.cpp index 1eb1bcfcc1..4c505d34fb 100644 --- a/src/sbml/packages/render/sbml/RadialGradient.cpp +++ b/src/sbml/packages/render/sbml/RadialGradient.cpp @@ -100,9 +100,12 @@ RadialGradient::RadialGradient(RenderPkgNamespaces *renderns) ,mFY(RelAbsVector(0.0,50.0)) ,mFZ(RelAbsVector(0.0,50.0)) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GradientBase). + // } @@ -158,14 +161,12 @@ RadialGradient::RadialGradient(RenderPkgNamespaces* renderns, const std::string& #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. RadialGradient::RadialGradient(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (GradientBase). + // } /** @endcond */ /* diff --git a/src/sbml/packages/render/sbml/Rectangle.cpp b/src/sbml/packages/render/sbml/Rectangle.cpp index 45d3c05c7e..0b85008387 100644 --- a/src/sbml/packages/render/sbml/Rectangle.cpp +++ b/src/sbml/packages/render/sbml/Rectangle.cpp @@ -103,9 +103,12 @@ Rectangle::Rectangle (RenderPkgNamespaces* renderns) , mRatio(util_NaN()) , mIsSetRatio(false) { - setElementNamespace(renderns->getURI()); - connectToChild(); - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -171,14 +174,12 @@ Rectangle::Rectangle(RenderPkgNamespaces* renderns, const std::string& id) #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. Rectangle::Rectangle(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -220,14 +221,12 @@ Rectangle::Rectangle(RenderPkgNamespaces* renderns, const std::string& id,const #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. Rectangle::Rectangle(const std::string& id,const RelAbsVector& x,const RelAbsVector& y,const RelAbsVector& z,const RelAbsVector& w,const RelAbsVector& h) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED @@ -267,14 +266,12 @@ Rectangle::Rectangle(RenderPkgNamespaces* renderns, const std::string& id,const #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. Rectangle::Rectangle(const std::string& id,const RelAbsVector& x,const RelAbsVector& y,const RelAbsVector& w,const RelAbsVector& h) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/RenderCubicBezier.cpp b/src/sbml/packages/render/sbml/RenderCubicBezier.cpp index 1f0b160a8c..8a8652fdaf 100644 --- a/src/sbml/packages/render/sbml/RenderCubicBezier.cpp +++ b/src/sbml/packages/render/sbml/RenderCubicBezier.cpp @@ -104,14 +104,12 @@ RenderCubicBezier::RenderCubicBezier (RenderPkgNamespaces* renderns): , mBasePoint2_Y(RelAbsVector(0.0, 0.0)) , mBasePoint2_Z(RelAbsVector(0.0, 0.0)) { - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (RenderPoint). + // } @@ -128,7 +126,8 @@ RenderCubicBezier::RenderCubicBezier (RenderPkgNamespaces* renderns): * @param bp1_y y coordinate of the end point. * @param bp1_z z coordinate of the end point. */ -RenderCubicBezier::RenderCubicBezier (RenderPkgNamespaces* renderns, const RelAbsVector& bp1_x,const RelAbsVector& bp1_y,const RelAbsVector& bp1_z,const RelAbsVector& bp2_x,const RelAbsVector& bp2_y,const RelAbsVector& bp2_z,const RelAbsVector& end_x,const RelAbsVector& end_y,const RelAbsVector& end_z):RenderPoint(renderns, end_x,end_y,end_z), +RenderCubicBezier::RenderCubicBezier (RenderPkgNamespaces* renderns, const RelAbsVector& bp1_x,const RelAbsVector& bp1_y,const RelAbsVector& bp1_z,const RelAbsVector& bp2_x,const RelAbsVector& bp2_y,const RelAbsVector& bp2_z,const RelAbsVector& end_x,const RelAbsVector& end_y,const RelAbsVector& end_z) + :RenderPoint(renderns, end_x,end_y,end_z), mBasePoint1_X(bp1_x), mBasePoint1_Y(bp1_y), mBasePoint1_Z(bp1_z), @@ -136,14 +135,12 @@ RenderCubicBezier::RenderCubicBezier (RenderPkgNamespaces* renderns, const RelAb mBasePoint2_Y(bp2_y), mBasePoint2_Z(bp2_z) { - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (RenderPoint). + // } diff --git a/src/sbml/packages/render/sbml/RenderCurve.cpp b/src/sbml/packages/render/sbml/RenderCurve.cpp index 1acdba1746..cb7b743a27 100644 --- a/src/sbml/packages/render/sbml/RenderCurve.cpp +++ b/src/sbml/packages/render/sbml/RenderCurve.cpp @@ -96,9 +96,12 @@ RenderCurve::RenderCurve(RenderPkgNamespaces *renderns) , mEndHead ("") , mRenderPoints (renderns) { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -149,14 +152,12 @@ RenderCurve::RenderCurve(RenderPkgNamespaces* renderns, const std::string& id) #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. RenderCurve::RenderCurve(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } #endif // OMIT_DEPRECATED /** @endcond */ diff --git a/src/sbml/packages/render/sbml/RenderGroup.cpp b/src/sbml/packages/render/sbml/RenderGroup.cpp index 0c38c30635..af26c08928 100644 --- a/src/sbml/packages/render/sbml/RenderGroup.cpp +++ b/src/sbml/packages/render/sbml/RenderGroup.cpp @@ -118,9 +118,12 @@ RenderGroup::RenderGroup(RenderPkgNamespaces *renderns) , mElements(renderns) , mElementName("g") { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } @@ -251,14 +254,12 @@ RenderGroup::RenderGroup(RenderPkgNamespaces* renderns, const std::string& id) : #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. RenderGroup::RenderGroup(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/RenderInformationBase.cpp b/src/sbml/packages/render/sbml/RenderInformationBase.cpp index 90b5f96410..3d534b589f 100644 --- a/src/sbml/packages/render/sbml/RenderInformationBase.cpp +++ b/src/sbml/packages/render/sbml/RenderInformationBase.cpp @@ -246,14 +246,14 @@ RenderInformationBase::RenderInformationBase(RenderPkgNamespaces* renderns, cons std::cerr << "Warning. RenderInformationBase::RenderInformationBase(const std::string& id) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS setId(id); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); + // set the element namespace of this object + setElementNamespace(renderns->getURI()); - // connect child elements to this element. - connectToChild(); + // connect child elements to this element. + connectToChild(); - // load package extensions bound with this object (if any) - loadPlugins(renderns); + // load package extensions bound with this object (if any) + loadPlugins(renderns); } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/Text.cpp b/src/sbml/packages/render/sbml/Text.cpp index 167a6d75c2..c4f359e063 100644 --- a/src/sbml/packages/render/sbml/Text.cpp +++ b/src/sbml/packages/render/sbml/Text.cpp @@ -105,9 +105,12 @@ Text::Text (RenderPkgNamespaces* renderns) mVTextAnchor(V_TEXTANCHOR_UNSET), mText("") { - setElementNamespace(renderns->getURI()); connectToChild(); - loadPlugins(renderns); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ @@ -187,14 +190,12 @@ Text::Text(RenderPkgNamespaces* renderns, const std::string& id,const RelAbsVect #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. Text::Text(const std::string& id,const RelAbsVector& x,const RelAbsVector& y,const RelAbsVector& z) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED diff --git a/src/sbml/packages/render/sbml/Transformation2D.cpp b/src/sbml/packages/render/sbml/Transformation2D.cpp index a58776d794..1086b263ec 100644 --- a/src/sbml/packages/render/sbml/Transformation2D.cpp +++ b/src/sbml/packages/render/sbml/Transformation2D.cpp @@ -105,14 +105,12 @@ Transformation2D::Transformation2D(RenderPkgNamespaces *renderns) , mElementName("transformation2D") { this->updateMatrix2D(); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /* @@ -190,20 +188,19 @@ Transformation2D::~Transformation2D() /* * Constructor with id and values for the matrix. */ -Transformation2D::Transformation2D(RenderPkgNamespaces* renderns, const double matrix[6]):Transformation(renderns) +Transformation2D::Transformation2D(RenderPkgNamespaces* renderns, const double matrix[6]) + :Transformation(renderns) { #ifdef DEPRECATION_WARNINGS std::cerr << "Warning. Transformation2D::Transformation2D(const double matrix[6]) is deprecated." << std::endl; #endif // DEPRECATION_WARNINGS this->setMatrix2D(matrix); - // set the element namespace of this object - setElementNamespace(renderns->getURI()); - - // connect child elements to this element. - connectToChild(); - - // load package extensions bound with this object (if any) - loadPlugins(renderns); + connectToChild(); + // + // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions + // in this constuctor because the functions are properly invoked in the constructor of the + // base class (Transformation). + // } /** @endcond */ #endif // OMIT_DEPRECATED From 341dce5351705a2b98899dcef1230d10a1ecbb8b Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Wed, 11 Feb 2026 11:36:20 -0800 Subject: [PATCH 2/3] KeyValuePair is not actually a subclass of Transformation. --- src/sbml/packages/fbc/sbml/KeyValuePair.cpp | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/sbml/packages/fbc/sbml/KeyValuePair.cpp b/src/sbml/packages/fbc/sbml/KeyValuePair.cpp index f8ee6c9c7b..cf4fc73a3f 100644 --- a/src/sbml/packages/fbc/sbml/KeyValuePair.cpp +++ b/src/sbml/packages/fbc/sbml/KeyValuePair.cpp @@ -76,12 +76,9 @@ KeyValuePair::KeyValuePair(FbcPkgNamespaces *fbcns) , mValue ("") , mUri ("") { + setElementNamespace(fbcns->getURI()); connectToChild(); - // - // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions - // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). - // + loadPlugins(fbcns); } From 7d327210606d6120b87ae321bed9213a85ae18a9 Mon Sep 17 00:00:00 2001 From: Lucian Smith Date: Wed, 11 Feb 2026 12:24:37 -0800 Subject: [PATCH 3/3] Fix comments. --- src/sbml/packages/distrib/sbml/UncertParameter.cpp | 2 +- src/sbml/packages/distrib/sbml/UncertSpan.cpp | 2 +- src/sbml/packages/distrib/sbml/Uncertainty.cpp | 2 +- src/sbml/packages/fbc/sbml/FbcAnd.cpp | 2 +- src/sbml/packages/fbc/sbml/FbcOr.cpp | 2 +- src/sbml/packages/fbc/sbml/GeneProductRef.cpp | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/sbml/packages/distrib/sbml/UncertParameter.cpp b/src/sbml/packages/distrib/sbml/UncertParameter.cpp index 474b1f23a2..58b4811e98 100644 --- a/src/sbml/packages/distrib/sbml/UncertParameter.cpp +++ b/src/sbml/packages/distrib/sbml/UncertParameter.cpp @@ -99,7 +99,7 @@ UncertParameter::UncertParameter(DistribPkgNamespaces *distribns) // // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). + // base class (DistribBase). // } diff --git a/src/sbml/packages/distrib/sbml/UncertSpan.cpp b/src/sbml/packages/distrib/sbml/UncertSpan.cpp index d63818660d..4c2282eec5 100644 --- a/src/sbml/packages/distrib/sbml/UncertSpan.cpp +++ b/src/sbml/packages/distrib/sbml/UncertSpan.cpp @@ -91,7 +91,7 @@ UncertSpan::UncertSpan(DistribPkgNamespaces *distribns) // // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). + // base class (UncertParameter). // } diff --git a/src/sbml/packages/distrib/sbml/Uncertainty.cpp b/src/sbml/packages/distrib/sbml/Uncertainty.cpp index 35efafe6fb..8859482e49 100644 --- a/src/sbml/packages/distrib/sbml/Uncertainty.cpp +++ b/src/sbml/packages/distrib/sbml/Uncertainty.cpp @@ -84,7 +84,7 @@ Uncertainty::Uncertainty(DistribPkgNamespaces *distribns) // // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). + // base class (DistribBase). // } diff --git a/src/sbml/packages/fbc/sbml/FbcAnd.cpp b/src/sbml/packages/fbc/sbml/FbcAnd.cpp index 4a3810535c..1d41d4cb24 100644 --- a/src/sbml/packages/fbc/sbml/FbcAnd.cpp +++ b/src/sbml/packages/fbc/sbml/FbcAnd.cpp @@ -84,7 +84,7 @@ FbcAnd::FbcAnd (FbcPkgNamespaces* fbcns) // // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). + // base class (FbcAssociation). // } diff --git a/src/sbml/packages/fbc/sbml/FbcOr.cpp b/src/sbml/packages/fbc/sbml/FbcOr.cpp index 427331c96d..578c77d812 100644 --- a/src/sbml/packages/fbc/sbml/FbcOr.cpp +++ b/src/sbml/packages/fbc/sbml/FbcOr.cpp @@ -85,7 +85,7 @@ FbcOr::FbcOr (FbcPkgNamespaces* fbcns) // // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). + // base class (FbcAssociation). // } diff --git a/src/sbml/packages/fbc/sbml/GeneProductRef.cpp b/src/sbml/packages/fbc/sbml/GeneProductRef.cpp index 145d667926..350e7b0ad1 100644 --- a/src/sbml/packages/fbc/sbml/GeneProductRef.cpp +++ b/src/sbml/packages/fbc/sbml/GeneProductRef.cpp @@ -81,7 +81,7 @@ GeneProductRef::GeneProductRef (FbcPkgNamespaces* fbcns) // // (NOTE) Developers don't have to invoke setElementNamespace or loadPlugins functions // in this constuctor because the functions are properly invoked in the constructor of the - // base class (Transformation). + // base class (FbcAssociation). // }