Merge pull request #264 from sbmlteam/fbc-fixes

Fbc v3 fixes

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

@@ -701,8 +701,8 @@ LIBSBML_EXTERN
 const char*
 FbcVariableType_toString(FbcVariableType_t fvt)
 {
-  int min = FBC_FBCVARIABLETYPE_LINEAR;
-  int max = FBC_FBCVARIABLETYPE_INVALID;
+  int min = FBC_VARIABLE_TYPE_LINEAR;
+  int max = FBC_VARIABLE_TYPE_INVALID;
 
   if (fvt < min || fvt > max)
   {
@@ -715,7 +715,7 @@ FbcVariableType_toString(FbcVariableType_t fvt)
 
 /*
  * Returns the #FbcVariableType_t enumeration corresponding to the given string
- * or @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t} if there is
+ * or @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t} if there is
  * no such match.
  */
 LIBSBML_EXTERN
@@ -733,7 +733,7 @@ FbcVariableType_fromString(const char* code)
     }
   }
 
-  return FBC_FBCVARIABLETYPE_INVALID;
+  return FBC_VARIABLE_TYPE_INVALID;
 }
 
 
@@ -745,8 +745,8 @@ LIBSBML_EXTERN
 int
 FbcVariableType_isValid(FbcVariableType_t fvt)
 {
-  int min = FBC_FBCVARIABLETYPE_LINEAR;
-  int max = FBC_FBCVARIABLETYPE_INVALID;
+  int min = FBC_VARIABLE_TYPE_LINEAR;
+  int max = FBC_VARIABLE_TYPE_INVALID;
 
   if (fvt < min || fvt >= max)
   {

src/sbml/packages/fbc/extension/FbcExtension.h

@@ -479,9 +479,9 @@ typedef enum
  */
 typedef enum
 {
-  FBC_FBCVARIABLETYPE_LINEAR          /*!< The fbc fbcvariabletype is @c "linear". */
-, FBC_FBCVARIABLETYPE_QUADRATIC       /*!< The fbc fbcvariabletype is @c "quadratic". */
-, FBC_FBCVARIABLETYPE_INVALID         /*!< Invalid FbcVariableType value. */
+  FBC_VARIABLE_TYPE_LINEAR          /*!< The fbc fbcvariabletype is @c "linear". */
+, FBC_VARIABLE_TYPE_QUADRATIC       /*!< The fbc fbcvariabletype is @c "quadratic". */
+, FBC_VARIABLE_TYPE_INVALID         /*!< Invalid FbcVariableType value. */
 } FbcVariableType_t;
 
 
@@ -494,7 +494,7 @@ typedef enum
  * "linear",
  * "quadratic",
  * "invalid FbcVariableType value",
- * or @c NULL if the value is @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID,
+ * or @c NULL if the value is @sbmlconstant{FBC_VARIABLE_TYPE_INVALID,
  * FbcVariableType_t} or another invalid enumeration value.
  *
  * @copydetails doc_returned_unowned_char
@@ -510,18 +510,18 @@ FbcVariableType_toString(FbcVariableType_t fvt);
 
 /**
  * Returns the #FbcVariableType_t enumeration corresponding to the given string
- * or @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t} if there is
+ * or @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t} if there is
  * no such match.
  *
  * @param code the string to convert to a #FbcVariableType_t.
  *
  * @return the corresponding #FbcVariableType_t or
- * @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t} if no match is
+ * @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t} if no match is
  * found.
  *
  * @note The matching is case-sensitive: "linear" will return
- * @sbmlconstant{FBC_FBCVARIABLETYPE_LINEAR, FbcVariableType_t}, but "Linear"
- * will return @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t}.
+ * @sbmlconstant{FBC_VARIABLE_TYPE_LINEAR, FbcVariableType_t}, but "Linear"
+ * will return @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t}.
  *
  * @if conly
  * @memberof Fbc_t
@@ -539,9 +539,9 @@ FbcVariableType_fromString(const char* code);
  * @param fvt the #FbcVariableType_t enumeration to query.
  *
  * @return @c 1 (true) if the #FbcVariableType_t is
- * @sbmlconstant{FBC_FBCVARIABLETYPE_LINEAR, FbcVariableType_t}, or
- * @sbmlconstant{FBC_FBCVARIABLETYPE_QUADRATIC, FbcVariableType_t};
- * @c 0 (false) otherwise (including @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID,
+ * @sbmlconstant{FBC_VARIABLE_TYPE_LINEAR, FbcVariableType_t}, or
+ * @sbmlconstant{FBC_VARIABLE_TYPE_QUADRATIC, FbcVariableType_t};
+ * @c 0 (false) otherwise (including @sbmlconstant{FBC_VARIABLE_TYPE_INVALID,
  * FbcVariableType_t}).
  *
  * @if conly

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

@@ -185,7 +185,7 @@ FbcReactionPlugin::writeElements (XMLOutputStream& stream) const
   // dont want to write <fbc:geneProductAssociation/> 
   // so check it actual has something in
   if (isSetGeneProductAssociation() == true && getLevel() == 3 
-    && getPackageVersion() == 2 && getGeneProductAssociation()->getAssociation() != NULL) 
+    && getPackageVersion() > 1 && getGeneProductAssociation()->getAssociation() != NULL) 
   { 
     mGeneProductAssociation->write(stream);
   } 

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

@@ -68,7 +68,7 @@ FluxObjective::FluxObjective (unsigned int level, unsigned int version, unsigned
   , mReaction ("")
   , mCoefficient (numeric_limits<double>::quiet_NaN())
   , mIsSetCoefficient (false)
-  , mVariableType (FBC_FBCVARIABLETYPE_INVALID)
+  , mVariableType (FBC_VARIABLE_TYPE_INVALID)
 {
   // set an SBMLNamespaces derived object of this package
   setSBMLNamespacesAndOwn(new FbcPkgNamespaces(level, version, pkgVersion));
@@ -85,7 +85,7 @@ FluxObjective::FluxObjective (FbcPkgNamespaces* fbcns)
   , mReaction ("")
   , mCoefficient (numeric_limits<double>::quiet_NaN())
   , mIsSetCoefficient (false)
-  , mVariableType (FBC_FBCVARIABLETYPE_INVALID)
+  , mVariableType (FBC_VARIABLE_TYPE_INVALID)
 {
   // set the element namespace of this object
   setElementNamespace(fbcns->getURI());
@@ -256,7 +256,7 @@ FluxObjective::isSetCoefficient() const
 bool
 FluxObjective::isSetVariableType() const
 {
-  return (mVariableType != FBC_FBCVARIABLETYPE_INVALID);
+  return (mVariableType != FBC_VARIABLE_TYPE_INVALID);
 }
 
 
@@ -317,7 +317,7 @@ FluxObjective::setVariableType(const FbcVariableType_t variableType)
   {
     if (FbcVariableType_isValid(variableType) == 0)
     {
-      mVariableType = FBC_FBCVARIABLETYPE_INVALID;
+      mVariableType = FBC_VARIABLE_TYPE_INVALID;
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
     else
@@ -347,7 +347,7 @@ FluxObjective::setVariableType(const std::string& variableType)
   {
     mVariableType = FbcVariableType_fromString(variableType.c_str());
 
-    if (mVariableType == FBC_FBCVARIABLETYPE_INVALID)
+    if (mVariableType == FBC_VARIABLE_TYPE_INVALID)
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -444,7 +444,7 @@ FluxObjective::unsetCoefficient()
 int
 FluxObjective::unsetVariableType()
 {
-  mVariableType = FBC_FBCVARIABLETYPE_INVALID;
+  mVariableType = FBC_VARIABLE_TYPE_INVALID;
   return LIBSBML_OPERATION_SUCCESS;
 }
 
@@ -1525,7 +1525,7 @@ FluxObjective_getVariableType(const FluxObjective_t * fo)
 {
   if (fo == NULL)
   {
-    return FBC_FBCVARIABLETYPE_INVALID;
+    return FBC_VARIABLE_TYPE_INVALID;
   }
 
   return fo->getVariableType();

src/sbml/packages/fbc/sbml/FluxObjective.h

@@ -235,9 +235,9 @@ class LIBSBML_EXTERN FluxObjective : public SBase
    * @if clike The value is drawn from the enumeration @ref FbcVariableType_t
    * @endif
    * The possible values returned by this method are:
-   * @li @sbmlconstant{FBC_FBCVARIABLETYPE_LINEAR, FbcVariableType_t}
-   * @li @sbmlconstant{FBC_FBCVARIABLETYPE_QUADRATIC, FbcVariableType_t}
-   * @li @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t}
+   * @li @sbmlconstant{FBC_VARIABLE_TYPE_LINEAR, FbcVariableType_t}
+   * @li @sbmlconstant{FBC_VARIABLE_TYPE_QUADRATIC, FbcVariableType_t}
+   * @li @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t}
    */
   FbcVariableType_t getVariableType() const;
 
@@ -1167,9 +1167,9 @@ FluxObjective_getCoefficient(const FluxObjective_t * fo);
  * @if clike The value is drawn from the enumeration @ref FbcVariableType_t
  * @endif
  * The possible values returned by this method are:
- * @li @sbmlconstant{FBC_FBCVARIABLETYPE_LINEAR, FbcVariableType_t}
- * @li @sbmlconstant{FBC_FBCVARIABLETYPE_QUADRATIC, FbcVariableType_t}
- * @li @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t}
+ * @li @sbmlconstant{FBC_VARIABLE_TYPE_LINEAR, FbcVariableType_t}
+ * @li @sbmlconstant{FBC_VARIABLE_TYPE_QUADRATIC, FbcVariableType_t}
+ * @li @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t}
  *
  * @memberof FluxObjective_t
  */

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

@@ -1067,7 +1067,7 @@ KeyValuePair::writeAttributes(XMLOutputStream& stream) const
   unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && version == 1 && pkgVersion == 3)
+  if (level == 3 && pkgVersion == 3)
   {
     writeL3V1V3Attributes(stream);
   }

src/sbml/packages/fbc/sbml/UserDefinedConstraintComponent.cpp

@@ -66,7 +66,7 @@ UserDefinedConstraintComponent::UserDefinedConstraintComponent(
   , mCoefficient (util_NaN())
   , mIsSetCoefficient (false)
   , mVariable ("")
-  , mVariableType (FBC_FBCVARIABLETYPE_INVALID)
+  , mVariableType (FBC_VARIABLE_TYPE_INVALID)
 {
   setSBMLNamespacesAndOwn(new FbcPkgNamespaces(level, version, pkgVersion));
 }
@@ -82,7 +82,7 @@ UserDefinedConstraintComponent::UserDefinedConstraintComponent(FbcPkgNamespaces
   , mCoefficient (util_NaN())
   , mIsSetCoefficient (false)
   , mVariable ("")
-  , mVariableType (FBC_FBCVARIABLETYPE_INVALID)
+  , mVariableType (FBC_VARIABLE_TYPE_INVALID)
 {
   setElementNamespace(fbcns->getURI());
   loadPlugins(fbcns);
@@ -260,7 +260,7 @@ UserDefinedConstraintComponent::isSetVariable() const
 bool
 UserDefinedConstraintComponent::isSetVariableType() const
 {
-  return (mVariableType != FBC_FBCVARIABLETYPE_INVALID);
+  return (mVariableType != FBC_VARIABLE_TYPE_INVALID);
 }
 
 
@@ -380,7 +380,7 @@ UserDefinedConstraintComponent::setVariableType(const FbcVariableType_t
   {
     if (FbcVariableType_isValid(variableType) == 0)
     {
-      mVariableType = FBC_FBCVARIABLETYPE_INVALID;
+      mVariableType = FBC_VARIABLE_TYPE_INVALID;
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
     else
@@ -412,7 +412,7 @@ UserDefinedConstraintComponent::setVariableType(const std::string&
   {
     mVariableType = FbcVariableType_fromString(variableType.c_str());
 
-    if (mVariableType == FBC_FBCVARIABLETYPE_INVALID)
+    if (mVariableType == FBC_VARIABLE_TYPE_INVALID)
     {
       return LIBSBML_INVALID_ATTRIBUTE_VALUE;
     }
@@ -514,7 +514,7 @@ UserDefinedConstraintComponent::unsetVariable()
 int
 UserDefinedConstraintComponent::unsetVariableType()
 {
-  mVariableType = FBC_FBCVARIABLETYPE_INVALID;
+  mVariableType = FBC_VARIABLE_TYPE_INVALID;
   return LIBSBML_OPERATION_SUCCESS;
 }
 
@@ -1060,10 +1060,10 @@ UserDefinedConstraintComponent::readAttributes(const XMLAttributes& attributes,
         log->logPackageError("fbc", FbcUserDefinedConstraintLOUserDefinedConstraintComponentsAllowedCoreAttributes,
           pkgVersion, level, version, details, getLine(), getColumn());
       }
-      else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == NotSchemaConformant)
-      {
-        getErrorLog()->remove(NotSchemaConformant);
-      }
+      else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == NotSchemaConformant)
+      {
+        getErrorLog()->remove(NotSchemaConformant);
+      }
     }
   }
 
@@ -1091,10 +1091,10 @@ UserDefinedConstraintComponent::readAttributes(const XMLAttributes& attributes,
           FbcUserDefinedConstraintComponentAllowedCoreAttributes, pkgVersion,
             level, version, details, getLine(), getColumn());
       }
-      else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == NotSchemaConformant)
-      {
-        getErrorLog()->remove(NotSchemaConformant);
-      }
+      else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == NotSchemaConformant)
+      {
+        getErrorLog()->remove(NotSchemaConformant);
+      }
     }
   }
 
@@ -1294,7 +1294,7 @@ UserDefinedConstraintComponent::writeAttributes(XMLOutputStream& stream) const
   unsigned int version = getVersion();
   unsigned int pkgVersion = getPackageVersion();
 
-  if (level == 3 && version == 1 && pkgVersion == 3)
+  if (level == 3 && pkgVersion == 3)
   {
     writeL3V1V3Attributes(stream);
   }
@@ -1477,7 +1477,7 @@ UserDefinedConstraintComponent_getVariableType(const
 {
   if (udcc == NULL)
   {
-    return FBC_FBCVARIABLETYPE_INVALID;
+    return FBC_VARIABLE_TYPE_INVALID;
   }
 
   return udcc->getVariableType();

src/sbml/packages/fbc/sbml/UserDefinedConstraintComponent.h

@@ -222,9 +222,9 @@ class LIBSBML_EXTERN UserDefinedConstraintComponent : public SBase
    * @if clike The value is drawn from the enumeration @ref FbcVariableType_t
    * @endif
    * The possible values returned by this method are:
-   * @li @sbmlconstant{FBC_FBCVARIABLETYPE_LINEAR, FbcVariableType_t}
-   * @li @sbmlconstant{FBC_FBCVARIABLETYPE_QUADRATIC, FbcVariableType_t}
-   * @li @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t}
+   * @li @sbmlconstant{FBC_VARIABLE_TYPE_LINEAR, FbcVariableType_t}
+   * @li @sbmlconstant{FBC_VARIABLE_TYPE_QUADRATIC, FbcVariableType_t}
+   * @li @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t}
    */
   FbcVariableType_t getVariableType() const;
 
@@ -1032,9 +1032,9 @@ UserDefinedConstraintComponent_getVariable(const
  * @if clike The value is drawn from the enumeration @ref FbcVariableType_t
  * @endif
  * The possible values returned by this method are:
- * @li @sbmlconstant{FBC_FBCVARIABLETYPE_LINEAR, FbcVariableType_t}
- * @li @sbmlconstant{FBC_FBCVARIABLETYPE_QUADRATIC, FbcVariableType_t}
- * @li @sbmlconstant{FBC_FBCVARIABLETYPE_INVALID, FbcVariableType_t}
+ * @li @sbmlconstant{FBC_VARIABLE_TYPE_LINEAR, FbcVariableType_t}
+ * @li @sbmlconstant{FBC_VARIABLE_TYPE_QUADRATIC, FbcVariableType_t}
+ * @li @sbmlconstant{FBC_VARIABLE_TYPE_INVALID, FbcVariableType_t}
  *
  * @memberof UserDefinedConstraintComponent_t
  */