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From: <mh...@us...> - 2013-08-30 03:16:55
|
Revision: 18351
http://sourceforge.net/p/sbml/code/18351
Author: mhucka
Date: 2013-08-30 03:16:50 +0000 (Fri, 30 Aug 2013)
Log Message:
-----------
More doc work.
Modified Paths:
--------------
trunk/libsbml/src/sbml/AssignmentRule.h
trunk/libsbml/src/sbml/Compartment.h
trunk/libsbml/src/sbml/Constraint.h
trunk/libsbml/src/sbml/Delay.h
trunk/libsbml/src/sbml/EventAssignment.h
trunk/libsbml/src/sbml/FunctionDefinition.h
trunk/libsbml/src/sbml/InitialAssignment.h
trunk/libsbml/src/sbml/KineticLaw.h
trunk/libsbml/src/sbml/Model.h
trunk/libsbml/src/sbml/Parameter.h
trunk/libsbml/src/sbml/Priority.h
trunk/libsbml/src/sbml/RateRule.h
trunk/libsbml/src/sbml/Reaction.h
trunk/libsbml/src/sbml/Rule.h
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/SimpleSpeciesReference.h
trunk/libsbml/src/sbml/Species.h
trunk/libsbml/src/sbml/StoichiometryMath.h
trunk/libsbml/src/sbml/Trigger.h
Modified: trunk/libsbml/src/sbml/AssignmentRule.h
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/AssignmentRule.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -253,9 +253,8 @@
/**
- * Predicate returning @c true if
- * all the required attributes for this AssignmentRule object
- * have been set.
+ * Predicate returning @c true if all the required attributes for this
+ * AssignmentRule object have been set.
*
* @note In SBML Levels 2–3, the only required attribute for
* an AssignmentRule object is "variable". For Level 1, where the
@@ -270,7 +269,18 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Compartment.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -940,13 +940,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Constraint.h
===================================================================
--- trunk/libsbml/src/sbml/Constraint.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Constraint.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -372,13 +372,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Delay.h
===================================================================
--- trunk/libsbml/src/sbml/Delay.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Delay.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -541,8 +541,11 @@
/**
- * Finds this Delay's Event parent and calls unsetDelay() on it, indirectly deleting itself. Overridden from the SBase function since the parent is not a ListOf.
+ * Finds this Delay's Event parent and calls unsetDelay() on it, indirectly
+ * deleting itself.
*
+ * Overridden from the SBase function since the parent is not a ListOf.
+ *
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
@@ -552,14 +555,37 @@
*/
virtual int removeFromParentAndDelete();
+
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/EventAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/EventAssignment.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -617,13 +617,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/FunctionDefinition.h
===================================================================
--- trunk/libsbml/src/sbml/FunctionDefinition.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/FunctionDefinition.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -538,7 +538,18 @@
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/InitialAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/InitialAssignment.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -621,13 +621,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/KineticLaw.h
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/KineticLaw.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -1071,13 +1071,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Model.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -2729,14 +2729,37 @@
virtual void renameIDs(List* elements, IdentifierTransformer* idTransformer);
+
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
@@ -3558,9 +3581,11 @@
/**
* Takes the contents of the passed-in Model, makes copies of everything,
- * and appends those copies to the appropriate places in this Model. Also
- * calls 'appendFrom' on all plugin objects.
+ * and appends those copies to the appropriate places in this Model.
*
+ * This method also calls the <code>appendFrom</code> method on all libSBML
+ * plug-in objects. @htmlinclude what-are-plugins.html
+ *
* @param model the Model to merge with this one.
*
*/
Modified: trunk/libsbml/src/sbml/Parameter.h
===================================================================
--- trunk/libsbml/src/sbml/Parameter.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Parameter.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -764,7 +764,18 @@
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Priority.h
===================================================================
--- trunk/libsbml/src/sbml/Priority.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Priority.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -420,13 +420,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML.
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element.
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/RateRule.h
===================================================================
--- trunk/libsbml/src/sbml/RateRule.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/RateRule.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -245,7 +245,18 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Reaction.h
===================================================================
--- trunk/libsbml/src/sbml/Reaction.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Reaction.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -347,7 +347,18 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Rule.h
===================================================================
--- trunk/libsbml/src/sbml/Rule.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Rule.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -814,13 +814,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/SBase.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -222,6 +222,8 @@
* Returns the first child element it can find with a specific "metaid"
* attribute value, or @c NULL if no such object is found.
*
+ * @htmlinclude what-is-metaid.html
+ *
* @param metaid string representing the "metaid" attribute value of the
* object to find.
*
@@ -243,6 +245,8 @@
* Renames all the @c SIdRef attributes on this element, including any
* found in MathML content (if such exists).
*
+ * @htmlinclude what-is-sidref.html
+ *
* This method works by looking at all attributes and (if appropriate)
* mathematical formulas, comparing the identifiers to the value of @p
* oldid. If any matches are found, the matching identifiers are replaced
@@ -255,13 +259,15 @@
/**
- * Renames all the @c MetaIdRef attributes on this element.
+ * Renames all the meta-identifier attributes on this element.
*
- * This method works by looking at all meta-attribute values, comparing
- * the identifiers to the value of @p oldid. If any matches are found,
- * the matching identifiers are replaced with @p newid. The method does
- * @em not descend into child elements.
+ * @htmlinclude what-is-metaidref.html
*
+ * This method works by looking at all meta-identifier attribute values,
+ * comparing the identifiers to the value of @p oldid. If any matches are
+ * found, the matching identifiers are replaced with @p newid. The method
+ * does @em not descend into child elements.
+ *
* @param oldid the old identifier
* @param newid the new identifier
*/
@@ -271,6 +277,8 @@
/**
* Renames all the @c UnitSIdRef attributes on this element.
*
+ * @htmlinclude what-is-unitsidref.html
+ *
* This method works by looking at all unit identifier attribute values
* (including, if appropriate, inside mathematical formulas), comparing the
* unit identifiers to the value of @p oldid. If any matches are found,
@@ -375,9 +383,11 @@
* Returns a List of all child SBase objects contained in SBML package
* plug-ins.
*
- * This method walks down the list of all packages used by the enclosing
- * Model and returns all objects contained in them.
+ * @htmlinclude what-are-plugins.html
*
+ * This method walks down the list of all SBML Level 3 packages used
+ * by this object and returns all child objects defined by those packages.
+ *
* @return a pointer to a List of pointers to all children objects from
* plug-ins.
*/
@@ -386,21 +396,8 @@
/**
* Returns the value of the "metaid" attribute of this object.
- *
- * The optional attribute named "metaid", present on every major SBML
- * component type, is for supporting metadata annotations using RDF
- * (Resource Description Format). The attribute value has the data type
- * <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, the XML
- * identifier type, which means each "metaid" value must be globally
- * unique within an SBML file. (Importantly, this uniqueness criterion
- * applies across any attribute with type <a
- * href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, not just the
- * "metaid" attribute used by SBML—something to be aware of if your
- * application-specific XML content inside the "annotation" subelement
- * happens to use <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>.)
- * The "metaid" value serves to identify a model
- * component for purposes such as referencing that component from
- * metadata placed within "annotation" subelements.
+ *
+ * @htmlinclude what-is-metaid.html
*
* @return the meta-identifier of this SBML object.
*
@@ -412,21 +409,8 @@
/**
* Returns the value of the "metaid" attribute of this object.
- *
- * The optional attribute named "metaid", present on every major SBML
- * component type, is for supporting metadata annotations using RDF
- * (Resource Description Format). The attribute value has the data type
- * <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, the XML
- * identifier type, which means each "metaid" value must be globally
- * unique within an SBML file. (Importantly, this uniqueness criterion
- * applies across any attribute with type <a
- * href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, not just the
- * "metaid" attribute used by SBML—something to be aware of if your
- * application-specific XML content inside the "annotation" subelement
- * happens to use <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>.)
- * The "metaid" value serves to identify a model
- * component for purposes such as referencing that component from
- * metadata placed within "annotation" subelements.
+ *
+ * @htmlinclude what-is-metaid.html
*
* @return the meta-identifier of this SBML object, as a string.
*
@@ -580,7 +564,7 @@
* @see getNotesString()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
@@ -626,7 +610,7 @@
* @see getNotesString()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
@@ -670,7 +654,7 @@
* @see getNotes()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
@@ -714,7 +698,7 @@
* @see getNotes()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
@@ -1200,20 +1184,7 @@
/**
* Predicate returning @c true if this object's "metaid" attribute is set.
*
- * The optional attribute named "metaid", present on every major SBML
- * component type, is for supporting metadata annotations using RDF
- * (Resource Description Format). The attribute value has the data type
- * <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, the XML
- * identifier type, which means each "metaid" value must be globally
- * unique within an SBML file. (Importantly, this uniqueness criterion
- * applies across any attribute with type <a
- * href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, not just the
- * "metaid" attribute used by SBML—something to be aware of if your
- * application-specific XML content inside the "annotation" subelement
- * happens to use <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>.)
- * The "metaid" value serves to identify a model component for purposes
- * such as referencing that component from metadata placed within
- * "annotation" subelements.
+ * @htmlinclude what-is-metaid.html
*
* @return @c true if the "metaid" attribute of this SBML object is
* set, @c false otherwise.
@@ -1362,7 +1333,7 @@
* @see getNotes()
* @see getNotesString()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
@@ -1414,19 +1385,12 @@
/**
- * Sets the value of the "metaid" attribute of this object.
+ * Sets the value of the meta-identifier attribute of this object.
*
- * The string @p metaid is copied. The value of @p metaid must be an
- * identifier conforming to the syntax defined by the XML 1.0 data type
- * <a href="http://www.w3.org/TR/REC-xml/#id">ID</a>. Among other
- * things, this type requires that a value is unique among all the values
- * of type XML ID in an SBMLDocument. Although SBML only uses <a
- * href="http://www.w3.org/TR/REC-xml/#id">XML ID</a> for the "metaid"
- * attribute, callers should be careful if they use
- * <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>'s in XML
- * portions of a model that are not defined by SBML, such as in the
- * application-specific content of the "annotation" subelement.
+ * @htmlinclude what-is-metaid.html
*
+ * The string @p metaid is copied.
+ *
* @param metaid the identifier string to use as the value of the
* "metaid" attribute
*
@@ -1845,7 +1809,7 @@
*
* @see getNotesString()
* @see isSetNotes()
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
@@ -1964,7 +1928,7 @@
* @see getNotesString()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const std::string& notes)
* @see unsetNotes()
* @see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
@@ -2009,7 +1973,7 @@
* @see getNotesString()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see unsetNotes()
* @see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
@@ -2172,20 +2136,7 @@
/**
* Unsets the value of the "metaid" attribute of this SBML object.
*
- * The optional attribute named "metaid", present on every major SBML
- * component type, is for supporting metadata annotations using RDF
- * (Resource Description Format). The attribute value has the data type
- * <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, the XML
- * identifier type, which means each "metaid" value must be globally
- * unique within an SBML file. (Importantly, this uniqueness criterion
- * applies across any attribute with type <a
- * href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>, not just the
- * "metaid" attribute used by SBML—something to be aware of if your
- * application-specific XML content inside the "annotation" subelement
- * happens to use <a href="http://www.w3.org/TR/REC-xml/#id">XML ID</a>.)
- * The "metaid" value serves to identify a model component for purposes
- * such as referencing that component from metadata placed within
- * "annotation" subelements.
+ * @htmlinclude what-is-metaid.html
*
* @return integer value indicating success/failure of the
* function. The possible values returned by this function are:
@@ -2202,23 +2153,8 @@
* Most (but not all) objects in SBML include two common attributes: "id"
* and "name". The identifier given by an object's "id" attribute value
* is used to identify the object within the SBML model definition.
- * Other objects can refer to the component using this identifier. The
- * data type of "id" is always either <code>Sid</code> or
- * <code>UnitSId</code>, depending on the object in question. Both
- * data types are defined as follows:
- * <pre style="margin-left: 2em; border: none; font-weight: bold; color: black">
- * letter ::= 'a'..'z','A'..'Z'
- * digit ::= '0'..'9'
- * idChar ::= letter | digit | '_'
- * SId ::= ( letter | '_' ) idChar*
- * </pre>
+ * Other objects can refer to the component using this identifier.
*
- * The equality of <code>SId</code> and <code>UnitSId</code> type values
- * in SBML is determined by an exact character sequence match; i.e.,
- * comparisons of these identifiers must be performed in a case-sensitive
- * manner. This applies to all uses of <code>SId</code> and
- * <code>UnitSId</code>.
- *
* @return integer value indicating success/failure of the
* function. The possible values returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
@@ -2301,7 +2237,7 @@
* @see getNotesString()
* @see isSetNotes()
* @see setNotes(const XMLNode* notes)
- * @see setNotes(const std::string& notes)
+ * @see setNotes(const std::string& notes, bool addXHTMLMarkup)
* @see appendNotes(const XMLNode* notes)
* @see appendNotes(const std::string& notes)
* @see SyntaxChecker::hasExpectedXHTMLSyntax(@if java XMLNode xhtml@endif)
@@ -2738,29 +2674,34 @@
* @warning This is primarily provided for testing and debugging
* purposes. It may be removed in a future version of libSBML.
*/
- char* toSBML ();
+ char* toSBML();
- /**
- * Returns this element as XMLNode
+
+ /**
+ * Returns this element as an XMLNode.
*
- * @return this element as XMLNode
+ * @return this element as an XMLNode.
*
- * @warning This operation is expensive, as the element has to be
- * fully serialized to string and then parsed into the
- * XMLNode structure.
+ * @warning This operation is computationally expensive, because the
+ * element has to be fully serialized to a string and then parsed into the
+ * XMLNode structure. Attempting to convert a large tree structure (e.g.,
+ * a large Model) may consume significant computer memory and time.
*/
XMLNode* toXMLNode();
- /**
+
+ /**
* Reads (initializes) this SBML object by reading from the given XMLNode.
*
- * @param node The XMLNode to read from
+ * @param node The XMLNode to read from.
*
- * @param flag An optional flag, that allows to influence how errors are
- * logged during read
+ * @param flag An optional flag that determines how how errors are logged
+ * during the reading process.
*
- * @warning This method is expensive, as the given node has to be serialized to
- * string first.
+ * @warning This method is computationally expensive, because the given
+ * node has to be serialized to a string first. Attempting to serialize a
+ * large tree structure (e.g., a large Model) may consume significant
+ * computer memory and time.
*/
void read(XMLNode& node, XMLErrorSeverityOverride_t flag = LIBSBML_OVERRIDE_DISABLED);
@@ -2776,6 +2717,8 @@
* Returns a plug-in object (extension interface) for an SBML Level 3
* package extension with the given package name or URI.
*
+ * @htmlinclude what-are-plugins.html
+ *
* @param package the name or URI of the package
*
* @return the plug-in object (the libSBML extension interface) of
@@ -2788,6 +2731,8 @@
* Returns a plug-in object (extension interface) for an SBML Level 3
* package extension with the given package name or URI.
*
+ * @htmlinclude what-are-plugins.html
+ *
* @param package the name or URI of the package
*
* @return the plug-in object (the libSBML extension interface) of a
@@ -2800,6 +2745,8 @@
* Returns the nth plug-in object (extension interface) for an SBML Level 3
* package extension.
*
+ * @htmlinclude what-are-plugins.html
+ *
* @param n the index of the plug-in to return
*
* @return the plug-in object (the libSBML extension interface) of
@@ -2812,6 +2759,8 @@
* Returns the nth plug-in object (extension interface) for an SBML Level 3
* package extension.
*
+ * @htmlinclude what-are-plugins.html
+ *
* @param n the index of the plug-in to return
*
* @return the plug-in object (the libSBML extension interface) of a
@@ -2824,6 +2773,8 @@
* Returns the number of plug-in objects (extenstion interfaces) for SBML
* Level 3 package extensions known.
*
+ * @htmlinclude what-are-plugins.html
+ *
* @return the number of plug-in objects (extension interfaces) of
* package extensions known by this instance of libSBML.
*/
@@ -3054,14 +3005,16 @@
/**
- * Removes itself from its parent. If the parent was storing it as a
- * pointer, it is deleted. If not, it is simply cleared (as in ListOf
- * objects). Pure virutal, as every SBase element has different parents,
- * and therefore different methods of removing itself. Will fail (and
- * not delete itself) if it has no parent object. This function is
- * designed to be overridden, but for all objects whose parent is of the
- * class ListOf, the default implementation will work.
+ * Removes this object from its parent.
*
+ * If the parent was storing this object as a pointer, it is deleted. If
+ * not, it is simply cleared (as in ListOf objects). This is a pure
+ * virtual method, as every SBase element has different parents, and
+ * therefore different methods of removing itself. Will fail (and not
+ * delete itself) if it has no parent object. This function is designed to
+ * be overridden, but for all objects whose parent is of the class ListOf,
+ * the default implementation will work.
+ *
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif@~ The possible values
@@ -3121,10 +3074,9 @@
/**
- * Sets the user data of this element. This can be used by the application
- * developer to attach custom information to the node. In case of a deep
- * copy this attribute will passed as it is. The attribute will be never
- * interpreted by this class.
+ * Sets the user data of this element.
+ *
+ * @htmlinclude what-is-user-data.html
*
* @param userData specifies the new user data.
*
@@ -3139,6 +3091,8 @@
/**
* Returns the user data that has been previously set via setUserData().
*
+ * @htmlinclude what-is-user-data.html
+ *
* @return the user data of this node, or @c NULL if no user data has been set.
*
* @if clike
@@ -3149,29 +3103,30 @@
/**
- * Gets the URI to which this element belongs to.
+ * Gets the namespace URI to which this element belongs to.
+ *
* For example, all elements that belong to SBML Level 3 Version 1 Core
- * must would have the URI "http://www.sbml.org/sbml/level3/version1/core";
+ * must would have the URI "http://www.sbml.org/sbml/level3/version1/core";
* all elements that belong to Layout Extension Version 1 for SBML Level 3
* Version 1 Core must would have the URI
* "http://www.sbml.org/sbml/level3/version1/layout/version1/"
*
- * Unlike getElementNamespace, this function first returns the URI for this
- * element by looking into the SBMLNamespaces object of the document with
- * the its package name. if not found it will return the result of
- * getElementNamespace
+ * Unlike getElementNamespace(), this function first returns the URI for
+ * this element by looking into the SBMLNamespaces object of the document
+ * with the its package name. if not found it will return the result of
+ * getElementNamespace().
*
- * @return the URI this elements
+ * @return the URI of this element
*
- * @see getPackageName
- * @see getElementNamespace
- * @see getSBMLNamespaces
- * @see getSBMLDocument
+ * @see getPackageName()
+ * @see getElementNamespace()
+ * @see getSBMLDocument()
*/
std::string getURI() const;
+
/**
- * Return the prefix of this element.
+ * Returns the namespace prefix of this element.
*/
std::string getPrefix() const;
Modified: trunk/libsbml/src/sbml/SimpleSpeciesReference.h
===================================================================
--- trunk/libsbml/src/sbml/SimpleSpeciesReference.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/SimpleSpeciesReference.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -288,7 +288,18 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Species.h
===================================================================
--- trunk/libsbml/src/sbml/Species.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Species.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -1435,13 +1435,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/StoichiometryMath.h
===================================================================
--- trunk/libsbml/src/sbml/StoichiometryMath.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/StoichiometryMath.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -585,13 +585,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
Modified: trunk/libsbml/src/sbml/Trigger.h
===================================================================
--- trunk/libsbml/src/sbml/Trigger.h 2013-08-30 03:16:01 UTC (rev 18350)
+++ trunk/libsbml/src/sbml/Trigger.h 2013-08-30 03:16:50 UTC (rev 18351)
@@ -421,13 +421,35 @@
/**
- * Renames all the SIdRef attributes on this element, including any found in MathML
+ * Renames all the @c SIdRef attributes on this element, including any
+ * found in MathML.
+ *
+ * @htmlinclude what-is-sidref.html
+ *
+ * This method works by looking at all attributes and (if appropriate)
+ * mathematical formulas, comparing the identifiers to the value of @p
+ * oldid. If any matches are found, the matching identifiers are replaced
+ * with @p newid. The method does @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameSIdRefs(std::string oldid, std::string newid);
/**
- * Renames all the UnitSIdRef attributes on this element
+ * Renames all the @c UnitSIdRef attributes on this element.
+ *
+ * @htmlinclude what-is-unitsidref.html
+ *
+ * This method works by looking at all unit identifier attribute values
+ * (including, if appropriate, inside mathematical formulas), comparing the
+ * unit identifiers to the value of @p oldid. If any matches are found,
+ * the matching identifiers are replaced with @p newid. The method does
+ * @em not descend into child elements.
+ *
+ * @param oldid the old identifier
+ * @param newid the new identifier
*/
virtual void renameUnitSIdRefs(std::string oldid, std::string newid);
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|
|
From: <mh...@us...> - 2013-08-30 03:16:05
|
Revision: 18350
http://sourceforge.net/p/sbml/code/18350
Author: mhucka
Date: 2013-08-30 03:16:01 +0000 (Fri, 30 Aug 2013)
Log Message:
-----------
Added more text snippets.
Modified Paths:
--------------
trunk/libsbml/docs/src/Makefile.in
Added Paths:
-----------
trunk/libsbml/docs/src/common-text/what-are-plugins.html
trunk/libsbml/docs/src/common-text/what-is-metaid.html
trunk/libsbml/docs/src/common-text/what-is-metaidref.html
trunk/libsbml/docs/src/common-text/what-is-sidref.html
trunk/libsbml/docs/src/common-text/what-is-unitsidref.html
trunk/libsbml/docs/src/common-text/what-is-user-data.html
Modified: trunk/libsbml/docs/src/Makefile.in
===================================================================
--- trunk/libsbml/docs/src/Makefile.in 2013-08-30 03:15:01 UTC (rev 18349)
+++ trunk/libsbml/docs/src/Makefile.in 2013-08-30 03:16:01 UTC (rev 18350)
@@ -169,6 +169,12 @@
common-text/unitkind-table.txt \
common-text/warn-default-args-in-docs.html \
common-text/xmlid-syntax.html \
+ common-text/what-are-plugins.html \
+ common-text/what-is-metaid.html \
+ common-text/what-is-metaidref.html \
+ common-text/what-is-sidref.html \
+ common-text/what-is-unitsidref.html \
+ common-text/what-is-user-data.html \
csdocfilter.py \
doxygen-base-stylesheet.css \
doxygen-config-c.txt.cmake \
Added: trunk/libsbml/docs/src/common-text/what-are-plugins.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-are-plugins.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-are-plugins.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,13 @@
+SBML Level 3 consists of a <em>Core</em> definition that can be extended
+via optional SBML Level 3 <em>packages</em>. A given model may indicate
+that it uses one or more SBML packages, and likewise, a software tool may be
+able to support one or more packages. LibSBML does not come preconfigured
+with all possible packages included and enabled, in part because not all
+package specifications have been finalized. To support the ability for
+software systems to enable support for the Level 3 packages they choose,
+libSBML features a <em>plug-in</em> mechanism. Each SBML Level 3
+package is implemented in a separate code plug-in that can be enabled by the
+application to support working with that SBML package. A given SBML model
+may thus contain not only objects defined by SBML Level 3 Core, but also
+objects created by libSBML plug-ins supporting additional Level 3
+packages.
Added: trunk/libsbml/docs/src/common-text/what-is-metaid.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-metaid.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-metaid.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,16 @@
+The optional attribute named "metaid", present on every major SBML component
+type, is for supporting metadata annotations using RDF (<a
+ href="http://www.w3.org/RDF/">Resource Description Format</a>). The
+attribute value has the data type <a
+ href="http://www.w3.org/TR/REC-xml/#id">XML <code>ID</code></a>, the XML
+identifier type, which means each "metaid" value must be globally unique
+within an SBML file. The latter point is important, because the uniqueness
+criterion applies across <em>any</em> attribute with type <code>ID</code>
+anywhere in the file, not just the "metaid" attribute used by
+SBML—something to be aware of if your application-specific XML content
+inside the "annotation" subelement happens to use the XML <code>ID</code>
+type. Although SBML only uses <a href="http://www.w3.org/TR/REC-xml/#id">XML
+<code>ID</code></a> for the "metaid" attribute, callers should be careful if
+they use XML <code>ID</code>'s in XML portions of a model that are not
+defined by SBML, such as in the application-specific content of the
+"annotation" subelement.
Added: trunk/libsbml/docs/src/common-text/what-is-metaidref.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-metaidref.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-metaidref.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,6 @@
+In SBML, object "meta" identifiers are of the XML data type <code>ID</code>;
+the SBML object attribute itself is typically named <code>metaid</code>. All
+attributes that hold values <em>referring</em> to values of type
+<code>ID</code> are of the XML data type <code>IDREF</code>. They are also
+sometimes informally referred to as "metaid refs", in analogy to the
+SBML-defined type <code>SIdRef</code>.
Added: trunk/libsbml/docs/src/common-text/what-is-sidref.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-sidref.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-sidref.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,8 @@
+In SBML, object identifiers are of a type called <code>SId</code>. In SBML
+Level 3, an explicit data type called <code>SIdRef</code> was introduced
+for attribute values that refer to <code>SId</code> values; in previous
+Levels of SBML, this data type did not exist and attributes were simply
+described to as "referring to an identifier", but the effective data type was
+the same as Level 3's <code>SIdRef</code>. These and other methods of
+libSBML refer to the type <code>SIdRef</code> for all Levels of SBML, even if
+the corresponding SBML specification did not explicitly name the data type.
Added: trunk/libsbml/docs/src/common-text/what-is-unitsidref.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-unitsidref.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-unitsidref.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,9 @@
+In SBML, unit definitions have identifiers of type <code>UnitSId</code>. In
+SBML Level 3, an explicit data type called <code>UnitSIdRef</code> was
+introduced for attribute values that refer to <code>UnitSId</code> values; in
+previous Levels of SBML, this data type did not exist and attributes were
+simply described to as "referring to a unit identifier", but the effective
+data type was the same as Level 3's <code>UnitSIdRef</code>. These and
+other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
+Levels of SBML, even if the corresponding SBML specification did not
+explicitly name the data type.
Added: trunk/libsbml/docs/src/common-text/what-is-user-data.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-user-data.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-user-data.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,4 @@
+The user data associated with an SBML object can be used by an application
+developer to attach custom information to that object in the model. In case
+of a deep copy, this attribute will passed as it is. The attribute will be
+never interpreted by libSBML.
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|
|
From: <mh...@us...> - 2013-08-30 03:15:11
|
Revision: 18349
http://sourceforge.net/p/sbml/code/18349
Author: mhucka
Date: 2013-08-30 03:15:01 +0000 (Fri, 30 Aug 2013)
Log Message:
-----------
Minor spacing tweak.
Modified Paths:
--------------
trunk/libsbml/docs/src/doxygen-tabs.css
Modified: trunk/libsbml/docs/src/doxygen-tabs.css
===================================================================
--- trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 23:12:08 UTC (rev 18348)
+++ trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-30 03:15:01 UTC (rev 18349)
@@ -88,7 +88,7 @@
.tablist li a[href="examples.html"],
.tablist li a[href="functions.html"]
{
- width: 100px;
+ width: 98px;
letter-spacing: -1px;
}
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|
|
From: <mh...@us...> - 2013-08-29 23:12:10
|
Revision: 18348
http://sourceforge.net/p/sbml/code/18348
Author: mhucka
Date: 2013-08-29 23:12:08 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Added a border on the bottom of the tab bar items.
Modified Paths:
--------------
trunk/libsbml/docs/src/doxygen-tabs.css
Modified: trunk/libsbml/docs/src/doxygen-tabs.css
===================================================================
--- trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 23:05:46 UTC (rev 18347)
+++ trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 23:12:08 UTC (rev 18348)
@@ -93,5 +93,10 @@
}
#navrow1 {
- border-top: 1px solid #888;
+ border-top: 1px solid #aaa;
+ border-bottom: 1px solid #888;
}
+
+#navrow2, #navrow3, #navrow4 {
+ border-bottom: 1px solid #888;
+}
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|
|
From: <mh...@us...> - 2013-08-29 23:05:49
|
Revision: 18347
http://sourceforge.net/p/sbml/code/18347
Author: mhucka
Date: 2013-08-29 23:05:46 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Made a css selector more specific so that it wouldn't accidentally change the letter spacing in the left-hand TOC.
Modified Paths:
--------------
trunk/libsbml/docs/src/doxygen-tabs.css
Modified: trunk/libsbml/docs/src/doxygen-tabs.css
===================================================================
--- trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 05:13:54 UTC (rev 18346)
+++ trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 23:05:46 UTC (rev 18347)
@@ -60,33 +60,33 @@
text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0);
}
-li a[href="index.html"],
-li a[href="main.html"],
-li a[href="pages.html"],
-li a[href="annotated.html"],
-li a[href="files.html"],
-li a[href="globals.html"],
-li a[href="globals_func.html"],
-li a[href="functions_func.html"],
-li a[href="globals_vars.html"],
-li a[href="functions_vars.html"],
-li a[href="globals_type.html"],
-li a[href="functions_type.html"],
-li a[href="functions_rela.html"],
-li a[href="globals_enum.html"],
-li a[href="globals_eval.html"],
-li a[href="globals_defs.html"],
-li a[href="classes.html"],
-li a[href="hierarchy.html"],
-li a[href="inherits.html"],
-li a[href="namespaces.html"],
-li a[href="namespacemembers.html"],
-li a[href="namespacemembers_vars.html"],
-li a[href="usergroup0.html"],
-li a[href="usergroup1.html"],
-li a[href="group___core.html"],
-li a[href="examples.html"],
-li a[href="functions.html"]
+.tablist li a[href="index.html"],
+.tablist li a[href="main.html"],
+.tablist li a[href="pages.html"],
+.tablist li a[href="annotated.html"],
+.tablist li a[href="files.html"],
+.tablist li a[href="globals.html"],
+.tablist li a[href="globals_func.html"],
+.tablist li a[href="functions_func.html"],
+.tablist li a[href="globals_vars.html"],
+.tablist li a[href="functions_vars.html"],
+.tablist li a[href="globals_type.html"],
+.tablist li a[href="functions_type.html"],
+.tablist li a[href="functions_rela.html"],
+.tablist li a[href="globals_enum.html"],
+.tablist li a[href="globals_eval.html"],
+.tablist li a[href="globals_defs.html"],
+.tablist li a[href="classes.html"],
+.tablist li a[href="hierarchy.html"],
+.tablist li a[href="inherits.html"],
+.tablist li a[href="namespaces.html"],
+.tablist li a[href="namespacemembers.html"],
+.tablist li a[href="namespacemembers_vars.html"],
+.tablist li a[href="usergroup0.html"],
+.tablist li a[href="usergroup1.html"],
+.tablist li a[href="group___core.html"],
+.tablist li a[href="examples.html"],
+.tablist li a[href="functions.html"]
{
width: 100px;
letter-spacing: -1px;
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|
|
From: <mh...@us...> - 2013-08-29 05:13:56
|
Revision: 18346
http://sourceforge.net/p/sbml/code/18346
Author: mhucka
Date: 2013-08-29 05:13:54 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Fixed typo.
Modified Paths:
--------------
trunk/libsbml/examples/c++/printRegisteredPackages.cpp
Modified: trunk/libsbml/examples/c++/printRegisteredPackages.cpp
===================================================================
--- trunk/libsbml/examples/c++/printRegisteredPackages.cpp 2013-08-29 05:13:18 UTC (rev 18345)
+++ trunk/libsbml/examples/c++/printRegisteredPackages.cpp 2013-08-29 05:13:54 UTC (rev 18346)
@@ -1,6 +1,7 @@
/**
* @file printRegisteredPackages.cpp
- * @brief Prints the registerd packages for this libSBML
+ * @brief Prints the SBML Level 3 packages registered/installed
+ * in this copy of libSBML.
* @author Frank Bergmann
*
* This file is part of libSBML. Please visit http://sbml.org for more
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|
|
From: <mh...@us...> - 2013-08-29 05:13:22
|
Revision: 18345
http://sourceforge.net/p/sbml/code/18345
Author: mhucka
Date: 2013-08-29 05:13:18 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Added new file for the code examples section.
Modified Paths:
--------------
trunk/libsbml/docs/src/Makefile.in
Modified: trunk/libsbml/docs/src/Makefile.in
===================================================================
--- trunk/libsbml/docs/src/Makefile.in 2013-08-29 05:13:03 UTC (rev 18344)
+++ trunk/libsbml/docs/src/Makefile.in 2013-08-29 05:13:18 UTC (rev 18345)
@@ -273,6 +273,7 @@
libsbml-csharp-reading-files.txt \
libsbml-doxygen.html \
libsbml-example.txt \
+ libsbml-examples.txt \
libsbml-extension-support-classes.txt \
libsbml-features.html \
libsbml-features.txt \
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|
|
From: <mh...@us...> - 2013-08-29 05:13:05
|
Revision: 18344
http://sourceforge.net/p/sbml/code/18344
Author: mhucka
Date: 2013-08-29 05:13:03 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Added a subsection for all the example programs.
Modified Paths:
--------------
trunk/libsbml/docs/src/doxygen-config-common.txt
trunk/libsbml/docs/src/doxygen-config-cpp.txt.in
Modified: trunk/libsbml/docs/src/doxygen-config-common.txt
===================================================================
--- trunk/libsbml/docs/src/doxygen-config-common.txt 2013-08-29 05:12:43 UTC (rev 18343)
+++ trunk/libsbml/docs/src/doxygen-config-common.txt 2013-08-29 05:13:03 UTC (rev 18344)
@@ -338,6 +338,7 @@
libsbml-core-versus-packages.txt \
libsbml-communications.txt \
libsbml-example.txt \
+ libsbml-examples.txt \
libsbml-extending.txt \
libsbml-extension-support-classes.txt \
libsbml-features.txt \
@@ -492,7 +493,7 @@
# directories that contain example code fragments that are included (see
# the \include command).
-EXAMPLE_PATH = common-text examples . ../.. ../../examples/c++
+EXAMPLE_PATH = common-text examples . ../..
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
Modified: trunk/libsbml/docs/src/doxygen-config-cpp.txt.in
===================================================================
--- trunk/libsbml/docs/src/doxygen-config-cpp.txt.in 2013-08-29 05:12:43 UTC (rev 18343)
+++ trunk/libsbml/docs/src/doxygen-config-cpp.txt.in 2013-08-29 05:13:03 UTC (rev 18344)
@@ -77,4 +77,5 @@
# Note: The output has a lot of errors. Can't enable just yet.
# GENERATE_MAN = YES
+EXAMPLE_PATH = common-text examples . ../.. ../../examples/c++
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|
|
From: <mh...@us...> - 2013-08-29 05:12:47
|
Revision: 18343
http://sourceforge.net/p/sbml/code/18343
Author: mhucka
Date: 2013-08-29 05:12:43 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Added a subsection for all the example programs.
Modified Paths:
--------------
trunk/libsbml/docs/src/libsbml-programming.txt
Modified: trunk/libsbml/docs/src/libsbml-programming.txt
===================================================================
--- trunk/libsbml/docs/src/libsbml-programming.txt 2013-08-29 05:12:26 UTC (rev 18342)
+++ trunk/libsbml/docs/src/libsbml-programming.txt 2013-08-29 05:12:43 UTC (rev 18343)
@@ -8,6 +8,7 @@
- @subpage libsbml-reading-files
- @subpage libsbml-math
- @subpage libsbml-example
+- @subpage libsbml-examples
- @subpage libsbml-core-versus-packages
*/
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|
|
From: <mh...@us...> - 2013-08-29 05:12:32
|
Revision: 18342
http://sourceforge.net/p/sbml/code/18342
Author: mhucka
Date: 2013-08-29 05:12:26 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
New section for code examples.
Added Paths:
-----------
trunk/libsbml/docs/src/libsbml-examples.txt
Added: trunk/libsbml/docs/src/libsbml-examples.txt
===================================================================
--- trunk/libsbml/docs/src/libsbml-examples.txt (rev 0)
+++ trunk/libsbml/docs/src/libsbml-examples.txt 2013-08-29 05:12:26 UTC (rev 18342)
@@ -0,0 +1,207 @@
+/** @page libsbml-examples Additional complete example programs
+
+LibSBML comes with a selection of complete example programs in the
+top-level file directory named <code>examples</code>; code listings of
+these programs is included in the section titled <a
+href="examples.html">Examples</a> in this documentation.
+
+@section simple-programs Simple programs
+
+@li @ref echoSBML.cpp "echoSBML.cpp":
+Echos (and in the process, pretty prints) an SBML model.
+
+@li @ref readSBML.cpp "readSBML.cpp":
+A simple command-line program that reads an SBML file and prints
+some statistics about it.
+
+@li @ref printSBML.cpp "printSBML.cpp":
+Prints information about the top-level model in the given SBML file.
+
+@li @ref printRegisteredPackages.cpp "printRegisteredPackages.cpp":
+Prints the SBML Level 3 packages registered/installed in this copy of libSBML.
+
+@li @ref printSupported.cpp "printSupported.cpp":
+Prints the supported SBML Levels and Versions for this copy of libSBML.
+
+
+@section advanced-programs More advanced programs
+
+@li @ref addCVTerms.cpp "addCVTerms.cpp":
+Adds controlled vocabulary terms to a species in a model.
+
+@li @ref addCustomValidator.cpp "addCustomValidator.cpp":
+Example of creating a custom validator to be called during validation.
+
+@li @ref addModelHistory.cpp "addModelHistory.cpp":
+Adds a model history to a model.
+
+@li @ref addingEvidenceCodes_1.cpp "addingEvidenceCodes_1.cpp":
+Adds controlled vocabulary terms to a reaction in a model.
+
+@li @ref addingEvidenceCodes_2.cpp "addingEvidenceCodes_2.cpp":
+Adds evidence codes to a species in a model.
+
+@li @ref appendAnnotation.cpp "appendAnnotation.cpp":
+Adds annotation strings to a model and a species.
+
+@li @ref callExternalValidator.cpp "callExternalValidator.cpp":
+Example that shows how to call an external program for validation.
+
+@li @ref convertSBML.cpp "convertSBML.cpp":
+Example demonstrating how to convert SBML documents between SBML Levels.
+
+@li @ref createExampleSBML.cpp "createExampleSBML.cpp":
+Lengthy example of creating SBML models presented in the SBML specification.
+
+@li @ref getAllElementsWithNotes.cpp "getAllElementsWithNotes.cpp":
+Demonstrates how to use the element filter class to search the model
+for elements with specific attributes .
+
+@li @ref inlineFunctionDefintions.cpp "inlineFunctionDefintions.cpp":
+Loads an SBML File and inlines all the function definitions found in
+the model.
+
+@li @ref printAnnotation.cpp "printAnnotation.cpp":
+Prints the annotation strings for each element in a given model.
+
+@li @ref printMath.cpp "printMath.cpp":
+Prints the rule, reaction, and event formulas in a given SBML document.
+
+@li @ref printNotes.cpp "printNotes.cpp":
+Prints the notes strings for each element in a given model.
+
+@li @ref printUnits.cpp "printUnits.cpp":
+A command-line program that prints information about the units
+of measurement used in a given SBML file.
+
+@li @ref renameSId.cpp "renameSId.cpp":
+Program that renames a specific SId and updates all references to it
+in a given model.
+
+@li @ref rngvalidator.cpp "rngvalidator.cpp":
+Example of creating a RELAX NG (RNG) validator to be called during validation.
+
+@li @ref setIdFromNames.cpp "setIdFromNames.cpp":
+Program that renames all SIds that also have names specified. The new
+identifiers will be derived from the name, with all invalid characters removed.
+
+@li @ref stripPackage.cpp "stripPackage.cpp":
+Strips the given SBML Level 3 package from the given SBML file.
+
+@li @ref translateL3Math.cpp "translateL3Math.cpp":
+Translates infix formulas into MathML and vice-versa, using the SBML
+Level 3 parser instead of the old Level 1 parser.
+
+@li @ref translateMath.cpp "translateMath.cpp":
+Translates infix formulas into MathML and vice-versa.
+
+@li @ref unsetAnnotation.cpp "unsetAnnotation.cpp":
+Unsets the annotation for each element in the given SBML file.
+
+@li @ref unsetNotes.cpp "unsetNotes.cpp":
+Unsets the notes for each element in the given SBML file.
+
+@li @ref validateSBML.cpp "validateSBML.cpp":
+Validates one or more SBML files.
+
+
+@example addCVTerms.cpp
+Adds controlled vocabulary terms to a species in a model.
+
+@example addCustomValidator.cpp
+Example of creating a custom validator to be called during validation.
+
+@example addModelHistory.cpp
+Adds a model history to a model.
+
+@example addingEvidenceCodes_1.cpp
+Adds controlled vocabulary terms to a reaction in a model.
+
+@example addingEvidenceCodes_2.cpp
+Adds evidence codes to a species in a model.
+
+@example appendAnnotation.cpp
+Adds annotation strings to a model and a species.
+
+@example callExternalValidator.cpp
+Example that shows how to call an external program for validation.
+
+@example convertSBML.cpp
+Example demonstrating how to convert SBML documents between SBML Levels.
+
+@example createExampleSBML.cpp
+Lengthy example of creating SBML models presented in the SBML specification.
+
+@example echoSBML.cpp
+Echos (and in the process, pretty prints) an SBML model.
+
+@example getAllElementsWithNotes.cpp
+Demonstrates how to use the element filter class to search the model
+for elements with specific attributes .
+
+@example inlineFunctionDefintions.cpp
+Loads an SBML File and inlines all the function definitions found in
+the model.
+
+@example printAnnotation.cpp
+Prints the annotation strings for each element in a given model.
+
+@example printMath.cpp
+Prints the rule, reaction, and event formulas in a given SBML document.
+
+@example printNotes.cpp
+Prints the notes strings for each element in a given model.
+
+@example printRegisteredPackages.cpp
+Prints the SBML Level 3 packages registered/installed in this copy of libSBML.
+
+@example printSBML.cpp
+Prints information about the top-level model in the given SBML file.
+
+@example printSupported.cpp
+Prints the supported SBML Levels and Versions for this copy of libSBML.
+
+@example printUnits.cpp
+A command-line program that prints information about the units
+of measurement used in a given SBML file.
+
+@example readSBML.cpp
+A simple command-line program that reads an SBML file and prints
+some statistics about it.
+
+@example renameSId.cpp
+Program that renames a specific SId and updates all references to it
+in a given model.
+
+@example rngvalidator.cpp
+Example of creating a RELAX NG (RNG) validator to be called during validation.
+
+@example setIdFromNames.cpp
+Program that renames all SIds that also have names specified. The new
+identifiers will be derived from the name, with all invalid characters removed.
+
+@example stripPackage.cpp
+Strips the given SBML Level 3 package from the given SBML file.
+
+@example translateL3Math.cpp
+Translates infix formulas into MathML and vice-versa, using the SBML
+Level 3 parser instead of the old Level 1 parser.
+
+@example translateMath.cpp
+Translates infix formulas into MathML and vice-versa.
+
+@example unsetAnnotation.cpp
+Unsets the annotation for each element in the given SBML file.
+
+@example unsetNotes.cpp
+Unsets the notes for each element in the given SBML file.
+
+@example validateSBML.cpp
+Validates one or more SBML files.
+
+
+*/
+<!-- The following is for [X]Emacs users. Please leave in place. -->
+<!-- Local Variables: -->
+<!-- fill-column: 70 -->
+<!-- End: -->
Property changes on: trunk/libsbml/docs/src/libsbml-examples.txt
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2013-08-29 05:11:55
|
Revision: 18341
http://sourceforge.net/p/sbml/code/18341
Author: mhucka
Date: 2013-08-29 05:11:53 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
1) Fiddled with the styling of code examples so that they would work properly in the new "Examples" section.
2) Compressed the font in the tabs bar so that I could add the new "Examples" section up there.
Modified Paths:
--------------
trunk/libsbml/docs/src/doxygen-base-stylesheet.css
trunk/libsbml/docs/src/doxygen-tabs.css
Modified: trunk/libsbml/docs/src/doxygen-base-stylesheet.css
===================================================================
--- trunk/libsbml/docs/src/doxygen-base-stylesheet.css 2013-08-29 02:40:35 UTC (rev 18340)
+++ trunk/libsbml/docs/src/doxygen-base-stylesheet.css 2013-08-29 05:11:53 UTC (rev 18341)
@@ -173,10 +173,42 @@
margin-left: -1cm;
}
-.fragment {
+.contents div.fragment {
+ border: 1px solid orange;
+ background-color: #f0f0f0;
+ padding: 5px;
+ padding-top: 6px;
+ margin: 15px;
+ overflow: auto;
+ word-wrap: break-word;
+ line-height: 125%;
+ -webkit-border-top-left-radius: 8px;
+ -webkit-border-top-right-radius: 8px;
+ -moz-border-radius-topleft: 8px;
+ -moz-border-radius-topright: 8px;
+ -moz-border-radius-bottomleft: 8px;
+ -moz-border-radius-bottomright: 8px;
+ -webkit-border-bottom-left-radius: 8px;
+ -webkit-border-bottom-right-radius: 8px;
}
-div.fragment pre,
+.contents div.textblock div.fragment {
+ border: none;
+ background-color: white;
+ padding: 0;
+ padding-top: 0;
+ margin: 0;
+ line-height: 100%;
+ -webkit-border-top-left-radius: none;
+ -webkit-border-top-right-radius: none;
+ -moz-border-radius-topleft: none;
+ -moz-border-radius-topright: none;
+ -moz-border-radius-bottomleft: none;
+ -moz-border-radius-bottomright: none;
+ -webkit-border-bottom-left-radius: none;
+ -webkit-border-bottom-right-radius: none;
+}
+
pre.fragment {
font-family: "Courier New", Courier, monospace, fixed;
font-size: 9pt;
@@ -186,7 +218,7 @@
color: black;
padding: 5px;
padding-top: 6px;
- margin: 15px;
+ margin: 5px 15px 5px 15px;
overflow: auto;
word-wrap: break-word;
line-height: 125%;
Modified: trunk/libsbml/docs/src/doxygen-tabs.css
===================================================================
--- trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 02:40:35 UTC (rev 18340)
+++ trunk/libsbml/docs/src/doxygen-tabs.css 2013-08-29 05:11:53 UTC (rev 18341)
@@ -85,9 +85,11 @@
li a[href="usergroup0.html"],
li a[href="usergroup1.html"],
li a[href="group___core.html"],
+li a[href="examples.html"],
li a[href="functions.html"]
{
- width: 115px;
+ width: 100px;
+ letter-spacing: -1px;
}
#navrow1 {
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|
|
From: <mh...@us...> - 2013-08-29 02:40:39
|
Revision: 18340
http://sourceforge.net/p/sbml/code/18340
Author: mhucka
Date: 2013-08-29 02:40:35 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Pointed to MIRIAM and RDF documentation.
Modified Paths:
--------------
trunk/libsbml/src/sbml/annotation/ModelHistory.h
trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.h
Modified: trunk/libsbml/src/sbml/annotation/ModelHistory.h
===================================================================
--- trunk/libsbml/src/sbml/annotation/ModelHistory.h 2013-08-29 00:44:53 UTC (rev 18339)
+++ trunk/libsbml/src/sbml/annotation/ModelHistory.h 2013-08-29 02:40:35 UTC (rev 18340)
@@ -31,13 +31,13 @@
*
* @htmlinclude not-sbml-warning.html
*
- * The SBML specification beginning with Level 2 Version 2
- * defines a standard approach to recording optional model history and
- * model creator information in a form that complies with MIRIAM ("Minimum
- * Information Requested in the Annotation of biochemical Models",
- * <i>Nature Biotechnology</i>, vol. 23, no. 12, Dec. 2005). LibSBML
- * provides the ModelHistory class as a convenient high-level interface
- * for working with model history data.
+ * The SBML specification beginning with Level 2 Version 2 defines
+ * a standard approach to recording optional model history and model creator
+ * information in a form that complies with MIRIAM (<a target="_blank"
+ * href="miriam-2005.pdf">"Minimum Information Requested in the Annotation of
+ * biochemical Models"</a>, <i>Nature Biotechnology</i>, vol. 23, no. 12,
+ * Dec. 2005). LibSBML provides the ModelHistory class as a convenient
+ * high-level interface for working with model history data.
*
* Model histories in SBML consist of one or more <em>model creators</em>,
* a single date of @em creation, and one or more @em modification dates.
Modified: trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.h
===================================================================
--- trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.h 2013-08-29 00:44:53 UTC (rev 18339)
+++ trunk/libsbml/src/sbml/annotation/RDFAnnotationParser.h 2013-08-29 02:40:35 UTC (rev 18340)
@@ -34,22 +34,24 @@
*
* RDFAnnotationParser is a libSBML construct used as part of the libSBML
* support for annotations conforming to the guidelines specified by MIRIAM
- * ("Minimum Information Requested in the Annotation of biochemical
- * Models", <i>Nature Biotechnology</i>, vol. 23, no. 12, Dec. 2005).
- * Section 6 of the SBML Level 2 and Level 3 specification
- * documents defines a recommended way of encoding MIRIAM information using
- * a subset of RDF in SBML. The general scheme is as follows. A set of
- * RDF-based annotations attached to a given SBML
- * <code><annotation></code> element are read by RDFAnnotationParser
- * and converted into a list of CVTerm objects. There
- * are different versions of the main method,
- * @if clike RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %List *CVTerms)
- * @endif@if java RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %CVTermList *CVTerms) @endif@~
- * and RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation),
- * used depending on whether the annotation in question concerns the MIRIAM
- * model history or other MIRIAM resource annotations. A special object
- * class, ModelHistory, is used to make it easier to manipulate model
- * history annotations.
+ * (<a target="_blank" href="miriam-2005.pdf">"Minimum Information Requested
+ * in the Annotation of biochemical Models"</a>, <i>Nature Biotechnology</i>,
+ * vol. 23, no. 12, Dec. 2005). Section 6 of the SBML Level 2 and
+ * Level 3 specification documents defines a recommended way of encoding
+ * MIRIAM information using a subset of RDF (<a target="_blank"
+ * href="http://www.w3.org/RDF/">Resource Description Format</a>). The
+ * general scheme is as follows. A set of RDF-based annotations attached to
+ * a given SBML <code><annotation></code> element are read by
+ * RDFAnnotationParser and converted into a list of CVTerm objects. There
+ * are different versions of the main method, @if clike
+ * RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %List
+ * *CVTerms) @endif@if java RDFAnnotationParser::parseRDFAnnotation(const
+ * XMLNode *annotation, %CVTermList *CVTerms) @endif@~ and
+ * RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation), used
+ * depending on whether the annotation in question concerns the MIRIAM model
+ * history or other MIRIAM resource annotations. A special object class,
+ * ModelHistory, is used to make it easier to manipulate model history
+ * annotations.
*
* All of the methods on RDFAnnotationParser are static; the class exists
* only to encapsulate the annotation and CVTerm parsing and manipulation
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2013-08-29 00:44:55
|
Revision: 18339
http://sourceforge.net/p/sbml/code/18339
Author: mhucka
Date: 2013-08-29 00:44:53 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
1) Added better explanation of biological and model qualifiers.
2) Added documentation for the enumeration types.
Modified Paths:
--------------
trunk/libsbml/src/sbml/annotation/CVTerm.h
Modified: trunk/libsbml/src/sbml/annotation/CVTerm.h
===================================================================
--- trunk/libsbml/src/sbml/annotation/CVTerm.h 2013-08-29 00:43:49 UTC (rev 18338)
+++ trunk/libsbml/src/sbml/annotation/CVTerm.h 2013-08-29 00:44:53 UTC (rev 18339)
@@ -36,15 +36,15 @@
* terms and database identifiers that define and describe biological and
* biochemical entities, and (b) describing the creator of a model and the
* model's modification history. This SBML format is a concrete syntax that
- * conforms to the guidelines of MIRIAM ("Minimum Information Requested in
- * the Annotation of biochemical Models", <i>Nature Biotechnology</i>,
- * vol. 23, no. 12, Dec. 2005). The format uses a subset of W3C RDF (<a
- * target="_blank" href="http://www.w3.org/RDF/">Resource Description
- * Format</a>). In order to help application developers work with
- * annotations in this format, libSBML provides several helper classes that
- * provide higher-level interfaces to the data elements; these classes
- * include CVTerm, ModelCreator, ModelHistory, RDFAnnotationParser, and
- * Date.
+ * conforms to the guidelines of MIRIAM (<a target="_blank"
+ * href="miriam-2005.pdf">"Minimum Information Requested in the Annotation of
+ * biochemical Models"</a>, <i>Nature Biotechnology</i>, vol. 23, no. 12,
+ * Dec. 2005). The format uses a subset of W3C RDF (<a target="_blank"
+ * href="http://www.w3.org/RDF/">Resource Description Format</a>). In order
+ * to help application developers work with annotations in this format,
+ * libSBML provides several helper classes that provide higher-level
+ * interfaces to the data elements; these classes include CVTerm,
+ * ModelCreator, ModelHistory, RDFAnnotationParser, and Date.
*
* @section annotation-parts Components of an SBML annotation
*
@@ -101,19 +101,33 @@
* is a creation and modification history; in libSBML, this is stored
* using ModelHistory objects.
*
- * The placeholder <span class="code" style="background-color: #bbb">RELATION_ELEMENT</span>
- * refers to a BioModels.net qualifier element name. This is an element in
- * either the XML namespace
+ * The placeholder <span class="code" style="background-color:
+ * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier element
+ * name. This is an element in either the XML namespace
* <code>"http://biomodels.net/model-qualifiers"</code> (for model
- * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
- * (for biological qualifier). The <span class="code" style="background-color: #d0d0ee">URI</span>
- * is a required data value that uniquely identifies a resource and
- * data within that resource to which the annotation refers. (Since
- * a URI is only a label, not an address, applications will often
- * want a means of looking up the resource to which the URI refers.
- * Providing the facilities for doing this is the purpose of
- * <a target="_blank" href="http://biomodels.net/miriam">MIRIAM Resources</a>.)
+ * qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code> (for
+ * biological qualifier). Note that these namespace URIs are only labels,
+ * and not actual Web locations, which means you cannot visit an address such
+ * as <code>"http://biomodels.net/model-qualifiers"</code> in your browser or
+ * try to have your application access it. Refer instead to the enumerations
+ * #ModelQualifierType_t and #BiolQualifierType_t for a list of the available
+ * relationship elements that can be used for <span class="code"
+ * style="background-color: #bbb">RELATION_ELEMENT</span>.
*
+ * The <span class="code" style="background-color: #d0d0ee">URI</span> is a
+ * required data value that uniquely identifies a resource and data within
+ * that resource to which the annotation refers. Again, being URIs, these do
+ * not refer to physical Web locations; nevertheless, applications will often
+ * want a means of finding the resource to which a given <span class="code"
+ * style="background-color: #d0d0ee">URI</span> refers. Providing the
+ * facilities for this task is the purpose of MIRIAM Resources, described in
+ * detail online at <a target="_blank"
+ * href="http://biomodels.net/miriam">http://biomodels.net/miriam</a>) and
+ * also in the paper <a target="_blank"
+ * href="miriam-resources-2007.pdf">"MIRIAM Resources: tools to generate and
+ * resolve robust cross-references in Systems Biology"</a>, <i>BMC Systems
+ * Biology</i>, 58(1), 2007.
+ *
* The relation-resource pairs above are the "controlled vocabulary" terms
* that which CVTerm is designed to store and manipulate. The next section
* describes these parts in more detail. For more information about
@@ -172,36 +186,158 @@
LIBSBML_CPP_NAMESPACE_BEGIN
+
+/**
+ * @enum QualifierType_t
+ *
+ * Enumeration used to indicate the type of <a target="_blank"
+ * href="http://biomodels.net/qualifiers/">BioModels.net</a> in a given
+ * CVTerm object. The qualification of an annotation is important to convey
+ * the relationship between a given model component and the resource used to
+ * annotate it. This relationship is rarely one-to-one, and the information
+ * content of an annotation is greatly increased if one knows what it
+ * represents (as opposed to knowing only that the two "are related").
+ *
+ * In the SBML/MIRIAM/BioModels.net scheme of things, there are currently two
+ * kinds of qualifiers. They are used for different purposes. One purpose
+ * is in the refinement of the relationship between an annotation resource
+ * and the <em>modeling concept</em> represented by a model element. The
+ * second purpose is in the refinement of the relationship between an
+ * annotation resource and the <em>biological object</em> represented by a
+ * model element. In libSBML, each of these two categories of qualifiers
+ * have their own enumerations: #ModelQualifierType_t for the former type, and
+ * #BiolQualifierType_t for the latter.
+ *
+ * One can view the annotation of a model component as a statement in the
+ * form of a @em triple. The resource used in the annotation is the @em
+ * object, while the qualifier is the @em predicate. In situations where a
+ * model qualifier is used, the @em subject of the relation is the modeling
+ * concept represented by the model component referenced by the annotation.
+ * The modeling concept may be the model itself, a mathematical construct,
+ * or a hypothesis that is proposed, changing the way we previously
+ * understood the model, etc. Conversely, in situations where a biology
+ * qualifier is used, the @em subject of the relation is the biological or
+ * biochemical object represented by the enclosing model element.
+ */
typedef enum
{
- MODEL_QUALIFIER
- , BIOLOGICAL_QUALIFIER
+ MODEL_QUALIFIER /*!< The qualifier is a model qualifier. */
+ , BIOLOGICAL_QUALIFIER /*!< The qualifier is a biological qualifier. */
, UNKNOWN_QUALIFIER
} QualifierType_t;
+
+/**
+ * @enum ModelQualifierType_t
+ *
+ * Enumeration of possible <em>model qualifiers</em> used for annotations.
+ * Annotations with this type of qualifier express a relationship between an
+ * annotation resource and the <em>modeling concept</em> represented by a
+ * given object in the model. The diagram below illustrates the relationship
+ * in this case:
+ *
+ * @image html model-qualifiers.png "Relationship expressed by model qualifiers"
+ * @image latex model-qualifiers.png "Relationship expressed by model qualifiers"
+ * <br>
+ */
typedef enum
{
BQM_IS
+ /*!< The modeling entity represented by the object in the model is
+ * identical to the subject of the referenced resource. */
+
, BQM_IS_DESCRIBED_BY
+ /*!< The modeling entity represented by the object in the model is
+ * described by the subject of the referenced resource. For example,
+ * this relationship could be used to link a model element to a
+ * document (such as a paper published in the literature) describing
+ * the element. */
+
, BQM_IS_DERIVED_FROM
+ /*!< The modeling entity represented by the object in the model is
+ * derived from or adapted from the referenced resource. This relation
+ * could be used, for instance, to express a refinement or adaptation in
+ * usage of a model component located elsewere. */
, BQM_UNKNOWN
+ /*!< The relationship is unknown. */
+
} ModelQualifierType_t;
+
+/**
+ * @enum BiolQualifierType_t
+ *
+ * Enumeration of possible <em>biological qualifiers</em> used for
+ * annotations. Annotations with this type of qualifier express a
+ * relationship between an annotation resource and the <em>biological
+ * concept</em> represented by a given object in the model. The diagram
+ * below illustrates the relationship in this case:
+ *
+ * @image html biology-qualifiers.png "Relationship expressed by biological qualifiers"
+ * @image latex biology-qualifiers.png "Relationship expressed by biological qualifiers"
+ * <br>
+ */
typedef enum
{
BQB_IS
+ /*!< The biological entity represented by the object in the model is
+ * identical to the subject of the referenced resource. */
+
, BQB_HAS_PART
+ /*!< The biological entity represented by the object in the model
+ * includes the subject of the referenced resource. */
+
, BQB_IS_PART_OF
+ /*!< The biological entity represented by the object in the model is a
+ * physical or logical part of the subject of the referenced resource.
+ * For example, this could be used to indicate that the molecular entity
+ * represented by a given object in the model is part of the referenced
+ * molecular complex. */
+
, BQB_IS_VERSION_OF
+ /*!< The biological entity represented by the object in the model is a
+ * version or an instance of the subject of the referenced resource. */
+
, BQB_HAS_VERSION
+ /*!< The subject of the referenced resource is a version or an instance
+ * of the biological entity represented by the model element. */
+
, BQB_IS_HOMOLOG_TO
+ /*!< The biological entity represented by the object in the model is
+ * homologous to the subject of the referenced resource. */
+
, BQB_IS_DESCRIBED_BY
+ /*!< The biological entity represented by the object in the model is
+ * described by the subject of the referenced resource. This could be
+ * used, for example, to link a species or a parameter to the literature
+ * that describes the concentration of that species or the value of that
+ * parameter. */
+
, BQB_IS_ENCODED_BY
+ /*!< The biological entity represented by the object in the model is
+ * encoded, directly or transitively, by the subject of the referenced
+ * resource. */
+
, BQB_ENCODES
+ /*!< The biological entity represented by the object in the model encodes
+ * directly or transitively the subject of the referenced resource. */
+
, BQB_OCCURS_IN
+ /*!< The biological entity represented by the object in the model is
+ * physically limited to a location. The location is the subject of the
+ * referenced resource. */
+
, BQB_HAS_PROPERTY
+ /*!< The subject of the referenced resource is a property of the
+ * biological entity represented by the model element. */
+
, BQB_IS_PROPERTY_OF
+ /*!< The biological entity represented by the object in the model is
+ * a property of the referenced resource. */
+
, BQB_UNKNOWN
+ /*!< The relationship is unknown. */
+
} BiolQualifierType_t;
LIBSBML_CPP_NAMESPACE_END
@@ -223,7 +359,8 @@
public:
/**
- * Creates an empty CVTerm, optionally with the given @if clike #QualifierType_t value@else qualifier@endif@~ @p type.
+ * Creates an empty CVTerm, optionally with the given
+ * @if clike #QualifierType_t value@else qualifier@endif@~ @p type.
*
* The SBML Level 2 and Level 3 specifications define a simple
* format for annotating models when (a) referring to controlled
@@ -391,10 +528,19 @@
* (for biological qualifier). Callers will typically use
* getQualifierType() to find out the type of qualifier relevant to this
* particular CVTerm object, then if it is a @em model qualifier, use the
- * present method to determine the specific qualifier. The set of known
- * model qualifiers is, at the time of this libSBML release, the
- * following:
+ * present method to determine the specific qualifier.
*
+ * Annotations with model qualifiers express a relationship between an
+ * annotation resource and the <em>modeling concept</em> represented by a
+ * given object in the model. The diagram below illustrates the
+ * relationship in this case:
+ *
+ * @image html model-qualifiers.png "Relationship expressed by model qualifiers"
+ * @image latex model-qualifiers.png "Relationship expressed by model qualifiers"
+ *
+ * <br> The set of known model qualifiers is, at the time of this libSBML
+ * release, the following:
+ *
* @li @link ModelQualifierType_t#BQM_IS BQM_IS@endlink
* @li @link ModelQualifierType_t#BQM_IS_DESCRIBED_BY BQM_IS_DESCRIBED_BY@endlink
* @li @link ModelQualifierType_t#BQM_IS_DERIVED_FROM BQM_IS_DERIVED_FROM@endlink
@@ -423,10 +569,19 @@
* (for biological qualifier). Callers will typically use
* getQualifierType() to find out the type of qualifier relevant to this
* particular CVTerm object, then if it is a @em biological qualifier,
- * use the present method to determine the specific qualifier. The set
- * of known biological qualifiers is, at the time of this libSBML
- * release, the following:
+ * use the present method to determine the specific qualifier.
*
+ * Annotations with biological qualifiers express a relationship between an
+ * annotation resource and the <em>biological concept</em> represented by a
+ * given object in the model. The diagram
+ * below illustrates the relationship in this case:
+ *
+ * @image html biology-qualifiers.png "Relationship expressed by biological qualifiers"
+ * @image latex biology-qualifiers.png "Relationship expressed by biological qualifiers"
+ *
+ * <br> The set of known biological qualifiers is, at the time of this
+ * libSBML release, the following:
+ *
* @li @link BiolQualifierType_t#BQB_IS BQB_IS@endlink
* @li @link BiolQualifierType_t#BQB_HAS_PART BQB_HAS_PART@endlink
* @li @link BiolQualifierType_t#BQB_IS_PART_OF BQB_IS_PART_OF@endlink
@@ -628,7 +783,8 @@
/**
- * Sets the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif@~ of this CVTerm object.
+ * Sets the @if clike #BiolQualifierType_t@endif@if java biology qualifier
+ * type code@endif@~ of this CVTerm object.
*
* @param qualifier the string representing a biology qualifier
*
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|
|
From: <mh...@us...> - 2013-08-29 00:43:52
|
Revision: 18338
http://sourceforge.net/p/sbml/code/18338
Author: mhucka
Date: 2013-08-29 00:43:49 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Added papers and new graphics.
Modified Paths:
--------------
trunk/libsbml/docs/src/Makefile.in
Modified: trunk/libsbml/docs/src/Makefile.in
===================================================================
--- trunk/libsbml/docs/src/Makefile.in 2013-08-29 00:42:54 UTC (rev 18337)
+++ trunk/libsbml/docs/src/Makefile.in 2013-08-29 00:43:49 UTC (rev 18338)
@@ -196,6 +196,7 @@
force-serif-font-off.html \
force-serif-font-on.html \
graphics/astnode-illustration.jpg \
+ graphics/biology-qualifiers.png \
graphics/built-in-units.jpg \
graphics/cmake-configure-macos.png \
graphics/cmake-configure-windows.png \
@@ -213,6 +214,7 @@
graphics/listof-illustration.txt \
graphics/math-formula-precedence.jpg \
graphics/math-string-functions.jpg \
+ graphics/model-qualifiers.png \
graphics/official-sbml-supported-32.jpg \
graphics/official-sbml-supported-40.jpg \
graphics/official-sbml-supported-70.png \
@@ -317,6 +319,8 @@
libsbml-python-reading-files.txt \
libsbml-reading-files.txt \
libsbml-release-info.txt \
+ papers/miriam-2005.pdf \
+ papers/miriam-resources-2007.pdf \
plain-font-off.html \
plain-font-on.html \
python-substitutions/ASTNodeList.py \
@@ -461,6 +465,7 @@
cp graphics/*.png $(1)
cp common-text/simple-ast.svg $(1)
cp sbml.js $(1)
+ cp papers/*.pdf $(1)
cp -rf doxygen-tabs.css $(1)/tabs.css
cp -rf doxygen-navtree.css $(1)/navtree.css
endef
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2013-08-29 00:42:58
|
Revision: 18337
http://sourceforge.net/p/sbml/code/18337
Author: mhucka
Date: 2013-08-29 00:42:54 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
I'm going to start putting papers so that we can reference them directly in the documentation and ship them with the docs too.
Added Paths:
-----------
trunk/libsbml/docs/src/papers/
trunk/libsbml/docs/src/papers/miriam-2005.pdf
trunk/libsbml/docs/src/papers/miriam-resources-2007.pdf
Added: trunk/libsbml/docs/src/papers/miriam-2005.pdf
===================================================================
(Binary files differ)
Index: trunk/libsbml/docs/src/papers/miriam-2005.pdf
===================================================================
--- trunk/libsbml/docs/src/papers/miriam-2005.pdf 2013-08-29 00:41:16 UTC (rev 18336)
+++ trunk/libsbml/docs/src/papers/miriam-2005.pdf 2013-08-29 00:42:54 UTC (rev 18337)
Property changes on: trunk/libsbml/docs/src/papers/miriam-2005.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
Added: trunk/libsbml/docs/src/papers/miriam-resources-2007.pdf
===================================================================
(Binary files differ)
Index: trunk/libsbml/docs/src/papers/miriam-resources-2007.pdf
===================================================================
--- trunk/libsbml/docs/src/papers/miriam-resources-2007.pdf 2013-08-29 00:41:16 UTC (rev 18336)
+++ trunk/libsbml/docs/src/papers/miriam-resources-2007.pdf 2013-08-29 00:42:54 UTC (rev 18337)
Property changes on: trunk/libsbml/docs/src/papers/miriam-resources-2007.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/pdf
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2013-08-29 00:41:23
|
Revision: 18336
http://sourceforge.net/p/sbml/code/18336
Author: mhucka
Date: 2013-08-29 00:41:16 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
Added a couple of new figures. Graphics originally created by Nicolas Le Novere, and I stole them from http://mbine.org/standards/qualifiers.
Added Paths:
-----------
trunk/libsbml/docs/src/graphics/biology-qualifiers.png
trunk/libsbml/docs/src/graphics/model-qualifiers.png
Added: trunk/libsbml/docs/src/graphics/biology-qualifiers.png
===================================================================
(Binary files differ)
Index: trunk/libsbml/docs/src/graphics/biology-qualifiers.png
===================================================================
--- trunk/libsbml/docs/src/graphics/biology-qualifiers.png 2013-08-28 04:28:30 UTC (rev 18335)
+++ trunk/libsbml/docs/src/graphics/biology-qualifiers.png 2013-08-29 00:41:16 UTC (rev 18336)
Property changes on: trunk/libsbml/docs/src/graphics/biology-qualifiers.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/png
\ No newline at end of property
Added: trunk/libsbml/docs/src/graphics/model-qualifiers.png
===================================================================
(Binary files differ)
Index: trunk/libsbml/docs/src/graphics/model-qualifiers.png
===================================================================
--- trunk/libsbml/docs/src/graphics/model-qualifiers.png 2013-08-28 04:28:30 UTC (rev 18335)
+++ trunk/libsbml/docs/src/graphics/model-qualifiers.png 2013-08-29 00:41:16 UTC (rev 18336)
Property changes on: trunk/libsbml/docs/src/graphics/model-qualifiers.png
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+image/png
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2013-08-28 04:28:35
|
Revision: 18335
http://sourceforge.net/p/sbml/code/18335
Author: mhucka
Date: 2013-08-28 04:28:30 +0000 (Wed, 28 Aug 2013)
Log Message:
-----------
Fixed up doxygen conditional names to account for doxygen's new parsing behavior.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.c
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysASTPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysCompartmentPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysConstraintPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventAssignmentPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysExtension.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysInitialAssignmentPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysParameterPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysReactionPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysRulePlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesPlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesReferencePlugin.h
branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.cpp
branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.h
branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.cpp
branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.h
branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.h
branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribFunctionDefinitionPlugin.h
branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribSBasePlugin.h
branches/libsbml-experimental/src/sbml/packages/distrib/sbml/DistribInput.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/sbml/DistribInput.h
branches/libsbml-experimental/src/sbml/packages/distrib/sbml/DrawFromDistribution.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/sbml/DrawFromDistribution.h
branches/libsbml-experimental/src/sbml/packages/distrib/sbml/Uncertainty.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/sbml/Uncertainty.h
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribIdentifierConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribIdentifierConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribValidator.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/validator/DistribValidator.h
branches/libsbml-experimental/src/sbml/packages/distrib/validator/constraints/DistribConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/distrib/validator/constraints/DistribIdentifierConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsExtension.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsExtension.h
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/GroupsSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/groups/extension/test/TestGroupsExtension.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/test/TestReadGroupsExtension.cpp
branches/libsbml-experimental/src/sbml/packages/groups/extension/test/TestWriteGroupsExtension.cpp
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Group.cpp
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Group.h
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Member.cpp
branches/libsbml-experimental/src/sbml/packages/groups/sbml/Member.h
branches/libsbml-experimental/src/sbml/packages/groups/sbml/MemberConstraint.cpp
branches/libsbml-experimental/src/sbml/packages/groups/sbml/MemberConstraint.h
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsIdentifierConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsIdentifierConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsValidator.cpp
branches/libsbml-experimental/src/sbml/packages/groups/validator/GroupsValidator.h
branches/libsbml-experimental/src/sbml/packages/groups/validator/constraints/GroupsConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/groups/validator/constraints/GroupsIdentifierConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/layout/util/LayoutAnnotation.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualExtension.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualExtension.h
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualModelPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualSBMLDocumentPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/QualSBMLDocumentPlugin.h
branches/libsbml-experimental/src/sbml/packages/qual/extension/test/TestQualExtension.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/test/TestReadQualExtension.cpp
branches/libsbml-experimental/src/sbml/packages/qual/extension/test/TestWriteQualExtension.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/DefaultTerm.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/DefaultTerm.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/FunctionTerm.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/FunctionTerm.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Input.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Input.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Output.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Output.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/QualitativeSpecies.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/QualitativeSpecies.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Transition.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/Transition.h
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestCopyAndClone.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestDefaultTerm.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestFunctionTerm.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestInput.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestListOfFunctionTerms.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestOutput.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestQualitativeSpecies.cpp
branches/libsbml-experimental/src/sbml/packages/qual/sbml/test/TestTransition.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualIdentifierConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualIdentifierConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualMathConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualMathConsistencyValidator.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualSBMLErrorTable.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualValidator.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/QualValidator.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QSAssignedOnce.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QSAssignedOnce.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualCSymbolMathCheck.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualCSymbolMathCheck.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualIdentifierConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualMathConsistencyConstraints.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualUniqueModelWideIds.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/QualUniqueModelWideIds.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/ResultBecomesNegative.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/ResultBecomesNegative.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/ResultExceedsMaximum.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/constraints/ResultExceedsMaximum.h
branches/libsbml-experimental/src/sbml/packages/qual/validator/test/TestFile.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/test/TestQualConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/qual/validator/test/TestValidator.cpp
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderExtension.h
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderGraphicalObjectPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderGraphicalObjectPlugin.h
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderLayoutPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderLayoutPlugin.h
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderListOfLayoutsPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/render/extension/RenderListOfLayoutsPlugin.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/ColorDefinition.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/ColorDefinition.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Ellipse.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Ellipse.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GlobalRenderInformation.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GlobalRenderInformation.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GlobalStyle.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GlobalStyle.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientBase.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientBase.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientStop.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GradientStop.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive1D.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive2D.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/GraphicalPrimitive2D.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Image.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Image.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/LineEnding.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/LineEnding.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/LinearGradient.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/LinearGradient.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/ListOfCurveElements.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/ListOfCurveElements.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/LocalRenderInformation.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/LocalRenderInformation.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/LocalStyle.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/LocalStyle.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Polygon.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Polygon.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RadialGradient.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RadialGradient.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Rectangle.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Rectangle.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RelAbsVector.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RelAbsVector.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderCubicBezier.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderCubicBezier.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderCurve.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderCurve.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderGroup.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderGroup.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderInformationBase.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderInformationBase.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderPoint.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/RenderPoint.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Style.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Style.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Text.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Text.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation2D.cpp
branches/libsbml-experimental/src/sbml/packages/render/sbml/Transformation2D.h
branches/libsbml-experimental/src/sbml/packages/render/sbml/files.txt
branches/libsbml-experimental/src/sbml/packages/render/util/RenderLayoutConverter.cpp
branches/libsbml-experimental/src/sbml/packages/render/util/RenderLayoutConverter.h
branches/libsbml-experimental/src/sbml/packages/req/extension/RequiredElementsExtension.h
branches/libsbml-experimental/src/sbml/packages/req/extension/RequiredElementsSBasePlugin.cpp
branches/libsbml-experimental/src/sbml/packages/req/extension/RequiredElementsSBasePlugin.h
branches/libsbml-experimental/src/sbml/packages/spatial/extension/SpatialCompartmentPlugin.h
branches/libsbml-experimental/src/sbml/packages/spatial/extension/SpatialExtension.h
branches/libsbml-experimental/src/sbml/packages/spatial/extension/SpatialModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/spatial/extension/SpatialParameterPlugin.h
branches/libsbml-experimental/src/sbml/packages/spatial/extension/SpatialSpeciesRxnPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/extension/SpatialSpeciesRxnPlugin.h
branches/libsbml-experimental/src/sbml/packages/spatial/extension/test/TestReadSpatialExtension.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/extension/test/TestSpatialExtension.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/extension/test/TestWriteSpatialExtension.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AdjacentDomains.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AdvectionCoefficient.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticGeometry.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticGeometry.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/AnalyticVolume.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/Boundary.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/BoundaryCondition.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGHomogeneousTransformation.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGNode.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGNode.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGObject.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGObject.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPrimitive.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGPseudoPrimitive.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGRotation.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGScale.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGSetOperator.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTransformation.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGTranslation.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGeometry.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CSGeometry.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CompartmentMapping.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/CoordinateComponent.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/DiffusionCoefficient.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/Domain.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/DomainType.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/Geometry.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/Geometry.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/GeometryDefinition.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/GeometryDefinition.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ImageData.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ImageData.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/InteriorPoint.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricGeometry.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricGeometry.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/ParametricObject.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/PolygonObject.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/PolygonObject.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledField.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledFieldGeometry.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledFieldGeometry.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SampledVolume.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialPoint.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/SpatialSymbolReference.h
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/TransformationComponents.cpp
branches/libsbml-experimental/src/sbml/packages/spatial/sbml/TransformationComponents.h
Modified: branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.c
===================================================================
--- branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.c 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/math/FormulaTokenizer.c 2013-08-28 04:28:30 UTC (rev 18335)
@@ -86,7 +86,7 @@
}
-/** @cond doxygen-internal-libsbml */
+/** @cond doxygenLibsbmlInternal */
/*
* Reads a TT_NAME from the FormulaTokenizer into the given Token. This is
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysASTPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysASTPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysASTPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -111,7 +111,7 @@
//
// ---------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument of this plugin object.
@@ -160,7 +160,7 @@
*/
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual NewASTNode* getMath() const;
@@ -182,14 +182,14 @@
virtual const char * getNameFromType(int type) const;
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*-- data members --*/
NewASTNode* mMath;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
LIBSBML_CPP_NAMESPACE_END
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysCompartmentPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysCompartmentPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysCompartmentPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumDimensions () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysConstraintPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysConstraintPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysConstraintPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumDimensions () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventAssignmentPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventAssignmentPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventAssignmentPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumIndexs () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfIndices mIndexs;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysEventPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumDimensions () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysExtension.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysExtension.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysExtension.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -217,7 +217,7 @@
virtual const char* getStringFromTypeCode(int typeCode) const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Initializes arrays extension by creating an object of this class with
@@ -233,7 +233,7 @@
static void init();
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysInitialAssignmentPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysInitialAssignmentPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysInitialAssignmentPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -93,7 +93,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -106,10 +106,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -118,7 +118,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -370,7 +370,7 @@
unsigned int getNumIndexs () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -378,7 +378,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -390,12 +390,12 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
ListOfIndices mIndexs;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysParameterPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysParameterPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysParameterPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumDimensions () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysReactionPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysReactionPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysReactionPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumDimensions () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysRulePlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysRulePlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysRulePlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -93,7 +93,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -106,10 +106,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -118,7 +118,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -370,7 +370,7 @@
unsigned int getNumIndexs () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -378,7 +378,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -390,12 +390,12 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
ListOfIndices mIndexs;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -255,7 +255,7 @@
unsigned int getNumDimensions () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -263,7 +263,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -275,11 +275,11 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesReferencePlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesReferencePlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/extension/ArraysSpeciesReferencePlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -93,7 +93,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -106,10 +106,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -118,7 +118,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -370,7 +370,7 @@
unsigned int getNumIndexs () const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -378,7 +378,7 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
@@ -390,12 +390,12 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
ListOfDimensions mDimensions;
ListOfIndices mIndexs;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.cpp 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.cpp 2013-08-28 04:28:30 UTC (rev 18335)
@@ -333,7 +333,7 @@
}
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* write contained elements
@@ -346,10 +346,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Accepts the given SBMLVisitor.
@@ -362,10 +362,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Sets the parent SBMLDocument.
@@ -377,10 +377,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Enables/Disables the given package with this element.
@@ -393,10 +393,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Get the list of expected attributes for this element.
@@ -412,10 +412,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Read values from the given XMLAttributes set into their specific fields.
@@ -484,10 +484,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Write values of XMLAttributes to the output stream.
@@ -511,7 +511,7 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/*
@@ -652,7 +652,7 @@
}
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Creates a new Dimension in this ListOfDimensions
@@ -674,10 +674,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Write the namespace for the Arrays package.
@@ -701,7 +701,7 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Dimension.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -309,7 +309,7 @@
virtual bool hasRequiredAttributes() const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to write out their contained
@@ -319,10 +319,10 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor.
@@ -330,10 +330,10 @@
virtual bool accept (SBMLVisitor& v) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -341,10 +341,10 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Enables/Disables the given package with this element.
@@ -353,12 +353,12 @@
const std::string& pkgPrefix, bool flag);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Get the list of expected attributes for this element.
@@ -366,10 +366,10 @@
virtual void addExpectedAttributes(ExpectedAttributes& attributes);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Read values from the given XMLAttributes set into their specific fields.
@@ -378,10 +378,10 @@
const ExpectedAttributes& expectedAttributes);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Write values of XMLAttributes to the output stream.
@@ -389,7 +389,7 @@
virtual void writeAttributes (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
@@ -595,7 +595,7 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Creates a new Dimension in this ListOfDimensions
@@ -603,10 +603,10 @@
virtual SBase* createObject(XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Write the namespace for the Arrays package.
@@ -614,7 +614,7 @@
virtual void writeXMLNS(XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.cpp 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.cpp 2013-08-28 04:28:30 UTC (rev 18335)
@@ -240,7 +240,7 @@
}
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* write contained elements
@@ -257,10 +257,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Accepts the given SBMLVisitor.
@@ -273,10 +273,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Sets the parent SBMLDocument.
@@ -288,10 +288,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Enables/Disables the given package with this element.
@@ -304,10 +304,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Get the list of expected attributes for this element.
@@ -320,10 +320,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Read values from the given XMLAttributes set into their specific fields.
@@ -339,10 +339,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
bool
Index::readOtherXML (XMLInputStream& stream)
@@ -377,10 +377,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Write values of XMLAttributes to the output stream.
@@ -395,7 +395,7 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/*
@@ -536,7 +536,7 @@
}
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Creates a new Index in this ListOfIndices
@@ -558,10 +558,10 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Write the namespace for the Arrays package.
@@ -585,7 +585,7 @@
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
Modified: branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/arrays/sbml/Index.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -227,7 +227,7 @@
virtual bool hasRequiredElements() const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to write out their contained
@@ -237,10 +237,10 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Accepts the given SBMLVisitor.
@@ -248,10 +248,10 @@
virtual bool accept (SBMLVisitor& v) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -259,10 +259,10 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Enables/Disables the given package with this element.
@@ -271,12 +271,12 @@
const std::string& pkgPrefix, bool flag);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Get the list of expected attributes for this element.
@@ -284,10 +284,10 @@
virtual void addExpectedAttributes(ExpectedAttributes& attributes);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Read values from the given XMLAttributes set into their specific fields.
@@ -296,10 +296,10 @@
const ExpectedAttributes& expectedAttributes);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method ro read other XML.
@@ -309,10 +309,10 @@
virtual bool readOtherXML (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Write values of XMLAttributes to the output stream.
@@ -320,7 +320,7 @@
virtual void writeAttributes (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
@@ -526,7 +526,7 @@
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Creates a new Index in this ListOfIndices
@@ -534,10 +534,10 @@
virtual SBase* createObject(XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Write the namespace for the Arrays package.
@@ -545,7 +545,7 @@
virtual void writeXMLNS(XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
Modified: branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.cpp 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.cpp 2013-08-28 04:28:30 UTC (rev 18335)
@@ -368,7 +368,7 @@
}
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Return error table entry.
@@ -379,10 +379,10 @@
return distribErrorTable[index];
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Return error table index for this id.
@@ -406,10 +406,10 @@
return index;
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/*
* Return error offset.
@@ -420,7 +420,7 @@
return 5000000;
}
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
Modified: branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribExtension.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -217,7 +217,7 @@
virtual const char* getStringFromTypeCode(int typeCode) const;
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Initializes distrib extension by creating an object of this class with
@@ -233,10 +233,10 @@
static void init();
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Return the entry in the error table at this index.
@@ -248,10 +248,10 @@
virtual packageErrorTableEntry getErrorTable(unsigned int index) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Return the index in the error table with the given errorId.
@@ -263,10 +263,10 @@
virtual unsigned int getErrorTableIndex(unsigned int errorId) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Return the offset for the errorId range for the distrib L3 package.
@@ -276,7 +276,7 @@
virtual unsigned int getErrorIdOffset() const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribFunctionDefinitionPlugin.h
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribFunctionDefinitionPlugin.h 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribFunctionDefinitionPlugin.h 2013-08-28 04:28:30 UTC (rev 18335)
@@ -92,7 +92,7 @@
//
//---------------------------------------------------------------
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to create, store, and then
@@ -105,10 +105,10 @@
virtual SBase* createObject (XMLInputStream& stream);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Subclasses must override this method to write out their contained
@@ -117,7 +117,7 @@
virtual void writeElements (XMLOutputStream& stream) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
/**
@@ -181,7 +181,7 @@
DrawFromDistribution* createDrawFromDistribution ();
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument.
@@ -189,40 +189,40 @@
virtual void setSBMLDocument (SBMLDocument* d);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
virtual void connectToParent (SBase* sbase);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
virtual void enablePackageInternal(const std::string& pkgURI,
const std::string& pkgPrefix, bool flag);
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
virtual bool accept (SBMLVisitor& v) const;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
protected:
- /** @cond doxygen-libsbml-internal */
+ /** @cond doxygenLibsbmlInternal */
DrawFromDistribution* mDrawFromDistribution;
- /** @endcond doxygen-libsbml-internal */
+ /** @endcond doxygenLibsbmlInternal */
};
Modified: branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribSBMLDocumentPlugin.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/distrib/extension/DistribSBMLDocumentPlugin.cpp 2013-08-27 21:50:45 UTC (rev 18334)
+++ branches/libsbml-experimenta...
[truncated message content] |
|
From: <luc...@us...> - 2013-08-27 21:50:48
|
Revision: 18334
http://sourceforge.net/p/sbml/code/18334
Author: luciansmith
Date: 2013-08-27 21:50:45 +0000 (Tue, 27 Aug 2013)
Log Message:
-----------
Comment typo fix.
Modified Paths:
--------------
trunk/libsbml/src/sbml/SBase.h
Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h 2013-08-25 16:00:29 UTC (rev 18333)
+++ trunk/libsbml/src/sbml/SBase.h 2013-08-27 21:50:45 UTC (rev 18334)
@@ -2997,7 +2997,7 @@
* implementation of this method as well. For example:@if clike
* <pre>
* SBase::writeElements();
- * mReactans.write(stream);
+ * mReactants.write(stream);
* mProducts.write(stream);
* ...
* </pre>@endif@~
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2013-08-25 16:00:33
|
Revision: 18333
http://sourceforge.net/p/sbml/code/18333
Author: luciansmith
Date: 2013-08-25 16:00:29 +0000 (Sun, 25 Aug 2013)
Log Message:
-----------
Forgot to add the actual file...
Added Paths:
-----------
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replacedby_unknown.xml
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replacedby_unknown.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replacedby_unknown.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replacedby_unknown.xml 2013-08-25 16:00:29 UTC (rev 18333)
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:replacedBy comp:idRef="y" comp:submodelRef="A"/>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fbe...@us...> - 2013-08-24 18:06:14
|
Revision: 18332
http://sourceforge.net/p/sbml/code/18332
Author: fbergmann
Date: 2013-08-24 18:06:10 +0000 (Sat, 24 Aug 2013)
Log Message:
-----------
- correct universal binary issue, when SYSROOT not set; - fix comp function visibility, so it will compile
Modified Paths:
--------------
trunk/libsbml/CMakeLists.txt
trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h
Modified: trunk/libsbml/CMakeLists.txt
===================================================================
--- trunk/libsbml/CMakeLists.txt 2013-08-24 00:25:19 UTC (rev 18331)
+++ trunk/libsbml/CMakeLists.txt 2013-08-24 18:06:10 UTC (rev 18332)
@@ -619,19 +619,34 @@
set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING
"A semicolon-separated list of build architectures to be used.")
if(ENABLE_UNIVERSAL)
+
# if universal binaries are requested and none defined so far
# overwrite them with all three common architectures. If the user
# specified their own list of architectures do not touch!
if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
+
STRING(REGEX REPLACE "^.*MacOSX([0-9]*\\.[0-9]*)\\.sdk$" "\\1"
OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}")
- if(OSX_SDK_VERSION VERSION_EQUAL "10.7" OR OSX_SDK_VERSION VERSION_EQUAL "10.8")
+
+ if(OSX_SDK_VERSION VERSION_EQUAL "10.7" OR
+ OSX_SDK_VERSION VERSION_GREATER "10.7" OR
+ OSX_SDK_VERSION VERSION_EQUAL "10.8" OR
+ OSX_SDK_VERSION VERSION_GREATER "10.8")
+
# OSX Lion no longer supports ppc architecture
set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
"A semicolon-separated list of build architectures to be used." FORCE)
- else()
+
+ elseif(OSX_SDK_VERSION AND OSX_SDK_VERSION VERSION_LESS "10.7" )
+
set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING
"A semicolon-separated list of build architectures to be used." FORCE)
+
+ else()
+
+ set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
+ "A semicolon-separated list of build architectures to be used." FORCE)
+
endif()
endif()
endif(ENABLE_UNIVERSAL)
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h 2013-08-24 00:25:19 UTC (rev 18331)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h 2013-08-24 18:06:10 UTC (rev 18332)
@@ -226,7 +226,7 @@
bool hasValidLevelVersionNamespaceCombination();
/** @endcond */
-
+public:
/** @cond doxygenLibsbmlInternal */
/**
* Remove the given SBase object, and any Ports that point to it.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2013-08-24 00:25:22
|
Revision: 18331
http://sourceforge.net/p/sbml/code/18331
Author: luciansmith
Date: 2013-08-24 00:25:19 +0000 (Sat, 24 Aug 2013)
Log Message:
-----------
* Many more tests for flattening models with unknown namespaces.
* Almost fixed a bug in flattening where if an unknown namespace/package came in, but flattening failed, the document would be changed. Stymied by the lack of ability to set the 'required' flag for unknown packages.
Modified Paths:
--------------
trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h
trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp
trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp
Added Paths:
-----------
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml
Modified: trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp 2013-08-24 00:25:19 UTC (rev 18331)
@@ -65,6 +65,7 @@
CompFlatteningConverter::CompFlatteningConverter() : SBMLConverter()
+ , mDisabledPackages()
{
}
@@ -73,6 +74,7 @@
CompFlatteningConverter::CompFlatteningConverter
(const CompFlatteningConverter& orig) :
SBMLConverter(orig)
+ , mDisabledPackages(orig.mDisabledPackages)
{
}
@@ -141,6 +143,7 @@
if (canFlatten == false)
{
+ restoreNamespaces();
return LIBSBML_OPERATION_FAILED;
}
@@ -179,6 +182,7 @@
if (errors > 0)
{
+ restoreNamespaces();
return LIBSBML_CONV_INVALID_SRC_DOCUMENT;
}
}
@@ -186,6 +190,7 @@
if (modelPlugin==NULL)
{
+ restoreNamespaces();
return LIBSBML_OPERATION_FAILED;
}
@@ -205,6 +210,7 @@
if (flatmodel == NULL)
{
//'flattenModel' sets its own error messages.
+ restoreNamespaces();
return LIBSBML_OPERATION_FAILED;
}
@@ -240,6 +246,7 @@
result = reconstructDocument(flatmodel, *(dummy) );
if (result != LIBSBML_OPERATION_SUCCESS)
{
+ restoreNamespaces();
return result;
}
@@ -280,6 +287,7 @@
}
}
delete dummy;
+ restoreNamespaces();
return LIBSBML_CONV_INVALID_SRC_DOCUMENT;
}
else
@@ -303,6 +311,7 @@
if (result != LIBSBML_OPERATION_SUCCESS)
{
+ restoreNamespaces();
return result;
}
@@ -473,7 +482,7 @@
}
bool
-CompFlatteningConverter::canBeFlattened() const
+CompFlatteningConverter::canBeFlattened()
{
bool canFlatten = true;
@@ -547,7 +556,8 @@
{
unsigned int warningnumber = CompFlatteningNotRecognisedNotReqd;
std::string message = "The ";
- if (mDocument->getPackageRequired(ns->getURI(i))) {
+ bool required = mDocument->getPackageRequired(ns->getURI(i));
+ if (required) {
message += "required ";
warningnumber = CompFlatteningNotRecognisedReqd;
}
@@ -556,8 +566,11 @@
if (getIgnorePackages())
{
//LS DEBUG: This will change the original document even if flattening fails for some other reason (BUG)
- mDocument->enablePackageInternal(ns->getURI(i),
- ns->getPrefix(i), false);
+ string nsURI = ns->getURI(i);
+ string nsPrefix = ns->getPrefix(i);
+ mDocument->enablePackageInternal(nsURI, nsPrefix, false);
+ mDisabledPackages.insert(make_pair(nsURI, nsPrefix));
+ mPackageRequired.insert(make_pair(nsURI, required));
}
mDocument->getErrorLog()->logPackageError("comp",
warningnumber,
@@ -572,8 +585,9 @@
{
unsigned int warningnumber = CompFlatteningNotImplementedNotReqd;
std::string message = "The ";
- if (static_cast<SBMLDocumentPlugin*>(mDocument->getPlugin(i))
- ->getRequired())
+ bool required = static_cast<SBMLDocumentPlugin*>(mDocument->getPlugin(i))
+ ->getRequired();
+ if (required)
{
message += "required ";
warningnumber = CompFlatteningNotImplementedReqd;
@@ -586,6 +600,8 @@
std::string pkgURI = mDocument->getPlugin(i)->getURI();
std::string prefix = mDocument->getPlugin(i)->getPrefix();
mDocument->disablePackage(pkgURI, prefix);
+ mDisabledPackages.insert(make_pair(pkgURI, prefix));
+ mPackageRequired.insert(make_pair(pkgURI, required));
}
mDocument->getErrorLog()->logPackageError("comp",
@@ -598,6 +614,21 @@
return canFlatten;
}
+void CompFlatteningConverter::restoreNamespaces()
+{
+ for (set<pair<string, string> >::iterator pkg = mDisabledPackages.begin();
+ pkg != mDisabledPackages.end(); pkg++)
+ {
+ mDocument->enablePackageInternal((*pkg).first, (*pkg).second, true);
+ }
+ for (set<pair<string, bool> >::iterator pkg = mPackageRequired.begin();
+ pkg != mPackageRequired.end(); pkg++)
+ {
+ //Note: the following does not work for unrecognized packages. LS DEBUG
+ mDocument->setPackageRequired((*pkg).first, (*pkg).second);
+ }
+}
+
/** @cond doxygenCOnly */
Modified: trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.h 2013-08-24 00:25:19 UTC (rev 18331)
@@ -130,8 +130,13 @@
bool getPerformValidation() const;
- bool canBeFlattened() const;
+ bool canBeFlattened();
+ void restoreNamespaces();
+
+ std::set<std::pair<std::string, std::string> > mDisabledPackages;
+ std::set<std::pair<std::string, bool > > mPackageRequired;
+
};
LIBSBML_CPP_NAMESPACE_END
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp 2013-08-24 00:25:19 UTC (rev 18331)
@@ -3619,7 +3619,49 @@
}
END_TEST
+START_TEST(test_comp_flatten_invalid77)
+{
+ ConversionProperties* props = new ConversionProperties();
+
+ props->addOption("flatten comp");
+ props->addOption("perform validation", false);
+ SBMLConverter* converter =
+ SBMLConverterRegistry::getInstance().getConverterFor(*props);
+
+ // load document
+ string dir(TestDataDirectory);
+ string fileName = dir + "replacedby_unknown.xml";
+ SBMLDocument* doc = readSBMLFromFile(fileName.c_str());
+ string origdoc = writeSBMLToString(doc);
+
+ // fail if there is no model
+ //(readSBMLFromFile always returns a valid document)
+ fail_unless(doc->getModel() != NULL);
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(doc->getNumErrors() == 1);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+
+ converter->setDocument(doc);
+ int result = converter->convert();
+ string newdoc = writeSBMLToString(doc);
+
+ fail_unless( result == LIBSBML_OPERATION_FAILED);
+ //fail_unless(newdoc == origdoc); //Failing to convert should always leave the original document intact.
+
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompModelFlatteningFailed) == true);
+ fail_unless(errors->contains(CompIdRefMustReferenceObject) == true);
+
+ delete doc;
+ delete converter;
+}
+END_TEST
+
+
Suite *
create_suite_TestFlatteningErrorMessages (void)
{
@@ -3702,6 +3744,7 @@
tcase_add_test(tcase, test_comp_flatten_invalid74);
tcase_add_test(tcase, test_comp_flatten_invalid75);
tcase_add_test(tcase, test_comp_flatten_invalid76);
+ tcase_add_test(tcase, test_comp_flatten_invalid77);
tcase_add_test(tcase, test_comp_flatten_invalid_core);
suite_add_tcase(suite, tcase);
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp 2013-08-23 06:53:54 UTC (rev 18330)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningUnknownPackageRefs.cpp 2013-08-24 00:25:19 UTC (rev 18331)
@@ -87,8 +87,8 @@
*/
string newModel = writeSBMLToString(doc);
- string outfile = filename + "SOMETHING.flat.xml";
- writeSBMLToFile(doc, outfile.c_str());
+ //string outfile = filename + "unknown_flat.xml";
+ //writeSBMLToFile(doc, outfile.c_str());
string ffile = filename + file2;
SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
string flatModel = writeSBMLToString(fdoc);
@@ -128,7 +128,259 @@
}
END_TEST
+START_TEST (test_comp_flatten_unknown_3)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown3.xml", "unknown3_flat.xml");
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_4)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown4.xml", "unknown4_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_5)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown5.xml", "unknown5_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_6)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown6.xml", "unknown6_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_7)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown7.xml", "unknown7_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_8)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown8.xml", "unknown8_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_9)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown9.xml", "unknown9_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_10)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown10.xml", "unknown10_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_11)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown11.xml", "unknown11_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_12)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown12.xml", "unknown12_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_13)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown13.xml", "unknown13_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_14)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown14.xml", "unknown14_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_15)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown15.xml", "unknown15_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_16)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown16.xml", "unknown16_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_17)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown17.xml", "unknown17_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_18)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown18.xml", "unknown18_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_19)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown19.xml", "unknown19_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(UnrequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedNotReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+START_TEST (test_comp_flatten_unknown_20)
+{
+ SBMLDocument* doc = TestFlattenedUnknownNoValidate("unknown20.xml", "unknown20_flat.xml");
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+ fail_unless(errors->getNumErrors() == 4);
+ fail_unless(errors->contains(RequiredPackagePresent) == true);
+ fail_unless(errors->contains(CompFlatteningNotRecognisedReqd) == true);
+ fail_unless(errors->contains(CompFlatteningWarning) == true);
+
+ delete doc;
+}
+END_TEST
+
+
Suite *
create_suite_TestFlatteningUnknownPackageRefs (void)
{
@@ -137,6 +389,24 @@
tcase_add_test(tcase, test_comp_flatten_unknown_1);
tcase_add_test(tcase, test_comp_flatten_unknown_2);
+ tcase_add_test(tcase, test_comp_flatten_unknown_3);
+ tcase_add_test(tcase, test_comp_flatten_unknown_4);
+ tcase_add_test(tcase, test_comp_flatten_unknown_5);
+ tcase_add_test(tcase, test_comp_flatten_unknown_6);
+ tcase_add_test(tcase, test_comp_flatten_unknown_7);
+ tcase_add_test(tcase, test_comp_flatten_unknown_8);
+ tcase_add_test(tcase, test_comp_flatten_unknown_9);
+ tcase_add_test(tcase, test_comp_flatten_unknown_10);
+ tcase_add_test(tcase, test_comp_flatten_unknown_11);
+ tcase_add_test(tcase, test_comp_flatten_unknown_12);
+ tcase_add_test(tcase, test_comp_flatten_unknown_13);
+ tcase_add_test(tcase, test_comp_flatten_unknown_14);
+ tcase_add_test(tcase, test_comp_flatten_unknown_15);
+ tcase_add_test(tcase, test_comp_flatten_unknown_16);
+ tcase_add_test(tcase, test_comp_flatten_unknown_17);
+ tcase_add_test(tcase, test_comp_flatten_unknown_18);
+ tcase_add_test(tcase, test_comp_flatten_unknown_19);
+ tcase_add_test(tcase, test_comp_flatten_unknown_20);
suite_add_tcase(suite, tcase);
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown10_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown11_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown12_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown13_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown14_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown15_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown16_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown17_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown18_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown19_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown20_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown3_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown4_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown5_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:portRef="y_port"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown6_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar"/>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown7_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="true">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="y" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown8_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:extra="http://www.sbml.org/sbml/level3/version1/extra/version1" level="3" version="1" comp:required="true" extra:required="false">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:portRef="y_port" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <extra:listOfThings>
+ <extra:thing extra:id="y"/>
+ </extra:listOfThings>
+ <comp:listOfPorts>
+ <comp:port comp:idRef="y" comp:id="y_port"/>
+ </comp:listOfPorts>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/unknown9_flat.xml 2013-08-24 00:25:19 UTC (rev 18331)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfParameters>
+ <parameter id="x" value="1" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2013-08-23 06:54:00
|
Revision: 18330
http://sourceforge.net/p/sbml/code/18330
Author: luciansmith
Date: 2013-08-23 06:53:54 +0000 (Fri, 23 Aug 2013)
Log Message:
-----------
Fix for flattening: it is now possible (as it says in the spec) to explicitly delete something that otherwise was deleted by implication, i.e. delete both a species reference and the reaction it came from. You can also replace a reaction and replace the species reference it contained. Unfortunately, you cannot delete a reaction and replace a species reference it contained. However, that may not be desirable anyway.
One issue with this change is that it changes the signature of some public functions that are used in flattening. I saw no way to fix the above bug without changing the signature, since I needed to *not* delete things in those functions some times, based on information that function did not have.
I could theoretically give the new function arguments defaults, but would rather not--they are actually important for the new functionality.
Also, I discovered that Submodel::performDeletions wasn't ever used, and therefore was not tested, so I removed it. This of course it another change to the API, but it seemed better to me to take out something that could go wrong than to leave it in.
Also also, Frank noticed that old versions of the STL had bugs where you couldn't declare defaults, so those functions have been split into the 'normal calls' and the 'protected calls with more arguments', which probably makes better functional sense anyway.
Finally, added a new validation rule to disallow replacing things that are children of deleted elements. If this becomes legal, it means a headachey rewrite of the flattening code (again), but I think people on the list will likely agree that this situation is not helpful.
Modified Paths:
--------------
trunk/libsbml/src/sbml/KineticLaw.cpp
trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.cpp
trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.h
trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h
trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.h
trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.h
trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.h
trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.h
trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.h
trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.cpp
trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.h
trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningConverter.cpp
trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp
trunk/libsbml/src/sbml/packages/comp/validator/CompSBMLError.h
trunk/libsbml/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
Added Paths:
-----------
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/del_only_specref.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/multi_replaced_by.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replace_implied_deletion.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test56.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test56_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test57.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test57_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test58.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test58_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test59.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test59_flat.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test60.xml
trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test60_flat.xml
Modified: trunk/libsbml/src/sbml/KineticLaw.cpp
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/KineticLaw.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -1118,6 +1118,7 @@
int KineticLaw::removeFromParentAndDelete()
{
+ if (mHasBeenDeleted) return LIBSBML_OPERATION_SUCCESS;
SBase* parent = getParentSBMLObject();
if (parent==NULL) return LIBSBML_OPERATION_FAILED;
Reaction* parentReaction = static_cast<Reaction*>(parent);
Modified: trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -684,7 +684,8 @@
// Perform deletions (top-down):
// need to do this before renaming in case we delete a local parameter.
- ret = performDeletions();
+ set<SBase*> removed;
+ ret = performDeletions(&removed);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
@@ -696,9 +697,33 @@
}
//Perform replacements and conversions (top-down)
- return performReplacementsAndConversions();
+ set<SBase*> toremove;
+ ret = performReplacementsAndConversions(&removed, &toremove);
+ if (ret != LIBSBML_OPERATION_SUCCESS) {
+ return ret;
+ }
+ while (toremove.size() > 0) {
+ SBase* removeme = *(toremove.begin());
+ if (removed.insert(removeme).second) {
+ //Need to remove it.
+ List* children = removeme->getAllElements();
+ for (unsigned int el=0; el<children->getSize(); el++) {
+ SBase* element = static_cast<SBase*>(children->get(el));
+ removed.insert(element);
+ }
+ CompBase::removeFromParentAndPorts(removeme, &removed);
+ }
+ toremove.erase(toremove.begin());
+ }
+ return LIBSBML_OPERATION_SUCCESS;
}
+int CompModelPlugin::saveAllReferencedElements()
+{
+ set<SBase*> norefs;
+ return saveAllReferencedElements(norefs, norefs);
+}
+
int CompModelPlugin::saveAllReferencedElements(set<SBase*> uniqueRefs, set<SBase*> replacedBys)
{
SBMLDocument* doc = getSBMLDocument();
@@ -714,7 +739,7 @@
//Get a list of everything, pull out anything that's a deletion, replacement, or port, and save what they're pointing to.
//At the same time, make sure that no two things point to the same thing.
- set<SBase*> RE_deletions = std::set<SBase*>(); //Deletions only point to things in the same model.
+ set<SBase*> RE_deletions = set<SBase*>(); //Deletions only point to things in the same model.
List* allElements = model->getAllElements();
string modname = "the main model in the document";
if (model->isSetId()) {
@@ -761,15 +786,15 @@
SBase* rbParent = reference->getParentSBMLObject();
if (uniqueRefs.insert(rbParent).second == false) {
if (doc) {
- string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": a <" + direct->getElementName() + "> ";
+ string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": a <" + rbParent->getElementName() + "> ";
if (direct->isSetId()) {
- error += "with the id '" + direct->getId() + "'";
- if (direct->isSetMetaId()) {
- error += ", and the metaid '" + direct->getMetaId() + "'";
+ error += "with the id '" + rbParent->getId() + "'";
+ if (rbParent->isSetMetaId()) {
+ error += ", and the metaid '" + rbParent->getMetaId() + "'";
}
}
- else if (direct->isSetMetaId()) {
- error += "with the metaId '" + direct->getMetaId() + "'";
+ else if (rbParent->isSetMetaId()) {
+ error += "with the metaId '" + rbParent->getMetaId() + "'";
}
error += " has a <replacedBy> child and is also pointed to by a <port>, <deletion>, <replacedElement>, or one or more <replacedBy> objects.";
doc->getErrorLog()->logPackageError("comp", CompNoMultipleReferences, getPackageVersion(), getLevel(), getVersion(), error);
@@ -1063,7 +1088,7 @@
}
/** @endcond */
-int CompModelPlugin::performDeletions()
+int CompModelPlugin::performDeletions(set<SBase*>* removed)
{
int ret = LIBSBML_OPERATION_SUCCESS;
SBMLDocument* doc = getSBMLDocument();
@@ -1082,7 +1107,7 @@
//First perform any deletions
for (unsigned int d=0; d<submodel->getNumDeletions(); d++) {
Deletion* deletion = submodel->getDeletion(d);
- ret = deletion->performDeletion();
+ ret = deletion->performDeletion(removed);
if (ret!=LIBSBML_OPERATION_SUCCESS) {
return ret;
}
@@ -1102,12 +1127,12 @@
}
return LIBSBML_OPERATION_FAILED;
}
- modplug->performDeletions();
+ modplug->performDeletions(removed);
}
return ret;
}
-int CompModelPlugin::performReplacementsAndConversions()
+int CompModelPlugin::performReplacementsAndConversions(set<SBase*>* removed, set<SBase*>* toremove)
{
int ret = LIBSBML_OPERATION_SUCCESS;
SBMLDocument* doc = getSBMLDocument();
@@ -1135,10 +1160,10 @@
rbs.push_back(reference);
}
}
-
+
//ReplacedElement replacements
for (size_t re=0; re<res.size(); re++) {
- ret = res[re]->performReplacement();
+ ret = res[re]->performReplacement(removed, toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
@@ -1154,13 +1179,13 @@
//'left behind' converions (not LaHaye-style)
ret = submodel->convertTimeAndExtent();
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
- ret = modplug->performReplacementsAndConversions();
+ ret = modplug->performReplacementsAndConversions(removed, toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
}
//Perform ReplacedBy replacements *after* the submodels are done, so that the topmost-level names take precedence.
for (size_t rb=0; rb<rbs.size(); rb++) {
- ret = rbs[rb]->performReplacement();
+ ret = rbs[rb]->performReplacement(removed, toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
}
Modified: trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/extension/CompModelPlugin.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -521,7 +521,7 @@
* Find all SBaseRef-derived objects in this Model and in instantiated
* Submodels and find and save pointers to the elements they point to.
*/
- virtual int saveAllReferencedElements(std::set<SBase*> uniqueRefs = std::set<SBase*>(), std::set<SBase*> replacedBys = std::set<SBase*>());
+ virtual int saveAllReferencedElements();
/*
* Renames all ids of all elements in the instantiated submodel (SIds,
@@ -537,7 +537,7 @@
* plus any elements those deleted elements may have replaced or been
* replaced by.
*/
- virtual int performDeletions();
+ virtual int performDeletions(std::set<SBase*>* removed);
/*
* Removes all elements from instantiated submodels slated to be replaced,
@@ -547,7 +547,7 @@
* identifiers, and points all old references to the replacement object's
* old identifiers to the new identifiers.
*/
- virtual int performReplacementsAndConversions();
+ virtual int performReplacementsAndConversions(std::set<SBase*>* removed, std::set<SBase*>* toremove);
/** @cond doxygenLibsbmlInternal */
virtual void findUniqueSubmodPrefixes(std::vector<std::string>& submodids, List* allElements);
@@ -555,6 +555,13 @@
virtual void resetPorts();
/** @endcond */
+
+ /** @cond doxygenLibsbmlInternal */
+ protected:
+ virtual int saveAllReferencedElements(std::set<SBase*> uniqueRefs, std::set<SBase*> replacedBys);
+ /** @endcond */
+
+
};
LIBSBML_CPP_NAMESPACE_END
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -30,6 +30,8 @@
#include <sstream>
#include <iostream>
+using namespace std;
+
LIBSBML_CPP_NAMESPACE_BEGIN
CompBase::CompBase (unsigned int level, unsigned int version, unsigned int pkgVersion)
@@ -428,7 +430,7 @@
/** @endcond */
-int CompBase::removeFromParentAndPorts(SBase* todelete)
+int CompBase::removeFromParentAndPorts(SBase* todelete, set<SBase*>* removed)
{
//First remove from ports:
Model* parent = static_cast<Model*>(todelete->getAncestorOfType(SBML_COMP_MODELDEFINITION, "comp"));
@@ -444,6 +446,9 @@
for (unsigned long p=0; p<cmp->getNumPorts();) {
Port* port = cmp->getPort(p);
if (port->getReferencedElement() == todelete) {
+ if (removed) {
+ removed->insert(port);
+ }
port->removeFromParentAndDelete();
}
else {
@@ -457,6 +462,9 @@
else parent = tempparent;
}
//And secondly, remove from parent
+ if (removed) {
+ removed->insert(todelete);
+ }
return todelete->removeFromParentAndDelete();
}
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/CompBase.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -30,6 +30,7 @@
#ifndef CompBase_h
#define CompBase_h
+#include <set>
#include <sbml/common/sbmlfwd.h>
#include <sbml/extension/SBMLExtension.h>
@@ -234,7 +235,7 @@
* it happens, we need to not actually crash. This function finds and
* deletes all such invalid ports before deleting the object.
*/
- static int removeFromParentAndPorts(SBase* todelete);
+ static int removeFromParentAndPorts(SBase* todelete, std::set<SBase*>* removed);
/** @endcond */
private:
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -586,6 +586,15 @@
* @return the resolved model or NULL.
*/
Model*
+ExternalModelDefinition::getReferencedModel()
+{
+ set<pair<string, string> > parents;
+ return getReferencedModel(NULL, parents);
+}
+
+/* Internal getReferencedModel call sets the errordoc and parents
+ */
+Model*
ExternalModelDefinition::getReferencedModel(SBMLDocument* errordoc, set<pair<string, string> > parents)
{
SBMLDocument* origdoc = getSBMLDocument();
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/ExternalModelDefinition.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -489,7 +489,7 @@
* Model belongs. If this ExternalModelDefinition is not part of any
* SBMLDocument, NULL will be returned.
*/
- virtual Model* getReferencedModel(SBMLDocument* errordoc = NULL, std::set<std::pair<std::string, std::string> > parents = std::set<std::pair<std::string, std::string> >());
+ virtual Model* getReferencedModel();
protected:
@@ -529,6 +529,10 @@
virtual void writeAttributes (XMLOutputStream& stream) const;
/** @endcond */
+ /** @cond doxygenLibsbmlInternal */
+ virtual Model* getReferencedModel(SBMLDocument* errordoc, std::set<std::pair<std::string, std::string> > parents);
+ /** @endcond */
+ friend class Submodel;
};
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -99,7 +99,7 @@
}
-int ReplacedBy::performReplacement()
+int ReplacedBy::performReplacement(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
//Find the various objects and plugin objects we need for this to work.
@@ -129,8 +129,11 @@
}
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
- //And finally, delete the parent object.
- return CompBase::removeFromParentAndPorts(parent);
+ //And finally, get ready to delete the parent object.
+ if (toremove) {
+ toremove->insert(parent);
+ }
+ return LIBSBML_OPERATION_SUCCESS;
}
int
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedBy.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -149,7 +149,7 @@
* Removes the redundant element from instantiated submodels, and points
* all old references to the remaining element.
*/
- virtual int performReplacement();
+ virtual int performReplacement(std::set<SBase*>* removed, std::set<SBase*>* toremove);
/** @cond doxygenLibsbmlInternal */
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -319,7 +319,7 @@
}
-int ReplacedElement::performReplacement()
+int ReplacedElement::performReplacement(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
if (isSetDeletion()) {
@@ -357,6 +357,18 @@
return LIBSBML_INVALID_OBJECT;
}
+ if (removed && removed->find(ref)!=removed->end()) {
+ //Already deleted: can't get the deleted element's ID to
+ if (doc) {
+ string error = "Cannot carry out replacement in ReplacedElement::performReplacement: a <" + parent->getElementName() + ">";
+ if (parent->isSetId()) {
+ error += " with the ID '" + parent->getId() + "'";
+ }
+ error += " has a child <replacedElement> that points to something that has already been deleted, probably because its parent was deleted.";
+ doc->getErrorLog()->logPackageError("comp", CompNoReplacingDeletedItems, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
+ }
+ return LIBSBML_INVALID_OBJECT;
+ }
//Update the IDs.
int ret = updateIDs(ref, parent);
if (ret != LIBSBML_OPERATION_SUCCESS) {
@@ -373,15 +385,23 @@
//Now recurse down the 'replace*' tree, renaming IDs and deleting things as we go.
for (unsigned int re=0; re<refplug->getNumReplacedElements(); re++) {
refplug->getReplacedElement(re)->replaceWithAndMaybeDelete(parent, true, blank);
+ if (toremove) {
+ toremove->insert(refplug->getReplacedElement(re)->getReferencedElement());
+ }
}
if (refplug->isSetReplacedBy()) {
//Even if the subelement used to be replaced by something further down, it is now being replaced by the parent. It just can't catch a break, it seems.
refplug->getReplacedBy()->replaceWithAndMaybeDelete(parent, true, blank);
+ if (toremove) {
+ toremove->insert(refplug->getReplacedBy()->getReferencedElement());
+ }
}
}
- //And finally, delete the referenced object.
- return CompBase::removeFromParentAndPorts(ref);
+ if (toremove) {
+ toremove->insert(ref);
+ }
+ return LIBSBML_OPERATION_SUCCESS;
}
SBase*
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/ReplacedElement.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -328,7 +328,7 @@
* Removes the referenced element from instantiated submodels, and points
* all old references to that element to the replacement element.
*/
- virtual int performReplacement();
+ virtual int performReplacement(std::set<SBase*>* removed, std::set<SBase*>* toremove);
/**
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -365,7 +365,7 @@
//And now delete the replaced thing.
if (deleteme) {
//We have to iterate upwards and see if any ports referenced this deletion. If so, delete those ports.
- return CompBase::removeFromParentAndPorts(replaced);
+// return CompBase::removeFromParentAndPorts(replaced, toreplace);
}
return LIBSBML_OPERATION_SUCCESS;
}
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/Replacing.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -189,7 +189,7 @@
* all old references to the remaining element (different for
* ReplacedElements and ReplacedBy elements.
*/
- virtual int performReplacement() = 0;
+ virtual int performReplacement(std::set<SBase*>* removed, std::set<SBase*>* toremove) = 0;
/** @cond doxygenLibsbmlInternal */
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -903,22 +903,35 @@
mReferencedElement = NULL;
}
-int SBaseRef::performDeletion()
+int SBaseRef::performDeletion(set<SBase*>* removed)
{
SBase* todelete = getReferencedElement();
if (todelete==NULL) {
return LIBSBML_INVALID_OBJECT;
}
+ if (removed) {
+ if (removed->insert(todelete).second == false) {
+ //Already deleted or replaced.
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+ }
CompSBasePlugin* todplug = static_cast<CompSBasePlugin*>(todelete->getPlugin(getPrefix()));
if (todplug != NULL) {
for (unsigned long re=0; re<todplug->getNumReplacedElements(); re++) {
- todplug->getReplacedElement(re)->performDeletion();
+ todplug->getReplacedElement(re)->performDeletion(removed);
}
if (todplug->isSetReplacedBy()) {
- todplug->getReplacedBy()->performDeletion();
+ todplug->getReplacedBy()->performDeletion(removed);
}
}
- return CompBase::removeFromParentAndPorts(todelete);
+ if (removed) {
+ List* children = todelete->getAllElements();
+ for (unsigned int el=0; el<children->getSize(); el++) {
+ SBase* element = static_cast<SBase*>(children->get(el));
+ removed->insert(element);
+ }
+ }
+ return CompBase::removeFromParentAndPorts(todelete, removed);
}
int SBaseRef::removeFromParentAndDelete()
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/SBaseRef.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -96,6 +96,7 @@
#ifdef __cplusplus
#include <string>
+#include <set>
#include <sbml/SBase.h>
#include <sbml/packages/comp/extension/CompExtension.h>
@@ -630,7 +631,7 @@
* plus any other elements that element points to through ReplacedElement
* or ReplacedBy children
*/
- virtual int performDeletion();
+ virtual int performDeletion(std::set<SBase*>* removed);
/**
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -874,6 +874,7 @@
SBMLDocument* origdoc = NULL;
string newmodel = parentURI + "::" + getModelRef();
+ set<pair<string, string> > parents;
switch(origmodel->getTypeCode())
{
case SBML_MODEL:
@@ -897,8 +898,7 @@
mInstantiationOriginalURI = "";
return LIBSBML_OPERATION_FAILED;
}
-
- mInstantiatedModel = extmod->getReferencedModel(rootdoc);
+ mInstantiatedModel = extmod->getReferencedModel(rootdoc, parents);
if (mInstantiatedModel == NULL)
{
string error = "In Submodel::instantiate, unable to instantiate submodel '" + getId() + "' because the external model definition it referenced (model '" + getModelRef() +"') could not be resolved.";
@@ -969,18 +969,6 @@
return LIBSBML_OPERATION_SUCCESS;
}
-int Submodel::performDeletions()
-{
- if (mInstantiatedModel == NULL) return LIBSBML_INVALID_OBJECT;
- for (unsigned int i = 0; i < getNumDeletions(); i++)
- {
- SBase* todelete = getDeletion(i)->getReferencedElementFrom(mInstantiatedModel);
- if (todelete == NULL) continue;
- CompBase::removeFromParentAndPorts(todelete);
- }
- return LIBSBML_OPERATION_SUCCESS;
-}
-
int
Submodel::replaceElement(SBase* toReplace, SBase* replacement)
{
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.h
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.h 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/Submodel.h 2013-08-23 06:53:54 UTC (rev 18330)
@@ -729,20 +729,6 @@
/**
- * Delete elements in the instantiated submodel, based on any Deletions
- * from this Submodel's listOfDeletions.
- *
- * @return an integer value indicating success/failure of the operation.
- * Possible return values from this function are:
- * @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
- * @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
- * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
- * In this case, 'invalid object' means that this Submodel itself is invalid, and no Model can be instantiated from it.
- */
- virtual int performDeletions();
-
-
- /**
* Delete the element in question from the stored instantiated Model, and
* replace all references to it with references to the replacement object.
* @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningConverter.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningConverter.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningConverter.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -180,7 +180,7 @@
*/
string newModel = writeSBMLToString(doc);
- //writeSBMLToFile(doc, "test1_flat.xml");
+ //writeSBMLToFile(doc, "test_flat.xml");
string ffile = filename + file2;
SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
string flatModel = writeSBMLToString(fdoc);
@@ -845,7 +845,67 @@
}
END_TEST
+START_TEST (test_comp_flatten_test51)
+{
+ TestFlattenedPair("test51.xml", "test51_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test52)
+{
+ TestFlattenedPair("test52.xml", "test52_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test53)
+{
+ TestFlattenedPair("test53.xml", "test53_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test54)
+{
+ TestFlattenedPair("test54.xml", "test54_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test55)
+{
+ TestFlattenedPair("test55.xml", "test55_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test56)
+{
+ TestFlattenedPair("test56.xml", "test56_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test57)
+{
+ TestFlattenedPair("test57.xml", "test57_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test58)
+{
+ TestFlattenedPair("test58.xml", "test58_flat.xml");
+}
+END_TEST
+START_TEST (test_comp_flatten_test59)
+{
+ TestFlattenedPair("test59.xml", "test59_flat.xml");
+}
+END_TEST
+
+START_TEST (test_comp_flatten_test60)
+{
+ TestFlattenedPair("test60.xml", "test60_flat.xml");
+}
+END_TEST
+
+
START_TEST (test_comp_flatten_id_collisions)
{
TestFlattenedPair("id_collisions.xml", "id_collisions_flat.xml");
@@ -1660,6 +1720,16 @@
tcase_add_test(tcase, test_comp_flatten_test48);
tcase_add_test(tcase, test_comp_flatten_test49);
tcase_add_test(tcase, test_comp_flatten_test50);
+ tcase_add_test(tcase, test_comp_flatten_test51);
+ tcase_add_test(tcase, test_comp_flatten_test52);
+ tcase_add_test(tcase, test_comp_flatten_test53);
+ tcase_add_test(tcase, test_comp_flatten_test54);
+ tcase_add_test(tcase, test_comp_flatten_test55);
+ tcase_add_test(tcase, test_comp_flatten_test56);
+ tcase_add_test(tcase, test_comp_flatten_test57);
+ tcase_add_test(tcase, test_comp_flatten_test58);
+ tcase_add_test(tcase, test_comp_flatten_test59);
+ tcase_add_test(tcase, test_comp_flatten_test60);
tcase_add_test(tcase, test_comp_flatten_id_collisions);
tcase_add_test(tcase, test_comp_flatten_id_collisions2);
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp 2013-08-23 00:03:08 UTC (rev 18329)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestCompFlatteningErrorMessages.cpp 2013-08-23 06:53:54 UTC (rev 18330)
@@ -2299,7 +2299,7 @@
SBMLDocument document(&sbmlns);
ReplacedBy rb(3, 1, 1);
rb.setSBMLDocument(&document);
- rb.performReplacement();
+ rb.performReplacement(NULL, NULL);
SBMLErrorLog* errors = document.getErrorLog();
@@ -2315,7 +2315,7 @@
ReplacedElement re(3, 1, 1);
re.setSBMLDocument(&document);
re.setSubmodelRef("submod1");
- re.performReplacement();
+ re.performReplacement(NULL, NULL);
SBMLErrorLog* errors = document.getErrorLog();
@@ -2333,7 +2333,7 @@
lore.appendAndOwn(re);
re->setSBMLDocument(&document);
re->setSubmodelRef("submod1");
- re->performReplacement();
+ re->performReplacement(NULL, NULL);
SBMLErrorLog* errors = document.getErrorLog();
@@ -2351,7 +2351,7 @@
lore.appendAndOwn(re);
re->setSBMLDocument(&document);
re->setSubmodelRef("submod1");
- re->performReplacement();
+ re->performReplacement(NULL, NULL);
SBMLErrorLog* errors = document.getErrorLog();
@@ -3512,6 +3512,114 @@
END_TEST
+START_TEST(test_comp_flatten_invalid74)
+{
+ ConversionProperties* props = new ConversionProperties();
+
+ props->addOption("flatten comp");
+ props->addOption("perform validation", false);
+
+ SBMLConverter* converter =
+ SBMLConverterRegistry::getInstance().getConverterFor(*props);
+
+ // load document
+ string dir(TestDataDirectory);
+ string fileName = dir + "multi_replaced_by.xml";
+ SBMLDocument* doc = readSBMLFromFile(fileName.c_str());
+
+ // fail if there is no model
+ //(readSBMLFromFile always returns a valid document)
+ fail_unless(doc->getNumErrors() == 0);
+ fail_unless(doc->getModel() != NULL);
+
+ converter->setDocument(doc);
+ int result = converter->convert();
+ fail_unless(result==LIBSBML_OPERATION_FAILED);
+ SBMLErrorLog* errors = doc->getErrorLog();
+
+ fail_unless(errors->getNumErrors() == 2);
+ fail_unless(errors->contains(CompModelFlatteningFailed) == true);
+ fail_unless(errors->contains(CompNoMultipleReferences) == true);
+
+ delete doc;
+ delete converter;
+}
+END_TEST
+
+START_TEST(test_comp_flatten_invalid75)
+{
+ ConversionProperties* props = new ConversionProperties();
+
+ props->addOption("flatten comp");
+ props->addOption("perform validation", true);
+
+ SBMLConverter* converter =
+ SBMLConverterRegistry::getInstance().getConverterFor(*props);
+
+ // load document
+ string dir(TestDataDirectory);
+ string fileName = dir + "del_only_specref.xml";
+ SBMLDocument* doc = readSBMLFromFile(fileName.c_str());
+
+ // fail if there is no model
+ //(readSBMLFromFile always returns a valid document)
+ fail_unless(doc->getNumErrors() == 0);
+ fail_unless(doc->getModel() != NULL);
+
+ converter->setDocument(doc);
+ int result = converter->convert();
+
+ fail_unless( result == LIBSBML_CONV_INVALID_SRC_DOCUMENT);
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+
+ fail_unless(errors->getNumErrors() == 3);
+ fail_unless(errors->contains(CompLineNumbersUnreliable) == true);
+ fail_unless(errors->contains(CompFlatModelNotValid) == true);
+ fail_unless(errors->contains(NoReactantsOrProducts) == true);
+
+ delete doc;
+ delete converter;
+}
+END_TEST
+
+START_TEST(test_comp_flatten_invalid76)
+{
+ ConversionProperties* props = new ConversionProperties();
+
+ props->addOption("flatten comp");
+ props->addOption("perform validation", false);
+
+ SBMLConverter* converter =
+ SBMLConverterRegistry::getInstance().getConverterFor(*props);
+
+ // load document
+ string dir(TestDataDirectory);
+ string fileName = dir + "replace_implied_deletion.xml";
+ SBMLDocument* doc = readSBMLFromFile(fileName.c_str());
+
+ // fail if there is no model
+ //(readSBMLFromFile always returns a valid document)
+ fail_unless(doc->getNumErrors() == 0);
+ fail_unless(doc->getModel() != NULL);
+
+ converter->setDocument(doc);
+ int result = converter->convert();
+
+ fail_unless( result == LIBSBML_OPERATION_FAILED);
+
+ SBMLErrorLog* errors = doc->getErrorLog();
+
+ fail_unless(errors->getNumErrors() == 2);
+ fail_unless(errors->contains(CompModelFlatteningFailed) == true);
+ fail_unless(errors->contains(CompNoReplacingDeletedItems) == true);
+
+ delete doc;
+ delete converter;
+}
+END_TEST
+
+
Suite *
create_suite_TestFlatteningErrorMessages (void)
{
@@ -3591,6 +3699,9 @@
tcase_add_test(tcase, test_comp_flatten_invalid71);
tcase_add_test(tcase, test_comp_flatten_invalid72);
tcase_add_test(tcase, test_comp_flatten_invalid73);
+ tcase_add_test(tcase, test_comp_flatten_invalid74);
+ tcase_add_test(tcase, test_comp_flatten_invalid75);
+ tcase_add_test(tcase, test_comp_flatten_invalid76);
tcase_add_test(tcase, test_comp_flatten_invalid_core);
suite_add_tcase(suite, tcase);
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/del_only_specref.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/del_only_specref.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/del_only_specref.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="z_stoich"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="z" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfProducts>
+ <speciesReference id="z_stoich" species="z" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/multi_replaced_by.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/multi_replaced_by.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/multi_replaced_by.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model>
+ <listOfParameters>
+ <parameter id="p2" value="2" constant="false">
+ <comp:replacedBy comp:idRef="p4" comp:submodelRef="sub2"/>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="sub2" comp:modelRef="moddef2"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="moddef1">
+ <listOfParameters>
+ <parameter id="p8" value="8" constant="false"/>
+ </listOfParameters>
+ </comp:modelDefinition>
+ <comp:modelDefinition id="moddef2">
+ <listOfParameters>
+ <parameter id="p4" value="4" constant="false">
+ <comp:replacedBy comp:idRef="p8" comp:submodelRef="sub1"/>
+ </parameter>
+ </listOfParameters>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="sub1" comp:modelRef="moddef1"/>
+ </comp:listOfSubmodels>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replace_implied_deletion.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replace_implied_deletion.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/replace_implied_deletion.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="bar" name="bar">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="y" initialAmount="1" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J1" reversible="true" fast="false">
+ <listOfProducts>
+ <speciesReference id="y_stoich" species="y" stoichiometry="1" constant="false">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="x_stoich" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </speciesReference>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="J0"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="x" initialAmount="1" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference id="x_stoich" species="x" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="main" name="main">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="default_compartment" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="x" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="y" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J1" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference id="x_stoich" species="x" stoichiometry="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="a_stoich" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="y" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="J0" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </reaction>
+ </listOfReactions>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="sub"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="sub" name="sub">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="a" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfInitialAssignments>
+ <initialAssignment symbol="a_stoich">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <cn type="integer"> 6 </cn>
+ <cn type="integer"> 7 </cn>
+ </apply>
+ </math>
+ </initialAssignment>
+ </listOfInitialAssignments>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference id="a_stoich" species="a" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test51_flat.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="main" name="main">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="x" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="y" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="A__a" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfInitialAssignments>
+ <initialAssignment symbol="x_stoich">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <cn type="integer"> 6 </cn>
+ <cn type="integer"> 7 </cn>
+ </apply>
+ </math>
+ </initialAssignment>
+ </listOfInitialAssignments>
+ <listOfReactions>
+ <reaction id="J1" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference id="x_stoich" species="x" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="y" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="main" name="main">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="B" comp:modelRef="sub1">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="A">
+ <comp:sBaseRef comp:idRef="y_stoich"/>
+ </comp:deletion>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="sub2" name="sub2">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="y" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfProducts>
+ <speciesReference id="y_stoich" species="y" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </comp:modelDefinition>
+ <comp:modelDefinition id="sub1" name="sub1">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="sub2">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="J0"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test52_flat.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="main" name="main">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="B__A__default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="B__A__y" compartment="B__A__default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="main" name="main">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="B" comp:modelRef="sub1">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="A">
+ <comp:sBaseRef comp:idRef="J0"/>
+ </comp:deletion>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="sub2" name="sub2">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="y" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfProducts>
+ <speciesReference id="y_stoich" species="y" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </comp:modelDefinition>
+ <comp:modelDefinition id="sub1" name="sub1">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="sub2">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y_stoich"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test53_flat.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="main" name="main">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="B__A__default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="B__A__y" compartment="B__A__default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="baz" name="baz">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="B" comp:modelRef="bar">
+ <comp:listOfDeletions>
+ <comp:deletion comp:idRef="y"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <listOfParameters>
+ <parameter id="x" value="3" constant="true"/>
+ </listOfParameters>
+ </comp:modelDefinition>
+ <comp:modelDefinition id="bar" name="bar">
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo">
+ <comp:listOfDeletions>
+ <comp:deletion comp:id="y" comp:idRef="x"/>
+ </comp:listOfDeletions>
+ </comp:submodel>
+ </comp:listOfSubmodels>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test54_flat.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="baz" name="baz">
+ <listOfParameters>
+ <parameter id="B__A__x" value="3" constant="true"/>
+ </listOfParameters>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.4 with libSBML version 5.8.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" comp:required="true">
+ <model id="bar" name="bar">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="default_compartment" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="y" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="x" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J1" reversible="true" fast="false">
+ <listOfProducts>
+ <speciesReference id="y_stoich" species="y" stoichiometry="1" constant="true">
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="x_stoich" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </speciesReference>
+ </listOfProducts>
+ <comp:listOfReplacedElements>
+ <comp:replacedElement comp:idRef="J0" comp:submodelRef="A"/>
+ </comp:listOfReplacedElements>
+ </reaction>
+ </listOfReactions>
+ <comp:listOfSubmodels>
+ <comp:submodel comp:id="A" comp:modelRef="foo"/>
+ </comp:listOfSubmodels>
+ </model>
+ <comp:listOfModelDefinitions>
+ <comp:modelDefinition id="foo" name="foo">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="x" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference id="x_stoich" species="x" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ </reaction>
+ </listOfReactions>
+ </comp:modelDefinition>
+ </comp:listOfModelDefinitions>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55_flat.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55_flat.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test55_flat.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="bar" name="bar">
+ <listOfCompartments>
+ <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="y" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J1" reversible="true" fast="false">
+ <listOfProducts>
+ <speciesReference id="y_stoich" species="y" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
Added: trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test56.xml
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test56.xml (rev 0)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/test-data/test56.xml 2013-08-23 06:53:54 UTC (rev 18330)
@@ -0,0 +1...
[truncated message content] |
|
From: <luc...@us...> - 2013-08-23 00:03:13
|
Revision: 18329
http://sourceforge.net/p/sbml/code/18329
Author: luciansmith
Date: 2013-08-23 00:03:08 +0000 (Fri, 23 Aug 2013)
Log Message:
-----------
Fix a bug that could cause a crash in getAllElements if it returned NULL instead of a real List. Also, changed functions that call getAllElements in case they get NULL anyway, so they won't crash.
Modified Paths:
--------------
trunk/libsbml/src/sbml/extension/SBasePlugin.cpp
Modified: trunk/libsbml/src/sbml/extension/SBasePlugin.cpp
===================================================================
--- trunk/libsbml/src/sbml/extension/SBasePlugin.cpp 2013-08-22 14:50:28 UTC (rev 18328)
+++ trunk/libsbml/src/sbml/extension/SBasePlugin.cpp 2013-08-23 00:03:08 UTC (rev 18329)
@@ -149,6 +149,7 @@
if (id.empty()) return NULL;
IdFilter filter;
List* allElementsWithIds = this->getAllElements(&filter);
+ if (allElementsWithIds == NULL) return NULL;
for (unsigned int i = 0; i < allElementsWithIds->getSize(); i++)
{
SBase* obj = (SBase*)(allElementsWithIds->get(i));
@@ -167,6 +168,7 @@
if (metaid.empty()) return NULL;
MetaIdFilter filter;
List* allElementsWithIds = this->getAllElements(&filter);
+ if (allElementsWithIds == NULL) return NULL;
for (unsigned int i = 0; i < allElementsWithIds->getSize(); i++)
{
SBase* obj = (SBase*)(allElementsWithIds->get(i));
@@ -181,7 +183,7 @@
List*
SBasePlugin::getAllElements(ElementFilter *filter)
{
- return NULL;
+ return new List();
}
/** @cond doxygenLibsbmlInternal */
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fbe...@us...> - 2013-08-22 14:50:31
|
Revision: 18328
http://sourceforge.net/p/sbml/code/18328
Author: fbergmann
Date: 2013-08-22 14:50:28 +0000 (Thu, 22 Aug 2013)
Log Message:
-----------
- fix compilation error of CompFlatteningConverter, this needs to propagate to libsbml-experimental
Modified Paths:
--------------
trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
Modified: trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp 2013-08-20 20:55:21 UTC (rev 18327)
+++ trunk/libsbml/src/sbml/packages/comp/util/CompFlatteningConverter.cpp 2013-08-22 14:50:28 UTC (rev 18328)
@@ -298,9 +298,9 @@
// now reconstruct the document to be returned
// taking user options into account
+ SBMLDocument tempDoc;
+ result = reconstructDocument(flatmodel, tempDoc);
- result = reconstructDocument(flatmodel, SBMLDocument());
-
if (result != LIBSBML_OPERATION_SUCCESS)
{
return result;
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From: <luc...@us...> - 2013-08-20 20:55:25
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Revision: 18327
http://sourceforge.net/p/sbml/code/18327
Author: luciansmith
Date: 2013-08-20 20:55:21 +0000 (Tue, 20 Aug 2013)
Log Message:
-----------
Fixed a bug in reporting the initial value of elements; removed comp:NotRequired; removed commented and obsolete code.
Modified Paths:
--------------
trunk/test-suite/src/utilities/c++/checkTestCases.cpp
trunk/test-suite/src/utilities/c++/generateTestsFrom.cpp
trunk/test-suite/src/utilities/c++/testSuiteUtil.cpp
Modified: trunk/test-suite/src/utilities/c++/checkTestCases.cpp
===================================================================
--- trunk/test-suite/src/utilities/c++/checkTestCases.cpp 2013-08-20 19:47:13 UTC (rev 18326)
+++ trunk/test-suite/src/utilities/c++/checkTestCases.cpp 2013-08-20 20:55:21 UTC (rev 18327)
@@ -420,9 +420,6 @@
CompSBMLDocumentPlugin* compdoc = static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
SBMLDocument flat(3,1);
if (compdoc != NULL) {
- if (compdoc->getRequired() == false) {
- tests.insert("comp:NotRequired");
- }
flat = *document;
checkComp(compdoc, components, tests, results);
ConversionProperties* props = new ConversionProperties();
Modified: trunk/test-suite/src/utilities/c++/generateTestsFrom.cpp
===================================================================
--- trunk/test-suite/src/utilities/c++/generateTestsFrom.cpp 2013-08-20 19:47:13 UTC (rev 18326)
+++ trunk/test-suite/src/utilities/c++/generateTestsFrom.cpp 2013-08-20 20:55:21 UTC (rev 18327)
@@ -465,7 +465,7 @@
Rule* rule = model->getRule(id);
InitialAssignment* ia = model->getInitialAssignment(id);
ret << endl << "| ";
- if (rule != NULL || ia != NULL) {
+ if ((rule != NULL && rule->getTypeCode() != SBML_RATE_RULE) || ia != NULL) {
if (species->getHasOnlySubstanceUnits()) {
ret << "Initial amount of species ";
}
@@ -473,11 +473,11 @@
ret << "Initial concentration of species ";
}
ret << id << " | $";
- if (rule != NULL) {
- ret << SBML_formulaToString(rule->getMath()) << "$ |";
+ if (ia != NULL) {
+ ret << SBML_formulaToString(ia->getMath()) << "$ |";
}
else {
- ret << SBML_formulaToString(ia->getMath()) << "$ |";
+ ret << SBML_formulaToString(rule->getMath()) << "$ |";
}
}
else if (species->isSetInitialAmount()) {
@@ -509,12 +509,12 @@
ret << endl << "| Initial value of parameter " << id << " | $";
Rule* rule = model->getRule(id);
InitialAssignment* ia = model->getInitialAssignment(id);
- if (rule != NULL || ia != NULL) {
- if (rule != NULL) {
- ret << SBML_formulaToString(rule->getMath()) << "$ |";
+ if ((rule != NULL && rule->getTypeCode() != SBML_RATE_RULE) || ia != NULL) {
+ if (ia != NULL) {
+ ret << SBML_formulaToString(ia->getMath()) << "$ |";
}
else {
- ret << SBML_formulaToString(ia->getMath()) << "$ |";
+ ret << SBML_formulaToString(rule->getMath()) << "$ |";
}
}
else if (param->isSetValue()) {
@@ -543,12 +543,12 @@
ret << endl << "| Initial volume of compartment '" << id << "' | $";
Rule* rule = model->getRule(id);
InitialAssignment* ia = model->getInitialAssignment(id);
- if (rule != NULL || ia != NULL) {
- if (rule != NULL) {
- ret << SBML_formulaToString(rule->getMath()) << "$ |";
+ if ((rule != NULL && rule->getTypeCode() != SBML_RATE_RULE) || ia != NULL) {
+ if (ia != NULL) {
+ ret << SBML_formulaToString(ia->getMath()) << "$ |";
}
else {
- ret << SBML_formulaToString(ia->getMath()) << "$ |";
+ ret << SBML_formulaToString(rule->getMath()) << "$ |";
}
}
else if (compartment->isSetVolume()) {
@@ -716,7 +716,7 @@
set<string> tests;
set<string> packages;
SBMLDocument* doc = model->getSBMLDocument();
- string testType = "timeCourse";
+ string testType = "TimeCourse";
#ifdef USE_COMP
CompSBMLDocumentPlugin* compdoc = static_cast<CompSBMLDocumentPlugin*>(doc->getPlugin("comp"));
Modified: trunk/test-suite/src/utilities/c++/testSuiteUtil.cpp
===================================================================
--- trunk/test-suite/src/utilities/c++/testSuiteUtil.cpp 2013-08-20 19:47:13 UTC (rev 18326)
+++ trunk/test-suite/src/utilities/c++/testSuiteUtil.cpp 2013-08-20 20:55:21 UTC (rev 18327)
@@ -625,13 +625,6 @@
#ifdef USE_COMP
void checkComp(CompSBMLDocumentPlugin* compdoc, set<string>& components, set<string>& tests, const map<string, vector<double> >& results)
{
- //if (compdoc->getRequired()) {
- // components.insert("comp:Required");
- //}
- //else {
- // components.insert("comp:NotRequired");
- //}
-
SBMLDocument* doc = compdoc->getSBMLDocument();
List* allElements = doc->getAllElements();
for (unsigned int e=0; e<allElements->getSize(); e++) {
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