Allow FBC objects to be used in both L3v1 and L3v2 core documents.

Fixes #360

src/sbml/packages/fbc/extension/FbcModelPlugin.cpp

@@ -656,10 +656,6 @@ int
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != bound->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != bound->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;
@@ -907,10 +903,6 @@ FbcModelPlugin::addObjective(const Objective* o)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != o->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != o->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;
@@ -1087,10 +1079,6 @@ FbcModelPlugin::addGeneProduct(const GeneProduct* gp)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != gp->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != gp->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;
@@ -1309,10 +1297,6 @@ int
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != association->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != association->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;
@@ -1534,10 +1518,6 @@ FbcModelPlugin::addUserDefinedConstraint(const UserDefinedConstraint* udc)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != udc->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != udc->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;

src/sbml/packages/fbc/extension/FbcReactionPlugin.cpp

@@ -422,10 +422,6 @@ FbcReactionPlugin::setGeneProductAssociation(const GeneProductAssociation* geneP
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != geneProductAssociation->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != geneProductAssociation->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;

src/sbml/packages/fbc/extension/FbcSBasePlugin.cpp

@@ -190,10 +190,6 @@ FbcSBasePlugin::addKeyValuePair(const KeyValuePair* kvp)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != kvp->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != kvp->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;

src/sbml/packages/fbc/sbml/Association.cpp

@@ -620,7 +620,7 @@ Association::readAttributes (const XMLAttributes& attributes,
     logEmptyString(mReference, sbmlLevel, sbmlVersion, "<gene>");
   }
   if (!SyntaxChecker::isValidSBMLSId(mReference)) 
-    logError(InvalidIdSyntax, getLevel(), getVersion(), 
+    logError(InvalidIdSyntax, sbmlLevel, sbmlVersion,
     "The syntax of the attribute reference='" + mReference + "' does not conform.");
 
 }

src/sbml/packages/fbc/sbml/FbcAnd.cpp

@@ -242,10 +242,6 @@ FbcAnd::addAssociation(const FbcAssociation* fa)
   {
     return LIBSBML_PKG_VERSION_MISMATCH;
   }
-  else if (getVersion() != fa->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const SBase *>(fa)) == false)
   {
     return LIBSBML_NAMESPACES_MISMATCH;

src/sbml/packages/fbc/sbml/FbcAssociation.cpp

@@ -912,10 +912,6 @@ ListOfFbcAssociations::addFbcAssociation(const FbcAssociation* fa)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != fa->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const SBase *>(fa)) == false)
   {
     return LIBSBML_NAMESPACES_MISMATCH;

src/sbml/packages/fbc/sbml/FbcOr.cpp

@@ -249,10 +249,6 @@ FbcOr::addAssociation(const FbcAssociation* fa)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != fa->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (getPackageVersion() != fa->getPackageVersion())
   {
     return LIBSBML_PKG_VERSION_MISMATCH;

src/sbml/packages/fbc/sbml/FluxObjective.cpp

@@ -343,11 +343,9 @@ FluxObjective::setCoefficient(double coefficient)
 int
 FluxObjective::setVariableType(const FbcVariableType_t variableType)
 {
-  unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     if (FbcVariableType_isValid(variableType) == 0)
     {
@@ -373,11 +371,9 @@ FluxObjective::setVariableType(const FbcVariableType_t variableType)
 int
 FluxObjective::setVariableType(const std::string& variableType)
 {
-  unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     mVariableType = FbcVariableType_fromString(variableType.c_str());
 
@@ -550,8 +546,6 @@ FluxObjective::hasRequiredAttributes () const
 {
   bool allPresent = true;
 
-  unsigned int level = getLevel();
-  unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
   if (isSetReaction() == false)
@@ -560,7 +554,7 @@ FluxObjective::hasRequiredAttributes () const
   if (isSetCoefficient() == false)
     allPresent = false;
 
-  if (level == 3 && version == 1 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     if (isSetVariableType() == false)
     {
@@ -974,16 +968,14 @@ FluxObjective::addExpectedAttributes(ExpectedAttributes& attributes)
 {
   SBase::addExpectedAttributes(attributes);
 
-  unsigned int level = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
   attributes.add("id");
   attributes.add("name");
   attributes.add("reaction");
   attributes.add("coefficient");
 
-  if (level == 3 && coreVersion == 1 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     attributes.add("variableType");
     attributes.add("reaction2");
@@ -1162,7 +1154,7 @@ FluxObjective::readAttributes (const XMLAttributes& attributes,
   // 
 
   std::string variableType;
-  if (pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     assigned = attributes.readInto("variableType", variableType);
 
@@ -1352,10 +1344,6 @@ ListOfFluxObjectives::addFluxObjective(const FluxObjective* fo)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != fo->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const SBase *>(fo)) == false)
   {
     return LIBSBML_NAMESPACES_MISMATCH;

src/sbml/packages/fbc/sbml/GeneAssociation.cpp

@@ -391,10 +391,6 @@ int
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != association->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else
   {
     if (mAssociation != NULL)

src/sbml/packages/fbc/sbml/GeneProduct.cpp

@@ -1071,10 +1071,6 @@ ListOfGeneProducts::addGeneProduct(const GeneProduct* gp)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != gp->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const SBase *>(gp)) == false)
   {
     return LIBSBML_NAMESPACES_MISMATCH;

src/sbml/packages/fbc/sbml/KeyValuePair.cpp

@@ -235,10 +235,9 @@ KeyValuePair::isSetUri() const
 int
 KeyValuePair::setId(const std::string& id)
 {
-  unsigned int coreLevel = getLevel();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     return SyntaxChecker::checkAndSetSId(id, mId);
   }
@@ -255,10 +254,9 @@ KeyValuePair::setId(const std::string& id)
 int
 KeyValuePair::setName(const std::string& name)
 {
-  unsigned int coreLevel = getLevel();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     mName = name;
     return LIBSBML_OPERATION_SUCCESS;
@@ -276,10 +274,9 @@ KeyValuePair::setName(const std::string& name)
 int
 KeyValuePair::setKey(const std::string& key)
 {
-  unsigned int coreLevel = getLevel();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     mKey = key;
     return LIBSBML_OPERATION_SUCCESS;
@@ -297,10 +294,9 @@ KeyValuePair::setKey(const std::string& key)
 int
 KeyValuePair::setValue(const std::string& value)
 {
-  unsigned int coreLevel = getLevel();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     mValue = value;
     return LIBSBML_OPERATION_SUCCESS;
@@ -318,10 +314,9 @@ KeyValuePair::setValue(const std::string& value)
 int
 KeyValuePair::setUri(const std::string& uri)
 {
-  unsigned int coreLevel = getLevel();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     mUri = uri;
     return LIBSBML_OPERATION_SUCCESS;
@@ -458,11 +453,9 @@ KeyValuePair::hasRequiredAttributes() const
 {
   bool allPresent = true;
 
-  unsigned int level = getLevel();
-  unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && version == 1 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     if (isSetKey() == false)
     {
@@ -854,10 +847,9 @@ KeyValuePair::addExpectedAttributes(ExpectedAttributes& attributes)
 {
   SBase::addExpectedAttributes(attributes);
 
-  unsigned int level = getLevel();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     attributes.add("id");
     attributes.add("name");
@@ -936,7 +928,7 @@ KeyValuePair::readAttributes(const XMLAttributes& attributes,
     }
   }
 
-  if (level == 3 && version == 1 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     readL3V1V3Attributes(attributes);
   }
@@ -1063,11 +1055,9 @@ KeyValuePair::writeAttributes(XMLOutputStream& stream) const
 {
   SBase::writeAttributes(stream);
 
-  unsigned int level = getLevel();
-  unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     writeL3V1V3Attributes(stream);
   }

src/sbml/packages/fbc/sbml/ListOfKeyValuePairs.cpp

@@ -156,11 +156,9 @@ ListOfKeyValuePairs::setXmlns(const XMLNamespaces* xmlns, const std::string& pre
 int
 ListOfKeyValuePairs::setXmlns(const std::string& xmlns)
 {
-  unsigned int coreLevel = getLevel();
-  unsigned int coreVersion = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (coreLevel == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     mXmlns = xmlns;
     return LIBSBML_OPERATION_SUCCESS;
@@ -286,10 +284,6 @@ ListOfKeyValuePairs::addKeyValuePair(const KeyValuePair* kvp)
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != kvp->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const
     SBase*>(kvp)) == false)
   {
@@ -382,11 +376,9 @@ ListOfKeyValuePairs::hasRequiredAttributes() const
 {
   bool allPresent = true;
 
-  unsigned int level = getLevel();
-  unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     if (isSetXmlns() == false)
     {
@@ -483,7 +475,7 @@ ListOfKeyValuePairs::readAttributes(const XMLAttributes& attributes,
     }
   }
 
-  if (level == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     readL3V1V3Attributes(attributes);
   }
@@ -550,11 +542,9 @@ ListOfKeyValuePairs::writeAttributes(XMLOutputStream& stream) const
 {
   ListOf::writeAttributes(stream);
 
-  unsigned int level = getLevel();
-  unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && pkgVersion == 3)
+  if (pkgVersion >= 3)
   {
     writeL3V1V3Attributes(stream);
   }

src/sbml/packages/fbc/sbml/ListOfUserDefinedConstraintComponents.cpp

@@ -231,10 +231,6 @@ ListOfUserDefinedConstraintComponents::addUserDefinedConstraintComponent(const
   {
     return LIBSBML_LEVEL_MISMATCH;
   }
-  else if (getVersion() != udcc->getVersion())
-  {
-    return LIBSBML_VERSION_MISMATCH;
-  }
   else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const
     SBase*>(udcc)) == false)
   {