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From: <sar...@us...> - 2016-10-27 07:56:35
|
Revision: 23643
http://sourceforge.net/p/sbml/code/23643
Author: sarahkeating
Date: 2016-10-27 07:56:31 +0000 (Thu, 27 Oct 2016)
Log Message:
-----------
clean up the generic functions for manipulating attributes
Modified Paths:
--------------
trunk/libsbml/src/sbml/AlgebraicRule.cpp
trunk/libsbml/src/sbml/AlgebraicRule.h
trunk/libsbml/src/sbml/AssignmentRule.cpp
trunk/libsbml/src/sbml/AssignmentRule.h
trunk/libsbml/src/sbml/Compartment.cpp
trunk/libsbml/src/sbml/Compartment.h
trunk/libsbml/src/sbml/CompartmentType.cpp
trunk/libsbml/src/sbml/CompartmentType.h
trunk/libsbml/src/sbml/Constraint.cpp
trunk/libsbml/src/sbml/Constraint.h
trunk/libsbml/src/sbml/Delay.cpp
trunk/libsbml/src/sbml/Delay.h
trunk/libsbml/src/sbml/Event.cpp
trunk/libsbml/src/sbml/Event.h
trunk/libsbml/src/sbml/EventAssignment.cpp
trunk/libsbml/src/sbml/EventAssignment.h
trunk/libsbml/src/sbml/FunctionDefinition.cpp
trunk/libsbml/src/sbml/FunctionDefinition.h
trunk/libsbml/src/sbml/InitialAssignment.cpp
trunk/libsbml/src/sbml/InitialAssignment.h
trunk/libsbml/src/sbml/KineticLaw.cpp
trunk/libsbml/src/sbml/KineticLaw.h
trunk/libsbml/src/sbml/LocalParameter.cpp
trunk/libsbml/src/sbml/LocalParameter.h
trunk/libsbml/src/sbml/Model.cpp
trunk/libsbml/src/sbml/Model.h
trunk/libsbml/src/sbml/ModifierSpeciesReference.cpp
trunk/libsbml/src/sbml/ModifierSpeciesReference.h
trunk/libsbml/src/sbml/Parameter.cpp
trunk/libsbml/src/sbml/Parameter.h
trunk/libsbml/src/sbml/Priority.cpp
trunk/libsbml/src/sbml/Priority.h
trunk/libsbml/src/sbml/RateRule.cpp
trunk/libsbml/src/sbml/RateRule.h
trunk/libsbml/src/sbml/Reaction.cpp
trunk/libsbml/src/sbml/Reaction.h
trunk/libsbml/src/sbml/Rule.cpp
trunk/libsbml/src/sbml/Rule.h
trunk/libsbml/src/sbml/SBase.cpp
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/SimpleSpeciesReference.cpp
trunk/libsbml/src/sbml/SimpleSpeciesReference.h
trunk/libsbml/src/sbml/Species.cpp
trunk/libsbml/src/sbml/Species.h
trunk/libsbml/src/sbml/SpeciesReference.cpp
trunk/libsbml/src/sbml/SpeciesReference.h
trunk/libsbml/src/sbml/SpeciesType.cpp
trunk/libsbml/src/sbml/SpeciesType.h
trunk/libsbml/src/sbml/Trigger.cpp
trunk/libsbml/src/sbml/Trigger.h
trunk/libsbml/src/sbml/Unit.cpp
trunk/libsbml/src/sbml/Unit.h
trunk/libsbml/src/sbml/UnitDefinition.cpp
trunk/libsbml/src/sbml/UnitDefinition.h
trunk/libsbml/src/sbml/test/TestAttributeFunctions.cpp
Modified: trunk/libsbml/src/sbml/AlgebraicRule.cpp
===================================================================
--- trunk/libsbml/src/sbml/AlgebraicRule.cpp 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/AlgebraicRule.cpp 2016-10-27 07:56:31 UTC (rev 23643)
@@ -137,6 +137,254 @@
}
/** @endcond */
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::getAttribute(const std::string& attributeName,
+ bool& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::getAttribute(const std::string& attributeName,
+ int& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::getAttribute(const std::string& attributeName,
+ unsigned int& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::getAttribute(const std::string& attributeName,
+ const char* value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this AlgebraicRule's attribute
+ * "attributeName" is set.
+ */
+bool
+AlgebraicRule::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = Rule::isSetAttribute(attributeName);
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::setAttribute(const std::string& attributeName, int value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::setAttribute(const std::string& attributeName,
+ unsigned int value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::setAttribute(const std::string& attributeName,
+ const char* value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this AlgebraicRule.
+ */
+int
+AlgebraicRule::unsetAttribute(const std::string& attributeName)
+{
+ int value = Rule::unsetAttribute(attributeName);
+
+ return value;
+}
+
+/** @endcond */
+
+
+
#endif /* __cplusplus */
Modified: trunk/libsbml/src/sbml/AlgebraicRule.h
===================================================================
--- trunk/libsbml/src/sbml/AlgebraicRule.h 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/AlgebraicRule.h 2016-10-27 07:56:31 UTC (rev 23643)
@@ -202,6 +202,284 @@
virtual bool hasRequiredAttributes() const ;
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ double& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ unsigned int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ const char* value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this AlgebraicRule's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this AlgebraicRule's attribute "attributeName" has been
+ * set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, bool value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, int value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, double value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ unsigned int value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, const char*
+ value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this AlgebraicRule.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
protected:
/** @cond doxygenLibsbmlInternal */
bool mInternalIdOnly;
Modified: trunk/libsbml/src/sbml/AssignmentRule.cpp
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.cpp 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/AssignmentRule.cpp 2016-10-27 07:56:31 UTC (rev 23643)
@@ -129,11 +129,24 @@
}
}
+/** @cond doxygenLibsbmlInternal */
-#ifndef SWIG
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
+ bool& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+ return return_value;
+}
+/** @endcond */
+
+
/** @cond doxygenLibsbmlInternal */
/*
@@ -141,9 +154,63 @@
*/
int
AssignmentRule::getAttribute(const std::string& attributeName,
+ int& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
+ unsigned int& value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
std::string& value) const
{
- int return_value = SBase::getAttribute(attributeName, value);
+ int return_value = Rule::getAttribute(attributeName, value);
if (return_value == LIBSBML_OPERATION_SUCCESS)
{
@@ -163,13 +230,32 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
+ const char* value) const
+{
+ int return_value = Rule::getAttribute(attributeName, value);
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+ if (attributeName == "variable")
+ {
+ value = getVariable().c_str();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ return return_value;
+}
-#ifndef SWIG
+/** @endcond */
@@ -182,7 +268,7 @@
bool
AssignmentRule::isSetAttribute(const std::string& attributeName) const
{
- bool value = SBase::isSetAttribute(attributeName);
+ bool value = Rule::isSetAttribute(attributeName);
if (attributeName == "variable")
{
@@ -196,26 +282,85 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+ return return_value;
+}
+/** @endcond */
-#ifndef SWIG
+/** @cond doxygenLibsbmlInternal */
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::setAttribute(const std::string& attributeName, int value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+ return return_value;
+}
+
+/** @endcond */
+
+
+
/** @cond doxygenLibsbmlInternal */
/*
* Sets the value of the "attributeName" attribute of this AssignmentRule.
*/
int
+AssignmentRule::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
AssignmentRule::setAttribute(const std::string& attributeName,
+ unsigned int value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::setAttribute(const std::string& attributeName,
const std::string& value)
{
- int return_value = SBase::setAttribute(attributeName, value);
+ int return_value = Rule::setAttribute(attributeName, value);
if (attributeName == "variable")
{
@@ -229,16 +374,29 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::setAttribute(const std::string& attributeName,
+ const char* value)
+{
+ int return_value = Rule::setAttribute(attributeName, value);
+ if (attributeName == "variable")
+ {
+ return_value = setVariable(value);
+ }
+ return return_value;
+}
+/** @endcond */
-#ifndef SWIG
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -247,7 +405,7 @@
int
AssignmentRule::unsetAttribute(const std::string& attributeName)
{
- int value = SBase::unsetAttribute(attributeName);
+ int value = Rule::unsetAttribute(attributeName);
if (attributeName == "variable")
{
@@ -262,10 +420,8 @@
-#endif /* !SWIG */
-
#endif /* __cplusplus */
Modified: trunk/libsbml/src/sbml/AssignmentRule.h
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.h 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/AssignmentRule.h 2016-10-27 07:56:31 UTC (rev 23643)
@@ -290,26 +290,115 @@
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
virtual int getAttribute(const std::string& attributeName,
- std::string& value) const;
+ double& value) const;
/** @endcond */
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ unsigned int& value) const;
+ /** @endcond */
- #ifndef SWIG
+ /** @cond doxygenLibsbmlInternal */
+ /**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+ /** @endcond */
+
+
/** @cond doxygenLibsbmlInternal */
/**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ const char* value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
* Predicate returning @c true if this AssignmentRule's attribute
* "attributeName" is set.
*
@@ -324,16 +413,44 @@
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, bool value);
+ /** @endcond */
- #ifndef SWIG
+ /** @cond doxygenLibsbmlInternal */
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, int value);
+ /** @endcond */
+
+
/** @cond doxygenLibsbmlInternal */
/**
@@ -347,23 +464,72 @@
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*/
+ virtual int setAttribute(const std::string& attributeName, double value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
virtual int setAttribute(const std::string& attributeName,
- const std::string& value);
+ unsigned int value);
/** @endcond */
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+ /** @endcond */
- #ifndef SWIG
+ /** @cond doxygenLibsbmlInternal */
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, const char*
+ value);
+ /** @endcond */
+
+
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/Compartment.cpp 2016-10-27 07:56:31 UTC (rev 23643)
@@ -1000,10 +1000,10 @@
}
-#ifndef SWIG
+
/** @cond doxygenLibsbmlInternal */
/*
@@ -1032,16 +1032,23 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName, int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+ return return_value;
+}
+/** @endcond */
-#ifndef SWIG
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1068,6 +1075,11 @@
value = getVolume();
return_value = LIBSBML_OPERATION_SUCCESS;
}
+ else if (attributeName == "spatialDimensions")
+ {
+ value = getSpatialDimensionsAsDouble();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
return return_value;
}
@@ -1076,16 +1088,6 @@
-
-#endif /* !SWIG */
-
-
-
-
-#ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1115,16 +1117,6 @@
-
-#endif /* !SWIG */
-
-
-
-
-#ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1164,13 +1156,42 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ const char* value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+ if (attributeName == "units")
+ {
+ value = getUnits().c_str();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "outside")
+ {
+ value = getOutside().c_str();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = getCompartmentType().c_str();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ return return_value;
+}
-#ifndef SWIG
+/** @endcond */
@@ -1221,16 +1242,6 @@
-
-#endif /* !SWIG */
-
-
-
-
-#ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1253,16 +1264,23 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName, int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+ return return_value;
+}
+/** @endcond */
-#ifndef SWIG
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1281,6 +1299,10 @@
{
return_value = setVolume(value);
}
+ else if (attributeName == "spatialDimensions")
+ {
+ return_value = setSpatialDimensions(value);
+ }
return return_value;
}
@@ -1289,16 +1311,6 @@
-
-#endif /* !SWIG */
-
-
-
-
-#ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1322,16 +1334,6 @@
-
-#endif /* !SWIG */
-
-
-
-
-#ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1363,16 +1365,36 @@
+/** @cond doxygenLibsbmlInternal */
-#endif /* !SWIG */
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName, const char* value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+ if (attributeName == "units")
+ {
+ return_value = setUnits(value);
+ }
+ else if (attributeName == "outside")
+ {
+ return_value = setOutside(value);
+ }
+ else if (attributeName == "compartmentType")
+ {
+ return_value = setCompartmentType(value);
+ }
+ return return_value;
+}
+/** @endcond */
-#ifndef SWIG
-
/** @cond doxygenLibsbmlInternal */
/*
@@ -1419,11 +1441,6 @@
-
-#endif /* !SWIG */
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/Compartment.h 2016-10-27 07:56:31 UTC (rev 23643)
@@ -1315,6 +1315,8 @@
virtual bool hasRequiredAttributes() const;
+
+
#ifndef SWIG
@@ -1339,16 +1341,25 @@
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, int& value) const;
+ /** @endcond */
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1369,16 +1380,6 @@
-
- #endif /* !SWIG */
-
-
-
-
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1399,16 +1400,6 @@
-
- #endif /* !SWIG */
-
-
-
-
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1429,16 +1420,26 @@
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ const char* value) const;
+ /** @endcond */
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1456,16 +1457,6 @@
-
- #endif /* !SWIG */
-
-
-
-
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1485,16 +1476,25 @@
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, int value);
+ /** @endcond */
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1514,16 +1514,6 @@
-
- #endif /* !SWIG */
-
-
-
-
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1544,16 +1534,6 @@
-
- #endif /* !SWIG */
-
-
-
-
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1574,16 +1554,26 @@
+ /** @cond doxygenLibsbmlInternal */
- #endif /* !SWIG */
+ /**
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, const char*
+ value);
+ /** @endcond */
- #ifndef SWIG
-
-
-
/** @cond doxygenLibsbmlInternal */
/**
@@ -1605,6 +1595,7 @@
#endif /* !SWIG */
+
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/CompartmentType.cpp
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.cpp 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/CompartmentType.cpp 2016-10-27 07:56:31 UTC (rev 23643)
@@ -304,7 +304,256 @@
}
+
/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::getAttribute(const std::string& attributeName,
+ bool& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::getAttribute(const std::string& attributeName,
+ int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::getAttribute(const std::string& attributeName,
+ unsigned int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::getAttribute(const std::string& attributeName,
+ const char* value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this CompartmentType's attribute
+ * "attributeName" is set.
+ */
+bool
+CompartmentType::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::setAttribute(const std::string& attributeName, int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::setAttribute(const std::string& attributeName,
+ unsigned int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::setAttribute(const std::string& attributeName,
+ const char* value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this CompartmentType.
+ */
+int
+CompartmentType::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
Modified: trunk/libsbml/src/sbml/CompartmentType.h
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.h 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/CompartmentType.h 2016-10-27 07:56:31 UTC (rev 23643)
@@ -308,6 +308,286 @@
virtual bool hasRequiredAttributes() const;
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ double& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ unsigned int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ const char* value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this CompartmentType's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this CompartmentType's attribute "attributeName" has
+ * been set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, bool value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, int value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, double value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ unsigned int value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, const char*
+ value);
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this CompartmentType.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/Constraint.cpp
===================================================================
--- trunk/libsbml/src/sbml/Constraint.cpp 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/Constraint.cpp 2016-10-27 07:56:31 UTC (rev 23643)
@@ -464,9 +464,252 @@
return allPresent;
}
+/** @cond doxygenLibsbmlInternal */
+/*
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::getAttribute(const std::string& attributeName, bool& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
/** @cond doxygenLibsbmlInternal */
+
/*
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::getAttribute(const std::string& attributeName, int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::getAttribute(const std::string& attributeName,
+ unsigned int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::getAttribute(const std::string& attributeName,
+ const char* value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this Constraint's attribute "attributeName"
+ * is set.
+ */
+bool
+Constraint::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::setAttribute(const std::string& attributeName, int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::setAttribute(const std::string& attributeName, unsigned int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::setAttribute(const std::string& attributeName, const char* value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this Constraint.
+ */
+int
+Constraint::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+/** @cond doxygenLibsbmlInternal */
+/*
* Subclasses should override this method to read (and store) XHTML,
* MathML, etc. directly from the XMLInputStream.
*
Modified: trunk/libsbml/src/sbml/Constraint.h
===================================================================
--- trunk/libsbml/src/sbml/Constraint.h 2016-10-25 17:44:36 UTC (rev 23642)
+++ trunk/libsbml/src/sbml/Constraint.h 2016-10-27 07:56:31 UTC (rev 23643)
@@ -397,6 +397,286 @@
virtual bool hasRequiredElements() const;
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ double& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ unsigned int& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Constraint.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ const char* value) const;
+
+ /** @endcond */
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this Constraint's attribute "attributeName"
+ * is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c tr...
[truncated message content] |
|
From: <mh...@us...> - 2016-10-25 17:44:39
|
Revision: 23642
http://sourceforge.net/p/sbml/code/23642
Author: mhucka
Date: 2016-10-25 17:44:36 +0000 (Tue, 25 Oct 2016)
Log Message:
-----------
Removed because it's folded into the JIB paper cover page now.
Removed Paths:
-------------
trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex
Deleted: trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex 2016-10-23 20:57:08 UTC (rev 23641)
+++ trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex 2016-10-25 17:44:36 UTC (rev 23642)
@@ -1 +0,0 @@
-Biological models often contain components that are related to one another. The \emph{SBML Level~3 Version~1 Core} specification does not directly provide a mechanism for defining these relationships, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactical constructs. The SBML \emph{Groups} package for SBML Level~3 adds the necessary features to SBML to allow grouping of related model elements. The package enables a modeler to include definitions of groups and nested groups, each of which may be annotated to convey why that group was created, and what it represents.
|
|
From: <mh...@us...> - 2016-10-23 20:57:10
|
Revision: 23641
http://sourceforge.net/p/sbml/code/23641
Author: mhucka
Date: 2016-10-23 20:57:08 +0000 (Sun, 23 Oct 2016)
Log Message:
-----------
Semi-final cover page for JIB submission.
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.bst
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.cls
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.aux
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.bbl
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.blg
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fdb_latexmk
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fls
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.log
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.out
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.pdf
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.synctex.gz
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.tex
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/sbgn_PD-level1.pdf
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/auto/
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/auto/sbml-groups-jib-cover-page.el
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/jib.bst
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/jib.cls
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/sbml-groups-jib-cover-page.pdf
trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/sbml-groups-jib-cover-page.tex
Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.bst
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.bst (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.bst 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,1211 @@
+%%
+%% This is file `jib.bst',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% merlin.mbs (with options: `seq-no,vonx,nm-init,ed-au,nmlm,x10,x0,m3,mcite,mct-3,mct-x2,xmth,num-xser,edpar,blk-au.blk-tit,xedn,and-xcom,etal-xc,url,url-nt,nfss,')
+%% ----------------------------------------
+%% *** Bibliography file for the Journal of Integrative Bioinformatics ***
+%%
+%% Copyright 1994-2011 Patrick W Daly
+ % ===============================================================
+ % IMPORTANT NOTICE:
+ % This bibliographic style (bst) file has been generated from one or
+ % more master bibliographic style (mbs) files, listed above.
+ %
+ % This generated file can be redistributed and/or modified under the terms
+ % of the LaTeX Project Public License Distributed from CTAN
+ % archives in directory macros/latex/base/lppl.txt; either
+ % version 1 of the License, or any later version.
+ % ===============================================================
+ % Name and version information of the main mbs file:
+ % \ProvidesFile{merlin.mbs}[2011/03/28 4.32 (PWD, AO, DPC)]
+ % For use with BibTeX version 0.99a or later
+ %-------------------------------------------------------------------
+ % This bibliography style file is intended for texts in ENGLISH
+ % This is a numerical citation style, and as such is standard LaTeX.
+ % It requires no extra package to interface to the main text.
+ % The form of the \bibitem entries is
+ % \bibitem{key}...
+ % Usage of \cite is as follows:
+ % \cite{key} ==>> [#]
+ % \cite[chap. 2]{key} ==>> [#, chap. 2]
+ % where # is a number determined by the ordering in the reference list.
+ % The order in the reference list is that by which the works were originally
+ % cited in the text, or that in the database.
+ %---------------------------------------------------------------------
+
+ENTRY
+ { address
+ author
+ booktitle
+ chapter
+ edition
+ editor
+ eid
+ howpublished
+ institution
+ journal
+ key
+ month
+ note
+ number
+ organization
+ pages
+ publisher
+ school
+ series
+ title
+ type
+ url
+ volume
+ year
+ }
+ {}
+ { label }
+INTEGERS { output.state before.all mid.sentence after.sentence after.block }
+FUNCTION {init.state.consts}
+{ #0 'before.all :=
+ #1 'mid.sentence :=
+ #2 'after.sentence :=
+ #3 'after.block :=
+}
+STRINGS { s t}
+FUNCTION {output.nonnull}
+{ 's :=
+ output.state mid.sentence =
+ { ", " * write$ }
+ { output.state after.block =
+ { add.period$ write$
+ newline$
+ "\newblock " write$
+ }
+ { output.state before.all =
+ 'write$
+ { add.period$ " " * write$ }
+ if$
+ }
+ if$
+ mid.sentence 'output.state :=
+ }
+ if$
+ s
+}
+FUNCTION {output}
+{ duplicate$ empty$
+ 'pop$
+ 'output.nonnull
+ if$
+}
+FUNCTION {output.check}
+{ 't :=
+ duplicate$ empty$
+ { pop$ "empty " t * " in " * cite$ * warning$ }
+ 'output.nonnull
+ if$
+}
+FUNCTION {fin.entry}
+{ add.period$
+ write$
+ newline$
+}
+
+FUNCTION {new.block}
+{ output.state before.all =
+ 'skip$
+ { after.block 'output.state := }
+ if$
+}
+FUNCTION {new.sentence}
+{ output.state after.block =
+ 'skip$
+ { output.state before.all =
+ 'skip$
+ { after.sentence 'output.state := }
+ if$
+ }
+ if$
+}
+FUNCTION {add.blank}
+{ " " * before.all 'output.state :=
+}
+
+FUNCTION {date.block}
+{
+ new.block
+}
+
+FUNCTION {not}
+{ { #0 }
+ { #1 }
+ if$
+}
+FUNCTION {and}
+{ 'skip$
+ { pop$ #0 }
+ if$
+}
+FUNCTION {or}
+{ { pop$ #1 }
+ 'skip$
+ if$
+}
+FUNCTION {new.block.checka}
+{ empty$
+ 'skip$
+ 'new.block
+ if$
+}
+FUNCTION {new.block.checkb}
+{ empty$
+ swap$ empty$
+ and
+ 'skip$
+ 'new.block
+ if$
+}
+FUNCTION {new.sentence.checka}
+{ empty$
+ 'skip$
+ 'new.sentence
+ if$
+}
+FUNCTION {new.sentence.checkb}
+{ empty$
+ swap$ empty$
+ and
+ 'skip$
+ 'new.sentence
+ if$
+}
+FUNCTION {field.or.null}
+{ duplicate$ empty$
+ { pop$ "" }
+ 'skip$
+ if$
+}
+FUNCTION {emphasize}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "\emph{" swap$ * "}" * }
+ if$
+}
+FUNCTION {tie.or.space.prefix}
+{ duplicate$ text.length$ #3 <
+ { "~" }
+ { " " }
+ if$
+ swap$
+}
+
+FUNCTION {capitalize}
+{ "u" change.case$ "t" change.case$ }
+
+FUNCTION {space.word}
+{ " " swap$ * " " * }
+ % Here are the language-specific definitions for explicit words.
+ % Each function has a name bbl.xxx where xxx is the English word.
+ % The language selected here is ENGLISH
+FUNCTION {bbl.and}
+{ "and"}
+
+FUNCTION {bbl.etal}
+{ "et~al." }
+
+FUNCTION {bbl.editors}
+{ "editors" }
+
+FUNCTION {bbl.editor}
+{ "editor" }
+
+FUNCTION {bbl.edby}
+{ "edited by" }
+
+FUNCTION {bbl.edition}
+{ "edition" }
+
+FUNCTION {bbl.volume}
+{ "volume" }
+
+FUNCTION {bbl.of}
+{ "of" }
+
+FUNCTION {bbl.number}
+{ "number" }
+
+FUNCTION {bbl.nr}
+{ "no." }
+
+FUNCTION {bbl.in}
+{ "in" }
+
+FUNCTION {bbl.pages}
+{ "pages" }
+
+FUNCTION {bbl.page}
+{ "page" }
+
+FUNCTION {bbl.chapter}
+{ "chapter" }
+
+FUNCTION {bbl.techrep}
+{ "Technical Report" }
+
+FUNCTION {bbl.mthesis}
+{ "Master's thesis" }
+
+FUNCTION {bbl.phdthesis}
+{ "Ph.D. thesis" }
+
+MACRO {jan} {"January"}
+
+MACRO {feb} {"February"}
+
+MACRO {mar} {"March"}
+
+MACRO {apr} {"April"}
+
+MACRO {may} {"May"}
+
+MACRO {jun} {"June"}
+
+MACRO {jul} {"July"}
+
+MACRO {aug} {"August"}
+
+MACRO {sep} {"September"}
+
+MACRO {oct} {"October"}
+
+MACRO {nov} {"November"}
+
+MACRO {dec} {"December"}
+
+MACRO {acmcs} {"ACM Computing Surveys"}
+
+MACRO {acta} {"Acta Informatica"}
+
+MACRO {cacm} {"Communications of the ACM"}
+
+MACRO {ibmjrd} {"IBM Journal of Research and Development"}
+
+MACRO {ibmsj} {"IBM Systems Journal"}
+
+MACRO {ieeese} {"IEEE Transactions on Software Engineering"}
+
+MACRO {ieeetc} {"IEEE Transactions on Computers"}
+
+MACRO {ieeetcad}
+ {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}
+
+MACRO {ipl} {"Information Processing Letters"}
+
+MACRO {jacm} {"Journal of the ACM"}
+
+MACRO {jcss} {"Journal of Computer and System Sciences"}
+
+MACRO {scp} {"Science of Computer Programming"}
+
+MACRO {sicomp} {"SIAM Journal on Computing"}
+
+MACRO {tocs} {"ACM Transactions on Computer Systems"}
+
+MACRO {tods} {"ACM Transactions on Database Systems"}
+
+MACRO {tog} {"ACM Transactions on Graphics"}
+
+MACRO {toms} {"ACM Transactions on Mathematical Software"}
+
+MACRO {toois} {"ACM Transactions on Office Information Systems"}
+
+MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}
+
+MACRO {tcs} {"Theoretical Computer Science"}
+FUNCTION {bibinfo.check}
+{ swap$
+ duplicate$ missing$
+ {
+ pop$ pop$
+ ""
+ }
+ { duplicate$ empty$
+ {
+ swap$ pop$
+ }
+ { swap$
+ pop$
+ }
+ if$
+ }
+ if$
+}
+FUNCTION {bibinfo.warn}
+{ swap$
+ duplicate$ missing$
+ {
+ swap$ "missing " swap$ * " in " * cite$ * warning$ pop$
+ ""
+ }
+ { duplicate$ empty$
+ {
+ swap$ "empty " swap$ * " in " * cite$ * warning$
+ }
+ { swap$
+ pop$
+ }
+ if$
+ }
+ if$
+}
+INTEGERS { nameptr namesleft numnames }
+
+
+STRINGS { bibinfo}
+
+FUNCTION {format.names}
+{ 'bibinfo :=
+ duplicate$ empty$ 'skip$ {
+ 's :=
+ "" 't :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr
+ "{f.~}{vv~}{ll}{, jj}"
+ format.name$
+ bibinfo bibinfo.check
+ 't :=
+ nameptr #1 >
+ {
+ nameptr #3
+ #1 + =
+ numnames #0
+ #10 +
+ > and
+ { "others" 't :=
+ #1 'namesleft := }
+ 'skip$
+ if$
+ namesleft #1 >
+ { ", " * t * }
+ {
+ s nameptr "{ll}" format.name$ duplicate$ "others" =
+ { 't := }
+ { pop$ }
+ if$
+ t "others" =
+ {
+ " " * bbl.etal *
+ }
+ {
+ bbl.and
+ space.word * t *
+ }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+ } if$
+}
+FUNCTION {format.names.ed}
+{
+ format.names
+}
+FUNCTION {format.authors}
+{ author "author" format.names
+}
+FUNCTION {get.bbl.editor}
+{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ }
+
+FUNCTION {format.editors}
+{ editor "editor" format.names duplicate$ empty$ 'skip$
+ {
+ " " *
+ get.bbl.editor
+ "(" swap$ * ")" *
+ *
+ }
+ if$
+}
+FUNCTION {format.note}
+{
+ url empty$
+ 'skip$
+ { "\urlprefix\url{" url * "}" * output }
+ if$
+ note empty$
+ { "" }
+ { note #1 #1 substring$
+ duplicate$ "{" =
+ 'skip$
+ { output.state mid.sentence =
+ { "l" }
+ { "u" }
+ if$
+ change.case$
+ }
+ if$
+ note #2 global.max$ substring$ * "note" bibinfo.check
+ }
+ if$
+}
+
+FUNCTION {format.title}
+{ title
+ duplicate$ empty$ 'skip$
+ { "t" change.case$ }
+ if$
+ "title" bibinfo.check
+}
+FUNCTION {output.bibitem}
+{ newline$
+ "\bibitem{" write$
+ cite$ write$
+ "}" write$
+ newline$
+ ""
+ before.all 'output.state :=
+}
+
+FUNCTION {n.dashify}
+{
+ 't :=
+ ""
+ { t empty$ not }
+ { t #1 #1 substring$ "-" =
+ { t #1 #2 substring$ "--" = not
+ { "--" *
+ t #2 global.max$ substring$ 't :=
+ }
+ { { t #1 #1 substring$ "-" = }
+ { "-" *
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+ }
+ if$
+ }
+ { t #1 #1 substring$ *
+ t #2 global.max$ substring$ 't :=
+ }
+ if$
+ }
+ while$
+}
+
+FUNCTION {word.in}
+{ bbl.in capitalize
+ " " * }
+
+FUNCTION {format.date}
+{
+ ""
+ duplicate$ empty$
+ year "year" bibinfo.check duplicate$ empty$
+ { swap$ 'skip$
+ { "there's a month but no year in " cite$ * warning$ }
+ if$
+ *
+ }
+ { swap$ 'skip$
+ {
+ swap$
+ " " * swap$
+ }
+ if$
+ *
+ }
+ if$
+}
+FUNCTION {format.btitle}
+{ title "title" bibinfo.check
+ duplicate$ empty$ 'skip$
+ {
+ emphasize
+ }
+ if$
+}
+FUNCTION {either.or.check}
+{ empty$
+ 'pop$
+ { "can't use both " swap$ * " fields in " * cite$ * warning$ }
+ if$
+}
+FUNCTION {format.bvolume}
+{ volume empty$
+ { "" }
+ { bbl.volume volume tie.or.space.prefix
+ "volume" bibinfo.check * *
+ series "series" bibinfo.check
+ duplicate$ empty$ 'pop$
+ { swap$ bbl.of space.word * swap$
+ emphasize * }
+ if$
+ "volume and number" number either.or.check
+ }
+ if$
+}
+FUNCTION {format.number.series}
+{ volume empty$
+ { number empty$
+ { series field.or.null }
+ { series empty$
+ { number "number" bibinfo.check }
+ { output.state mid.sentence =
+ { bbl.number }
+ { bbl.number capitalize }
+ if$
+ number tie.or.space.prefix "number" bibinfo.check * *
+ bbl.in space.word *
+ series "series" bibinfo.check *
+ }
+ if$
+ }
+ if$
+ }
+ { "" }
+ if$
+}
+
+FUNCTION {format.edition}
+{ edition duplicate$ empty$ 'skip$
+ {
+ output.state mid.sentence =
+ { "l" }
+ { "t" }
+ if$ change.case$
+ "edition" bibinfo.check
+ " " * bbl.edition *
+ }
+ if$
+}
+INTEGERS { multiresult }
+FUNCTION {multi.page.check}
+{ 't :=
+ #0 'multiresult :=
+ { multiresult not
+ t empty$ not
+ and
+ }
+ { t #1 #1 substring$
+ duplicate$ "-" =
+ swap$ duplicate$ "," =
+ swap$ "+" =
+ or or
+ { #1 'multiresult := }
+ { t #2 global.max$ substring$ 't := }
+ if$
+ }
+ while$
+ multiresult
+}
+FUNCTION {format.pages}
+{ pages duplicate$ empty$ 'skip$
+ { duplicate$ multi.page.check
+ {
+ bbl.pages swap$
+ n.dashify
+ }
+ {
+ bbl.page swap$
+ }
+ if$
+ tie.or.space.prefix
+ "pages" bibinfo.check
+ * *
+ }
+ if$
+}
+FUNCTION {format.journal.pages}
+{ pages duplicate$ empty$ 'pop$
+ { swap$ duplicate$ empty$
+ { pop$ pop$ format.pages }
+ {
+ ":" *
+ swap$
+ n.dashify
+ "pages" bibinfo.check
+ *
+ }
+ if$
+ }
+ if$
+}
+FUNCTION {format.journal.eid}
+{ eid "eid" bibinfo.check
+ duplicate$ empty$ 'pop$
+ { swap$ duplicate$ empty$ 'skip$
+ {
+ ":" *
+ }
+ if$
+ swap$ *
+ }
+ if$
+}
+FUNCTION {format.vol.num.pages}
+{ volume field.or.null
+ duplicate$ empty$ 'skip$
+ {
+ "volume" bibinfo.check
+ }
+ if$
+ number "number" bibinfo.check duplicate$ empty$ 'skip$
+ {
+ swap$ duplicate$ empty$
+ { "there's a number but no volume in " cite$ * warning$ }
+ 'skip$
+ if$
+ swap$
+ "(" swap$ * ")" *
+ }
+ if$ *
+ eid empty$
+ { format.journal.pages }
+ { format.journal.eid }
+ if$
+}
+
+FUNCTION {format.chapter.pages}
+{ chapter empty$
+ 'format.pages
+ { type empty$
+ { bbl.chapter }
+ { type "l" change.case$
+ "type" bibinfo.check
+ }
+ if$
+ chapter tie.or.space.prefix
+ "chapter" bibinfo.check
+ * *
+ pages empty$
+ 'skip$
+ { ", " * format.pages * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.booktitle}
+{
+ booktitle "booktitle" bibinfo.check
+ emphasize
+}
+FUNCTION {format.in.ed.booktitle}
+{ format.booktitle duplicate$ empty$ 'skip$
+ {
+ editor "editor" format.names.ed duplicate$ empty$ 'pop$
+ {
+ " " *
+ get.bbl.editor
+ "(" swap$ * "), " *
+ * swap$
+ * }
+ if$
+ word.in swap$ *
+ }
+ if$
+}
+FUNCTION {empty.misc.check}
+{ author empty$ title empty$ howpublished empty$
+ month empty$ year empty$ note empty$
+ and and and and and
+ { "all relevant fields are empty in " cite$ * warning$ }
+ 'skip$
+ if$
+}
+FUNCTION {format.thesis.type}
+{ type duplicate$ empty$
+ 'pop$
+ { swap$ pop$
+ "t" change.case$ "type" bibinfo.check
+ }
+ if$
+}
+FUNCTION {format.tr.number}
+{ number "number" bibinfo.check
+ type duplicate$ empty$
+ { pop$ bbl.techrep }
+ 'skip$
+ if$
+ "type" bibinfo.check
+ swap$ duplicate$ empty$
+ { pop$ "t" change.case$ }
+ { tie.or.space.prefix * * }
+ if$
+}
+FUNCTION {format.article.crossref}
+{
+ key duplicate$ empty$
+ { pop$
+ journal duplicate$ empty$
+ { "need key or journal for " cite$ * " to crossref " * crossref * warning$ }
+ { "journal" bibinfo.check emphasize word.in swap$ * }
+ if$
+ }
+ { word.in swap$ * " " *}
+ if$
+ " \cite{" * crossref * "}" *
+}
+FUNCTION {format.crossref.editor}
+{ editor #1 "{vv~}{ll}" format.name$
+ "editor" bibinfo.check
+ editor num.names$ duplicate$
+ #2 >
+ { pop$
+ "editor" bibinfo.check
+ " " * bbl.etal
+ *
+ }
+ { #2 <
+ 'skip$
+ { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
+ {
+ "editor" bibinfo.check
+ " " * bbl.etal
+ *
+ }
+ {
+ bbl.and space.word
+ * editor #2 "{vv~}{ll}" format.name$
+ "editor" bibinfo.check
+ *
+ }
+ if$
+ }
+ if$
+ }
+ if$
+}
+FUNCTION {format.book.crossref}
+{ volume duplicate$ empty$
+ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
+ pop$ word.in
+ }
+ { bbl.volume
+ capitalize
+ swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word *
+ }
+ if$
+ editor empty$
+ editor field.or.null author field.or.null =
+ or
+ { key empty$
+ { series empty$
+ { "need editor, key, or series for " cite$ * " to crossref " *
+ crossref * warning$
+ "" *
+ }
+ { series emphasize * }
+ if$
+ }
+ { key * }
+ if$
+ }
+ { format.crossref.editor * }
+ if$
+ " \cite{" * crossref * "}" *
+}
+FUNCTION {format.incoll.inproc.crossref}
+{
+ editor empty$
+ editor field.or.null author field.or.null =
+ or
+ { key empty$
+ { format.booktitle duplicate$ empty$
+ { "need editor, key, or booktitle for " cite$ * " to crossref " *
+ crossref * warning$
+ }
+ { word.in swap$ * }
+ if$
+ }
+ { word.in key * " " *}
+ if$
+ }
+ { word.in format.crossref.editor * " " *}
+ if$
+ " \cite{" * crossref * "}" *
+}
+FUNCTION {format.org.or.pub}
+{ 't :=
+ ""
+ address empty$ t empty$ and
+ 'skip$
+ {
+ t empty$
+ { address "address" bibinfo.check *
+ }
+ { t *
+ address empty$
+ 'skip$
+ { ", " * address "address" bibinfo.check * }
+ if$
+ }
+ if$
+ }
+ if$
+}
+FUNCTION {format.publisher.address}
+{ publisher "publisher" bibinfo.warn format.org.or.pub
+}
+
+FUNCTION {format.organization.address}
+{ organization "organization" bibinfo.check format.org.or.pub
+}
+
+FUNCTION {article}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.title "title" output.check
+ new.block
+ crossref missing$
+ {
+ journal
+ "journal" bibinfo.check
+ emphasize
+ "journal" output.check
+ format.vol.num.pages output
+ format.date "year" output.check
+ }
+ { format.article.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ new.block
+ format.note output
+ fin.entry
+}
+FUNCTION {book}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ new.block
+ format.btitle "title" output.check
+ crossref missing$
+ { format.bvolume output
+ new.block
+ format.number.series output
+ new.sentence
+ format.publisher.address output
+ }
+ {
+ new.block
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.edition output
+ format.date "year" output.check
+ new.block
+ format.note output
+ fin.entry
+}
+FUNCTION {booklet}
+{ output.bibitem
+ format.authors output
+ new.block
+ format.title "title" output.check
+ new.block
+ howpublished "howpublished" bibinfo.check output
+ address "address" bibinfo.check output
+ format.date output
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {inbook}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ new.block
+ format.btitle "title" output.check
+ crossref missing$
+ {
+ format.bvolume output
+ format.chapter.pages "chapter and pages" output.check
+ new.block
+ format.number.series output
+ new.sentence
+ format.publisher.address output
+ }
+ {
+ format.chapter.pages "chapter and pages" output.check
+ new.block
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.edition output
+ format.date "year" output.check
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {incollection}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.title "title" output.check
+ new.block
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ format.bvolume output
+ format.number.series output
+ format.chapter.pages output
+ new.sentence
+ format.publisher.address output
+ format.edition output
+ format.date "year" output.check
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.chapter.pages output
+ }
+ if$
+ new.block
+ format.note output
+ fin.entry
+}
+FUNCTION {inproceedings}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.title "title" output.check
+ new.block
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ format.bvolume output
+ format.number.series output
+ format.pages output
+ new.sentence
+ publisher empty$
+ { format.organization.address output }
+ { organization "organization" bibinfo.check output
+ format.publisher.address output
+ }
+ if$
+ format.date "year" output.check
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ new.block
+ format.note output
+ fin.entry
+}
+FUNCTION {conference} { inproceedings }
+FUNCTION {manual}
+{ output.bibitem
+ author empty$
+ { organization "organization" bibinfo.check
+ duplicate$ empty$ 'pop$
+ { output
+ address "address" bibinfo.check output
+ }
+ if$
+ }
+ { format.authors output.nonnull }
+ if$
+ new.block
+ format.btitle "title" output.check
+ author empty$
+ { organization empty$
+ {
+ address new.block.checka
+ address "address" bibinfo.check output
+ }
+ 'skip$
+ if$
+ }
+ {
+ organization address new.block.checkb
+ organization "organization" bibinfo.check output
+ address "address" bibinfo.check output
+ }
+ if$
+ format.edition output
+ format.date output
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {mastersthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.btitle
+ "title" output.check
+ new.block
+ bbl.mthesis format.thesis.type output.nonnull
+ school "school" bibinfo.warn output
+ address "address" bibinfo.check output
+ format.date "year" output.check
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {misc}
+{ output.bibitem
+ format.authors output
+ title howpublished new.block.checkb
+ format.title output
+ howpublished new.block.checka
+ howpublished "howpublished" bibinfo.check output
+ format.date output
+ new.block
+ format.note output
+ fin.entry
+ empty.misc.check
+}
+FUNCTION {phdthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.btitle
+ "title" output.check
+ new.block
+ bbl.phdthesis format.thesis.type output.nonnull
+ school "school" bibinfo.warn output
+ address "address" bibinfo.check output
+ format.date "year" output.check
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {proceedings}
+{ output.bibitem
+ editor empty$
+ { organization "organization" bibinfo.check output
+ }
+ { format.editors output.nonnull }
+ if$
+ new.block
+ format.btitle "title" output.check
+ format.bvolume output
+ format.number.series output
+ editor empty$
+ { publisher empty$
+ 'skip$
+ {
+ new.sentence
+ format.publisher.address output
+ }
+ if$
+ }
+ { publisher empty$
+ {
+ new.sentence
+ format.organization.address output }
+ {
+ new.sentence
+ organization "organization" bibinfo.check output
+ format.publisher.address output
+ }
+ if$
+ }
+ if$
+ format.date "year" output.check
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {techreport}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.title
+ "title" output.check
+ new.block
+ format.tr.number output.nonnull
+ institution "institution" bibinfo.warn output
+ address "address" bibinfo.check output
+ format.date "year" output.check
+ new.block
+ format.note output
+ fin.entry
+}
+
+FUNCTION {unpublished}
+{ output.bibitem
+ format.authors "author" output.check
+ new.block
+ format.title "title" output.check
+ format.date output
+ new.block
+ format.note "note" output.check
+ fin.entry
+}
+
+FUNCTION {default.type} { misc }
+READ
+STRINGS { longest.label }
+INTEGERS { number.label longest.label.width }
+FUNCTION {initialize.longest.label}
+{ "" 'longest.label :=
+ #1 'number.label :=
+ #0 'longest.label.width :=
+}
+FUNCTION {longest.label.pass}
+{ number.label int.to.str$ 'label :=
+ number.label #1 + 'number.label :=
+ label width$ longest.label.width >
+ { label 'longest.label :=
+ label width$ 'longest.label.width :=
+ }
+ 'skip$
+ if$
+}
+EXECUTE {initialize.longest.label}
+ITERATE {longest.label.pass}
+FUNCTION {begin.bib}
+{ preamble$ empty$
+ 'skip$
+ { preamble$ write$ newline$ }
+ if$
+ "\begin{thebibliography}{" longest.label * "}" *
+ write$ newline$
+ "\providecommand{\url}[1]{\texttt{#1}}"
+ write$ newline$
+ "\providecommand{\urlprefix}{URL }"
+ write$ newline$
+}
+EXECUTE {begin.bib}
+EXECUTE {init.state.consts}
+ITERATE {call.type$}
+FUNCTION {end.bib}
+{ newline$
+ "\end{thebibliography}" write$ newline$
+}
+EXECUTE {end.bib}
+%% End of customized bst file
+%%
+%% End of file `jib.bst'.
Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.cls
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.cls (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib.cls 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,203 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{jib}[2012/08/06 v2.0 by Stephan Weise]
+\DeclareOption*{%
+ \PassOptionsToClass{\CurrentOption}{article}}
+\ProcessOptions
+% article.cls Version: 2004/02/16 v1.4f
+\LoadClass[12pt]{article}
+% calc -> Tools Package
+% textcomp -> base Package
+% url -> ltxmisc Package
+\RequirePackage{calc}[1998/07/07 v4.1b Infix arithmetic (KKT,FJ)]
+\RequirePackage{url}[2004/03/15 ver 3.1 Verb mode for urls, etc.]
+\RequirePackage{listings}[2004/09/07 1.3 Carsten Heinz]
+\RequirePackage{caption}[2004/07/16 v3.0c Customising captions (AS)]
+\RequirePackage{textcomp}[2004/02/22 v1.99f Standard LaTeX package]
+\RequirePackage{times}[2004/02/22 v1.99f Standard LaTeX package]
+% graphicx -> graphics Package
+% epsfig -> graphics Package
+\RequirePackage{graphicx}[1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)]
+\RequirePackage{epsfig}[1999/02/16 v1.7a (e)psfig emulation (SPQR)]
+% vmargin Package
+\RequirePackage{vmargin}[2004/07/15 V2.5 set document margins (VK)]
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% In Case of using latex compiler (Standard)
+%\RequirePackage[dvipdfm]{hyperref}[2003/11/30 v6.74m Hypertext links for LaTeX]
+
+% In Case of using pdflatex compiler
+\RequirePackage{hyperref}[2003/11/30 v6.74m Hypertext links for LaTeX]
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\hypersetup{
+ naturalnames=true,
+ hypertexnames=false,
+ pageanchor=false,
+ plainpages=false,
+ breaklinks=true,
+ colorlinks=true,
+ linkcolor=black,
+ citecolor=black,
+ urlcolor=black,
+ filecolor=black,
+ bookmarks=true,
+ bookmarksopen=true,
+}
+
+\RequirePackage{eso-pic}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Titelseitendefinition
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\newenvironment{jibtitlepage}{%
+ \sffamily%
+ \newcounter{institution}
+ \renewcommand{\theinstitution}{\arabic{institution}}
+ \newcommand{\addjibinstitution}{%
+ \@ifstar{\@addjibinstitution}
+ {\@addjibinstitutionwithreference}}
+ \newcommand{\@addjibinstitution}[1]{
+ \begin{center}{\small ##1}\end{center}}
+ \newcommand{\@addjibinstitutionwithreference}[2]{%
+ \begin{center}%
+ \refstepcounter{institution}\label{##1}%
+ \textsuperscript{\scriptsize{\theinstitution}}{\small ##2}%
+ \end{center}}
+
+ \newcommand{\jibtitle}[1]{\begin{center}\large\bfseries ##1\end{center}}
+ \newcommand{\iref}[2][]{\textsuperscript{\scriptsize{\ref{##2}##1}}}
+ \newcommand{\jibauthor}[1]{\begin{center}\small\bfseries ##1\end{center}}
+
+ \newcommand{\jibfootnotemark}{}
+ \newcommand{\jibfurtherfootnotes}{}
+ \renewcommand{\@makefnmark}{\textsuperscript{\scriptsize{\jibfootnotemark\jibfurtherfootnotes}}}%
+ \renewcommand\@makefntext[1]{%
+ \parindent 1em%
+ \noindent
+ \hb@xt@1.8em{\hss\textsuperscript{\scriptsize{\jibfootnotemark}}}##1}
+ \newcommand{\jibauthorfootnote}[3][]{%
+ \renewcommand{\jibfurtherfootnotes}{##1}%
+ \renewcommand{\jibfootnotemark}{##2}%
+ \footnote{##3}}
+}
+{\setcounter{footnote}{0}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Definition des Satzspiegels und Seitenlayouts
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\setpapersize{A4}
+%\setlength{\paperwidth}{210mm}
+%\setlength{\paperheight}{297mm}
+\setmarginsrb{1in}%Rand links
+ {12.5mm}%Rand oben
+ {1in}%Rand rechts
+ {12.5mm}%Rand unten
+ {1cm}%Kopfhoehe
+ {1cm}%Kopfabstand
+ {2cm}%Fusshoehe
+ {2.25cm}%Fussabstand
+
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{1.5ex plus.2ex minus.2ex}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% URL-Definitionen und Anpassungen
+%% Infos: Package url
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\url@emailstyle{%
+ \@ifundefined{selectfont}{\def\UrlFont{\sf}}{\def\UrlFont{\sffamily}}}
+\DeclareUrlCommand\email{\urlstyle{email}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Header/Footer-Definition
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\def\jibvolume#1{\gdef\@jibvolume{#1}}\jibvolume{00}
+\def\jibissue#1{\gdef\@jibissue{#1}}\jibissue{00}
+\def\jibpages#1{\gdef\@jibpages{#1}}\jibpages{0000}
+\def\jibyear#1{\def\@jibyear{#1}}\jibyear{0000}
+
+\def\jibfooter{\footnotesize\sffamily doi:10.2390/biecoll-jib-\@jibyear-\@jibpages \hfil \thepage}
+
+\def\ps@jibheadings{%
+ \renewcommand{\@oddfoot}{\jibfooter}%
+ \renewcommand{\@evenfoot}{\jibfooter}%
+ \renewcommand{\@evenhead}{\leftmark\hfil\rightmark}%
+ \renewcommand{\@oddhead}{\leftmark\hfil\rightmark}%
+ }
+
+\newcommand{\makeHeaderFooter}[1]{
+\markboth{\footnotesize\sffamily Journal of Integrative Bioinformatics, \@jibvolume(\@jibissue):\@jibpages, \@jibyear}{\href{http://journal.imbio.de/}{\footnotesize\sffamily http://journal.imbio.de/}}}
+\makeHeaderFooter{}
+\pagestyle{jibheadings}
+
+% Copyright
+\AddToShipoutPictureFG{%
+ \put(635,60){%
+ \rotatebox{90}{\scriptsize{
+ \begin{minipage}[t]{200mm}
+ \textcolor[rgb]{0.67,0.67,0.67}{Copyright \@jibyear~The Author(s). Published by Journal of Integrative Bioinformatics. \\
+ This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (http://creativecommons.org/licenses/by-nc-nd/3.0/).}
+ \end{minipage}
+ }}%
+ }%
+}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Abstract ohne Indent
+%% - nutzt intern die Quotation-Umgebung zum Erzeugen des Abstracts
+%% (im notitlepage und onecolumn Modus
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\renewcommand{\abstractname}{Summary}
+\renewenvironment{quotation}
+ {\list{}{\listparindent 0em%
+ \itemindent \listparindent
+ \rightmargin \leftmargin
+ \parsep \z@ \@plus\p@}%
+ \item\relax}
+ {\endlist}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Font-Anpassung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\renewcommand\section{\@startsection {section}{1}{\z@}%
+ {-3.5ex \@plus -1ex \@minus -.2ex}%
+ {2.3ex \@plus.2ex}%
+ {\normalfont\sffamily\large\bfseries}}
+\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
+ {-3.25ex\@plus -1ex \@minus -.2ex}%
+ {1.5ex \@plus .2ex}%
+ {\normalfont\sffamily\normalsize\bfseries}}
+\renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}%
+ {-3.25ex\@plus -1ex \@minus -.2ex}%
+ {1.5ex \@plus .2ex}%
+ {\normalfont\sffamily\normalsize}}
+\renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}%
+ {3.25ex \@plus1ex \@minus.2ex}%
+ {-1em}%
+ {\normalfont\sffamily\normalsize\bfseries}}
+\renewcommand\subparagraph{\@startsection{subparagraph}{5}{\parindent}%
+ {3.25ex \@plus1ex \@minus .2ex}%
+ {-1em}%
+ {\normalfont\sffamily\normalsize\bfseries}}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Caption Anpassung fuer Figuren- und Tabellenunterschriften
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\captionsetup{font={footnotesize,bf},%
+ margin=0.7cm,%
+ parskip=5pt,%
+ aboveskip=0pt,%
+ belowskip=0pt}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Sonderzeichenanpassung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% \texorpdfstring{...}, weil z.B. \textreg eventuell in section, subsection etc. genutzt wird
+%% und hyperref bzw. in bookmarks Probleme mit Sonderzeichen auftreten
+%% werden die originalen Befehle, wie \textregistered etc., verwendet, treten keine Probleme auf
+\newcommand{\textreg}{\texorpdfstring{\textsuperscript{\textregistered}}{\textregistered}}
+\newcommand{\textcright}{\texorpdfstring{\textsuperscript{\textcopyright}}{\textcopyright}}
Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.aux
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.aux (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.aux 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,25 @@
+\relax
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\newlabel{embl}{{1}{1}{\relax }{institution.1}{}}
+\newlabel{csbe}{{2}{1}{\relax }{institution.2}{}}
+\newlabel{edin}{{3}{1}{\relax }{institution.3}{}}
+\newlabel{caltec}{{4}{1}{\relax }{institution.4}{}}
+\newlabel{ipk}{{5}{1}{\relax }{institution.5}{}}
+\newlabel{mskcc}{{6}{1}{\relax }{institution.6}{}}
+\newlabel{sri}{{7}{1}{\relax }{institution.7}{}}
+\newlabel{sbi}{{8}{1}{\relax }{institution.8}{}}
+\newlabel{hert}{{9}{1}{\relax }{institution.9}{}}
Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.bbl
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.bbl (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.bbl 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,21 @@
+\begin{thebibliography}{1}
+\providecommand{\url}[1]{\texttt{#1}}
+\providecommand{\urlprefix}{URL }
+
+\bibitem{jibBook}
+F.~Surname.
+\newblock \emph{This is a book title}, volume 123 of \emph{Series name}.
+\newblock Publisher name, 2012.
+
+\bibitem{jibArticle}
+F.~Surname.
+\newblock This is an article title.
+\newblock \emph{Journal name}, 1(2):10--20, 2012.
+
+\bibitem{jibProceedings}
+F.~Surname.
+\newblock This is the title of a proceedings article.
+\newblock In E.~EditorSurname (editor), \emph{Prooceedings title}, volume 234
+ of \emph{Series name}, pages 20--30. Publisher name, 2012.
+
+\end{thebibliography}
Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.blg
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.blg (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.blg 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,50 @@
+This is BibTeX, Version 0.99d (TeX Live 2012)
+Capacity: max_strings=35307, hash_size=35307, hash_prime=30011
+The top-level auxiliary file: jib_example.aux
+The style file: jib.bst
+Database file #1: jib_references.bib
+Warning--can't use both author and editor fields in jibBook
+Warning--can't use both volume and number fields in jibBook
+Warning--can't use both volume and number fields in jibProceedings
+You've used 3 entries,
+ 2225 wiz_defined-function locations,
+ 522 strings with 4307 characters,
+and the built_in function-call counts, 1069 in all, are:
+= -- 70
+> -- 16
+< -- 3
++ -- 7
+- -- 4
+* -- 72
+:= -- 122
+add.period$ -- 10
+call.type$ -- 3
+change.case$ -- 4
+chr.to.int$ -- 0
+cite$ -- 6
+duplicate$ -- 108
+empty$ -- 116
+format.name$ -- 4
+if$ -- 229
+int.to.chr$ -- 0
+int.to.str$ -- 3
+missing$ -- 27
+newline$ -- 20
+num.names$ -- 5
+pop$ -- 33
+preamble$ -- 1
+purify$ -- 0
+quote$ -- 0
+skip$ -- 25
+stack$ -- 0
+substring$ -- 43
+swap$ -- 80
+text.length$ -- 3
+text.prefix$ -- 0
+top$ -- 0
+type$ -- 0
+warning$ -- 3
+while$ -- 9
+width$ -- 4
+write$ -- 39
+(There were 3 warnings)
Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fdb_latexmk
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fdb_latexmk (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fdb_latexmk 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,110 @@
+# Fdb version 3
+["pdflatex"] 1434626938 "jib_example.tex" "jib_example.pdf" "jib_example" 1434626940
+ "/usr/local/texlive/2012/texmf-dist/fonts/enc/dvips/base/8r.enc" 1165713224 4850 80dc9bab7f31fb78a000ccfed0e27cab ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/map/fontname/texfonts.map" 1272929888 3287 e6b82fe08f5336d4d5ebc73fb1152e87 ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/helvetic/phvb7t.tfm" 1136768653 2240 eb56c13537f4d8a0bd3fafc25572b1bd ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/helvetic/phvb8r.tfm" 1136768653 4484 b828043cbd581d289d955903c1339981 ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/helvetic/phvr7t.tfm" 1136768653 2520 53e01eef820ca829e42c1333c3fd02b9 ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/helvetic/phvr8r.tfm" 1136768653 4712 9ef4d7d106579d4b136e1529e1a4533c ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/times/ptmb7t.tfm" 1136768653 2172 fd0c924230362ff848a33632ed45dc23 ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/times/ptmb8r.tfm" 1136768653 4524 6bce29db5bc272ba5f332261583fee9c ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/times/ptmr7t.tfm" 1136768653 2124 2601a75482e9426d33db523edf23570a ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/adobe/times/ptmr8r.tfm" 1136768653 4408 25b74d011a4c66b7f212c0cc3c90061b ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/public/cm/cmmi10.tfm" 1136768653 1528 abec98dbc43e172678c11b3b9031252a ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/public/cm/cmmi12.tfm" 1136768653 1524 4414a8315f39513458b80dfc63bff03a ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/public/cm/cmmi6.tfm" 1136768653 1512 f21f83efb36853c0b70002322c1ab3ad ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/public/cm/cmmi8.tfm" 1136768653 1520 eccf95517727cb11801f4f1aee3a21b4 ""
+ "/usr/local/texlive/2012/texmf-dist/fonts/tfm/public/cm/cmr10.tfm" 1136768653 1296 45809c5a464d5f32c8f98ba97c1bb47f ""
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Added: trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fls
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fls (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/jib-submission-2006/JIB-LaTeX-Template/jib_example.fls 2016-10-23 20:57:08 UTC (rev 23641)
@@ -0,0 +1,718 @@
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[truncated message content] |
|
From: <fbe...@us...> - 2016-10-20 15:03:33
|
Revision: 23640
http://sourceforge.net/p/sbml/code/23640
Author: fbergmann
Date: 2016-10-20 15:03:30 +0000 (Thu, 20 Oct 2016)
Log Message:
-----------
- allow ':' and '-' to be used in gene product associations
Modified Paths:
--------------
trunk/libsbml/src/sbml/packages/fbc/sbml/Association.cpp
trunk/libsbml/src/sbml/packages/fbc/sbml/FbcAssociation.cpp
Modified: trunk/libsbml/src/sbml/packages/fbc/sbml/Association.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/fbc/sbml/Association.cpp 2016-10-20 09:49:19 UTC (rev 23639)
+++ trunk/libsbml/src/sbml/packages/fbc/sbml/Association.cpp 2016-10-20 15:03:30 UTC (rev 23640)
@@ -291,6 +291,8 @@
Association* a = new Association();
a->setType(GENE_ASSOCIATION);
std::string name = node->getName();
+ replaceAllSubStrings(name, "__MINUS__", "-");
+ replaceAllSubStrings(name, "__COLON__", ":");
replaceAllSubStrings(name, "__DOT__", ".");
replaceAllSubStrings(name, "__ONE__" ,"1" );
replaceAllSubStrings(name, "__TWO__" ,"2" );
@@ -330,6 +332,8 @@
replaceAllSubStrings(tweaked, " AND ", " * ");
replaceAllSubStrings(tweaked, " or ", " + ");
replaceAllSubStrings(tweaked, " OR ", " + ");
+ replaceAllSubStrings(tweaked, "-", "__MINUS__");
+ replaceAllSubStrings(tweaked, ":", "__COLON__");
replaceAllSubStrings(tweaked, ".", "__DOT__");
replaceAllSubStrings(tweaked, "1", "__ONE__");
replaceAllSubStrings(tweaked, "2", "__TWO__");
Modified: trunk/libsbml/src/sbml/packages/fbc/sbml/FbcAssociation.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/fbc/sbml/FbcAssociation.cpp 2016-10-20 09:49:19 UTC (rev 23639)
+++ trunk/libsbml/src/sbml/packages/fbc/sbml/FbcAssociation.cpp 2016-10-20 15:03:30 UTC (rev 23640)
@@ -291,6 +291,8 @@
if (node->getType() == AST_NAME)
{
std::string name = node->getName();
+ replaceAllSubStrings(name, "__MINUS__", "-");
+ replaceAllSubStrings(name, "__COLON__", ":");
replaceAllSubStrings(name, "__DOT__", ".");
replaceAllSubStrings(name, "__ONE__", "1");
replaceAllSubStrings(name, "__TWO__", "2");
@@ -355,6 +357,8 @@
replaceAllSubStrings(tweaked, " AND ", " * ");
replaceAllSubStrings(tweaked, " or ", " + ");
replaceAllSubStrings(tweaked, " OR ", " + ");
+ replaceAllSubStrings(tweaked, "-", "__MINUS__");
+ replaceAllSubStrings(tweaked, ":", "__COLON__");
replaceAllSubStrings(tweaked, ".", "__DOT__");
replaceAllSubStrings(tweaked, "1", "__ONE__");
replaceAllSubStrings(tweaked, "2", "__TWO__");
|
|
From: <sar...@us...> - 2016-10-20 09:49:21
|
Revision: 23639
http://sourceforge.net/p/sbml/code/23639
Author: sarahkeating
Date: 2016-10-20 09:49:19 +0000 (Thu, 20 Oct 2016)
Log Message:
-----------
Modified Paths:
--------------
trunk/libsbml/src/sbml/packages/comp/extension/CompExtension.cpp
Modified: trunk/libsbml/src/sbml/packages/comp/extension/CompExtension.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/extension/CompExtension.cpp 2016-10-19 04:14:55 UTC (rev 23638)
+++ trunk/libsbml/src/sbml/packages/comp/extension/CompExtension.cpp 2016-10-20 09:49:19 UTC (rev 23639)
@@ -155,7 +155,7 @@
{
if (sbmlLevel == 3)
{
- if (sbmlVersion == 1)
+ if (sbmlVersion == 1 || sbmlVersion == 2)
{
if (pkgVersion == 1)
{
|
|
From: <luc...@us...> - 2016-10-19 04:14:58
|
Revision: 23638
http://sourceforge.net/p/sbml/code/23638
Author: luciansmith
Date: 2016-10-19 04:14:55 +0000 (Wed, 19 Oct 2016)
Log Message:
-----------
Allow SBML l3v2 when creating comp namespace.
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/packages/comp/extension/CompExtension.cpp
Modified: branches/libsbml-experimental/src/sbml/packages/comp/extension/CompExtension.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/packages/comp/extension/CompExtension.cpp 2016-10-19 04:14:22 UTC (rev 23637)
+++ branches/libsbml-experimental/src/sbml/packages/comp/extension/CompExtension.cpp 2016-10-19 04:14:55 UTC (rev 23638)
@@ -155,7 +155,7 @@
{
if (sbmlLevel == 3)
{
- if (sbmlVersion == 1)
+ if (sbmlVersion == 1 || sbmlVersion == 2)
{
if (pkgVersion == 1)
{
|
|
From: <luc...@us...> - 2016-10-19 04:14:24
|
Revision: 23637
http://sourceforge.net/p/sbml/code/23637
Author: luciansmith
Date: 2016-10-19 04:14:22 +0000 (Wed, 19 Oct 2016)
Log Message:
-----------
Remove space before for documentation.
Modified Paths:
--------------
trunk/libsbml/src/sbml/AssignmentRule.h
trunk/libsbml/src/sbml/Delay.h
trunk/libsbml/src/sbml/EventAssignment.h
trunk/libsbml/src/sbml/RateRule.h
trunk/libsbml/src/sbml/Reaction.h
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/common/common-documentation.h
trunk/libsbml/src/sbml/xml/XMLError.h
Modified: trunk/libsbml/src/sbml/AssignmentRule.h
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/AssignmentRule.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -88,7 +88,7 @@
* prior to Level 2 version 4) be the same as the units defined for
* the parameter.
*
- * <li> (For SBML Level 3 Version 2 only) <em>In the case of
+ * <li> (For SBML Level 3 Version 2 only) <em>In the case of
* an object from an SBML Level 3 package</em>, an AssignmentRule sets
* the referenced object's value (as defined by that package) to the
* value of the formula in math. The unit of measurement associated
Modified: trunk/libsbml/src/sbml/Delay.h
===================================================================
--- trunk/libsbml/src/sbml/Delay.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/Delay.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -173,7 +173,7 @@
* with SBML Level 2 Version 2, the units of that time are
* calculated based on the mathematical expression and the model quantities
* referenced by <code><ci></code> elements used within that
- * expression. (In SBML Level 2 Version 1, there exists an
+ * expression. (In SBML Level 2 Version 1, there exists an
* attribute on Event called "timeUnits". This attribute can be used to set
* the units of the Delay expression explicitly.) The method
* Delay::getDerivedUnitDefinition() returns what libSBML computes the units
Modified: trunk/libsbml/src/sbml/EventAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/EventAssignment.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -180,7 +180,7 @@
* and Level 3) or must (in previous Versions of Level 2) be
* identical to the units defined for the parameter.
*
- * <li> (For SBML Level 3 Version 2 only) <em>In the case of
+ * <li> (For SBML Level 3 Version 2 only) <em>In the case of
* an object from an SBML Level 3 package</em>, an EventAssignment sets
* the referenced object's value (as defined by that package) to the
* value of the formula in "math". The unit of measurement associated
Modified: trunk/libsbml/src/sbml/RateRule.h
===================================================================
--- trunk/libsbml/src/sbml/RateRule.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/RateRule.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -79,7 +79,7 @@
* version 4) be the Parameter object's "unit" attribute value divided
* by the model-wide unit of <em>time</em>.
*
- * <li> (For SBML Level 3 Version 2 only) <em>In the case of
+ * <li> (For SBML Level 3 Version 2 only) <em>In the case of
* an object from an SBML Level 3 package</em>, a RateRule sets the rate
* of change of the referenced object's value (as defined by that package)
* to the value of the formula in "math". The unit of measurement associated
Modified: trunk/libsbml/src/sbml/Reaction.h
===================================================================
--- trunk/libsbml/src/sbml/Reaction.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/Reaction.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -115,7 +115,7 @@
* The Reaction object class has another boolean attribute called "fast".
* This attribute is optional in SBML Level 2, with a default of @c
* false; it is mandatory in SBML Level 3 (with no default value).
- * In SBML Level 3 Version 2, a value of @c true for the "fast"
+ * In SBML Level 3 Version 2, a value of @c true for the "fast"
* attribute is deprecated in favor of all reactions having a "fast" value
* of @c false. It
* is used to indicate that a reaction occurs on a vastly faster time scale
Modified: trunk/libsbml/src/sbml/SBase.h
===================================================================
--- trunk/libsbml/src/sbml/SBase.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/SBase.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -1089,7 +1089,7 @@
* readers are urged to consult the appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more
- * in-depth explanations. The SBML Level 2 and 3
+ * in-depth explanations. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element
* content must be structured.
*
@@ -1497,7 +1497,7 @@
* readers are urged to consult the appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more
- * in-depth explanations. The SBML Level 2 and 3
+ * in-depth explanations. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element
* content must be structured.
*
@@ -1542,7 +1542,7 @@
* readers are urged to consult the appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more
- * in-depth explanations. The SBML Level 2 and 3
+ * in-depth explanations. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element
* content must be structured.
*
@@ -1631,7 +1631,7 @@
* readers are urged to consult the appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more
- * in-depth explanations. The SBML Level 2 and 3
+ * in-depth explanations. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element
* content must be structured.
*
@@ -1675,7 +1675,7 @@
* readers are urged to consult the appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more
- * in-depth explanations. The SBML Level 2 and 3
+ * in-depth explanations. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element
* content must be structured.
*
@@ -1915,7 +1915,7 @@
* readers are urged to consult the appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more
- * in-depth explanations. The SBML Level 2 and 3
+ * in-depth explanations. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element
* content must be structured.
*
Modified: trunk/libsbml/src/sbml/common/common-documentation.h
===================================================================
--- trunk/libsbml/src/sbml/common/common-documentation.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/common/common-documentation.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -578,7 +578,7 @@
* appropriate <a target="_blank"
* href="http://sbml.org/Documents/Specifications">SBML specification
* document</a> for the Level and Version of their model for more in-depth
- * explanations of using "notes" in SBML. The SBML Level 2 and 3
+ * explanations of using "notes" in SBML. The SBML Level 2 and 3
* specifications have considerable detail about how "notes" element content
* must be structured.
*
Modified: trunk/libsbml/src/sbml/xml/XMLError.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLError.h 2016-10-18 13:31:32 UTC (rev 23636)
+++ trunk/libsbml/src/sbml/xml/XMLError.h 2016-10-19 04:14:22 UTC (rev 23637)
@@ -72,7 +72,7 @@
* Each XMLError object also contains a category code; its value may be
* retrieved using the method XMLError::getCategory(). Category values
* are drawn from @if clike the enumeration <a class="el" href="#XMLErrorCategory_t">XMLErrorCategory_t</a> described below.@else a
- * set of constants whose names begin with the characters @c LIBSBML_CAT_, described below.@endif@~ Categories
+ * set of constants whose names begin with the characters @c LIBSBML_CAT_, described below.@endif@~ Categories
* are used by libSBML to provide more information to calling programs about
* the nature of a given error.
*
|
|
From: <fbe...@us...> - 2016-10-18 13:31:35
|
Revision: 23636
http://sourceforge.net/p/sbml/code/23636
Author: fbergmann
Date: 2016-10-18 13:31:32 +0000 (Tue, 18 Oct 2016)
Log Message:
-----------
- adapt python build script for experimental python builds
Modified Paths:
--------------
branches/libsbml-experimental/dev/utilities/build-python/build_conda.bat
branches/libsbml-experimental/dev/utilities/build-python/build_libsbml.bat
branches/libsbml-experimental/dev/utilities/build-python/build_python.bat
branches/libsbml-experimental/dev/utilities/build-python/python-src/CMakeLists.txt
branches/libsbml-experimental/dev/utilities/build-python/python-src/rename-files.cmake
branches/libsbml-experimental/dev/utilities/build-python/python-src/setup32.py.in
branches/libsbml-experimental/dev/utilities/build-python/python-src/setup64.py.in
branches/libsbml-experimental/dev/utilities/build-python/remove_files.bat
Property Changed:
----------------
branches/libsbml-experimental/dev/utilities/build-python/python-src/
Modified: branches/libsbml-experimental/dev/utilities/build-python/build_conda.bat
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/build_conda.bat 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/build_conda.bat 2016-10-18 13:31:32 UTC (rev 23636)
@@ -2,7 +2,7 @@
Setlocal EnableDelayedExpansion
SET THIS_DIR=%~dp0
SET LIBSBML_SRC=%THIS_DIR%\..\..\..\
-SET NAME=python-libsbml
+SET NAME=python-libsbml-experimental
pushd %THIS_DIR%
Modified: branches/libsbml-experimental/dev/utilities/build-python/build_libsbml.bat
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/build_libsbml.bat 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/build_libsbml.bat 2016-10-18 13:31:32 UTC (rev 23636)
@@ -27,9 +27,9 @@
SET PYTHON_64=c:\python27_64\python.exe
:: set up the packages to be used
-SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DENABLE_COMP=ON -DENABLE_FBC=ON -DENABLE_LAYOUT=ON -DENABLE_QUAL=ON -DENABLE_GROUPS=ON
+SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DENABLE_COMP=ON -DENABLE_FBC=ON -DENABLE_LAYOUT=ON -DENABLE_QUAL=ON -DENABLE_GROUPS=ON -DENABLE_RENDER=ON -DENABLE_ARRAYS=ON -DENABLE_DISTRIB=ON -DENABLE_DYN=ON -DENABLE_MULTI=ON -DENABLE_REQUIREDELEMENTS=ON -DENABLE_SPATIAL=ON
:: outcomment the next line if you want to use the new math layer
-SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DLIBSBML_USE_LEGACY_MATH=ON
+SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DLIBSBML_USE_LEGACY_MATH=OFF
:: shouldn't need to touch those
SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DWITH_STATIC_RUNTIME=ON
Modified: branches/libsbml-experimental/dev/utilities/build-python/build_python.bat
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/build_python.bat 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/build_python.bat 2016-10-18 13:31:32 UTC (rev 23636)
@@ -3,7 +3,7 @@
SET THIS_DIR=%~dp0
SET LIBSBML_SRC=%THIS_DIR%\..\..\..\
SET BUILD_DIR=%THIS_DIR%\build_32
-SET NAME=python-libsbml
+SET NAME=python-libsbml-experimental
pushd %THIS_DIR%\python-src
Index: branches/libsbml-experimental/dev/utilities/build-python/python-src
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/python-src 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/python-src 2016-10-18 13:31:32 UTC (rev 23636)
Property changes on: branches/libsbml-experimental/dev/utilities/build-python/python-src
___________________________________________________________________
Modified: svn:ignore
## -22,3 +22,4 ##
*.h
*.py
*.pth
+libsbml_experimental.egg-info
Modified: branches/libsbml-experimental/dev/utilities/build-python/python-src/CMakeLists.txt
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/python-src/CMakeLists.txt 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/python-src/CMakeLists.txt 2016-10-18 13:31:32 UTC (rev 23636)
@@ -62,7 +62,13 @@
-DUSE_QUAL
-DUSE_LAYOUT
-DUSE_GROUPS
- -DLIBSBML_USE_LEGACY_MATH
+ -DUSE_ARRAYS
+ -DUSE_DYN
+ -DUSE_DISTRIB
+ -DUSE_MULTI
+ -DUSE_REQUIREDELEMENTS
+ -DUSE_SPATIAL
+ -DUSE_RENDER
)
Modified: branches/libsbml-experimental/dev/utilities/build-python/python-src/rename-files.cmake
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/python-src/rename-files.cmake 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/python-src/rename-files.cmake 2016-10-18 13:31:32 UTC (rev 23636)
@@ -44,17 +44,17 @@
set (VERSIONS 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5)
foreach(version ${VERSIONS})
- if (EXISTS "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win32-py${version}.exe")
+ if (EXISTS "${OUT_DIR}/libsbml-experimental-${PACKAGE_VERSION}.win32-py${version}.exe")
file(RENAME
- "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win32-py${version}.exe"
- "${OUT_DIR}/libSBML-${PACKAGE_VERSION}-win-py${version}-x86.exe"
+ "${OUT_DIR}/libsbml-experimental-${PACKAGE_VERSION}.win32-py${version}.exe"
+ "${OUT_DIR}/libSBML-experimental-${PACKAGE_VERSION}-win-py${version}-x86.exe"
)
endif()
- if (EXISTS "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win-amd64-py${version}.exe")
+ if (EXISTS "${OUT_DIR}/libsbml-experimental-${PACKAGE_VERSION}.win-amd64-py${version}.exe")
file(RENAME
- "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win-amd64-py${version}.exe"
- "${OUT_DIR}/libSBML-${PACKAGE_VERSION}-win-py${version}-x64.exe"
+ "${OUT_DIR}/libsbml-experimental-${PACKAGE_VERSION}.win-amd64-py${version}.exe"
+ "${OUT_DIR}/libSBML-experimental-${PACKAGE_VERSION}-win-py${version}-x64.exe"
)
endif()
Modified: branches/libsbml-experimental/dev/utilities/build-python/python-src/setup32.py.in
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/python-src/setup32.py.in 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/python-src/setup32.py.in 2016-10-18 13:31:32 UTC (rev 23636)
@@ -35,7 +35,7 @@
except ImportError:
from distutils.core import setup, Extension
-setup(name = "libsbml",
+setup(name = "libsbml-experimental",
version = "${PACKAGE_VERSION}",
description = "LibSBML Python API",
long_description = ("LibSBML is a library for reading, writing and "+
Modified: branches/libsbml-experimental/dev/utilities/build-python/python-src/setup64.py.in
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/python-src/setup64.py.in 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/python-src/setup64.py.in 2016-10-18 13:31:32 UTC (rev 23636)
@@ -35,7 +35,7 @@
except ImportError:
from distutils.core import setup, Extension
-setup(name = "libsbml",
+setup(name = "libsbml-experimental",
version = "${PACKAGE_VERSION}",
description = "LibSBML Python API",
long_description = ("LibSBML is a library for reading, writing and "+
Modified: branches/libsbml-experimental/dev/utilities/build-python/remove_files.bat
===================================================================
--- branches/libsbml-experimental/dev/utilities/build-python/remove_files.bat 2016-10-18 09:47:40 UTC (rev 23635)
+++ branches/libsbml-experimental/dev/utilities/build-python/remove_files.bat 2016-10-18 13:31:32 UTC (rev 23636)
@@ -44,7 +44,7 @@
if exist python-src\b64_35 rd /s /q python-src\b64_35
if exist python-src\build rd /s /q python-src\build
if exist python-src\libsbml rd /s /q python-src\libsbml
-if exist python-src\libsbml.egg-info rd /s /q python-src\libsbml.egg-info
+if exist python-src\libsbml_experimental.egg-info rd /s /q python-src\libsbml_experimental.egg-info
if exist python-src\dist rd /s /q python-src\dist
if "%MODE%"=="TEMP" goto DONE
|
|
From: <sar...@us...> - 2016-10-18 09:47:42
|
Revision: 23635
http://sourceforge.net/p/sbml/code/23635
Author: sarahkeating
Date: 2016-10-18 09:47:40 +0000 (Tue, 18 Oct 2016)
Log Message:
-----------
reverted change
this code does NOT get called for an l3v2 model as there are so many more ids to check; so it should not change
Modified Paths:
--------------
trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp
Modified: trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp 2016-10-17 21:08:52 UTC (rev 23634)
+++ trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp 2016-10-18 09:47:40 UTC (rev 23635)
@@ -107,49 +107,49 @@
//void
//IdBase::checkId (const SBase& x)
//{
-//// if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+//// if (x.isSetId()) doCheckId(x.getId(), x);
//}
void
IdBase::checkId (const Model& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const FunctionDefinition& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const UnitDefinition& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const Compartment& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const Species& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const Parameter& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
@@ -175,14 +175,14 @@
void
IdBase::checkId (const Reaction& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const Event& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
@@ -196,25 +196,25 @@
void
IdBase::checkId (const CompartmentType& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const SpeciesType& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const SpeciesReference& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
IdBase::checkId (const ModifierSpeciesReference& x)
{
- if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
+ if (x.isSetId()) doCheckId(x.getId(), x);
}
void
|
|
From: <luc...@us...> - 2016-10-17 21:08:55
|
Revision: 23634
http://sourceforge.net/p/sbml/code/23634
Author: luciansmith
Date: 2016-10-17 21:08:52 +0000 (Mon, 17 Oct 2016)
Log Message:
-----------
Update ID-uniqueness validators to use *IdAttribute functions instead of *Id, since only the former will properly check the actual ID attributes in question.
Modified Paths:
--------------
trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp
trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp
Modified: trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp 2016-10-17 19:24:14 UTC (rev 23633)
+++ trunk/libsbml/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp 2016-10-17 21:08:52 UTC (rev 23634)
@@ -102,49 +102,49 @@
//void
//CompIdBase::checkId (const SBase& x)
//{
-//// if (x.isSetId()) doCheckId(x.getId(), x);
+//// if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
//}
void
CompIdBase::checkId (const Model& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Submodel& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Port& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Deletion& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const ReplacedElement& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const ReplacedBy& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
@@ -152,48 +152,48 @@
void
CompIdBase::checkId (const ModelDefinition& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const ExternalModelDefinition& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const FunctionDefinition& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const UnitDefinition& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Compartment& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Species& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Parameter& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
@@ -219,46 +219,46 @@
void
CompIdBase::checkId (const Reaction& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const Event& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const EventAssignment& x)
{
- if (x.isSetVariable()) doCheckId(x.getVariable(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const CompartmentType& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const SpeciesType& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const SpeciesReference& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
CompIdBase::checkId (const ModifierSpeciesReference& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
Modified: trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp
===================================================================
--- trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp 2016-10-17 19:24:14 UTC (rev 23633)
+++ trunk/libsbml/src/sbml/validator/constraints/IdBase.cpp 2016-10-17 21:08:52 UTC (rev 23634)
@@ -107,49 +107,49 @@
//void
//IdBase::checkId (const SBase& x)
//{
-//// if (x.isSetId()) doCheckId(x.getId(), x);
+//// if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
//}
void
IdBase::checkId (const Model& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const FunctionDefinition& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const UnitDefinition& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const Compartment& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const Species& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const Parameter& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
@@ -175,14 +175,14 @@
void
IdBase::checkId (const Reaction& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const Event& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
@@ -196,25 +196,25 @@
void
IdBase::checkId (const CompartmentType& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const SpeciesType& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const SpeciesReference& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
IdBase::checkId (const ModifierSpeciesReference& x)
{
- if (x.isSetId()) doCheckId(x.getId(), x);
+ if (x.isSetIdAttribute()) doCheckId(x.getIdAttribute(), x);
}
void
|
|
From: <fbe...@us...> - 2016-10-17 19:24:15
|
Revision: 23633
http://sourceforge.net/p/sbml/code/23633
Author: fbergmann
Date: 2016-10-17 19:24:14 +0000 (Mon, 17 Oct 2016)
Log Message:
-----------
- add a new example that will add a note to a given SBML file and element
Added Paths:
-----------
trunk/libsbml/examples/python/append_to_note.py
Added: trunk/libsbml/examples/python/append_to_note.py
===================================================================
--- trunk/libsbml/examples/python/append_to_note.py (rev 0)
+++ trunk/libsbml/examples/python/append_to_note.py 2016-10-17 19:24:14 UTC (rev 23633)
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+##
+## \file append_to_note.py
+## \brief adds to the notes of an element in a document
+##
+## This file takes three or four arguments;
+##
+## input-file - the input SBML file
+## id - the SBML Id of the element to which notes should be appended
+## string - the string to be added to the body of the existing note
+## output-file - an optional output file
+##
+## \author Frank T. Bergmann
+##
+## <!--------------------------------------------------------------------------
+## This sample program is distributed under a different license than the rest
+## of libSBML. This program uses the open-source MIT license, as follows:
+##
+## Copyright (c) 2013-2016 by the California Institute of Technology
+## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
+## and the University of Heidelberg (Germany), with support from the National
+## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
+##
+## Permission is hereby granted, free of charge, to any person obtaining a
+## copy of this software and associated documentation files (the "Software"),
+## to deal in the Software without restriction, including without limitation
+## the rights to use, copy, modify, merge, publish, distribute, sublicense,
+## and/or sell copies of the Software, and to permit persons to whom the
+## Software is furnished to do so, subject to the following conditions:
+##
+## The above copyright notice and this permission notice shall be included in
+## all copies or substantial portions of the Software.
+##
+## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+## DEALINGS IN THE SOFTWARE.
+##
+## Neither the name of the California Institute of Technology (Caltech), nor
+## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
+## of Heidelberg, nor the names of any contributors, may be used to endorse
+## or promote products derived from this software without specific prior
+## written permission.
+## ------------------------------------------------------------------------ -->
+
+import libsbml
+import sys
+
+def getBody(notes):
+ if notes == None:
+ return None
+ if notes.isStart() and notes.getName() == "body":
+ return notes
+ for i in range(notes.getNumChildren()):
+ current = getBody(notes.getChild(i))
+ if current != None:
+ return current;
+ return None
+
+def addToNotes(doc, id, stringToAdd):
+ element = doc.getElementBySId(id)
+ if element == None:
+ print ("Couldn't find element '{0}'".format(id))
+ exit(2)
+ notes = element.getNotes()
+ if notes == None:
+ print("Element '{0}' has no notes".format(id))
+ exit(3)
+ body = getBody(notes)
+ if body == None:
+ print ("Element '{0}' has no body".format(id))
+ exit(4)
+ print ("Body before change: ")
+ print (body.toXMLString())
+ body.addChild(libsbml.XMLNode_convertStringToXMLNode(stringToAdd))
+ print ("\nBody after change: ")
+ print (body.toXMLString())
+
+
+if __name__ == "__main__":
+ if len(sys.argv) < 4:
+ print ("usage append_to_note input-file id note-to-add [output-file]")
+ exit(1)
+
+ doc = libsbml.readSBMLFromFile(sys.argv[1])
+
+ if doc.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0:
+ print("Errors occurred loading the file")
+ doc.printErrors()
+ exit(1);
+
+ addToNotes(doc, sys.argv[2], sys.argv[3])
+
+ if len(sys.argv) > 4:
+ libsbml.writeSBMLToFile(doc, sys.argv[4])
|
|
From: <luc...@us...> - 2016-10-17 18:50:10
|
Revision: 23632
http://sourceforge.net/p/sbml/code/23632
Author: luciansmith
Date: 2016-10-17 18:50:08 +0000 (Mon, 17 Oct 2016)
Log Message:
-----------
Add a first draft of an abstract for JIB submission.
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex
Added: trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/groups/specification/abstract.tex 2016-10-17 18:50:08 UTC (rev 23632)
@@ -0,0 +1 @@
+Biological models often contain components that are related to one another. The \emph{SBML Level~3 Version~1 Core} specification does not directly provide a mechanism for defining these relationships, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactical constructs. The SBML \emph{Groups} package for SBML Level~3 adds the necessary features to SBML to allow grouping of related model elements. The package enables a modeler to include definitions of groups and nested groups, each of which may be annotated to convey why that group was created, and what it represents.
|
|
From: <fbe...@us...> - 2016-10-17 09:22:51
|
Revision: 23631
http://sourceforge.net/p/sbml/code/23631
Author: fbergmann
Date: 2016-10-17 09:22:49 +0000 (Mon, 17 Oct 2016)
Log Message:
-----------
- adjust path to reflect what sarah uses
Modified Paths:
--------------
trunk/libsbml/dev/utilities/build-python/build_libsbml.bat
trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat
Modified: trunk/libsbml/dev/utilities/build-python/build_libsbml.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_libsbml.bat 2016-10-15 11:55:59 UTC (rev 23630)
+++ trunk/libsbml/dev/utilities/build-python/build_libsbml.bat 2016-10-17 09:22:49 UTC (rev 23631)
@@ -23,8 +23,10 @@
::SET DEPENDENCY_DIR=\Development\libSBML-dependencies\install_vs12_release_x64
:: be sure to update to the correct python path
-SET PYTHON_32=c:\python27_32\python.exe
-SET PYTHON_64=c:\python27_64\python.exe
+::SET PYTHON_32=c:\python27_32\python.exe
+::SET PYTHON_64=c:\python27_64\python.exe
+SET PYTHON_32=c:\python32\python27\python.exe
+SET PYTHON_64=c:\python64\python27\python.exe
:: set up the packages to be used
SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DENABLE_COMP=ON -DENABLE_FBC=ON -DENABLE_LAYOUT=ON -DENABLE_QUAL=ON -DENABLE_GROUPS=ON
Modified: trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat 2016-10-15 11:55:59 UTC (rev 23630)
+++ trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat 2016-10-17 09:22:49 UTC (rev 23631)
@@ -10,8 +10,10 @@
SET MINOR=%2
SET CURRENT_DIR=%~dp0
SET SOURCE_32=.
-SET PTYHON_32=c:\Python%MAJOR%%MINOR%_32\python.exe
-SET PTYHON_64=c:\Python%MAJOR%%MINOR%_64\python.exe
+::SET PTYHON_32=c:\Python%MAJOR%%MINOR%_32\python.exe
+::SET PTYHON_64=c:\Python%MAJOR%%MINOR%_64\python.exe
+SET PTYHON_32=c:\Python32\Python%MAJOR%%MINOR%\python.exe
+SET PTYHON_64=c:\Python64\Python%MAJOR%%MINOR%\python.exe
SET BUILD_32=%SOURCE_32%\b32_%MAJOR%%MINOR%
SET BUILD_64=%SOURCE_32%\b64_%MAJOR%%MINOR%
|
|
From: <sar...@us...> - 2016-10-15 11:56:02
|
Revision: 23630
http://sourceforge.net/p/sbml/code/23630
Author: sarahkeating
Date: 2016-10-15 11:55:59 +0000 (Sat, 15 Oct 2016)
Log Message:
-----------
Merged revision(s) 23628-23629 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/src/sbml/test/TestAttributeFunctions.cpp
Property Changed:
----------------
branches/libsbml-experimental/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2016-10-15 11:54:03 UTC (rev 23629)
+++ branches/libsbml-experimental 2016-10-15 11:55:59 UTC (rev 23630)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -5,4 +5,4 ##
/branches/libsbml-experimental:23458-23459
/branches/libsbml-fengkai/multi-dev-base-on-experimental22472:22523-22669
/branches/libsbml-fengkai/multi-dev-based-on-experimental22472:22522
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-23392,23460-23627
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-23392,23460-23629
\ No newline at end of property
Modified: branches/libsbml-experimental/src/sbml/test/TestAttributeFunctions.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/test/TestAttributeFunctions.cpp 2016-10-15 11:54:03 UTC (rev 23629)
+++ branches/libsbml-experimental/src/sbml/test/TestAttributeFunctions.cpp 2016-10-15 11:55:59 UTC (rev 23630)
@@ -35,6 +35,7 @@
#include <sbml/SBase.h>
#include <sbml/Model.h>
+#include <sbml/SBMLTypes.h>
#include <check.h>
|
|
From: <sar...@us...> - 2016-10-15 11:54:05
|
Revision: 23629
http://sourceforge.net/p/sbml/code/23629
Author: sarahkeating
Date: 2016-10-15 11:54:03 +0000 (Sat, 15 Oct 2016)
Log Message:
-----------
add include needed in some cases
Modified Paths:
--------------
trunk/libsbml/src/sbml/test/TestAttributeFunctions.cpp
Modified: trunk/libsbml/src/sbml/test/TestAttributeFunctions.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestAttributeFunctions.cpp 2016-10-14 16:08:40 UTC (rev 23628)
+++ trunk/libsbml/src/sbml/test/TestAttributeFunctions.cpp 2016-10-15 11:54:03 UTC (rev 23629)
@@ -35,6 +35,7 @@
#include <sbml/SBase.h>
#include <sbml/Model.h>
+#include <sbml/SBMLTypes.h>
#include <check.h>
|
|
From: <sar...@us...> - 2016-10-14 16:08:45
|
Revision: 23628
http://sourceforge.net/p/sbml/code/23628
Author: sarahkeating
Date: 2016-10-14 16:08:40 +0000 (Fri, 14 Oct 2016)
Log Message:
-----------
Merged revision(s) 23602-23627 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-experimental/CMakeLists.txt
branches/libsbml-experimental/src/sbml/AssignmentRule.cpp
branches/libsbml-experimental/src/sbml/AssignmentRule.h
branches/libsbml-experimental/src/sbml/Compartment.cpp
branches/libsbml-experimental/src/sbml/Compartment.h
branches/libsbml-experimental/src/sbml/Event.cpp
branches/libsbml-experimental/src/sbml/Event.h
branches/libsbml-experimental/src/sbml/EventAssignment.cpp
branches/libsbml-experimental/src/sbml/EventAssignment.h
branches/libsbml-experimental/src/sbml/InitialAssignment.cpp
branches/libsbml-experimental/src/sbml/InitialAssignment.h
branches/libsbml-experimental/src/sbml/KineticLaw.cpp
branches/libsbml-experimental/src/sbml/KineticLaw.h
branches/libsbml-experimental/src/sbml/LocalParameter.cpp
branches/libsbml-experimental/src/sbml/LocalParameter.h
branches/libsbml-experimental/src/sbml/Model.cpp
branches/libsbml-experimental/src/sbml/Model.h
branches/libsbml-experimental/src/sbml/Parameter.cpp
branches/libsbml-experimental/src/sbml/Parameter.h
branches/libsbml-experimental/src/sbml/RateRule.cpp
branches/libsbml-experimental/src/sbml/RateRule.h
branches/libsbml-experimental/src/sbml/Reaction.cpp
branches/libsbml-experimental/src/sbml/Reaction.h
branches/libsbml-experimental/src/sbml/SBase.cpp
branches/libsbml-experimental/src/sbml/SBase.h
branches/libsbml-experimental/src/sbml/SimpleSpeciesReference.cpp
branches/libsbml-experimental/src/sbml/SimpleSpeciesReference.h
branches/libsbml-experimental/src/sbml/Species.cpp
branches/libsbml-experimental/src/sbml/Species.h
branches/libsbml-experimental/src/sbml/SpeciesReference.cpp
branches/libsbml-experimental/src/sbml/SpeciesReference.h
branches/libsbml-experimental/src/sbml/Trigger.cpp
branches/libsbml-experimental/src/sbml/Trigger.h
branches/libsbml-experimental/src/sbml/Unit.cpp
branches/libsbml-experimental/src/sbml/Unit.h
branches/libsbml-experimental/src/sbml/conversion/test/TestLevelVersionConverter.cpp
branches/libsbml-experimental/src/sbml/math/FormulaParser.c
branches/libsbml-experimental/src/sbml/math-legacy/ASTNode.cpp
branches/libsbml-experimental/src/sbml/math-legacy/FormulaParser.c
branches/libsbml-experimental/src/sbml/packages/comp/extension/test/TestRunner.c
branches/libsbml-experimental/src/sbml/packages/comp/sbml/test/TestRunner.c
branches/libsbml-experimental/src/sbml/packages/comp/util/test/TestRunner.c
branches/libsbml-experimental/src/sbml/packages/comp/validator/test/TestCompConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcModelPlugin.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/extension/FbcModelPlugin.h
branches/libsbml-experimental/src/sbml/packages/fbc/extension/test/TestRunner.c
branches/libsbml-experimental/src/sbml/packages/fbc/extension/test/TestWriteFbcExtension.cpp
branches/libsbml-experimental/src/sbml/packages/fbc/validator/test/TestFbcConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/groups/validator/test/TestGroupsConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/layout/validator/test/TestLayoutConsistencyValidator.cpp
branches/libsbml-experimental/src/sbml/packages/layout/validator/test/test-data/general-constraints/6010401-pass-00-01.xml
branches/libsbml-experimental/src/sbml/packages/layout/validator/test/test-data/general-constraints/6010401-pass-00-02.xml
branches/libsbml-experimental/src/sbml/packages/layout/validator/test/test-data/general-constraints/6020101-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/layout/validator/test/test-data/general-constraints/6020102-fail-01-01.xml
branches/libsbml-experimental/src/sbml/packages/layout/validator/test/test-data/general-constraints/6020103-fail-01-01.xml
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branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20617-fail-01-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20617-pass-00-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20617-pass-00-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20623-pass-00-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20623-pass-00-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20623-pass-00-03.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20623-pass-00-04.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-fail-01-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-fail-01-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-fail-01-03.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-fail-01-04.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-pass-00-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-pass-00-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-pass-00-03.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20705-pass-00-04.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20902-pass-00-22.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20902-pass-00-23.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20902-pass-00-30.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20902-pass-00-31.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-fail-01-16.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-fail-01-17.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-fail-01-24.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-fail-01-25.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-pass-00-16.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-pass-00-17.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20903-pass-00-24.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-fail-01-16.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-fail-01-17.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-fail-01-24.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-fail-01-25.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-pass-00-16.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-pass-00-17.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-pass-00-24.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/20904-pass-00-25.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21103-pass-00-10.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21103-pass-00-11.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21103-pass-00-13.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21232-pass-00-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21232-pass-00-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21232-pass-00-03.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-general-consistency-constraints/21232-pass-00-04.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-03.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-04.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-05.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-fail-01-06.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-01.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-02.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-03.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-04.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-05.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-06.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-07.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-10.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-11.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-12.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-13.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-16.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-mathml-constraints/10217-pass-00-17.xml
branches/libsbml-experimental/src/sbml/validator/test/test-data/sbml-unit-constraints/20509-fail-01-13-99508.xml
branches/libsbml-experimental/src/sbml/xml/XMLToken.cpp
branches/libsbml-experimental/src/sbml/xml/XMLToken.h
branches/libsbml-experimental/src/sbml/xml/test/TestXMLToken.c
Added Paths:
-----------
branches/libsbml-experimental/dev/utilities/build-python/
branches/libsbml-experimental/src/sbml/test/TestAttributeFunctions.cpp
Property Changed:
----------------
branches/libsbml-experimental/
branches/libsbml-experimental/src/sbml/packages/groups/validator/
Index: branches/libsbml-experimental
===================================================================
--- branches/libsbml-experimental 2016-10-14 16:04:02 UTC (rev 23627)
+++ branches/libsbml-experimental 2016-10-14 16:08:40 UTC (rev 23628)
Property changes on: branches/libsbml-experimental
___________________________________________________________________
Modified: svn:mergeinfo
## -5,4 +5,4 ##
/branches/libsbml-experimental:23458-23459
/branches/libsbml-fengkai/multi-dev-base-on-experimental22472:22523-22669
/branches/libsbml-fengkai/multi-dev-based-on-experimental22472:22522
-/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-23392,23460-23601
+/trunk/libsbml:18168-18171,18174-18194,18196-18201,18204,18207-18209,18211-18213,18215-18216,18226,18228-18292,18294-18388,18390-18443,18450-18454,18456-18458,18460-18462,18464,18466,18469-18520,18523-18561,18563,18565-18584,18586-18638,18640-18641,18644-18715,18717-18844,18846-19128,19130-19829,19831-23392,23460-23627
\ No newline at end of property
Modified: branches/libsbml-experimental/CMakeLists.txt
===================================================================
--- branches/libsbml-experimental/CMakeLists.txt 2016-10-14 16:04:02 UTC (rev 23627)
+++ branches/libsbml-experimental/CMakeLists.txt 2016-10-14 16:08:40 UTC (rev 23628)
@@ -34,6 +34,16 @@
cmake_minimum_required(VERSION 2.6)
project(libsbml)
+if(POLICY CMP0054)
+ cmake_policy(SET CMP0054 NEW)
+endif()
+
+if(POLICY CMP0058)
+ cmake_policy(SET CMP0058 NEW)
+endif()
+
+
+
set(LIBSBML_ROOT_SOURCE_DIR "${CMAKE_SOURCE_DIR}" CACHE PATH
"Path to the libSBML root source directory")
set(LIBSBML_ROOT_BINARY_DIR "${CMAKE_BINARY_DIR}" CACHE PATH
@@ -213,6 +223,8 @@
if(WITH_WALL)
if(MSVC OR USING_INTEL)
add_definitions(/W4)
+ string(REPLACE "/W3" "/W4" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+ string(REPLACE "/W3" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
else()
add_definitions(-Wall)
endif()
@@ -223,7 +235,7 @@
"Compile using 'strict includes' rules: libSBML header files won't
use SBMLTypes.h, among others." OFF)
if(LIBSBML_USE_STRICT_INCLUDES)
- add_definitions(-DLIBSBML_USE_STRICT_INCLUDES)
+ add_definitions(-DLIBSBML_USE_STRICT_INCLUDES)
endif(LIBSBML_USE_STRICT_INCLUDES)
mark_as_advanced(LIBSBML_USE_STRICT_INCLUDES)
@@ -307,18 +319,24 @@
set(LIBSBML_USE_CPP_NAMESPACE OFF)
if(WITH_CPP_NAMESPACE)
add_definitions(-DLIBSBML_USE_CPP_NAMESPACE=1)
- set(LIBSBML_USE_CPP_NAMESPACE ON)
+ set(LIBSBML_USE_CPP_NAMESPACE ON)
endif()
if(WITH_SWIG)
find_program(SWIG_EXECUTABLE
NAMES swig
PATHS
+ c:/swigwin-3.0.10
+ c:/swigwin-3.0.9
+ c:/swigwin-3.0.8
+ c:/swigwin-3.0.7
+ c:/swigwin-3.0.6
c:/swigwin-3.0.5
c:/swigwin-3.0.4
c:/swigwin-3.0.3
c:/swigwin-3.0.2
c:/swigwin-3.0.1
+ c:/swigwin-2.0.12
c:/swigwin-2.0.11
c:/swigwin-2.0.10
c:/swigwin-2.0.9
@@ -340,7 +358,7 @@
)
find_package(SWIG)
if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
- message(WARNING
+ message(WARNING
"You are using SWIG version ${SWIG_VERSION}. We strongly recommend
using version 2.0.4 or greater. For libSBML JavaScript support, you
will need version 3.0.1 at minimum.")
@@ -383,7 +401,7 @@
endif()
add_definitions( -DUSE_EXPAT )
- list(APPEND SWIG_EXTRA_ARGS -DUSE_EXPAT)
+ list(APPEND SWIG_EXTRA_ARGS -DUSE_EXPAT)
set(LIBSBML_XML_LIBRARY "expat")
set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBEXPAT_INCLUDE_DIR})
@@ -426,7 +444,7 @@
endif()
add_definitions( -DUSE_LIBXML )
- list(APPEND SWIG_EXTRA_ARGS -DUSE_LIBXML)
+ list(APPEND SWIG_EXTRA_ARGS -DUSE_LIBXML)
set(USE_LIBXML ON)
set(LIBSBML_XML_LIBRARY "libxml2")
@@ -530,7 +548,7 @@
set(USE_BZ2 ON)
add_definitions( -DUSE_BZ2 )
- list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
+ list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
# make sure that we have a valid bzip2 library
check_library_exists("${LIBBZ_LIBRARY}" "BZ2_bzCompressInit" "" LIBBZ_FOUND_SYMBOL)
@@ -617,7 +635,7 @@
endif()
set(USE_ZLIB ON)
add_definitions( -DUSE_ZLIB )
- list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB)
+ list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB)
# make sure that we have a valid zip library
check_library_exists("${LIBZ_LIBRARY}" "gzopen" "" LIBZ_FOUND_SYMBOL)
@@ -649,7 +667,7 @@
#
if(WITH_CSHARP)
- FILE(TO_CMAKE_PATH "$ENV{WINDIR}" windir)
+ FILE(TO_CMAKE_PATH "$ENV{WINDIR}" windir)
find_program(CSHARP_COMPILER
NAMES gmcs csc mcs
PATHS
@@ -723,7 +741,7 @@
message(WARNING "Libcheck is not compatible with Visual Studio 2003 (or earlier versions).")
endif()
- if (UNIX)
+ if (UNIX)
# setup valgrind
set(CMAKE_MEMORYCHECK_COMMAND valgrind)
set(CMAKE_MEMORYCHECK_COMMAND_OPTIONS
@@ -732,7 +750,7 @@
set(MEMCHECK_COMMAND
"${CMAKE_MEMORYCHECK_COMMAND} ${CMAKE_MEMORYCHECK_COMMAND_OPTIONS}")
separate_arguments(MEMCHECK_COMMAND)
- endif()
+ endif()
include(CTest)
@@ -848,7 +866,7 @@
endif(ENABLE_UNIVERSAL)
else(APPLE)
add_definitions(-DLINUX)
-
+
if(NOT CYGWIN)
# on cygwin all code is position independent so -fPIC is not needed
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing -fPIC")
@@ -881,35 +899,38 @@
if(${flag_var} MATCHES "/MD")
string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
endif(${flag_var} MATCHES "/MD")
-
+
endforeach(flag_var)
add_definitions( -D_MT)
endif(WITH_STATIC_RUNTIME)
+
+ # on VS enable multiprocessor build
+ SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP")
# Provide an easy way to use Visual Leak Detector (https://vld.codeplex.com)
- option(LIBSBML_USE_VLD "When running debug builds with MSVC use Visual Leak Detector." OFF)
- mark_as_advanced(LIBSBML_USE_VLD)
- if (LIBSBML_USE_VLD)
+ option(LIBSBML_USE_VLD "When running debug builds with MSVC use Visual Leak Detector." OFF)
+ mark_as_advanced(LIBSBML_USE_VLD)
+ if (LIBSBML_USE_VLD)
find_path(VLD_INCLUDE_DIR
NAMES vld.h
PATHS ${LIBSBML_DEPENDENCY_DIR}/include
- "$ENV{PROGRAMFILES}/Visual Leak Detector/include"
- "$ENV{PROGRAMFILES(X86)}/Visual Leak Detector/include"
+ "$ENV{PROGRAMFILES}/Visual Leak Detector/include"
+ "$ENV{PROGRAMFILES(X86)}/Visual Leak Detector/include"
DOC "Directory containing VLD files."
)
if (NOT VLD_INCLUDE_DIR)
message(WARNING "VLD is not found on your system, please ensure you installed it correctly.")
- else()
- include_directories(${VLD_INCLUDE_DIR})
- endif()
-
- add_definitions( -DLIBSBML_USE_VLD)
-
- endif (LIBSBML_USE_VLD)
+ else()
+ include_directories(${VLD_INCLUDE_DIR})
+ endif()
+
+ add_definitions( -DLIBSBML_USE_VLD)
+
+ endif (LIBSBML_USE_VLD)
- # CMake no longer creates PDB files for static libraries after 2.8.11
- # so we store debug information in the object files instead
- if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
+ # CMake no longer creates PDB files for static libraries after 2.8.11
+ # so we store debug information in the object files instead
+ if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
foreach(flag_var
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
@@ -917,19 +938,19 @@
CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
if(${flag_var} MATCHES "/Zi")
- STRING(REPLACE "/Zi" "/Z7" "${flag_var}" "${${flag_var}}")
+ STRING(REPLACE "/Zi" "/Z7" "${flag_var}" "${${flag_var}}")
endif(${flag_var} MATCHES "/Zi")
- endforeach(flag_var)
- endif()
-
+ endforeach(flag_var)
+ endif()
+
file(GLOB WIN32_BINARIES ${LIBSBML_DEPENDENCY_DIR}/bin/*.dll)
INSTALL(FILES ${WIN32_BINARIES} DESTINATION bin)
file(GLOB WIN32_DEPENDENCIES ${LIBSBML_DEPENDENCY_DIR}/lib/*.lib)
install(FILES ${WIN32_DEPENDENCIES} DESTINATION lib)
if(WITH_LIBXML)
- if (EXTRA_LIBS STREQUAL "")
- # populate EXTRA_LIBS variable
+ if (EXTRA_LIBS STREQUAL "")
+ # populate EXTRA_LIBS variable
find_library(LIBICONV_LIBRARY
NAMES libiconv.lib iconv.lib iconv
PATHS /usr/lib /usr/local/lib
@@ -937,17 +958,17 @@
${LIBSBML_DEPENDENCY_DIR}/lib
DOC "The file name of the libiconv library."
)
-
- set(ADDITIONAL_LIBS)
- if (EXISTS ${LIBICONV_LIBRARY})
- set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBICONV_LIBRARY};")
- endif()
- if (EXISTS ${LIBZ_LIBRARY})
- set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBZ_LIBRARY};")
- endif()
- set(EXTRA_LIBS "WS2_32.lib;${ADDITIONAL_LIBS}" CACHE STRING "List of additional libraries to link against." FORCE)
- endif()
- endif()
+
+ set(ADDITIONAL_LIBS)
+ if (EXISTS ${LIBICONV_LIBRARY})
+ set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBICONV_LIBRARY};")
+ endif()
+ if (EXISTS ${LIBZ_LIBRARY})
+ set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBZ_LIBRARY};")
+ endif()
+ set(EXTRA_LIBS "WS2_32.lib;${ADDITIONAL_LIBS}" CACHE STRING "List of additional libraries to link against." FORCE)
+ endif()
+ endif()
elseif(CYGWIN)
add_definitions(-DCYGWIN)
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DCYGWIN")
@@ -1087,7 +1108,7 @@
endif()
SET (PC_LIBDIR ${CMAKE_INSTALL_LIBDIR})
-if (${CMAKE_INSTALL_LIBDIR} STREQUAL "lib")
+if ("${CMAKE_INSTALL_LIBDIR}" STREQUAL "lib")
SET (PC_LIBDIR ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
endif()
@@ -1170,7 +1191,7 @@
message(STATUS " Using SWIG = ${SWIG_EXECUTABLE} (Version ${SWIG_VERSION})")
if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
- message(WARNING " You are using SWIG version ${SWIG_VERSION}. We strongly recommend at least version 2.0.4.")
+ message(WARNING " You are using SWIG version ${SWIG_VERSION}. We strongly recommend at least version 2.0.4.")
endif()
endif()
Modified: branches/libsbml-experimental/src/sbml/AssignmentRule.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/AssignmentRule.cpp 2016-10-14 16:04:02 UTC (rev 23627)
+++ branches/libsbml-experimental/src/sbml/AssignmentRule.cpp 2016-10-14 16:08:40 UTC (rev 23628)
@@ -129,6 +129,143 @@
}
}
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "variable")
+ {
+ value = getVariable();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this AssignmentRule's attribute
+ * "attributeName" is set.
+ */
+bool
+AssignmentRule::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "variable")
+ {
+ value = isSetVariable();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "variable")
+ {
+ return_value = setVariable(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "variable")
+ {
+ value = unsetVariable();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
#endif /* __cplusplus */
Modified: branches/libsbml-experimental/src/sbml/AssignmentRule.h
===================================================================
--- branches/libsbml-experimental/src/sbml/AssignmentRule.h 2016-10-14 16:04:02 UTC (rev 23627)
+++ branches/libsbml-experimental/src/sbml/AssignmentRule.h 2016-10-14 16:08:40 UTC (rev 23628)
@@ -271,6 +271,120 @@
virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this AssignmentRule's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this AssignmentRule's attribute "attributeName" has
+ * been set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
protected:
/** @cond doxygenLibsbmlInternal */
/* the validator classes need to be friends to access the
Modified: branches/libsbml-experimental/src/sbml/Compartment.cpp
===================================================================
--- branches/libsbml-experimental/src/sbml/Compartment.cpp 2016-10-14 16:04:02 UTC (rev 23627)
+++ branches/libsbml-experimental/src/sbml/Compartment.cpp 2016-10-14 16:08:40 UTC (rev 23628)
@@ -999,7 +999,432 @@
return allPresent;
}
+
+#ifndef SWIG
+
+
+
/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName, bool& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "constant")
+ {
+ value = getConstant();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "size")
+ {
+ value = getSize();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "volume")
+ {
+ value = getVolume();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ unsigned int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "spatialDimensions")
+ {
+ value = getSpatialDimensions();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "units")
+ {
+ value = getUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "outside")
+ {
+ value = getOutside();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = getCompartmentType();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this Compartment's attribute "attributeName"
+ * is set.
+ */
+bool
+Compartment::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "size")
+ {
+ value = isSetSize();
+ }
+ else if (attributeName == "volume")
+ {
+ value = isSetVolume();
+ }
+ else if (attributeName == "units")
+ {
+ value = isSetUnits();
+ }
+ else if (attributeName == "spatialDimensions")
+ {
+ value = isSetSpatialDimensions();
+ }
+ else if (attributeName == "constant")
+ {
+ value = isSetConstant();
+ }
+ else if (attributeName == "outside")
+ {
+ value = isSetOutside();
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = isSetCompartmentType();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "constant")
+ {
+ return_value = setConstant(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "size")
+ {
+ return_value = setSize(value);
+ }
+ else if (attributeName == "volume")
+ {
+ return_value = setVolume(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName,
+ unsigned int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "spatialDimensions")
+ {
+ return_value = setSpatialDimensions(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "units")
+ {
+ return_value = setUnits(value);
+ }
+ else if (attributeName == "outside")
+ {
+ return_value = setOutside(value);
+ }
+ else if (attributeName == "compartmentType")
+ {
+ return_value = setCompartmentType(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "size")
+ {
+ value = unsetSize();
+ }
+ else if (attributeName == "volume")
+ {
+ value = unsetVolume();
+ }
+ else if (attributeName == "units")
+ {
+ value = unsetUnits();
+ }
+ else if (attributeName == "spatialDimensions")
+ {
+ value = unsetSpatialDimensions();
+ }
+ else if (attributeName == "constant")
+ {
+ value = unsetConstant();
+ }
+ else if (attributeName == "outside")
+ {
+ value = unsetOutside();
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = unsetCompartmentType();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
Modified: branches/libsbml-experimental/src/sbml/Compartment.h
===================================================================
--- branches/libsbml-experimental/src/sbml/Compartment.h 2016-10-14 16:04:02 UTC (rev 23627)
+++ branches/libsbml-experimental/src/sbml/Compartment.h 2016-10-14 16:08:40 UTC (rev 23628)
@@ -1315,6 +1315,296 @@
virtual bool hasRequiredAttributes() const;
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ double& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" att...
[truncated message content] |
|
From: <sar...@us...> - 2016-10-14 16:04:05
|
Revision: 23627
http://sourceforge.net/p/sbml/code/23627
Author: sarahkeating
Date: 2016-10-14 16:04:02 +0000 (Fri, 14 Oct 2016)
Log Message:
-----------
added the generic attribute functions to facilitate matlab binding
Modified Paths:
--------------
trunk/libsbml/src/sbml/AssignmentRule.cpp
trunk/libsbml/src/sbml/AssignmentRule.h
trunk/libsbml/src/sbml/Compartment.cpp
trunk/libsbml/src/sbml/Compartment.h
trunk/libsbml/src/sbml/Event.cpp
trunk/libsbml/src/sbml/Event.h
trunk/libsbml/src/sbml/EventAssignment.cpp
trunk/libsbml/src/sbml/EventAssignment.h
trunk/libsbml/src/sbml/InitialAssignment.cpp
trunk/libsbml/src/sbml/InitialAssignment.h
trunk/libsbml/src/sbml/KineticLaw.cpp
trunk/libsbml/src/sbml/KineticLaw.h
trunk/libsbml/src/sbml/LocalParameter.cpp
trunk/libsbml/src/sbml/LocalParameter.h
trunk/libsbml/src/sbml/Model.cpp
trunk/libsbml/src/sbml/Model.h
trunk/libsbml/src/sbml/Parameter.cpp
trunk/libsbml/src/sbml/Parameter.h
trunk/libsbml/src/sbml/RateRule.cpp
trunk/libsbml/src/sbml/RateRule.h
trunk/libsbml/src/sbml/Reaction.cpp
trunk/libsbml/src/sbml/Reaction.h
trunk/libsbml/src/sbml/SBase.cpp
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/SimpleSpeciesReference.cpp
trunk/libsbml/src/sbml/SimpleSpeciesReference.h
trunk/libsbml/src/sbml/Species.cpp
trunk/libsbml/src/sbml/Species.h
trunk/libsbml/src/sbml/SpeciesReference.cpp
trunk/libsbml/src/sbml/SpeciesReference.h
trunk/libsbml/src/sbml/Trigger.cpp
trunk/libsbml/src/sbml/Trigger.h
trunk/libsbml/src/sbml/Unit.cpp
trunk/libsbml/src/sbml/Unit.h
trunk/libsbml/src/sbml/test/TestAttributeFunctions.cpp
trunk/libsbml/src/sbml/test/TestRunner.c
Modified: trunk/libsbml/src/sbml/AssignmentRule.cpp
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/AssignmentRule.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -129,6 +129,143 @@
}
}
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "variable")
+ {
+ value = getVariable();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this AssignmentRule's attribute
+ * "attributeName" is set.
+ */
+bool
+AssignmentRule::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "variable")
+ {
+ value = isSetVariable();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "variable")
+ {
+ return_value = setVariable(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this AssignmentRule.
+ */
+int
+AssignmentRule::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "variable")
+ {
+ value = unsetVariable();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
#endif /* __cplusplus */
Modified: trunk/libsbml/src/sbml/AssignmentRule.h
===================================================================
--- trunk/libsbml/src/sbml/AssignmentRule.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/AssignmentRule.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -271,6 +271,120 @@
virtual void renameSIdRefs(const std::string& oldid, const std::string& newid);
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this AssignmentRule's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this AssignmentRule's attribute "attributeName" has
+ * been set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this AssignmentRule.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
protected:
/** @cond doxygenLibsbmlInternal */
/* the validator classes need to be friends to access the
Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Compartment.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -999,7 +999,432 @@
return allPresent;
}
+
+#ifndef SWIG
+
+
+
/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName, bool& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "constant")
+ {
+ value = getConstant();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "size")
+ {
+ value = getSize();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "volume")
+ {
+ value = getVolume();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ unsigned int& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "spatialDimensions")
+ {
+ value = getSpatialDimensions();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "units")
+ {
+ value = getUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "outside")
+ {
+ value = getOutside();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = getCompartmentType();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this Compartment's attribute "attributeName"
+ * is set.
+ */
+bool
+Compartment::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "size")
+ {
+ value = isSetSize();
+ }
+ else if (attributeName == "volume")
+ {
+ value = isSetVolume();
+ }
+ else if (attributeName == "units")
+ {
+ value = isSetUnits();
+ }
+ else if (attributeName == "spatialDimensions")
+ {
+ value = isSetSpatialDimensions();
+ }
+ else if (attributeName == "constant")
+ {
+ value = isSetConstant();
+ }
+ else if (attributeName == "outside")
+ {
+ value = isSetOutside();
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = isSetCompartmentType();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "constant")
+ {
+ return_value = setConstant(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "size")
+ {
+ return_value = setSize(value);
+ }
+ else if (attributeName == "volume")
+ {
+ return_value = setVolume(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName,
+ unsigned int value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "spatialDimensions")
+ {
+ return_value = setSpatialDimensions(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "units")
+ {
+ return_value = setUnits(value);
+ }
+ else if (attributeName == "outside")
+ {
+ return_value = setOutside(value);
+ }
+ else if (attributeName == "compartmentType")
+ {
+ return_value = setCompartmentType(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this Compartment.
+ */
+int
+Compartment::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "size")
+ {
+ value = unsetSize();
+ }
+ else if (attributeName == "volume")
+ {
+ value = unsetVolume();
+ }
+ else if (attributeName == "units")
+ {
+ value = unsetUnits();
+ }
+ else if (attributeName == "spatialDimensions")
+ {
+ value = unsetSpatialDimensions();
+ }
+ else if (attributeName == "constant")
+ {
+ value = unsetConstant();
+ }
+ else if (attributeName == "outside")
+ {
+ value = unsetOutside();
+ }
+ else if (attributeName == "compartmentType")
+ {
+ value = unsetCompartmentType();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Compartment.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -1315,6 +1315,296 @@
virtual bool hasRequiredAttributes() const;
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ double& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ unsigned int& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this Compartment's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this Compartment's attribute "attributeName" has been
+ * set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, bool value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, double value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ unsigned int value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this Compartment.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/Event.cpp
===================================================================
--- trunk/libsbml/src/sbml/Event.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Event.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -1346,7 +1346,220 @@
/** @endcond */
+
+#ifndef SWIG
+
+
+
/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Event.
+ */
+int
+Event::getAttribute(const std::string& attributeName, bool& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "useValuesFromTriggerTime")
+ {
+ value = getUseValuesFromTriggerTime();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Event.
+ */
+int
+Event::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "timeUnits")
+ {
+ value = getTimeUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this Event's attribute "attributeName" is
+ * set.
+ */
+bool
+Event::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "useValuesFromTriggerTime")
+ {
+ value = isSetUseValuesFromTriggerTime();
+ }
+ else if (attributeName == "timeUnits")
+ {
+ value = isSetTimeUnits();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Event.
+ */
+int
+Event::setAttribute(const std::string& attributeName, bool value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "useValuesFromTriggerTime")
+ {
+ return_value = setUseValuesFromTriggerTime(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Event.
+ */
+int
+Event::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "timeUnits")
+ {
+ return_value = setTimeUnits(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this Event.
+ */
+int
+Event::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "useValuesFromTriggerTime")
+ {
+ value = unsetUseValuesFromTriggerTime();
+ }
+ else if (attributeName == "timeUnits")
+ {
+ value = unsetTimeUnits();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
Modified: trunk/libsbml/src/sbml/Event.h
===================================================================
--- trunk/libsbml/src/sbml/Event.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Event.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -1098,6 +1098,177 @@
void setInternalId(std::string id) { mInternalId = id; };
/** @endcond */
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Event.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName, bool& value)
+ const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this Event.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this Event's attribute "attributeName" is
+ * set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this Event's attribute "attributeName" has been set,
+ * otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Event.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, bool value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Event.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this Event.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/EventAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/EventAssignment.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -474,6 +474,141 @@
}
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this EventAssignment.
+ */
+int
+EventAssignment::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "variable")
+ {
+ value = getVariable();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this EventAssignment's attribute
+ * "attributeName" is set.
+ */
+bool
+EventAssignment::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "variable")
+ {
+ value = isSetVariable();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this EventAssignment.
+ */
+int
+EventAssignment::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "variable")
+ {
+ return_value = setVariable(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this EventAssignment.
+ */
+int
+EventAssignment::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "variable")
+ {
+ value = unsetVariable();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
void
EventAssignment::renameSIdRefs(const std::string& oldid, const std::string& newid)
{
Modified: trunk/libsbml/src/sbml/EventAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/EventAssignment.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -648,6 +648,118 @@
/** @endcond */
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this EventAssignment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this EventAssignment's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this EventAssignment's attribute "attributeName" has
+ * been set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this EventAssignment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this EventAssignment.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/InitialAssignment.cpp
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/InitialAssignment.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -452,6 +452,141 @@
}
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this InitialAssignment.
+ */
+int
+InitialAssignment::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "symbol")
+ {
+ value = getSymbol();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this InitialAssignment's attribute
+ * "attributeName" is set.
+ */
+bool
+InitialAssignment::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "symbol")
+ {
+ value = isSetSymbol();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this InitialAssignment.
+ */
+int
+InitialAssignment::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "symbol")
+ {
+ return_value = setSymbol(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this InitialAssignment.
+ */
+int
+InitialAssignment::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "symbol")
+ {
+ value = unsetSymbol();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
void
InitialAssignment::renameSIdRefs(const std::string& oldid, const std::string& newid)
{
Modified: trunk/libsbml/src/sbml/InitialAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/InitialAssignment.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -625,6 +625,119 @@
/** @endcond */
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this InitialAssignment.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this InitialAssignment's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this InitialAssignment's attribute "attributeName" has
+ * been set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this InitialAssignment.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this
+ * InitialAssignment.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/KineticLaw.cpp
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/KineticLaw.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -1139,6 +1139,158 @@
}
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this KineticLaw.
+ */
+int
+KineticLaw::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "timeUnits")
+ {
+ value = getTimeUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "substanceUnits")
+ {
+ value = getSubstanceUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this KineticLaw's attribute "attributeName"
+ * is set.
+ */
+bool
+KineticLaw::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "timeUnits")
+ {
+ value = isSetTimeUnits();
+ }
+ else if (attributeName == "substanceUnits")
+ {
+ value = isSetSubstanceUnits();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this KineticLaw.
+ */
+int
+KineticLaw::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "timeUnits")
+ {
+ return_value = setTimeUnits(value);
+ }
+ else if (attributeName == "substanceUnits")
+ {
+ return_value = setSubstanceUnits(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this KineticLaw.
+ */
+int
+KineticLaw::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "timeUnits")
+ {
+ value = unsetTimeUnits();
+ }
+ else if (attributeName == "substanceUnits")
+ {
+ value = unsetSubstanceUnits();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
void
KineticLaw::renameSIdRefs(const std::string& oldid, const std::string& newid)
{
Modified: trunk/libsbml/src/sbml/KineticLaw.h
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/KineticLaw.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -1022,6 +1022,118 @@
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this KineticLaw.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this KineticLaw's attribute "attributeName"
+ * is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this KineticLaw's attribute "attributeName" has been
+ * set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this KineticLaw.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this KineticLaw.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/LocalParameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/LocalParameter.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/LocalParameter.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -255,7 +255,221 @@
}
+
+#ifndef SWIG
+
+
+
/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this LocalParameter.
+ */
+int
+LocalParameter::getAttribute(const std::string& attributeName,
+ double& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "value")
+ {
+ value = getValue();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this LocalParameter.
+ */
+int
+LocalParameter::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "units")
+ {
+ value = getUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this LocalParameter's attribute
+ * "attributeName" is set.
+ */
+bool
+LocalParameter::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "value")
+ {
+ value = isSetValue();
+ }
+ else if (attributeName == "units")
+ {
+ value = isSetUnits();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this LocalParameter.
+ */
+int
+LocalParameter::setAttribute(const std::string& attributeName, double value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "value")
+ {
+ return_value = setValue(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this LocalParameter.
+ */
+int
+LocalParameter::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "units")
+ {
+ return_value = setUnits(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this LocalParameter.
+ */
+int
+LocalParameter::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "value")
+ {
+ value = unsetValue();
+ }
+ else if (attributeName == "units")
+ {
+ value = unsetUnits();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+/** @cond doxygenLibsbmlInternal */
/**
* Subclasses should override this method to get the list of
* expected attributes.
Modified: trunk/libsbml/src/sbml/LocalParameter.h
===================================================================
--- trunk/libsbml/src/sbml/LocalParameter.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/LocalParameter.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -356,6 +356,175 @@
/** @endcond */
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this LocalParameter.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ double& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Gets the value of the "attributeName" attribute of this LocalParameter.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this LocalParameter's attribute
+ * "attributeName" is set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this LocalParameter's attribute "attributeName" has
+ * been set, otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this LocalParameter.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName, double value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this LocalParameter.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this LocalParameter.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
protected:
/** @cond doxygenLibsbmlInternal */
/**
@@ -605,6 +774,8 @@
/** @endcond */
+
+
protected:
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/Model.cpp
===================================================================
--- trunk/libsbml/src/sbml/Model.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Model.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -3742,6 +3742,243 @@
return mEvents.remove(sid);
}
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Model.
+ */
+int
+Model::getAttribute(const std::string& attributeName,
+ std::string& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ return return_value;
+ }
+
+ if (attributeName == "substanceUnits")
+ {
+ value = getSubstanceUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "timeUnits")
+ {
+ value = getTimeUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "volumeUnits")
+ {
+ value = getVolumeUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "lengthUnits")
+ {
+ value = getLengthUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "areaUnits")
+ {
+ value = getAreaUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "extentUnits")
+ {
+ value = getExtentUnits();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (attributeName == "conversionFactor")
+ {
+ value = getConversionFactor();
+ return_value = LIBSBML_OPERATION_SUCCESS;
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Predicate returning @c true if this Model's attribute "attributeName" is
+ * set.
+ */
+bool
+Model::isSetAttribute(const std::string& attributeName) const
+{
+ bool value = SBase::isSetAttribute(attributeName);
+
+ if (attributeName == "substanceUnits")
+ {
+ value = isSetSubstanceUnits();
+ }
+ else if (attributeName == "timeUnits")
+ {
+ value = isSetTimeUnits();
+ }
+ else if (attributeName == "volumeUnits")
+ {
+ value = isSetVolumeUnits();
+ }
+ else if (attributeName == "lengthUnits")
+ {
+ value = isSetLengthUnits();
+ }
+ else if (attributeName == "areaUnits")
+ {
+ value = isSetAreaUnits();
+ }
+ else if (attributeName == "extentUnits")
+ {
+ value = isSetExtentUnits();
+ }
+ else if (attributeName == "conversionFactor")
+ {
+ value = isSetConversionFactor();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Sets the value of the "attributeName" attribute of this Model.
+ */
+int
+Model::setAttribute(const std::string& attributeName,
+ const std::string& value)
+{
+ int return_value = SBase::setAttribute(attributeName, value);
+
+ if (attributeName == "substanceUnits")
+ {
+ return_value = setSubstanceUnits(value);
+ }
+ else if (attributeName == "timeUnits")
+ {
+ return_value = setTimeUnits(value);
+ }
+ else if (attributeName == "volumeUnits")
+ {
+ return_value = setVolumeUnits(value);
+ }
+ else if (attributeName == "lengthUnits")
+ {
+ return_value = setLengthUnits(value);
+ }
+ else if (attributeName == "areaUnits")
+ {
+ return_value = setAreaUnits(value);
+ }
+ else if (attributeName == "extentUnits")
+ {
+ return_value = setExtentUnits(value);
+ }
+ else if (attributeName == "conversionFactor")
+ {
+ return_value = setConversionFactor(value);
+ }
+
+ return return_value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
+
+
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Unsets the value of the "attributeName" attribute of this Model.
+ */
+int
+Model::unsetAttribute(const std::string& attributeName)
+{
+ int value = SBase::unsetAttribute(attributeName);
+
+ if (attributeName == "substanceUnits")
+ {
+ value = unsetSubstanceUnits();
+ }
+ else if (attributeName == "timeUnits")
+ {
+ value = unsetTimeUnits();
+ }
+ else if (attributeName == "volumeUnits")
+ {
+ value = unsetVolumeUnits();
+ }
+ else if (attributeName == "lengthUnits")
+ {
+ value = unsetLengthUnits();
+ }
+ else if (attributeName == "areaUnits")
+ {
+ value = unsetAreaUnits();
+ }
+ else if (attributeName == "extentUnits")
+ {
+ value = unsetExtentUnits();
+ }
+ else if (attributeName == "conversionFactor")
+ {
+ value = unsetConversionFactor();
+ }
+
+ return value;
+}
+
+/** @endcond */
+
+
+
+
+#endif /* !SWIG */
int
Model::appendFrom(const Model* model)
{
Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Model.h 2016-10-14 16:04:02 UTC (rev 23627)
@@ -3088,7 +3088,119 @@
/** @endcond */
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
/**
+ * Gets the value of the "attributeName" attribute of this Model.
+ *
+ * @param attributeName, the name of the attribute to retrieve.
+ *
+ * @param value, the address of the value to record.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int getAttribute(const std::string& attributeName,
+ std::string& value) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Predicate returning @c true if this Model's attribute "attributeName" is
+ * set.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @return @c true if this Model's attribute "attributeName" has been set,
+ * otherwise @c false is returned.
+ */
+ virtual bool isSetAttribute(const std::string& attributeName) const;
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Sets the value of the "attributeName" attribute of this Model.
+ *
+ * @param attributeName, the name of the attribute to set.
+ *
+ * @param value, the value of the attribute to set.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int setAttribute(const std::string& attributeName,
+ const std::string& value);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+
+
+
+ #ifndef SWIG
+
+
+
+ /** @cond doxygenLibsbmlInternal */
+
+ /**
+ * Unsets the value of the "attributeName" attribute of this Model.
+ *
+ * @param attributeName, the name of the attribute to query.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ */
+ virtual int unsetAttribute(const std::string& attributeName);
+
+ /** @endcond */
+
+
+
+
+ #endif /* !SWIG */
+
+ /**
* Populates the internal list of derived units for this Model object.
*
* This method tells libSBML to (re)calculate all units for all components
Modified: trunk/libsbml/src/sbml/Parameter.cpp
===================================================================
--- trunk/libsbml/src/sbml/Parameter.cpp 2016-10-13 14:39:26 UTC (rev 23626)
+++ trunk/libsbml/src/sbml/Parameter.cpp 2016-10-14 16:04:02 UTC (rev 23627)
@@ -686,6 +686,297 @@
}
+
+
+#ifndef SWIG
+
+
+
+/** @cond doxygenLibsbmlInternal */
+
+/*
+ * Gets the value of the "attributeName" attribute of this Parameter.
+ */
+int
+Parameter::getAttribute(const std::string& attributeName, bool& value) const
+{
+ int return_value = SBase::getAttribute(attributeName, value);
+
+ if (return_value == LIBSBML_OPERATION_SUCCESS)
+ {
+ r...
[truncated message content] |
|
From: <fbe...@us...> - 2016-10-13 14:39:29
|
Revision: 23626
http://sourceforge.net/p/sbml/code/23626
Author: fbergmann
Date: 2016-10-13 14:39:26 +0000 (Thu, 13 Oct 2016)
Log Message:
-----------
- allow wheels to be created
Modified Paths:
--------------
trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat
Modified: trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat 2016-10-13 14:31:30 UTC (rev 23625)
+++ trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat 2016-10-13 14:39:26 UTC (rev 23626)
@@ -25,7 +25,7 @@
if "%MODE%" == "" set MODE=ALL
if "%MODE%" == "INSTALLER" GOTO INSTALLER
-if "%MODE%" == "WHEEL" GOTO INSTALLER
+if "%MODE%" == "WHEEL" GOTO WHEEL
if "%MODE%" == "TEST" GOTO TEST
|
|
From: <fbe...@us...> - 2016-10-13 14:31:33
|
Revision: 23625
http://sourceforge.net/p/sbml/code/23625
Author: fbergmann
Date: 2016-10-13 14:31:30 +0000 (Thu, 13 Oct 2016)
Log Message:
-----------
- rename binaries after creating them so they match the desired scheme
Modified Paths:
--------------
trunk/libsbml/dev/utilities/build-python/build_python.bat
Added Paths:
-----------
trunk/libsbml/dev/utilities/build-python/python-src/rename-files.cmake
Modified: trunk/libsbml/dev/utilities/build-python/build_python.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_python.bat 2016-10-13 14:09:41 UTC (rev 23624)
+++ trunk/libsbml/dev/utilities/build-python/build_python.bat 2016-10-13 14:31:30 UTC (rev 23625)
@@ -51,6 +51,9 @@
call buildV.bat 3 4 INSTALLER
call buildV.bat 3 5 INSTALLER
+:: move files
move dist\*.exe %THIS_DIR%\dist
+:: rename files
+cmake -DSRC_DIR=%LIBSBML_SRC% -DOUT_DIR=%THIS_DIR%\dist -P rename-files.cmake
popd
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/python-src/rename-files.cmake
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/rename-files.cmake (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/rename-files.cmake 2016-10-13 14:31:30 UTC (rev 23625)
@@ -0,0 +1,61 @@
+# cmake build script wrapping built libsbml python bindings into conda binaries
+#
+#
+
+if ("${SRC_DIR}" STREQUAL "" OR "${OUT_DIR}" STREQUAL "" )
+message(FATAL_ERROR
+"
+ Need the following parameters:
+ - SRC_DIR: the libsbml directory (containing VERSION.txt)
+ - OUT_DIR: the directory where the installers to be
+ renamed are
+
+")
+endif()
+
+set(LIBSBML_VERSION_MAJOR)
+set(LIBSBML_VERSION_MINOR)
+set(LIBSBML_VERSION_PATCH)
+set(LIBSBML_VERSION_RELEASE)
+set(LIBSBML_DOTTED_VERSION)
+
+if(EXISTS "${SRC_DIR}/VERSION.txt")
+
+ file(STRINGS "${SRC_DIR}/VERSION.txt" VersionString NEWLINE_CONSUME)
+ string(STRIP "${VersionString}" VersionString)
+ set(LIBSBML_DOTTED_VERSION ${VersionString})
+ string(REPLACE "." ";" VersionString "${VersionString}" )
+ string(REPLACE "-" ";" VersionString "${VersionString}" )
+ list(LENGTH VersionString versionLength)
+ list(GET VersionString 0 LIBSBML_VERSION_MAJOR )
+ list(GET VersionString 1 LIBSBML_VERSION_MINOR )
+ list(GET VersionString 2 LIBSBML_VERSION_PATCH )
+
+ if(${versionLength} GREATER 3)
+ list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
+ endif()
+
+endif()
+
+# version number needs to be calculated correctly
+MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_VERSION_MINOR} * 100 + ${LIBSBML_VERSION_PATCH}" )
+set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")
+
+set (VERSIONS 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5)
+foreach(version ${VERSIONS})
+
+ if (EXISTS "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win32-py${version}.exe")
+ file(RENAME
+ "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win32-py${version}.exe"
+ "${OUT_DIR}/libSBML-${PACKAGE_VERSION}-win-py${version}-x86.exe"
+ )
+ endif()
+
+ if (EXISTS "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win-amd64-py${version}.exe")
+ file(RENAME
+ "${OUT_DIR}/libsbml-${PACKAGE_VERSION}.win-amd64-py${version}.exe"
+ "${OUT_DIR}/libSBML-${PACKAGE_VERSION}-win-py${version}-x64.exe"
+ )
+ endif()
+
+endforeach()
|
|
From: <fbe...@us...> - 2016-10-13 14:09:44
|
Revision: 23624
http://sourceforge.net/p/sbml/code/23624
Author: fbergmann
Date: 2016-10-13 14:09:41 +0000 (Thu, 13 Oct 2016)
Log Message:
-----------
- specify files to be ignored
- added /bigobj to compile flags to allow larger files to be compiled
Modified Paths:
--------------
trunk/libsbml/dev/utilities/build-python/build_all.bat
trunk/libsbml/dev/utilities/build-python/build_python.bat
trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt
Property Changed:
----------------
trunk/libsbml/dev/utilities/build-python/
trunk/libsbml/dev/utilities/build-python/python-src/
Index: trunk/libsbml/dev/utilities/build-python
===================================================================
--- trunk/libsbml/dev/utilities/build-python 2016-10-13 13:42:38 UTC (rev 23623)
+++ trunk/libsbml/dev/utilities/build-python 2016-10-13 14:09:41 UTC (rev 23624)
Property changes on: trunk/libsbml/dev/utilities/build-python
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,6 ##
+build_32
+build_64
+dist
+install_32
+install_64
+swig
Modified: trunk/libsbml/dev/utilities/build-python/build_all.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_all.bat 2016-10-13 13:42:38 UTC (rev 23623)
+++ trunk/libsbml/dev/utilities/build-python/build_all.bat 2016-10-13 14:09:41 UTC (rev 23624)
@@ -2,7 +2,21 @@
SET BASE_DIR=%~dp0
Setlocal EnableDelayedExpansion
+:: build libsbml
call build_libsbml.bat
+
+:: create all python binaries
call build_python.bat
+
+:: create conda binaries in dist\conda
call build_conda.bat
-call remove_files.bat
\ No newline at end of file
+
+:: you can limit what will be deleted by providing some
+:: options here. They are:
+::
+:: ALL - delete all files created
+:: BUILD - delete build dirs
+:: INSTALL - delete install dirs
+:: TEMP - delete python temp files and dirs
+::
+call remove_files.bat
Modified: trunk/libsbml/dev/utilities/build-python/build_python.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_python.bat 2016-10-13 13:42:38 UTC (rev 23623)
+++ trunk/libsbml/dev/utilities/build-python/build_python.bat 2016-10-13 14:09:41 UTC (rev 23624)
@@ -12,12 +12,23 @@
:: create builds for different python versions
:: build in parallel (means that installers | wheels have to be created later)
+::
+:: if start is being used, the builds will be carried out in :: parallel. start needs the the argument EXIT_WHEN_DONE,
+:: otherwise the console window will remain open.
+::
+:: if call is being used that argument cannot be given
+:: otherwise the build will stop.
+::
+:: the lines below carry out the 2.5, 2.6 and 2.7 build
+:: in parallel, as well the 3.1, 3.2 and 3.3 build and the
+:: 3.4 and 3.5 build.
+::
start buildV.bat 2 5 BUILD EXIT_WHEN_DONE
start buildV.bat 2 6 BUILD EXIT_WHEN_DONE
call buildV.bat 2 7 BUILD
start buildV.bat 3 1 BUILD EXIT_WHEN_DONE
start buildV.bat 3 2 BUILD EXIT_WHEN_DONE
-start buildV.bat 3 3 BUILD EXIT_WHEN_DONE
+call buildV.bat 3 3 BUILD
start buildV.bat 3 4 BUILD EXIT_WHEN_DONE
call buildV.bat 3 5 BUILD
Index: trunk/libsbml/dev/utilities/build-python/python-src
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src 2016-10-13 13:42:38 UTC (rev 23623)
+++ trunk/libsbml/dev/utilities/build-python/python-src 2016-10-13 14:09:41 UTC (rev 23624)
Property changes on: trunk/libsbml/dev/utilities/build-python/python-src
___________________________________________________________________
Added: svn:ignore
## -0,0 +1,24 ##
+b32_25
+b32_26
+b32_27
+b32_31
+b32_32
+b32_33
+b32_34
+b32_35
+b64_25
+b64_26
+b64_27
+b64_31
+b64_32
+b64_33
+b64_34
+b64_35
+build
+dist
+libsbml
+libsbml.egg-info
+*.cpp
+*.h
+*.py
+*.pth
Modified: trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt 2016-10-13 13:42:38 UTC (rev 23623)
+++ trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt 2016-10-13 14:09:41 UTC (rev 23624)
@@ -179,6 +179,10 @@
PATHS ${LIB_PATH} ${DEP_DIR}/lib
)
+if (MSVC)
+add_definitions(/bigobj)
+endif()
+
set(LIBS
${LIBS} ${SBML_LIBRARY}
${XML_LIBRARY} ${ICONV_LIBRARY}
|
|
From: <fbe...@us...> - 2016-10-13 13:42:40
|
Revision: 23623
http://sourceforge.net/p/sbml/code/23623
Author: fbergmann
Date: 2016-10-13 13:42:38 +0000 (Thu, 13 Oct 2016)
Log Message:
-----------
- first version of standalone scripts to build / run / test windows python files
Added Paths:
-----------
trunk/libsbml/dev/utilities/build-python/
trunk/libsbml/dev/utilities/build-python/README.md
trunk/libsbml/dev/utilities/build-python/build_all.bat
trunk/libsbml/dev/utilities/build-python/build_conda.bat
trunk/libsbml/dev/utilities/build-python/build_libsbml.bat
trunk/libsbml/dev/utilities/build-python/build_python.bat
trunk/libsbml/dev/utilities/build-python/python-src/
trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt
trunk/libsbml/dev/utilities/build-python/python-src/buildPython32.bat
trunk/libsbml/dev/utilities/build-python/python-src/buildPython64.bat
trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat
trunk/libsbml/dev/utilities/build-python/python-src/configure-files.cmake
trunk/libsbml/dev/utilities/build-python/python-src/libsbml-python-installer-graphic.bmp
trunk/libsbml/dev/utilities/build-python/python-src/setup.py.in
trunk/libsbml/dev/utilities/build-python/python-src/setup32.py.in
trunk/libsbml/dev/utilities/build-python/python-src/setup64.py.in
trunk/libsbml/dev/utilities/build-python/python-src/setupStable.py.in
trunk/libsbml/dev/utilities/build-python/python-src/testPython.bat
trunk/libsbml/dev/utilities/build-python/remove_files.bat
trunk/libsbml/dev/utilities/build-python/source/
trunk/libsbml/dev/utilities/build-python/source/bld.bat
trunk/libsbml/dev/utilities/build-python/source/build.sh
trunk/libsbml/dev/utilities/build-python/source/create-conda-archives.cmake
trunk/libsbml/dev/utilities/build-python/source/egg-info
trunk/libsbml/dev/utilities/build-python/source/files
trunk/libsbml/dev/utilities/build-python/source/index.json
trunk/libsbml/dev/utilities/build-python/source/meta.yaml
trunk/libsbml/dev/utilities/build-python/source/recipe.json
Added: trunk/libsbml/dev/utilities/build-python/README.md
===================================================================
--- trunk/libsbml/dev/utilities/build-python/README.md (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/README.md 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,44 @@
+## Dependencies
+For the build to be working you will need to have the following installed:
+
+* cmake. After the installation the `cmake` executable is expected to be in the `PATH`.
+* Visual Studio: by default these scripts assume VS 2015 will be used.
+* libSBML-dependencies built for the VS version you are using (it will be using the static runtime) by default the scripts are expected to be in `\Development\libSBML-dependencies\install_vs14_release_x86_static` and `\Development\libSBML-dependencies\install_vs14_release_x86_static`.
+* python 2.6, 2.7, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5 (both 32 nd 64 bit): The scripts will assume that those files are in `c:\python%version%_%arch%`, so for example `c:\python27_32` for the python 2.7 32 bit version.
+* for the python version2 2.6, 2.7, 3.3, 3.4 and 3.5 you will need to have wheel installed, to create windows binary wheels.
+
+## Customizing the scripts
+Some customization of the scripts will be needed in case the conventions are not met. Specifically:
+
+* `build_libsbml.bat`: here you want to adjust the `SWIG`, `CMAKE_OPTIONS` for the build, the `PYTHON` location as well as the `DEPENDENCY_DIR` variables. The script also uses Ninja as build tool which allows for parallel compilation of libsbml. If you would prefer to use NMake, you want to adjust the `BUILD_COMMAND` and `GENERATOR` variable as well.
+* `build_python.bat`: by default three python builds will happen in parallel. If you prefer those builds to be run sequentially, then change the `start` statements to be `call` statements.
+* `python-src\buildV.bat`: this script is given the python major and minor version. Based on these you should be setting the `PYTHON_32` and `PYTHON_64` bit variable.
+
+## Creating Windows Python binaries
+The normal setuptools build process does not work for windows (as we have too many files that are passed along on the command line by setuptools). Thus these scripts are used to create the python binaries:
+
+
+### build_libsbml.bat
+This script basically creates a static build of libSBML (32 and 64 bit). The top of the file contains a number of variables that have to be adapted to the individual platform.
+
+### build_python.bat
+This script will create the different python binaries out of the files created by `build_libsbml.bat`, and once done will create the windows installers and python wheels.
+
+### build_conda.bat
+This script transforms the binaries build by `build_python.bat` and wraps them into anaconda files.
+
+### remove_files.bat
+This script removes all the temporary files created in the process of building the python bindings. The only exception being the `dist` folder that will hold the result of the build.
+
+### build_all.bat
+This script will call all the other scripts in order, building libSBML, creating the python binaries, and the conda packages. Finally all temporary files will be removed.
+
+## Support files
+Additionally this directory contains a number of support files and directories:
+
+* `python-src` this directory contains all the files needed to build the python files, installers and wheels
+* `create-conda-archives.cmake` and the `source` directories are there to create the conda binaries.
+
+
+---
+10/13/2016 3:33:18 PM Frank T. Bergmann
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/build_all.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_all.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/build_all.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,8 @@
+@echo off
+SET BASE_DIR=%~dp0
+Setlocal EnableDelayedExpansion
+
+call build_libsbml.bat
+call build_python.bat
+call build_conda.bat
+call remove_files.bat
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/build_conda.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_conda.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/build_conda.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,24 @@
+@echo off
+Setlocal EnableDelayedExpansion
+SET THIS_DIR=%~dp0
+SET LIBSBML_SRC=%THIS_DIR%\..\..\..\
+SET NAME=python-libsbml
+
+pushd %THIS_DIR%
+
+if not exist dist mkdir dist
+if not exist dist\conda-x86 mkdir dist\conda-x86
+if not exist dist\conda-x64 mkdir dist\conda-x64
+
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%THIS_DIR%\python-src\build\lib.win-amd64-3.5 -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P source\create-conda-archives.cmake
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%THIS_DIR%\python-src\build\lib.win-amd64-3.3 -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P source\create-conda-archives.cmake
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%THIS_DIR%\python-src\build\lib.win-amd64-2.7 -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P source\create-conda-archives.cmake
+move *.bz2 dist\conda-x64
+
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%THIS_DIR%\python-src\build\lib.win32-3.5 -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P source\create-conda-archives.cmake
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%THIS_DIR%\python-src\build\lib.win32-3.3 -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P source\create-conda-archives.cmake
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%THIS_DIR%\python-src\build\lib.win32-2.7 -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P source\create-conda-archives.cmake
+move *.bz2 dist\conda-x86
+
+rd /s /q out
+popd
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/build_libsbml.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_libsbml.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/build_libsbml.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,64 @@
+@echo off
+SET BASE_DIR=%~dp0
+Setlocal EnableDelayedExpansion
+
+:: swig win exectuable
+SET SWIG=C:\swigwin-3.0.10\swig.exe
+
+:: specify which VS you want to use
+SET VS_VERSION=14
+
+:: set the matching build command for the generator
+::SET BUILD_COMMAND=nmake
+SET BUILD_COMMAND=ninja
+
+:: set the generator to be used this could be VS, Nmake, Ninja
+::SET GENERATOR="NMake Makefiles"
+SET GENERATOR=Ninja -DCMAKE_CXX_COMPILER=cl -DCMAKE_C_COMPILER=cl
+
+
+:: libsbml depenendency dir (has to match architecture and vs version)
+SET DEPENDENCY_DIR_32=\Development\libSBML-dependencies\install_vs%VS_VERSION%_release_x86_static
+SET DEPENDENCY_DIR_64=\Development\libSBML-dependencies\install_vs%VS_VERSION%_release_x64_static
+::SET DEPENDENCY_DIR=\Development\libSBML-dependencies\install_vs12_release_x64
+
+:: be sure to update to the correct python path
+SET PYTHON_32=c:\python27_32\python.exe
+SET PYTHON_64=c:\python27_64\python.exe
+
+:: set up the packages to be used
+SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DENABLE_COMP=ON -DENABLE_FBC=ON -DENABLE_LAYOUT=ON -DENABLE_QUAL=ON -DENABLE_GROUPS=ON
+:: outcomment the next line if you want to use the new math layer
+SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DLIBSBML_USE_LEGACY_MATH=ON
+
+:: shouldn't need to touch those
+SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DWITH_STATIC_RUNTIME=ON
+SET CMAKE_OPTIONS=%CMAKE_OPTIONS% -DLIBSBML_SKIP_SHARED_LIBRARY=ON
+
+SET BUILD_DIR_32=%BASE_DIR%\build_32
+SET BUILD_DIR_64=%BASE_DIR%\build_64
+
+SET INSTALL_DIR_32=%BASE_DIR%\install_32
+SET INSTALL_DIR_64=%BASE_DIR%\install_64
+
+SET VSVARS="%ProgramFiles(x86)%\Microsoft Visual Studio %VS_VERSION%.0\VC\vcvarsall.bat"
+
+if not exist %BUILD_DIR_32% mkdir %BUILD_DIR_32%
+
+pushd %BUILD_DIR_32%
+SET ARCH=x86
+call %VSVARS% %ARCH%
+cmake -G %GENERATOR% %CMAKE_OPTIONS% -DLIBSBML_DEPENDENCY_DIR=%DEPENDENCY_DIR_32% -DWITH_PYTHON=ON -DPYTHON_EXECUTABLE=%PYTHON_32% -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=%INSTALL_DIR_32% ../../../../
+%BUILD_COMMAND%
+%BUILD_COMMAND% install
+popd
+
+
+if not exist %BUILD_DIR_64% mkdir %BUILD_DIR_64%
+pushd %BUILD_DIR_64%
+SET ARCH=amd64
+call %VSVARS% %ARCH%
+cmake -G %GENERATOR% %CMAKE_OPTIONS% -DLIBSBML_DEPENDENCY_DIR=%DEPENDENCY_DIR_64% -DWITH_PYTHON=ON -DPYTHON_EXECUTABLE=%PYTHON_64% -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=%INSTALL_DIR_64% ../../../../
+%BUILD_COMMAND%
+%BUILD_COMMAND% install
+popd
Added: trunk/libsbml/dev/utilities/build-python/build_python.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/build_python.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/build_python.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,45 @@
+@echo off
+Setlocal EnableDelayedExpansion
+SET THIS_DIR=%~dp0
+SET LIBSBML_SRC=%THIS_DIR%\..\..\..\
+SET BUILD_DIR=%THIS_DIR%\build_32
+SET NAME=python-libsbml
+
+pushd %THIS_DIR%\python-src
+
+:: configure files
+cmake -DSRC_DIR=%LIBSBML_SRC% -DBUILD_DIR=%BUILD_DIR% -DOUT_DIR=%THIS_DIR%\out -DNAME=%NAME% -P configure-files.cmake
+
+:: create builds for different python versions
+:: build in parallel (means that installers | wheels have to be created later)
+start buildV.bat 2 5 BUILD EXIT_WHEN_DONE
+start buildV.bat 2 6 BUILD EXIT_WHEN_DONE
+call buildV.bat 2 7 BUILD
+start buildV.bat 3 1 BUILD EXIT_WHEN_DONE
+start buildV.bat 3 2 BUILD EXIT_WHEN_DONE
+start buildV.bat 3 3 BUILD EXIT_WHEN_DONE
+start buildV.bat 3 4 BUILD EXIT_WHEN_DONE
+call buildV.bat 3 5 BUILD
+
+if not exist %THIS_DIR%\dist mkdir %THIS_DIR%\dist
+
+:: wheels
+call buildV.bat 2 7 WHEEL
+call buildV.bat 3 3 WHEEL
+call buildV.bat 3 4 WHEEL
+call buildV.bat 3 5 WHEEL
+move dist\*.whl %THIS_DIR%\dist
+
+:: create installers and wheels
+call buildV.bat 2 5 INSTALLER
+call buildV.bat 2 6 INSTALLER
+call buildV.bat 2 7 INSTALLER
+call buildV.bat 3 1 INSTALLER
+call buildV.bat 3 2 INSTALLER
+call buildV.bat 3 3 INSTALLER
+call buildV.bat 3 4 INSTALLER
+call buildV.bat 3 5 INSTALLER
+
+move dist\*.exe %THIS_DIR%\dist
+
+popd
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/CMakeLists.txt 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,220 @@
+###############################################################################
+#
+#
+#
+# Description : CMake build script for compiling and linking the
+# python bindings
+# Original author(s): Frank Bergmann <fbe...@ca...>
+# Organization : California Institute of Technology
+#
+# This file is supposed to be called by buildPython32.bat / buildPython64.bat
+#
+###############################################################################
+
+cmake_minimum_required(VERSION 2.8)
+project(_libsbml)
+
+include (CMakeTestCCompiler)
+include (CheckCSourceCompiles)
+include (CheckCXXSourceCompiles)
+include (CheckStructHasMember)
+include (CheckLibraryExists)
+include (CheckFunctionExists)
+include (CheckCCompilerFlag)
+include (CheckCSourceRuns)
+include (CheckSymbolExists)
+include (CheckTypeSize)
+
+find_package(PythonInterp REQUIRED)
+
+# determine the library path and include path
+# for the given interpreter
+get_filename_component(path "${PYTHON_EXECUTABLE}" PATH)
+file(GLOB python_lib "${path}/libs/python*.lib")
+foreach(lib ${python_lib})
+ get_filename_component(name "${lib}" NAME)
+ string(TOLOWER "${name}" lower)
+ if ("${lower}" STREQUAL "python3.lib"
+ OR "${lower}" MATCHES "_d.lib$"
+ OR "${lower}" MATCHES "debug"
+ OR "${lower}" MATCHES "optimized"
+ )
+ list(REMOVE_ITEM python_lib "${lib}")
+ endif()
+endforeach()
+set(PYTHON_LIBRARY ${python_lib})
+set(PYTHON_INCLUDE_DIR ${path}/include)
+find_package(PythonLibs REQUIRED)
+
+
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/../swig)
+if (CMAKE_SIZEOF_VOID_P EQUAL 4)
+include_directories(${CMAKE_SOURCE_DIR}/../../../win32/include)
+else()
+include_directories(${CMAKE_SOURCE_DIR}/../../../win64/include)
+endif()
+include_directories(${PYTHON_INCLUDE_DIRS})
+include_directories(${DEP_DIR}/include)
+
+add_definitions(-DUSE_COMP
+ -DUSE_FBC
+ -DUSE_QUAL
+ -DUSE_LAYOUT
+ -DUSE_GROUPS
+ -DLIBSBML_USE_LEGACY_MATH
+)
+
+
+# set build type default
+set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None (CMAKE_CXX_FLAGS or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel" FORCE )
+
+
+###############################################################################
+#
+# Set up remaining variables, add option for universal binaries
+#
+set(BUILD_DEFINITIONS)
+if(UNIX)
+ if(APPLE)
+ add_definitions(-DMACOSX)
+ set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DMACOSX")
+
+ # On OSX it is common to build universal binaries to support multiple
+ # processor architectures. The default behavior is not to build
+ # multiple architectures, as most users might not need that.
+ option(ENABLE_UNIVERSAL "Create Universal Binaries" OFF)
+
+ set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING "A semicolon separated list of build architectures to be used")
+ if(ENABLE_UNIVERSAL)
+ # if universal binaries are requested and none defined so far
+ # overwrite them with all three common architectures. If the user
+ # specified their own list of architectures do not touch!
+ if (CMAKE_OSX_ARCHITECTURES STREQUAL "")
+ set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING "A semicolon separated list of build architectures to be used" FORCE)
+ endif()
+ endif(ENABLE_UNIVERSAL)
+ else(APPLE)
+ add_definitions(-DLINUX)
+
+ if (NOT CYGWIN)
+ # on cygwin all code is position independent so -fPIC is not needed
+ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing -fPIC")
+ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing -fPIC")
+ endif()
+
+ set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DLINUX")
+ endif(APPLE)
+
+ add_definitions( -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\" -DPACKAGE_NAME=\"${PROJECT_NAME}\")
+ set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\" -DPACKAGE_NAME=\"${PROJECT_NAME}\"")
+
+else(UNIX)
+ add_definitions(-DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS)
+ set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS")
+ if(MSVC)
+ add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE)
+ set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -D_CRT_SECURE_NO_WARNINGS")
+ option(WITH_STATIC_RUNTIME "Compile using the static MSVC Runtime" OFF)
+ if (NOT WITHOUT_STATIC_RUNTIME)
+ foreach(flag_var
+ CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
+ CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
+ CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
+ CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
+
+ if(${flag_var} MATCHES "/MD")
+ string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
+ endif(${flag_var} MATCHES "/MD")
+ endforeach(flag_var)
+ add_definitions( -D_MT)
+ endif(NOT WITHOUT_STATIC_RUNTIME)
+
+ file(GLOB WIN32_BINARIES ${CMAKE_SOURCE_DIR}/dependencies/bin/*.dll)
+ INSTALL(FILES ${WIN32_BINARIES} DESTINATION bin)
+
+ elseif(CYGWIN)
+ add_definitions(-DCYGWIN)
+ set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DCYGWIN")
+ elseif(MINGW)
+ if(WITH_LIBXML)
+ # this is necessary to build with libxml2 on mingw
+ add_definitions(-DLIBXML_STATIC)
+ endif(WITH_LIBXML)
+ endif(MSVC)
+
+endif(UNIX)
+
+
+set(LIB_PATH)
+if (CMAKE_SIZEOF_VOID_P EQUAL 4)
+ set(LIB_PATH "${CMAKE_SOURCE_DIR}/../install_32/lib")
+ include_directories("${CMAKE_SOURCE_DIR}/../install_32/include")
+else()
+ set(LIB_PATH "${CMAKE_SOURCE_DIR}/../install_64/lib")
+ include_directories("${CMAKE_SOURCE_DIR}/../install_64/include")
+endif()
+
+
+
+find_library(SBML_LIBRARY
+ NAMES libsbml-static.lib
+ PATHS ${LIB_PATH} ${DEP_DIR}/lib
+)
+find_library(XML_LIBRARY
+ NAMES libxml2.lib
+ PATHS ${LIB_PATH} ${DEP_DIR}/lib
+)
+find_library(ICONV_LIBRARY
+ NAMES libiconv.lib iconv.lib
+ PATHS ${LIB_PATH} ${DEP_DIR}/lib
+)
+find_library(BZ2_LIBRARY
+ NAMES libbz2.lib bzip2.lib
+ PATHS ${LIB_PATH} ${DEP_DIR}/lib
+)
+
+find_library(ZLIB_LIBRARY
+ NAMES zdll.lib zlib.lib
+ PATHS ${LIB_PATH} ${DEP_DIR}/lib
+)
+
+set(LIBS
+ ${LIBS} ${SBML_LIBRARY}
+ ${XML_LIBRARY} ${ICONV_LIBRARY}
+ ${BZ2_LIBRARY} ${ZLIB_LIBRARY}
+ ${PYTHON_LIBRARIES}
+)
+
+
+# remove additional list for python3
+foreach(lib ${LIBS})
+ get_filename_component(name "${lib}" NAME)
+ string(TOLOWER "${name}" lower)
+ if ("${lower}" STREQUAL "python3.lib"
+ OR "${lower}" MATCHES "_d.lib$"
+ OR "${lower}" MATCHES "debug"
+ OR "${lower}" MATCHES "optimized"
+ )
+ list(REMOVE_ITEM LIBS "${lib}")
+ endif()
+endforeach()
+
+add_library(binding_python_lib SHARED libsbml_wrap.cpp)
+
+set_target_properties (binding_python_lib PROPERTIES OUTPUT_NAME "_libsbml")
+if (UNIX)
+ set_target_properties (binding_python_lib PROPERTIES PREFIX "")
+ set_target_properties (binding_python_lib PROPERTIES SUFFIX ".so")
+else()
+ if (CYGWIN)
+ set_target_properties (binding_python_lib PROPERTIES PREFIX "")
+ set_target_properties (binding_python_lib PROPERTIES SUFFIX ".dll")
+ else()
+ set(LIBS ${LIBS} ws2_32.lib)
+ set_target_properties (binding_python_lib PROPERTIES SUFFIX ".pyd")
+ endif()
+endif()
+
+target_link_libraries(binding_python_lib ${LIBS} )
+
Added: trunk/libsbml/dev/utilities/build-python/python-src/buildPython32.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/buildPython32.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/buildPython32.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,46 @@
+@echo off
+Setlocal EnableDelayedExpansion
+
+REM This file will build the python source dist 32 bit
+REM
+REM 2011/02/26 Frank Bergmann
+REM
+
+REM ensure visual studio is in the path
+if "%VS_VERSION%"=="" SET VS_VERSION=14
+if "%INCLUDE%"=="" call "%ProgramFiles(x86)%\Microsoft Visual Studio %VS_VERSION%.0\VC\vcvarsall.bat" x86
+
+REM set up directory variables
+SET BASE_DIR=%~dp0
+
+REM check argument
+SET PYTHON_INTERP=%1
+if "%PYTHON_INTERP%" == "" goto MISSING_INTERP
+
+SET DEP_DIR=%2
+if "%DEP_DIR%" == "" SET DEP_DIR=../../../win32/
+
+SET MAJOR=%3
+SET MINOR=%4
+
+SET BUILD_DIR=b32_%MAJOR%%MINOR%
+
+REM goto path
+pushd %BASE_DIR%
+
+REM create build dir
+if not exist %BUILD_DIR% mkdir %BUILD_DIR%
+cd %BUILD_DIR%
+cmake -G "NMake Makefiles" -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE="%PYTHON_INTERP%" -DDEP_DIR="%DEP_DIR%" ..
+nmake
+
+goto ALL_DONE
+
+:MISSING_INTERP
+echo.
+echo Please provide the python interpreter to use as first argument.
+echo.
+goto ALL_DONE
+
+:ALL_DONE
+popd
Added: trunk/libsbml/dev/utilities/build-python/python-src/buildPython64.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/buildPython64.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/buildPython64.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,47 @@
+@echo off
+Setlocal EnableDelayedExpansion
+
+REM This file will build the python source dist 64 bit
+REM
+REM 2011/02/26 Frank Bergmann
+REM
+
+REM ensure visual studio is in the path
+if "%VS_VERSION%"=="" SET VS_VERSION=14
+if "%INCLUDE%"=="" call "%ProgramFiles(x86)%\Microsoft Visual Studio %VS_VERSION%.0\VC\vcvarsall.bat" amd64
+
+REM set up directory variables
+SET BASE_DIR=%~dp0
+
+REM check argument
+SET PYTHON_INTERP=%1
+if "%PYTHON_INTERP%" == "" goto MISSING_INTERP
+
+
+SET DEP_DIR=%2
+if "%DEP_DIR%" == "" SET DEP_DIR=../../../win32/
+
+SET MAJOR=%3
+SET MINOR=%4
+
+SET BUILD_DIR=b64_%MAJOR%%MINOR%
+
+REM goto path
+pushd %BASE_DIR%
+
+REM create build dir
+if not exist %BUILD_DIR% mkdir %BUILD_DIR%
+cd %BUILD_DIR%
+cmake -G "NMake Makefiles" -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE="%PYTHON_INTERP%" -DDEP_DIR="%DEP_DIR%" ..
+nmake
+
+goto ALL_DONE
+
+:MISSING_INTERP
+echo.
+echo Please provide the python interpreter to use as first argument.
+echo.
+goto ALL_DONE
+
+:ALL_DONE
+popd
Added: trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/buildV.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,76 @@
+@echo off
+REM
+REM Python Build script that builds a particular level / version of python bindings
+REM
+REM Frank T. Bergmann 9/10/2014
+REM
+REM
+Setlocal EnableDelayedExpansion
+SET MAJOR=%1
+SET MINOR=%2
+SET CURRENT_DIR=%~dp0
+SET SOURCE_32=.
+SET PTYHON_32=c:\Python%MAJOR%%MINOR%_32\python.exe
+SET PTYHON_64=c:\Python%MAJOR%%MINOR%_64\python.exe
+SET BUILD_32=%SOURCE_32%\b32_%MAJOR%%MINOR%
+SET BUILD_64=%SOURCE_32%\b64_%MAJOR%%MINOR%
+
+:: supported modes BUILD | INSTALLER | WHEEL | ALL
+:: where: BUILD - only the 32 bit and 64bit bindings will be built
+:: TEST - only test the binaries (assumes a build was run before)
+:: INSTALLER - only the installers will be built (assumes a build was run before)
+:: WHEEL - only the wheels will be created (assumes a build was run before)
+:: ALL (anything else) - the files will be built, an installer created and the wheels
+SET MODE=%3
+if "%MODE%" == "" set MODE=ALL
+
+if "%MODE%" == "INSTALLER" GOTO INSTALLER
+if "%MODE%" == "WHEEL" GOTO INSTALLER
+if "%MODE%" == "TEST" GOTO TEST
+
+
+:BUILD
+:: 32 bit
+if exist %BUILD_32% rmdir /q /s %BUILD_32%
+call .\buildPython32.bat "%PTYHON_32%" ../install_32 %MAJOR% %MINOR%
+if not exist "%SOURCE_32%\build\lib.win32-%MAJOR%.%MINOR%" mkdir "%SOURCE_32%\build\lib.win32-%MAJOR%.%MINOR%"
+if not exist "%SOURCE_32%\build\lib.win32-%MAJOR%.%MINOR%\libsbml" mkdir "%SOURCE_32%\build\lib.win32-%MAJOR%.%MINOR%\libsbml"
+copy "%SOURCE_32%\libsbml\__init__.py" "%SOURCE_32%\build\lib.win32-%MAJOR%.%MINOR%\libsbml"
+move "%BUILD_32%\_libsbml.pyd" "%SOURCE_32%\build\lib.win32-%MAJOR%.%MINOR%\libsbml"
+
+:: 64 bit
+if exist %BUILD_64% rmdir /q /s %BUILD_64%
+call "%SOURCE_32%\buildPython64.bat" "%PTYHON_64%" ../install_64 %MAJOR% %MINOR%
+if not exist "%SOURCE_32%\build\lib.win-amd64-%MAJOR%.%MINOR%" mkdir "%SOURCE_32%\build\lib.win-amd64-%MAJOR%.%MINOR%"
+if not exist "%SOURCE_32%\build\lib.win-amd64-%MAJOR%.%MINOR%\libsbml" mkdir "%SOURCE_32%\build\lib.win-amd64-%MAJOR%.%MINOR%\libsbml"
+copy /y "%SOURCE_32%\libsbml\__init__.py" "%SOURCE_32%\build\lib.win-amd64-%MAJOR%.%MINOR%\libsbml"
+move "%BUILD_64%\_libsbml.pyd" "%SOURCE_32%\build\lib.win-amd64-%MAJOR%.%MINOR%\libsbml"
+
+:TEST
+SET OLD_PATH=%PATH%
+SET PATH=%PATH%;C:\Python32\Python%MAJOR%%MINOR%\DLLs
+call .\testPython.bat "%PTYHON_32%" %CURRENT_DIR%\build\lib.win32-%MAJOR%.%MINOR% ..\..\..\..\src\bindings\python\
+
+SET PATH=%OLD_PATH%;C:\Python64\Python%MAJOR%%MINOR%\DLLs
+call .\testPython.bat "%PTYHON_64%" %CURRENT_DIR%\build\lib.win-amd64-%MAJOR%.%MINOR% ..\..\..\..\src\bindings\python\
+
+if "%MODE%" == "BUILD" GOTO DONE
+if "%MODE%" == "TEST" GOTO DONE
+
+:INSTALLER
+:: 32 bit
+"%PTYHON_32%" setup32.py bdist_wininst --skip-build --target-version="%MAJOR%.%MINOR%" --bitmap libsbml-python-installer-graphic.bmp
+
+:: 64 bit
+"%PTYHON_64%" setup64.py bdist_wininst --skip-build --target-version="%MAJOR%.%MINOR%" --bitmap libsbml-python-installer-graphic.bmp
+
+goto DONE
+
+:WHEEL
+"%PTYHON_32%" setup.py bdist_wheel --skip-build
+"%PTYHON_64%" setup.py bdist_wheel --skip-build
+goto DONE
+
+:DONE
+
+if "%4"=="EXIT_WHEN_DONE" exit
Added: trunk/libsbml/dev/utilities/build-python/python-src/configure-files.cmake
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/configure-files.cmake (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/configure-files.cmake 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,72 @@
+# cmake build script wrapping built libsbml python bindings into conda binaries
+#
+#
+
+if ("${SRC_DIR}" STREQUAL "" OR "${BUILD_DIR}" STREQUAL "" OR "${NAME}" STREQUAL "" )
+message(FATAL_ERROR
+"
+ Need the following parameters:
+ - SRC_DIR: the libsbml directory (containing VERSION.txt)
+ - BUILD_DIR: the build directory where libsbml was build with SWIG
+ - NAME: the NAME of the package
+
+")
+endif()
+
+set(LIBSBML_VERSION_MAJOR)
+set(LIBSBML_VERSION_MINOR)
+set(LIBSBML_VERSION_PATCH)
+set(LIBSBML_VERSION_RELEASE)
+set(LIBSBML_DOTTED_VERSION)
+
+if(EXISTS "${SRC_DIR}/VERSION.txt")
+
+ file(STRINGS "${SRC_DIR}/VERSION.txt" VersionString NEWLINE_CONSUME)
+ string(STRIP "${VersionString}" VersionString)
+ set(LIBSBML_DOTTED_VERSION ${VersionString})
+ string(REPLACE "." ";" VersionString "${VersionString}" )
+ string(REPLACE "-" ";" VersionString "${VersionString}" )
+ list(LENGTH VersionString versionLength)
+ list(GET VersionString 0 LIBSBML_VERSION_MAJOR )
+ list(GET VersionString 1 LIBSBML_VERSION_MINOR )
+ list(GET VersionString 2 LIBSBML_VERSION_PATCH )
+
+ if(${versionLength} GREATER 3)
+ list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
+ endif()
+
+endif()
+
+# version number needs to be calculated correctly
+MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_VERSION_MINOR} * 100 + ${LIBSBML_VERSION_PATCH}" )
+set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")
+
+# configure files
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in ${CMAKE_CURRENT_SOURCE_DIR}/setup.py)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup32.py.in ${CMAKE_CURRENT_SOURCE_DIR}/setup32.py)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup64.py.in ${CMAKE_CURRENT_SOURCE_DIR}/setup64.py)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setupStable.py.in ${CMAKE_CURRENT_SOURCE_DIR}/setupStable.py)
+
+# copy files
+file(GLOB PYTHON_FILES
+ "${SRC_DIR}/src/bindings/python/*.h"
+ "${SRC_DIR}/src/bindings/python/*.cpp"
+ "${SRC_DIR}/src/bindings/python/*.cxx"
+ "${BUILD_DIR}/src/bindings/python/*.pth"
+ "${BUILD_DIR}/src/bindings/python/*.cpp"
+ "${BUILD_DIR}/src/bindings/python/*.h"
+)
+
+file(COPY ${PYTHON_FILES} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR})
+file(COPY "${BUILD_DIR}/src/bindings/python/libsbml.py" DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/libsbml/__init__.py)
+
+file(GLOB SWIG_FILES
+ "${SRC_DIR}/src/bindings/swig/*.h"
+ "${SRC_DIR}/src/bindings/swig/*.cpp"
+ "${SRC_DIR}/src/bindings/swig/*.cxx"
+ "${BUILD_DIR}/src/bindings/swig/*.cpp"
+ "${BUILD_DIR}/src/bindings/swig/*.h"
+)
+
+file(COPY ${SWIG_FILES} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/../swig)
+
Added: trunk/libsbml/dev/utilities/build-python/python-src/libsbml-python-installer-graphic.bmp
===================================================================
(Binary files differ)
Index: trunk/libsbml/dev/utilities/build-python/python-src/libsbml-python-installer-graphic.bmp
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/libsbml-python-installer-graphic.bmp 2016-10-11 15:37:25 UTC (rev 23622)
+++ trunk/libsbml/dev/utilities/build-python/python-src/libsbml-python-installer-graphic.bmp 2016-10-13 13:42:38 UTC (rev 23623)
Property changes on: trunk/libsbml/dev/utilities/build-python/python-src/libsbml-python-installer-graphic.bmp
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/libsbml/dev/utilities/build-python/python-src/setup.py.in
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/setup.py.in (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/setup.py.in 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,89 @@
+## @file setup.py
+## @brief Python distutils code for libSBML Python module (including dependencies)
+## @author Michael Hucka
+## @author Ben Bornstein
+## @author Ben Kovitz
+## @author Frank Bergmann (fbe...@ca...)
+##
+##<!---------------------------------------------------------------------------
+## This file is part of libSBML. Please visit http://sbml.org for more
+## information about SBML, and the latest version of libSBML.
+##
+## Copyright (C) 2013-2016 jointly by the following organizations:
+## 1. California Institute of Technology, Pasadena, CA, USA
+## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+## 3. University of Heidelberg, Heidelberg, Germany
+##
+## Copyright 2005-2010 California Institute of Technology.
+## Copyright 2002-2005 California Institute of Technology and
+## Japan Science and Technology Corporation.
+##
+## This library is free software; you can redistribute it and/or modify it
+## under the terms of the GNU Lesser General Public License as published by
+## the Free Software Foundation. A copy of the license agreement is provided
+## in the file named "LICENSE.txt" included with this software distribution
+## and also available online as http://sbml.org/software/libsbml/license.html
+##----------------------------------------------------------------------- -->*/
+
+import glob
+import os
+import sys
+import shutil
+import platform
+from distutils.sysconfig import get_config_vars
+
+current_dir = os.path.dirname(os.path.realpath(__file__))
+
+cfiles = []
+definitions = []
+packages = []
+current_os = ''
+inc_dirs = []
+basepath = ''
+libs = []
+lib_dirs = []
+try:
+ from setuptools import setup, Extension, Command
+except ImportError:
+ from distutils.core import setup, Extension
+
+setup(name = "${NAME}",
+ version = "${PACKAGE_VERSION}",
+ description = "LibSBML Python API",
+ long_description = ("LibSBML is a library for reading, writing and "+
+ "manipulating the Systems Biology Markup Language "+
+ "(SBML). It is written in ISO C and C++, supports "+
+ "SBML Levels 1, 2 and 3, and runs on Linux, Microsoft "+
+ "Windows, and Apple MacOS X. For more information "+
+ "about SBML, please see http://sbml.org."),
+ license = "LGPL",
+ author = "SBML Team",
+ author_email = "lib...@ca...",
+ url = "http://sbml.org",
+ packages = ["libsbml"],
+ package_dir = {'libsbml': 'libsbml'},
+ #data_files = [('lib/site-packages', ['libsbml.pth'])],
+ ext_package = "libsbml",
+ ext_modules = [Extension("_libsbml",
+ sources = cfiles,
+ define_macros = definitions
+ + [(current_os, None),
+ ('USE_EXPAT', None),
+ ('USE_ZLIB', None),
+ ('USE_BZ2', None)
+ ]
+ + packages,
+ include_dirs = inc_dirs +
+ [
+ basepath + "/",
+ basepath + "/sbml",
+ basepath + "/sbml/compress",
+ basepath + "/sbml/validator/constraints",
+ basepath + "/sbml/packages/comp/validator",
+ basepath + "/sbml/packages/comp/validator/constraints",
+ "."],
+ libraries = libs,
+ library_dirs = lib_dirs
+ )
+ ]
+)
Added: trunk/libsbml/dev/utilities/build-python/python-src/setup32.py.in
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/setup32.py.in (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/setup32.py.in 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,67 @@
+## @file setup.py
+## @brief Python distutils code for libSBML Python module
+## @author Michael Hucka
+## @author Ben Bornstein
+## @author Ben Kovitz
+## @author Frank Bergmann (fbe...@ca...)
+##
+##<!---------------------------------------------------------------------------
+## This file is part of libSBML. Please visit http://sbml.org for more
+## information about SBML, and the latest version of libSBML.
+##
+## Copyright (C) 2013-2016 jointly by the following organizations:
+## 1. California Institute of Technology, Pasadena, CA, USA
+## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+## 3. University of Heidelberg, Heidelberg, Germany
+##
+## Copyright 2005-2010 California Institute of Technology.
+## Copyright 2002-2005 California Institute of Technology and
+## Japan Science and Technology Corporation.
+##
+## This library is free software; you can redistribute it and/or modify it
+## under the terms of the GNU Lesser General Public License as published by
+## the Free Software Foundation. A copy of the license agreement is provided
+## in the file named "LICENSE.txt" included with this software distribution
+## and also available online as http://sbml.org/software/libsbml/license.html
+##----------------------------------------------------------------------- -->*/
+
+import platform
+
+# figure out whether this is a 64bit or 32 bit installation
+basepath = '../../../win32/'
+
+try:
+ from setuptools import setup, Extension, Command
+except ImportError:
+ from distutils.core import setup, Extension
+
+setup(name = "libsbml",
+ version = "${PACKAGE_VERSION}",
+ description = "LibSBML Python API",
+ long_description = ("LibSBML is a library for reading, writing and "+
+ "manipulating the Systems Biology Markup Language "+
+ "(SBML). It is written in ISO C and C++, supports "+
+ "SBML Levels 1, 2 and 3, and runs on Linux, Microsoft "+
+ "Windows, and Apple MacOS X. For more information "+
+ "about SBML, please see http://sbml.org."),
+ license = "LGPL",
+ author = "SBML Team",
+ author_email = "lib...@ca...",
+ url = "http://sbml.org",
+ packages = ["libsbml"],
+ package_dir = {'libsbml': 'libsbml'},
+ data_files = [#('Lib/site-packages/libsbml', [basepath + 'bin/libsbml.dll']),
+ ('Lib/site-packages', ['libsbml.pth'])],
+ ext_package = "libsbml",
+ ext_modules = [Extension("_libsbml",
+ sources = [ "libsbml_wrap.cpp"],
+ define_macros = [('WIN32', None),
+ ('USE_LAYOUT', None),
+ ('LIBSBML_EXPORTS', None)],
+ include_dirs = [basepath + "include",
+ basepath + "include/sbml", "."],
+ libraries = ["libsbml"],
+ library_dirs = [basepath + "lib"]
+ )
+ ]
+)
Added: trunk/libsbml/dev/utilities/build-python/python-src/setup64.py.in
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/setup64.py.in (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/setup64.py.in 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,67 @@
+## @file setup.py
+## @brief Python distutils code for libSBML Python module
+## @author Michael Hucka
+## @author Ben Bornstein
+## @author Ben Kovitz
+## @author Frank Bergmann (fbe...@ca...)
+##
+##<!---------------------------------------------------------------------------
+## This file is part of libSBML. Please visit http://sbml.org for more
+## information about SBML, and the latest version of libSBML.
+##
+## Copyright (C) 2013-2016 jointly by the following organizations:
+## 1. California Institute of Technology, Pasadena, CA, USA
+## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+## 3. University of Heidelberg, Heidelberg, Germany
+##
+## Copyright 2005-2010 California Institute of Technology.
+## Copyright 2002-2005 California Institute of Technology and
+## Japan Science and Technology Corporation.
+##
+## This library is free software; you can redistribute it and/or modify it
+## under the terms of the GNU Lesser General Public License as published by
+## the Free Software Foundation. A copy of the license agreement is provided
+## in the file named "LICENSE.txt" included with this software distribution
+## and also available online as http://sbml.org/software/libsbml/license.html
+##----------------------------------------------------------------------- -->*/
+
+import platform
+
+# figure out whether this is a 64bit or 32 bit installation
+basepath = '../../../win64/'
+
+try:
+ from setuptools import setup, Extension, Command
+except ImportError:
+ from distutils.core import setup, Extension
+
+setup(name = "libsbml",
+ version = "${PACKAGE_VERSION}",
+ description = "LibSBML Python API",
+ long_description = ("LibSBML is a library for reading, writing and "+
+ "manipulating the Systems Biology Markup Language "+
+ "(SBML). It is written in ISO C and C++, supports "+
+ "SBML Levels 1, 2 and 3, and runs on Linux, Microsoft "+
+ "Windows, and Apple MacOS X. For more information "+
+ "about SBML, please see http://sbml.org."),
+ license = "LGPL",
+ author = "SBML Team",
+ author_email = "lib...@ca...",
+ url = "http://sbml.org",
+ packages = ["libsbml"],
+ package_dir = {'libsbml': 'libsbml'},
+ data_files = [#('Lib/site-packages/libsbml', [basepath + 'bin/libsbml.dll']),
+ ('Lib/site-packages', ['libsbml.pth'])],
+ ext_package = "libsbml",
+ ext_modules = [Extension("_libsbml",
+ sources = [ "libsbml_wrap.cpp"],
+ define_macros = [('WIN32', None),
+ ('USE_LAYOUT', None),
+ ('LIBSBML_EXPORTS', None)],
+ include_dirs = [basepath + "include",
+ basepath + "include/sbml", "."],
+ libraries = ["libsbml"],
+ library_dirs = [basepath + "lib"]
+ )
+ ]
+)
Added: trunk/libsbml/dev/utilities/build-python/python-src/setupStable.py.in
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/setupStable.py.in (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/setupStable.py.in 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,135 @@
+## @file setup.py
+## @brief Python distutils code for libSBML Python module
+## @author Michael Hucka
+## @author Ben Bornstein
+## @author Ben Kovitz
+## @author Frank Bergmann (fbe...@ca...)
+##
+##<!---------------------------------------------------------------------------
+## This file is part of libSBML. Please visit http://sbml.org for more
+## information about SBML, and the latest version of libSBML.
+##
+## Copyright (C) 2013-2016 jointly by the following organizations:
+## 1. California Institute of Technology, Pasadena, CA, USA
+## 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+## 3. University of Heidelberg, Heidelberg, Germany
+##
+## Copyright 2005-2010 California Institute of Technology.
+## Copyright 2002-2005 California Institute of Technology and
+## Japan Science and Technology Corporation.
+##
+## This library is free software; you can redistribute it and/or modify it
+## under the terms of the GNU Lesser General Public License as published by
+## the Free Software Foundation. A copy of the license agreement is provided
+## in the file named "LICENSE.txt" included with this software distribution
+## and also available online as http://sbml.org/software/libsbml/license.html
+##----------------------------------------------------------------------- -->*/
+
+import glob
+import os
+import sys
+import shutil
+import platform
+from distutils.sysconfig import get_config_vars
+
+# remove -Wstrict-prototypes
+(opt,) = get_config_vars('OPT')
+if opt != None:
+ os.environ['OPT'] = " ".join(
+ flag for flag in opt.split() if flag != '-Wstrict-prototypes'
+ )
+
+# we need to switch the __init__.py file based on the python version
+# as python 3 uses a different syntax for metaclasses
+if sys.version_info >= (3,0):
+ # this is python 3.x
+ if (os.path.exists('./libsbml/__init__.py')):
+ os.remove('./libsbml/__init__.py')
+ shutil.copyfile('./script/libsbml3.py', './libsbml/__init__.py')
+else:
+ # this is an older python
+ if (os.path.exists('./libsbml/__init__.py')):
+ os.remove('./libsbml/__init__.py')
+ shutil.copyfile('./script/libsbml2.py', './libsbml/__init__.py')
+
+# figure out the os
+basepath = './base/'
+current_os = 'LINUX'
+lib_dirs = ['/usr/lib']
+inc_dirs = ['/usr/include/libxml2']
+libs = ['xml2', 'bz2', 'z']
+package_name = '"libsbml"'
+definitions = []
+packages = [
+ ('USE_COMP', None),
+ ('USE_GROUPS', None),
+ ('USE_QUAL', None),
+ ('USE_FBC', None),
+ ('USE_LAYOUT', None)
+]
+if platform.system() == 'Darwin':
+ current_os = 'DARWIN'
+elif platform.system() == 'Windows':
+ current_os = 'WIN32'
+ package_name = '\\"libsbml\\"'
+ definitions = [
+ ('LIBSBML_EXPORTS', None),
+ ('LIBLAX_STATIC', None)
+ ]
+ dependency_dir = 'D:\Development\libsbml_dependencies\install_vs9_release_x86'
+ inc_dirs= [ dependency_dir + '/include']
+ lib_dirs= [ dependency_dir + '/lib']
+ libs = ['libxml2', 'libbz2', 'zdll', 'libiconv', 'ws2_32']
+
+cfiles = [ basepath + 'libsbml_wrap.cpp' ]
+for root, dirs, files in os.walk(basepath + 'sbml'):
+ for file in files:
+ if file.endswith('.c') or file.endswith('.cpp'):
+ cfiles.append(os.path.join(root, file))
+
+try:
+ from setuptools import setup, Extension, Command
+except ImportError:
+ from distutils.core import setup, Extension
+
+
+setup(name = "${NAME}",
+ version = "${PACKAGE_VERSION}",
+ description = "LibSBML Python API",
+ long_description = ("LibSBML is a library for reading, writing and "+
+ "manipulating the Systems Biology Markup Language "+
+ "(SBML). It is written in ISO C and C++, supports "+
+ "SBML Levels 1, 2 and 3, and runs on Linux, Microsoft "+
+ "Windows, and Apple MacOS X. For more information "+
+ "about SBML, please see http://sbml.org."),
+ license = "LGPL",
+ author = "SBML Team",
+ author_email = "lib...@ca...",
+ url = "http://sbml.org",
+ packages = ["libsbml"],
+ package_dir = {'libsbml': 'libsbml'},
+ #data_files = [('lib/site-packages', ['libsbml.pth'])],
+ ext_package = "libsbml",
+ ext_modules = [Extension("_libsbml",
+ sources = cfiles,
+ define_macros = definitions
+ + [(current_os, None),
+ ('USE_LIBXML', None),
+ ('USE_ZLIB', None),
+ ('USE_BZ2', None)
+ ]
+ + packages,
+ include_dirs = inc_dirs +
+ [
+ basepath + "/",
+ basepath + "/sbml",
+ basepath + "/sbml/compress",
+ basepath + "/sbml/validator/constraints",
+ basepath + "/sbml/packages/comp/validator",
+ basepath + "/sbml/packages/comp/validator/constraints",
+ "."],
+ libraries = libs,
+ library_dirs = lib_dirs
+ )
+ ]
+)
Added: trunk/libsbml/dev/utilities/build-python/python-src/testPython.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/python-src/testPython.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/python-src/testPython.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,51 @@
+@echo off
+Setlocal EnableDelayedExpansion
+REM This file tests the python build
+REM it needs three arguments
+REM
+REM - python interpreter
+REM - directory of python build
+REM - test directory
+REM
+REM 2011/02/26 Frank Bergmann
+REM
+
+REM ensure visual studio is in the path
+if "%VS_VERSION%"=="" SET VS_VERSION=14
+if "%INCLUDE%"=="" call "%ProgramFiles(x86)%\Microsoft Visual Studio %VS_VERSION%.0\VC\vcvarsall.bat" x86
+
+
+REM set up directory variables
+SET BASE_DIR=%~dp0
+SET PYTHON_INTERP=%1
+SET PYTHON_BUILD=%2
+SET TEST_DIR=%3
+
+if "%PYTHON_INTERP%" == "" goto MISSING_ARGS
+if "%PYTHON_BUILD%" == "" goto MISSING_ARGS
+if "%TEST_DIR%" == "" goto MISSING_ARGS
+
+cd /d "%TEST_DIR%"
+
+echo.
+echo Testing Python bindings from: %PYTHON_BUILD%
+echo with python: %PYTHON_INTERP%
+echo and tests : %TEST_DIR%
+echo.
+SET PYTHONPATH=%PYTHON_BUILD%;%PYTHON_BUILD%\libsbml;%TEST_DIR%;%TEST_DIR%\test;.;test;test\sbml;test\annotation;test\math;test\xml;
+"%PYTHON_INTERP%" test.py
+
+goto ALL_DONE
+
+:MISSING_ARGS
+echo.
+echo Please call this script with three arguments:
+echo.
+echo - python interpreter
+echo - libSBML python build
+echo - libSBML python test directory
+echo.
+goto ALL_DONE
+
+:ALL_DONE
+cd /d %BASE_DIR%
Added: trunk/libsbml/dev/utilities/build-python/remove_files.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/remove_files.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/remove_files.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,65 @@
+@echo off
+:: removes all files that are no longer needed
+
+Setlocal EnableDelayedExpansion
+SET THIS_DIR=%~dp0
+
+SET MODE=%1
+:: supported Modes are
+:: ALL - delete all files created
+:: BUILD - delete build dirs
+:: INSTALL - delete install dirs
+:: TEMP - delete python temp files and dirs
+if "%MODE%"=="" SET MODE=ALL
+
+
+pushd %THIS_DIR%
+
+if "%MODE%"=="BUILD" goto BUILD
+if "%MODE%"=="INSTALL" goto INSTALL
+
+
+if exist swig rd /s /q swig
+del /q python-src\*.cpp
+del /q python-src\*.h
+del /q python-src\*.py
+del /q python-src\*.bak
+del /q python-src\*.pth
+
+if exist python-src\b32_25 rd /s /q python-src\b32_25
+if exist python-src\b32_26 rd /s /q python-src\b32_26
+if exist python-src\b32_27 rd /s /q python-src\b32_27
+if exist python-src\b32_31 rd /s /q python-src\b32_31
+if exist python-src\b32_32 rd /s /q python-src\b32_32
+if exist python-src\b32_33 rd /s /q python-src\b32_33
+if exist python-src\b32_34 rd /s /q python-src\b32_34
+if exist python-src\b32_35 rd /s /q python-src\b32_35
+if exist python-src\b64_25 rd /s /q python-src\b64_25
+if exist python-src\b64_26 rd /s /q python-src\b64_26
+if exist python-src\b64_27 rd /s /q python-src\b64_27
+if exist python-src\b64_31 rd /s /q python-src\b64_31
+if exist python-src\b64_32 rd /s /q python-src\b64_32
+if exist python-src\b64_33 rd /s /q python-src\b64_33
+if exist python-src\b64_34 rd /s /q python-src\b64_34
+if exist python-src\b64_35 rd /s /q python-src\b64_35
+if exist python-src\build rd /s /q python-src\build
+if exist python-src\libsbml rd /s /q python-src\libsbml
+if exist python-src\libsbml.egg-info rd /s /q python-src\libsbml.egg-info
+if exist python-src\dist rd /s /q python-src\dist
+if "%MODE%"=="TEMP" goto DONE
+
+:BUILD
+if exist build_32 rd /s /q build_32
+if exist build_64 rd /s /q build_64
+if "%MODE%"=="BUILD" goto DONE
+
+:INSTALL
+if exist install_32 rd /s /q install_32
+if exist install_64 rd /s /q install_64
+if "%MODE%"=="INSTALL" goto DONE
+
+
+:DONE
+if exist out rd /s /q out
+
+popd
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/source/bld.bat
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/bld.bat (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/bld.bat 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,8 @@
+"%PYTHON%" setup.py install
+if errorlevel 1 exit 1
+
+:: Add more build steps here, if they are necessary.
+
+:: See
+:: http://docs.continuum.io/conda/build.html
+:: for a list of environment variables that are set during the build process.
Added: trunk/libsbml/dev/utilities/build-python/source/build.sh
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/build.sh (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/build.sh 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+$PYTHON setup.py install
+
+# Add more build steps here, if they are necessary.
+
+# See
+# http://docs.continuum.io/conda/build.html
+# for a list of environment variables that are set during the build process.
Added: trunk/libsbml/dev/utilities/build-python/source/create-conda-archives.cmake
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/create-conda-archives.cmake (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/create-conda-archives.cmake 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,121 @@
+# cmake build script wrapping built libsbml python bindings into conda binaries
+#
+#
+
+if ("${SRC_DIR}" STREQUAL "" OR "${OUT_DIR}" STREQUAL "" OR "${BUILD_DIR}" STREQUAL "" OR "${NAME}" STREQUAL "" )
+message(FATAL_ERROR
+"
+ Need the following parameters:
+ - SRC_DIR: the libsbml directory (containing VERSION.txt)
+ - BUILD_DIR: the build directory containing libsbml as created
+ by setup tools for example 'lib.win32-2.7'
+ - OUT_DIR: the directory where to place the resulting bz2 file
+ - NAME: the NAME of the package
+
+")
+endif()
+
+set(LIBSBML_VERSION_MAJOR)
+set(LIBSBML_VERSION_MINOR)
+set(LIBSBML_VERSION_PATCH)
+set(LIBSBML_VERSION_RELEASE)
+set(LIBSBML_DOTTED_VERSION)
+
+if(EXISTS "${SRC_DIR}/VERSION.txt")
+
+ file(STRINGS "${SRC_DIR}/VERSION.txt" VersionString NEWLINE_CONSUME)
+ string(STRIP "${VersionString}" VersionString)
+ set(LIBSBML_DOTTED_VERSION ${VersionString})
+ string(REPLACE "." ";" VersionString "${VersionString}" )
+ string(REPLACE "-" ";" VersionString "${VersionString}" )
+ list(LENGTH VersionString versionLength)
+ list(GET VersionString 0 LIBSBML_VERSION_MAJOR )
+ list(GET VersionString 1 LIBSBML_VERSION_MINOR )
+ list(GET VersionString 2 LIBSBML_VERSION_PATCH )
+
+ if(${versionLength} GREATER 3)
+ list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
+ endif()
+
+endif()
+
+# version number needs to be calculated correctly
+MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_VERSION_MINOR} * 100 + ${LIBSBML_VERSION_PATCH}" )
+set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")
+
+# figure out python version and arch from the BUILD_DIR
+string(FIND ${BUILD_DIR} "lib." index)
+math(EXPR index "${index} + 4")
+string(SUBSTRING ${BUILD_DIR} ${index} -1 ARCH_VERSION)
+
+string(FIND ${ARCH_VERSION} "-" index REVERSE)
+string(SUBSTRING ${ARCH_VERSION} 0 ${index} BUILD_ARCH)
+math(EXPR index "${index} + 1")
+string(SUBSTRING ${ARCH_VERSION} ${index} -1 PYTHON_VERSION)
+string(REPLACE "." "" SHORT_VERSION "${PYTHON_VERSION}" )
+string(REPLACE "-" "_" OTHER_NAME "${NAME}")
+set(TARGET_NAME "${OTHER_NAME}-${PACKAGE_VERSION}-py${PYTHON_VERSION}")
+set(TARGET_DIR "${NAME}-${PACKAGE_VERSION}-py${SHORT_VERSION}_0")
+
+
+message(STATUS "creating archive for version: ${PACKAGE_VERSION}")
+message(STATUS " from : ${ARCH_VERSION}")
+message(STATUS " from : ${BUILD_ARCH}")
+message(STATUS " from : ${PYTHON_VERSION}")
+message(STATUS " from : ${SHORT_VERSION}")
+message(STATUS " cur : ${CMAKE_CURRENT_SOURCE_DIR}")
+message(STATUS " target : ${TARGET_NAME}")
+
+SET(SUBDIR "win-64")
+SET(ARCH "x86_64")
+if ("${BUILD_ARCH}" STREQUAL "win32")
+SET(SUBDIR "win-32")
+SET(ARCH "x86")
+endif()
+
+# create output dir
+if( NOT EXISTS "${OUT_DIR}")
+ execute_process( COMMAND ${CMAKE_COMMAND}
+ -E make_directory ${OUT_DIR})
+endif()
+
+# create temp dir
+execute_process( COMMAND ${CMAKE_COMMAND} -E make_directory ${TARGET_DIR})
+execute_process( COMMAND ${CMAKE_COMMAND} -E make_directory ${TARGET_DIR}/Lib)
+execute_process( COMMAND ${CMAKE_COMMAND} -E make_directory ${TARGET_DIR}/Lib/site-packages)
+execute_process( COMMAND ${CMAKE_COMMAND} -E make_directory ${TARGET_DIR}/Lib/site-packages/libsbml)
+execute_process( COMMAND ${CMAKE_COMMAND} -E make_directory ${TARGET_DIR}/info)
+execute_process( COMMAND ${CMAKE_COMMAND} -E make_directory ${TARGET_DIR}/info/recipe)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/egg-info
+ ${TARGET_DIR}/Lib/site-packages/${TARGET_NAME}.egg-info)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/bld.bat
+ ${TARGET_DIR}/info/recipe/bld.bat)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/build.sh
+ ${TARGET_DIR}/info/recipe/build.sh)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/meta.yaml
+ ${TARGET_DIR}/info/recipe/meta.yaml)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/files
+ ${TARGET_DIR}/info/files)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/index.json
+ ${TARGET_DIR}/info/index.json)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/source/recipe.json
+ ${TARGET_DIR}/info/recipe.json)
+
+file(GLOB BINARIES "${BUILD_DIR}/libsbml/*")
+file(COPY ${BINARIES} DESTINATION ${TARGET_DIR}/Lib/site-packages/libsbml)
+
+# create bz2
+execute_process(COMMAND ${CMAKE_COMMAND}
+ -E tar cjf ../${TARGET_DIR}.tar.bz2 info Lib
+ WORKING_DIRECTORY ${TARGET_DIR})
+
+# cleanup
+execute_process(COMMAND ${CMAKE_COMMAND}
+ -E remove_directory ${TARGET_DIR})
Added: trunk/libsbml/dev/utilities/build-python/source/egg-info
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/egg-info (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/egg-info 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: ${NAME}
+Version: ${PACKAGE_VERSION}
+Summary: LibSBML Python API
+Home-page: http://sbml.org
+Author: SBML Team
+Author-email: lib...@ca...
+License: LGPL
+Description: LibSBML is a library for reading, writing and manipulating the Systems Biology Markup Language (SBML). It is written in ISO C and C++, supports SBML Levels 1, 2 and 3, and runs on Linux, Microsoft Windows, and Apple MacOS X. For more information about SBML, please see http://sbml.org.
+Platform: UNKNOWN
Added: trunk/libsbml/dev/utilities/build-python/source/files
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/files (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/files 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,4 @@
+Lib/site-packages/libsbml/__init__.py
+Lib/site-packages/libsbml/__init__.pyc
+Lib/site-packages/libsbml/_libsbml.pyd
+Lib/site-packages/${TARGET_NAME}.egg-info
Added: trunk/libsbml/dev/utilities/build-python/source/index.json
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/index.json (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/index.json 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,13 @@
+{
+ "arch": "${ARCH}",
+ "build": "py${SHORT_VERSION}_0",
+ "build_number": 0,
+ "depends": [
+ "python ${PYTHON_VERSION}*"
+ ],
+ "license": "LGPL",
+ "name": "${NAME}",
+ "platform": "win",
+ "subdir": "${SUBDIR}",
+ "version": "${PACKAGE_VERSION}"
+}
\ No newline at end of file
Added: trunk/libsbml/dev/utilities/build-python/source/meta.yaml
===================================================================
--- trunk/libsbml/dev/utilities/build-python/source/meta.yaml (rev 0)
+++ trunk/libsbml/dev/utilities/build-python/source/meta.yaml 2016-10-13 13:42:38 UTC (rev 23623)
@@ -0,0 +1,60 @@
+package:
+ name: ${NAME}
+ version: "${PACKAGE_VERSION}"
+
+source:
+ fn: ${NAME}-${PACKAGE_VERSION}.tar.gz
+ url: https://pypi.python.org/packages/source/p/${NAME}/${NAME}-${PACKAGE_VERSION}.tar.gz
+
+# patches:
+ # List any patch files here
+ # - fix.patch
+
+# build:
+ # noarch_python: True
+ # preserve_egg_dir: True
+ # entry_points:
+ # Put any entry points (scripts to be generated automatically) here. The
+ # syn...
[truncated message content] |
|
From: <fbe...@us...> - 2016-10-11 15:37:27
|
Revision: 23622
http://sourceforge.net/p/sbml/code/23622
Author: fbergmann
Date: 2016-10-11 15:37:25 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
- disable warning for legacy math
Modified Paths:
--------------
trunk/libsbml/src/sbml/math-legacy/FormulaParser.c
Modified: trunk/libsbml/src/sbml/math-legacy/FormulaParser.c
===================================================================
--- trunk/libsbml/src/sbml/math-legacy/FormulaParser.c 2016-10-11 13:46:24 UTC (rev 23621)
+++ trunk/libsbml/src/sbml/math-legacy/FormulaParser.c 2016-10-11 15:37:25 UTC (rev 23622)
@@ -35,6 +35,10 @@
#include <sbml/math/FormulaTokenizer.h>
#include <sbml/math/FormulaParser.h>
+#ifdef _MSC_VER
+#pragma warning( disable: 4311)
+#pragma warning( disable: 4312)
+#endif
/** @cond doxygenLibsbmlInternal */
|
|
From: <fbe...@us...> - 2016-10-11 13:46:32
|
Revision: 23621
http://sourceforge.net/p/sbml/code/23621
Author: fbergmann
Date: 2016-10-11 13:46:24 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
- silence 64-bit warnings
Modified Paths:
--------------
trunk/libsbml/src/sbml/math/FormulaParser.c
trunk/libsbml/src/sbml/packages/comp/extension/test/TestRunner.c
trunk/libsbml/src/sbml/packages/comp/sbml/test/TestRunner.c
trunk/libsbml/src/sbml/packages/comp/util/test/TestRunner.c
trunk/libsbml/src/sbml/packages/comp/validator/test/TestCompConsistencyValidator.cpp
trunk/libsbml/src/sbml/packages/fbc/extension/test/TestRunner.c
trunk/libsbml/src/sbml/packages/fbc/validator/test/TestFbcConsistencyValidator.cpp
trunk/libsbml/src/sbml/packages/groups/validator/test/TestGroupsConsistencyValidator.cpp
trunk/libsbml/src/sbml/packages/layout/validator/test/TestLayoutConsistencyValidator.cpp
trunk/libsbml/src/sbml/packages/qual/extension/test/TestRunner.c
trunk/libsbml/src/sbml/packages/qual/sbml/test/TestRunner.c
trunk/libsbml/src/sbml/packages/qual/validator/test/TestQualConsistencyValidator.cpp
trunk/libsbml/src/sbml/validator/constraints/RateOfCycles.cpp
trunk/libsbml/src/sbml/validator/test/TestConsistencyValidator.cpp
Modified: trunk/libsbml/src/sbml/math/FormulaParser.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/math/FormulaParser.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -36,6 +36,10 @@
#include <sbml/math/FormulaParser.h>
#include <sbml/math/ASTTypes.h>
+#ifdef _MSC_VER
+#pragma warning( disable: 4311)
+#pragma warning( disable: 4312)
+#endif
/** @cond doxygenLibsbmlInternal */
/**
Modified: trunk/libsbml/src/sbml/packages/comp/extension/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/extension/test/TestRunner.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/comp/extension/test/TestRunner.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -70,7 +70,7 @@
setTestDataDirectory (void)
{
char *srcdir = getenv("srcdir");
- int length = (srcdir == NULL) ? 0 : strlen(srcdir);
+ int length = (srcdir == NULL) ? 0 : (int)strlen(srcdir);
/**
Modified: trunk/libsbml/src/sbml/packages/comp/sbml/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/sbml/test/TestRunner.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/comp/sbml/test/TestRunner.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -77,7 +77,7 @@
setTestDataDirectory (void)
{
char *srcdir = getenv("srcdir");
- int length = (srcdir == NULL) ? 0 : strlen(srcdir);
+ int length = (srcdir == NULL) ? 0 : (int)strlen(srcdir);
/**
Modified: trunk/libsbml/src/sbml/packages/comp/util/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/util/test/TestRunner.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/comp/util/test/TestRunner.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -144,7 +144,7 @@
setTestDataDirectory (void)
{
char *srcdir = getenv("srcdir");
- int length = (srcdir == NULL) ? 0 : strlen(srcdir);
+ int length = (srcdir == NULL) ? 0 : (int)strlen(srcdir);
/**
Modified: trunk/libsbml/src/sbml/packages/comp/validator/test/TestCompConsistencyValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/comp/validator/test/TestCompConsistencyValidator.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/comp/validator/test/TestCompConsistencyValidator.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -116,8 +116,8 @@
cout << msg << "." << endl;
set<TestFile> files = TestFile::getFilesIn(directory, begin, end, library);
- unsigned int passes = count_if(files.begin(), files.end(), tester);
- unsigned int failures = files.size() - passes;
+ unsigned int passes = (unsigned int)count_if(files.begin(), files.end(), tester);
+ unsigned int failures = (unsigned int)files.size() - passes;
double percent = (static_cast<double>(passes) / files.size()) * 100;
cout << static_cast<int>(percent) << "%: Checks: " << files.size();
Modified: trunk/libsbml/src/sbml/packages/fbc/extension/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/packages/fbc/extension/test/TestRunner.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/fbc/extension/test/TestRunner.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -47,7 +47,7 @@
setTestDataDirectory (void)
{
char *srcdir = getenv("srcdir");
- int length = (srcdir == NULL) ? 0 : strlen(srcdir);
+ int length = (srcdir == NULL) ? 0 : (int)strlen(srcdir);
/**
Modified: trunk/libsbml/src/sbml/packages/fbc/validator/test/TestFbcConsistencyValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/fbc/validator/test/TestFbcConsistencyValidator.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/fbc/validator/test/TestFbcConsistencyValidator.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -98,8 +98,8 @@
cout << msg << "." << endl;
set<TestFile> files = TestFile::getFilesIn(directory, begin, end, library);
- unsigned int passes = count_if(files.begin(), files.end(), tester);
- unsigned int failures = files.size() - passes;
+ unsigned int passes = (unsigned int)count_if(files.begin(), files.end(), tester);
+ unsigned int failures = (unsigned int)files.size() - passes;
double percent = (static_cast<double>(passes) / files.size()) * 100;
cout << static_cast<int>(percent) << "%: Checks: " << files.size();
Modified: trunk/libsbml/src/sbml/packages/groups/validator/test/TestGroupsConsistencyValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/groups/validator/test/TestGroupsConsistencyValidator.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/groups/validator/test/TestGroupsConsistencyValidator.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -98,8 +98,8 @@
cout << msg << "." << endl;
set<TestFile> files = TestFile::getFilesIn(directory, begin, end, library);
- unsigned int passes = count_if(files.begin(), files.end(), tester);
- unsigned int failures = files.size() - passes;
+ unsigned int passes = (unsigned int)count_if(files.begin(), files.end(), tester);
+ unsigned int failures = (unsigned int)files.size() - passes;
double percent = (static_cast<double>(passes) / files.size()) * 100;
cout << static_cast<int>(percent) << "%: Checks: " << files.size();
Modified: trunk/libsbml/src/sbml/packages/layout/validator/test/TestLayoutConsistencyValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/layout/validator/test/TestLayoutConsistencyValidator.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/layout/validator/test/TestLayoutConsistencyValidator.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -105,8 +105,8 @@
cout << msg << "." << endl;
set<TestFile> files = TestFile::getFilesIn(directory, begin, end, library);
- unsigned int passes = count_if(files.begin(), files.end(), tester);
- unsigned int failures = files.size() - passes;
+ unsigned int passes = (unsigned int)count_if(files.begin(), files.end(), tester);
+ unsigned int failures = (unsigned int)files.size() - passes;
double percent = (static_cast<double>(passes) / files.size()) * 100;
cout << static_cast<int>(percent) << "%: Checks: " << files.size();
Modified: trunk/libsbml/src/sbml/packages/qual/extension/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/packages/qual/extension/test/TestRunner.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/qual/extension/test/TestRunner.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -64,7 +64,7 @@
setTestDataDirectory (void)
{
char *srcdir = getenv("srcdir");
- int length = (srcdir == NULL) ? 0 : strlen(srcdir);
+ int length = (srcdir == NULL) ? 0 : (int)strlen(srcdir);
/**
Modified: trunk/libsbml/src/sbml/packages/qual/sbml/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/packages/qual/sbml/test/TestRunner.c 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/qual/sbml/test/TestRunner.c 2016-10-11 13:46:24 UTC (rev 23621)
@@ -72,7 +72,7 @@
setTestDataDirectory (void)
{
char *srcdir = getenv("srcdir");
- int length = (srcdir == NULL) ? 0 : strlen(srcdir);
+ int length = (srcdir == NULL) ? 0 : (int)strlen(srcdir);
/**
Modified: trunk/libsbml/src/sbml/packages/qual/validator/test/TestQualConsistencyValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/packages/qual/validator/test/TestQualConsistencyValidator.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/packages/qual/validator/test/TestQualConsistencyValidator.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -118,8 +118,8 @@
cout << msg << "." << endl;
set<TestFile> files = TestFile::getFilesIn(directory, begin, end, library);
- unsigned int passes = count_if(files.begin(), files.end(), tester);
- unsigned int failures = files.size() - passes;
+ unsigned int passes = (unsigned int)count_if(files.begin(), files.end(), tester);
+ unsigned int failures = (unsigned int)files.size() - passes;
double percent = (static_cast<double>(passes) / files.size()) * 100;
cout << static_cast<int>(percent) << "%: Checks: " << files.size();
Modified: trunk/libsbml/src/sbml/validator/constraints/RateOfCycles.cpp
===================================================================
--- trunk/libsbml/src/sbml/validator/constraints/RateOfCycles.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/validator/constraints/RateOfCycles.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -385,7 +385,7 @@
List* variables = ar->getMath()->getListOfNodes( ASTNode_isFunction );
for (size_t ns = 0; ns < variables->getSize(); ns++)
{
- ASTNode* node = static_cast<ASTNode*>( variables->get(ns) );
+ ASTNode* node = static_cast<ASTNode*>( variables->get((unsigned int)ns) );
if (node->getType() != AST_FUNCTION_RATE_OF)
{
continue;
@@ -405,7 +405,7 @@
List* variables = ia->getMath()->getListOfNodes( ASTNode_isFunction );
for (size_t ns = 0; ns < variables->getSize(); ns++)
{
- ASTNode* node = static_cast<ASTNode*>( variables->get(ns) );
+ ASTNode* node = static_cast<ASTNode*>( variables->get((unsigned int)ns) );
if (node->getType() != AST_FUNCTION_RATE_OF)
{
continue;
Modified: trunk/libsbml/src/sbml/validator/test/TestConsistencyValidator.cpp
===================================================================
--- trunk/libsbml/src/sbml/validator/test/TestConsistencyValidator.cpp 2016-10-11 12:51:10 UTC (rev 23620)
+++ trunk/libsbml/src/sbml/validator/test/TestConsistencyValidator.cpp 2016-10-11 13:46:24 UTC (rev 23621)
@@ -399,8 +399,8 @@
cout << msg << "." << endl;
set<TestFile> files = TestFile::getFilesIn(directory, begin, end, library);
- unsigned int passes = count_if(files.begin(), files.end(), tester);
- unsigned int failures = files.size() - passes;
+ unsigned int passes = (unsigned int)count_if(files.begin(), files.end(), tester);
+ unsigned int failures = (unsigned int)files.size() - passes;
double percent = (static_cast<double>(passes) / files.size()) * 100;
cout << static_cast<int>(percent) << "%: Checks: " << files.size();
|
|
From: <fbe...@us...> - 2016-10-11 12:51:13
|
Revision: 23620
http://sourceforge.net/p/sbml/code/23620
Author: fbergmann
Date: 2016-10-11 12:51:10 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
- issue #132073903: add setCharacters function to XMLToken
Modified Paths:
--------------
trunk/libsbml/src/sbml/xml/XMLToken.cpp
trunk/libsbml/src/sbml/xml/XMLToken.h
trunk/libsbml/src/sbml/xml/test/TestXMLToken.c
Modified: trunk/libsbml/src/sbml/xml/XMLToken.cpp
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLToken.cpp 2016-10-11 12:29:26 UTC (rev 23619)
+++ trunk/libsbml/src/sbml/xml/XMLToken.cpp 2016-10-11 12:51:10 UTC (rev 23620)
@@ -236,12 +236,26 @@
* @return the characters of this XML text.
*/
const string&
-XMLToken::getCharacters () const
+XMLToken::getCharacters() const
{
return mChars;
}
+int
+XMLToken::setCharacters(const std::string& chars)
+{
+ if (chars.empty())
+ {
+ return LIBSBML_OPERATION_FAILED;
+ }
+ else
+ {
+ mChars = chars;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
/*
* @return the column at which this XMLToken occurred.
*/
@@ -1277,7 +1291,7 @@
LIBLAX_EXTERN
XMLToken_t *
XMLToken_createWithTripleAttr (const XMLTriple_t *triple,
- const XMLAttributes_t *attr)
+ const XMLAttributes_t *attr)
{
if (triple == NULL || attr == NULL) return NULL;
return new(nothrow) XMLToken(*triple, *attr);
@@ -1287,8 +1301,8 @@
LIBLAX_EXTERN
XMLToken_t *
XMLToken_createWithTripleAttrNS (const XMLTriple_t *triple,
- const XMLAttributes_t *attr,
- const XMLNamespaces_t *ns)
+ const XMLAttributes_t *attr,
+ const XMLNamespaces_t *ns)
{
if (triple == NULL || attr == NULL || ns == NULL) return NULL;
return new(nothrow) XMLToken(*triple, *attr, *ns);
@@ -1334,7 +1348,22 @@
}
}
+LIBLAX_EXTERN
+int
+XMLToken_setCharacters(XMLToken_t *token, const char *text)
+{
+ if (token != NULL && text != NULL)
+ {
+ return token->setCharacters(text);
+ }
+ else
+ {
+ return LIBSBML_OPERATION_FAILED;
+ }
+}
+
+
LIBLAX_EXTERN
const char *
XMLToken_getCharacters (const XMLToken_t *token)
@@ -1393,9 +1422,9 @@
LIBLAX_EXTERN
int
XMLToken_addAttrWithNS ( XMLToken_t *token, const char* name
- , const char* value
- , const char* namespaceURI
- , const char* prefix )
+ , const char* value
+ , const char* namespaceURI
+ , const char* prefix )
{
if (token == NULL) return LIBSBML_INVALID_OBJECT;
return token->addAttr(name, value, namespaceURI, prefix);
Modified: trunk/libsbml/src/sbml/xml/XMLToken.h
===================================================================
--- trunk/libsbml/src/sbml/xml/XMLToken.h 2016-10-11 12:29:26 UTC (rev 23619)
+++ trunk/libsbml/src/sbml/xml/XMLToken.h 2016-10-11 12:51:10 UTC (rev 23620)
@@ -949,6 +949,25 @@
/**
+ * Sets the characters for this XMLToken
+ *
+ * This method only makes sense for XMLToken objects that contains text.
+ * If this method is called on a token that represents an XML start or end
+ * tag, it will return the code @sbmlconstant{LIBSBML_OPERATION_FAILED,
+ * OperationReturnValues_t}.
+ *
+ * @param chars string, characters to append to the text of this token.
+ *
+ * @copydetails doc_returns_success_code
+ * @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+ * @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+ *
+ * @see isText()
+ * @see isElement()
+ */
+ int setCharacters(const std::string& chars);
+
+ /**
* Appends characters to the text content of token.
*
* This method only makes sense for XMLToken objects that contains text.
@@ -1214,7 +1233,7 @@
LIBLAX_EXTERN
XMLToken_t *
XMLToken_createWithTripleAttr (const XMLTriple_t *triple,
- const XMLAttributes_t *attr);
+ const XMLAttributes_t *attr);
/**
@@ -1232,8 +1251,8 @@
LIBLAX_EXTERN
XMLToken_t *
XMLToken_createWithTripleAttrNS (const XMLTriple_t *triple,
- const XMLAttributes_t *attr,
- const XMLNamespaces_t *ns);
+ const XMLAttributes_t *attr,
+ const XMLNamespaces_t *ns);
/**
@@ -1294,6 +1313,22 @@
/**
+* Sets characters of this XML text content.
+*
+* @param token XMLToken_t structure whose characters to set.
+* @param text string, characters to set.
+*
+* @copydetails doc_returns_success_code
+* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
+* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
+**
+* @memberof XMLToken_t
+*/
+LIBLAX_EXTERN
+int
+XMLToken_setCharacters(XMLToken_t *token, const char *text);
+
+/**
* Returns the text of this element.
*
* @param token XMLToken_t structure to be queried.
@@ -1419,9 +1454,9 @@
LIBLAX_EXTERN
int
XMLToken_addAttrWithNS ( XMLToken_t *token, const char* name
- , const char* value
- , const char* namespaceURI
- , const char* prefix );
+ , const char* value
+ , const char* namespaceURI
+ , const char* prefix );
/**
Modified: trunk/libsbml/src/sbml/xml/test/TestXMLToken.c
===================================================================
--- trunk/libsbml/src/sbml/xml/test/TestXMLToken.c 2016-10-11 12:29:26 UTC (rev 23619)
+++ trunk/libsbml/src/sbml/xml/test/TestXMLToken.c 2016-10-11 12:51:10 UTC (rev 23620)
@@ -114,6 +114,10 @@
fail_unless(XMLToken_isEOF(token) == 0);
fail_unless(strcmp(XMLToken_getCharacters(token), "This is text") == 0);
+ fail_unless(XMLToken_append(token, " and more text") == 0);
+ fail_unless(strcmp(XMLToken_getCharacters(token), "This is text and more text") == 0);
+ fail_unless(XMLToken_setCharacters(token, "This is text too.") == 0);
+ fail_unless(strcmp(XMLToken_getCharacters(token), "This is text too.") == 0);
XMLToken_free(token);
}
|
|
From: <fbe...@us...> - 2016-10-11 12:29:28
|
Revision: 23619
http://sourceforge.net/p/sbml/code/23619
Author: fbergmann
Date: 2016-10-11 12:29:26 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
- remove more warnings
Modified Paths:
--------------
trunk/libsbml/src/sbml/conversion/test/TestLevelVersionConverter.cpp
trunk/libsbml/src/sbml/math-legacy/ASTNode.cpp
trunk/libsbml/src/sbml/test/TestWriteL3V2SBML.cpp
Modified: trunk/libsbml/src/sbml/conversion/test/TestLevelVersionConverter.cpp
===================================================================
--- trunk/libsbml/src/sbml/conversion/test/TestLevelVersionConverter.cpp 2016-10-11 10:26:27 UTC (rev 23618)
+++ trunk/libsbml/src/sbml/conversion/test/TestLevelVersionConverter.cpp 2016-10-11 12:29:26 UTC (rev 23619)
@@ -54,16 +54,16 @@
extern char *TestDataDirectory;
-static bool
-equalDouble (double a, double b)
-{
- bool result = fabs(a-b) < 1e-6;// sqrt(util_epsilon());
- if (!result)
- cerr << "not equal: " << a << " vs " << b
- << " difference: " << fabs(a-b)
- << endl;
- return result;
-}
+//static bool
+//equalDouble (double a, double b)
+//{
+// bool result = fabs(a-b) < 1e-6;// sqrt(util_epsilon());
+// if (!result)
+// cerr << "not equal: " << a << " vs " << b
+// << " difference: " << fabs(a-b)
+// << endl;
+// return result;
+//}
Modified: trunk/libsbml/src/sbml/math-legacy/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math-legacy/ASTNode.cpp 2016-10-11 10:26:27 UTC (rev 23618)
+++ trunk/libsbml/src/sbml/math-legacy/ASTNode.cpp 2016-10-11 12:29:26 UTC (rev 23619)
@@ -80,7 +80,7 @@
* ASTNodeType predicate
*/
#define ASTNodeType_isLogical(t) \
- ((t >= AST_LOGICAL_AND) && (t <= AST_LOGICAL_XOR) || t == AST_LOGICAL_IMPLIES)
+ (((t >= AST_LOGICAL_AND) && (t <= AST_LOGICAL_XOR)) || t == AST_LOGICAL_IMPLIES)
/**
* ASTNodeType predicate
Modified: trunk/libsbml/src/sbml/test/TestWriteL3V2SBML.cpp
===================================================================
--- trunk/libsbml/src/sbml/test/TestWriteL3V2SBML.cpp 2016-10-11 10:26:27 UTC (rev 23618)
+++ trunk/libsbml/src/sbml/test/TestWriteL3V2SBML.cpp 2016-10-11 12:29:26 UTC (rev 23619)
@@ -148,7 +148,7 @@
Model * m = D->createModel("");
XMLNode * ann = XMLNode::convertStringToXMLNode("test");
- (SBase*)(m->getListOfCompartments())->setAnnotation(ann);
+ ((SBase*)(m->getListOfCompartments()))->setAnnotation(ann);
delete ann;
string S = writeSBMLToStdString(D);
@@ -169,7 +169,7 @@
);
Model * m = D->createModel("");
- InitialAssignment *ia = m->createInitialAssignment();
+ /*InitialAssignment *ia =*/ m->createInitialAssignment();
string S = writeSBMLToStdString(D);
|