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From: <mh...@us...> - 2010-09-30 21:42:00
|
Revision: 12081
http://sbml.svn.sourceforge.net/sbml/?rev=12081&view=rev
Author: mhucka
Date: 2010-09-30 21:41:49 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
Bunches of doc adjustments for Python.
Modified Paths:
--------------
trunk/libsbml/docs/src/doxygen-config-python.txt.in
trunk/libsbml/src/sbml/Compartment.cpp
trunk/libsbml/src/sbml/Compartment.h
trunk/libsbml/src/sbml/CompartmentType.h
trunk/libsbml/src/sbml/Constraint.h
trunk/libsbml/src/sbml/Delay.h
trunk/libsbml/src/sbml/Event.h
trunk/libsbml/src/sbml/EventAssignment.h
trunk/libsbml/src/sbml/FunctionDefinition.h
trunk/libsbml/src/sbml/InitialAssignment.h
trunk/libsbml/src/sbml/KineticLaw.h
trunk/libsbml/src/sbml/ListOf.h
trunk/libsbml/src/sbml/LocalParameter.h
trunk/libsbml/src/sbml/Model.h
trunk/libsbml/src/sbml/Parameter.h
trunk/libsbml/src/sbml/Priority.h
trunk/libsbml/src/sbml/Reaction.h
trunk/libsbml/src/sbml/Rule.h
trunk/libsbml/src/sbml/SBMLDocument.h
trunk/libsbml/src/sbml/SBMLError.h
trunk/libsbml/src/sbml/SBMLErrorLog.h
trunk/libsbml/src/sbml/SBMLReader.h
trunk/libsbml/src/sbml/SBMLWriter.h
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/Species.h
trunk/libsbml/src/sbml/SpeciesReference.h
trunk/libsbml/src/sbml/SpeciesType.h
trunk/libsbml/src/sbml/StoichiometryMath.h
trunk/libsbml/src/sbml/Trigger.h
trunk/libsbml/src/sbml/Unit.h
trunk/libsbml/src/sbml/UnitDefinition.h
Modified: trunk/libsbml/docs/src/doxygen-config-python.txt.in
===================================================================
--- trunk/libsbml/docs/src/doxygen-config-python.txt.in 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/docs/src/doxygen-config-python.txt.in 2010-09-30 21:41:49 UTC (rev 12081)
@@ -61,7 +61,7 @@
# The ENABLED_SECTIONS tag can be used to enable conditional
# documentation sections, marked by \if sectionname ... \endif.
-ENABLED_SECTIONS = notcpp doxygen-python-only clike
+ENABLED_SECTIONS = notcpp doxygen-python-only python
# Because of how we construct the Python documentation, we don't want
# the first sentence to be assumed to be the brief description.
Modified: trunk/libsbml/src/sbml/Compartment.cpp
===================================================================
--- trunk/libsbml/src/sbml/Compartment.cpp 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Compartment.cpp 2010-09-30 21:41:49 UTC (rev 12081)
@@ -1676,24 +1676,7 @@
/**
- * Creates a new Compartment_t structure using the given SBML @p level
- * and @p version values.
- *
- * @param level an unsigned int, the SBML Level to assign to this
- * Compartment
- *
- * @param version an unsigned int, the SBML Version to assign to this
- * Compartment
- *
- * @return a pointer to the newly created Compartment_t structure.
- *
- * @note Once a Compartment has been added to an SBMLDocument, the @p
- * level and @p version for the document @em override those used to create
- * the Compartment. Despite this, the ability to supply the values at
- * creation time is an important aid to creating valid SBML. Knowledge of
- * the intended SBML Level and Version determine whether it is valid to
- * assign a particular value to an attribute, or whether it is valid to add
- * an object to an existing SBMLDocument.
+ * @copydoc Compartment::Compartment(unsigned int level, unsigned int version);
*/
LIBSBML_EXTERN
Compartment_t *
Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Compartment.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -371,7 +371,7 @@
* Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the
* method
- * @if clike setId()@endif@if java Compartment::setId(String id)@endif.
+ * @if clike setId()@endif@if python setId()@endif@if java Compartment::setId(String id)@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
@@ -516,14 +516,14 @@
* Get the size of this Compartment.
*
* This method is identical to
- * @if clike getVolume()@endif@if java Compartment::getVolume()@endif.
+ * @if clike getVolume()@endif@if python getVolume()@endif@if java Compartment::getVolume()@endif.
* In SBML Level 1, compartments are always three-dimensional
* constructs and only have volumes, whereas in SBML Level 2,
* compartments may be other than three-dimensional and therefore the
* "volume" attribute is named "size" in Level 2. LibSBML provides
* both
- * @if clike getSize()@endif@if java Compartment::getSize()@endif and
- * @if clike getVolume()@endif@if java Compartment::getVolume()@endif for
+ * @if clike getSize()@endif@if python getSize()@endif@if java Compartment::getSize()@endif and
+ * @if clike getVolume()@endif@if python getVolume()@endif@if java Compartment::getVolume()@endif for
* easier compatibility between SBML Levels.
*
* @return the value of the "size" attribute ("volume" in Level 1) of
@@ -539,14 +539,14 @@
* Get the volume of this Compartment.
*
* This method is identical to
- * @if clike getSize()@endif@if java Compartment::getSize()@endif. In
+ * @if clike getSize()@endif@if python getSize()@endif@if java Compartment::getSize()@endif. In
* SBML Level 1, compartments are always three-dimensional
* constructs and only have volumes, whereas in SBML Level 2,
* compartments may be other than three-dimensional and therefore the
* "volume" attribute is named "size" in Level 2. LibSBML provides
* both
- * @if clike getSize()@endif@if java Compartment::getSize()@endif and
- * @if clike getVolume()@endif@if java Compartment::getVolume()@endif
+ * @if clike getSize()@endif@if python getSize()@endif@if java Compartment::getSize()@endif and
+ * @if clike getVolume()@endif@if python getVolume()@endif@if java Compartment::getVolume()@endif
* for easier compatibility between SBML Levels.
*
* @return the value of the "volume" attribute ("size" in Level 2) of
@@ -575,7 +575,7 @@
* @note @htmlinclude unassigned-units-are-not-a-default.html
*
* @see isSetUnits()
- * @see @if clike setUnits()@endif@if java Compartment::setUnits(String sid)@endif
+ * @see @if clike setUnits()@endif@if python setUnits()@endif@if java Compartment::setUnits(String sid)@endif
* @see getSize()
*/
const std::string& getUnits () const;
@@ -641,11 +641,11 @@
* Compartment's "size" attribute has been set.
*
* This method is similar but not identical to
- * @if clike isSetVolume()@endif@if java Compartment::isSetVolume()@endif. The latter
+ * @if clike isSetVolume()@endif@if python isSetVolume()@endif@if java Compartment::isSetVolume()@endif. The latter
* should be used in the context of SBML Level 1 models instead of
- * @if clike isSetSize()@endif@if java Compartment::isSetSize()@endif
+ * @if clike isSetSize()@endif@if python isSetSize()@endif@if java Compartment::isSetSize()@endif
* because
- * @if clike isSetVolume()@endif@if java Compartment::isSetVolume()@endif
+ * @if clike isSetVolume()@endif@if python isSetVolume()@endif@if java Compartment::isSetVolume()@endif
* performs extra processing to take
* into account the difference in default values between SBML Levels 1
* and 2.
@@ -664,7 +664,7 @@
* "volume" attribute has been set.
*
* This method is similar but not identical to
- * @if clike isSetSize()@endif@if java Compartment::isSetSize()@endif. The latter
+ * @if clike isSetSize()@endif@if python isSetSize()@endif@if java Compartment::isSetSize()@endif. The latter
* should not be used in the context of SBML Level 1 models because this
* method performs extra processing to take into account
* the difference in default values between SBML Levels 1 and 2.
@@ -673,7 +673,7 @@
* above) of this Compartment has been set, @c false otherwise.
*
* @see isSetSize()
- * @see @if clike setVolume()@endif@if java Compartment::setVolume(double value)@endif
+ * @see @if clike setVolume()@endif@if python setVolume()@endif@if java Compartment::setVolume(double value)@endif
*
* @note The attribute "volume" only exists by that name in SBML
* Level 1. In Level 2 and above, the equivalent attribute is
@@ -825,7 +825,7 @@
* Compartment.
*
* This method is identical to
- * @if clike setVolume()@endif@if java Compartment::setVolume(double value)@endif
+ * @if clike setVolume()@endif@if python setVolume()@endif@if java Compartment::setVolume(double value)@endif
* and is provided for compatibility between
* SBML Level 1 and Level 2.
*
@@ -849,7 +849,7 @@
* Compartment.
*
* This method is identical to
- * @if clike setVolume()@endif@if java Compartment::setVolume(double value)@endif
+ * @if clike setVolume()@endif@if python setVolume()@endif@if java Compartment::setVolume(double value)@endif
* and is provided for compatibility between SBML Level 1 and
* Level 2.
*
@@ -1040,7 +1040,7 @@
*
* Note that unit declarations for Compartment objects are specified in
* terms of the @em identifier of a unit (e.g., using
- * @if clike setUnits()@endif@if java Compartment::setUnits(String sid)@endif), but
+ * @if clike setUnits()@endif@if python setUnits()@endif@if java Compartment::setUnits(String sid)@endif), but
* @em this method returns a UnitDefinition object, not a unit
* identifier. It does this by constructing an appropriate
* UnitDefinition. For SBML Level 2 models, it will do this even
@@ -1114,8 +1114,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or
@@ -1241,8 +1246,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -1264,8 +1274,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/CompartmentType.h
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/CompartmentType.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -166,7 +166,7 @@
* (identifier) attribute of a CompartmentType is required to have a value.
* Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the
- * method @if clike setId() @endif@if java setId(String id) @endif.
+ * method @if clike setId() @endif@if python setId() @endif@if java setId(String id) @endif.
*
* @param sbmlns an SBMLNamespaces object.
*
@@ -317,8 +317,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -426,8 +431,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -449,8 +459,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/Constraint.h
===================================================================
--- trunk/libsbml/src/sbml/Constraint.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Constraint.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -356,8 +356,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -485,8 +490,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -508,8 +518,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/Delay.h
===================================================================
--- trunk/libsbml/src/sbml/Delay.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Delay.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -467,8 +467,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
Modified: trunk/libsbml/src/sbml/Event.h
===================================================================
--- trunk/libsbml/src/sbml/Event.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Event.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -889,8 +889,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -1045,8 +1050,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -1068,8 +1078,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/EventAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/EventAssignment.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/EventAssignment.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -492,8 +492,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -645,8 +650,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -668,8 +678,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/FunctionDefinition.h
===================================================================
--- trunk/libsbml/src/sbml/FunctionDefinition.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/FunctionDefinition.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -431,8 +431,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -570,8 +575,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -593,8 +603,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/InitialAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/InitialAssignment.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -394,7 +394,7 @@
* The units are calculated based on the mathematical expression in the
* InitialAssignment and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -407,13 +407,13 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
* the units of <em>X</em>. <strong>It is important that callers also
* invoke the method</strong>
- * @if clike containsUndeclaredUnits()@endif@if java InitialAssignment::containsUndeclaredUnits()@endif
+ * @if clike containsUndeclaredUnits()@endif@if python containsUndeclaredUnits()@endif@if java InitialAssignment::containsUndeclaredUnits()@endif
* <strong>to determine whether this situation holds</strong>. Callers
* may wish to take suitable actions in those scenarios.
*
@@ -433,7 +433,7 @@
* The units are calculated based on the mathematical expression in the
* InitialAssignment and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -446,13 +446,13 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
* the units of <em>X</em>. <strong>It is important that callers also
* invoke the method</strong>
- * @if clike containsUndeclaredUnits()@endif@if java InitialAssignment::containsUndeclaredUnits()@endif
+ * @if clike containsUndeclaredUnits()@endif@if python containsUndeclaredUnits()@endif@if java InitialAssignment::containsUndeclaredUnits()@endif
* <strong>to determine whether this situation holds</strong>. Callers
* may wish to take suitable actions in those scenarios.
*
@@ -475,7 +475,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
@@ -494,7 +494,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
@@ -513,8 +513,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -667,8 +672,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -690,8 +700,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/KineticLaw.h
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/KineticLaw.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -200,7 +200,7 @@
* it as as a text string.
*
* This is fundamentally equivalent to
- * @if clike getMath()@endif@if java KineticLaw::getMath()@endif.
+ * @if clike getMath()@endif@if python getMath()@endif@if java KineticLaw::getMath()@endif.
* This variant is provided principally for compatibility compatibility
* with SBML Level 1.
*
@@ -226,7 +226,7 @@
* it as as an AST.
*
* This is fundamentally equivalent to
- * @if clike getFormula()@endif@if java KineticLaw::getFormula()@endif.
+ * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::getFormula()@endif.
* The latter is provided principally for compatibility compatibility
* with SBML Level 1, which represented mathematical formulas in
* text-string form.
@@ -273,10 +273,10 @@
* KineticLaw's "formula" attribute has been set
*
* This is functionally identical to the method
- * @if clike isSetMath()@endif@if java KineticLaw::isSetMath()@endif. It is
+ * @if clike isSetMath()@endif@if python isSetMath()@endif@if java KineticLaw::isSetMath()@endif. It is
* provided in order to mirror the parallel between
- * @if clike getFormula()@endif@if java KineticLaw::getFormula()@endif and
- * @if clike getMath()@endif@if java KineticLaw::getMath()@endif.
+ * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::getFormula()@endif and
+ * @if clike getMath()@endif@if python getMath()@endif@if java KineticLaw::getMath()@endif.
*
* @return @c true if the formula (meaning the @c math subelement) of
* this KineticLaw has been set, @c false otherwise.
@@ -299,10 +299,10 @@
* Kinetic's "math" subelement has been set
*
* This is identical to the method
- * @if clike isSetFormula()@endif@if java KineticLaw::isSetFormula()@endif.
+ * @if clike isSetFormula()@endif@if python isSetFormula()@endif@if java KineticLaw::isSetFormula()@endif.
* It is provided in order to mirror the parallel between
- * @if clike getFormula()@endif@if java KineticLaw::getFormula()@endif and
- * @if clike getMath()@endif@if java KineticLaw::getMath()@endif.
+ * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::getFormula()@endif and
+ * @if clike getMath()@endif@if python getMath()@endif@if java KineticLaw::getMath()@endif.
*
* @return @c true if the formula (meaning the @c math subelement) of
* this KineticLaw has been set, @c false otherwise.
@@ -376,7 +376,7 @@
* of the given ASTNode.
*
* This is fundamentally identical to
- * @if clike getFormula()@endif@if java KineticLaw::setFormula(String formula)@endif.
+ * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::setFormula(String formula)@endif.
* The latter is provided principally for compatibility compatibility with
* SBML Level 1, which represented mathematical formulas in text-string
* form.
@@ -498,7 +498,7 @@
* instance in the KineticLaw</em>. In addition, the caller should make
* sure to free the original object if it is no longer being used, or
* else a memory leak will result. Please see
- * @if clike createParameter()@endif@if java KineticLaw::createParameter()@endif
+ * @if clike createParameter()@endif@if python createParameter()@endif@if java KineticLaw::createParameter()@endif
* for a method that does not lead to these issues.
*
* @see createParameter()
@@ -529,7 +529,7 @@
* instance in the KineticLaw</em>. In addition, the caller should make
* sure to free the original object if it is no longer being used, or
* else a memory leak will result. Please see
- * @if clike createParameter()@endif@if java KineticLaw::createParameter()@endif
+ * @if clike createParameter()@endif@if python createParameter()@endif@if java KineticLaw::createParameter()@endif
* for a method that does not lead to these issues.
*
* @see createLocalParameter()
@@ -703,7 +703,7 @@
* The units are calculated based on the mathematical expression in the
* KineticLaw and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -716,7 +716,7 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
@@ -742,7 +742,7 @@
* The units are calculated based on the mathematical expression in the
* KineticLaw and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -755,7 +755,7 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
@@ -784,7 +784,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
@@ -803,7 +803,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
@@ -902,8 +902,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link
Modified: trunk/libsbml/src/sbml/ListOf.h
===================================================================
--- trunk/libsbml/src/sbml/ListOf.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/ListOf.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -266,8 +266,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -288,8 +293,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/LocalParameter.h
===================================================================
--- trunk/libsbml/src/sbml/LocalParameter.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/LocalParameter.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -194,7 +194,7 @@
* Thus, callers are cautioned to assign a value after calling this
* constructor if no identifier is provided as an argument. Setting the
* identifier can be accomplished using the method
- * @if clike setId()@endif@if java setId(String id)@endif.
+ * @if clike setId()@endif@if python setId()@endif@if java setId(String id)@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
@@ -344,8 +344,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link
@@ -449,8 +454,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link
@@ -473,8 +483,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Model.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -87,6 +87,7 @@
*
* LibSBML provides two main mechanisms for creating objects: class
* constructors (e.g., @if clike @link Species::Species() Species()
+ * @endlink @endif@if python @link Species::Species() Species()
* @endlink @endif@if java <a
* href="org/sbml/libsbml/Species.html">Species()</a> @endif), and
* <code>create<span class="placeholder"><em>Object</em></span>()</code>
@@ -156,6 +157,7 @@
@endverbatim
*
* The key point of the example above is that, because the @if clike
+ * Model::addSpecies() @endif@if python
* Model::addSpecies() @endif@if java Model::addSpecies(Species s) @endif
* call makes a copy of the object handed to it, care is needed both when
* attempting to make changes to the object, and when the original object
@@ -2739,8 +2741,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
Modified: trunk/libsbml/src/sbml/Parameter.h
===================================================================
--- trunk/libsbml/src/sbml/Parameter.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Parameter.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -222,7 +222,7 @@
* Thus, callers are cautioned to assign a value after calling this
* constructor if no identifier is provided as an argument. Setting the
* identifier can be accomplished using the method
- * @if clike setId()@endif@if java setId(String id)@endif.
+ * @if clike setId()@endif@if python setId()@endif@if java setId(String id)@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
@@ -631,8 +631,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or
@@ -751,8 +756,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link
@@ -775,8 +785,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for the objects contained in this ListOf
Modified: trunk/libsbml/src/sbml/Priority.h
===================================================================
--- trunk/libsbml/src/sbml/Priority.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Priority.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -214,8 +214,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
* is stored in an enumeration; in the Java language interface for
- * libSBML, the type codes are defined as static integer constants in
+ * libSBML, the type codes are defined as static integer constants in the
* interface class {@link libsbmlConstants}. The names of the type codes
+ * all begin with the characters @c SBML_. @endif@if python LibSBML attaches an
+ * identifying code to every kind of SBML object. These are known as
+ * <em>SBML type codes</em>. In the Python language interface for
+ * libSBML, the type codes are defined as static integer constants in the
+ * interface class {@link libsbml}. The names of the type codes
* all begin with the characters @c SBML_. @endif
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
Modified: trunk/libsbml/src/sbml/Reaction.h
===================================================================
--- trunk/libsbml/src/sbml/Reaction.h 2010-09-30 14:04:54 UTC (rev 12080)
+++ trunk/libsbml/src/sbml/Reaction.h 2010-09-30 21:41:49 UTC (rev 12081)
@@ -1169,8 +1169,13 @@
* identifying code to every kind of SBML object. These are known as
* <em>SBML type codes</em>. In other languages, the set of type codes
...
[truncated message content] |
|
From: <sar...@us...> - 2010-09-30 14:05:06
|
Revision: 12080
http://sbml.svn.sourceforge.net/sbml/?rev=12080&view=rev
Author: sarahkeating
Date: 2010-09-30 14:04:54 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
version number exists here too
Modified Paths:
--------------
trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfo.cs
trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfoTR.cs
Modified: trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfo.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfo.cs 2010-09-30 13:05:46 UTC (rev 12079)
+++ trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfo.cs 2010-09-30 14:04:54 UTC (rev 12080)
@@ -15,5 +15,5 @@
[assembly: Guid("14def7f4-5e60-4925-b81e-f297ad1c3265")]
-[assembly: AssemblyVersion("4.1.0.0")]
-[assembly: AssemblyFileVersion("4.1.0.0")]
+[assembly: AssemblyVersion("4.2.0.0")]
+[assembly: AssemblyFileVersion("4.2.0.0")]
Modified: trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfoTR.cs
===================================================================
--- trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfoTR.cs 2010-09-30 13:05:46 UTC (rev 12079)
+++ trunk/libsbml/src/bindings/csharp/Properties/AssemblyInfoTR.cs 2010-09-30 14:04:54 UTC (rev 12080)
@@ -32,5 +32,5 @@
// You can specify all the values or you can default the Build and Revision Numbers
// by using the '*' as shown below:
// [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.0.0.0")]
-[assembly: AssemblyFileVersion("1.0.0.0")]
+[assembly: AssemblyVersion("4.2.0.0")]
+[assembly: AssemblyFileVersion("4.2.0.0")]
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-30 13:05:53
|
Revision: 12079
http://sbml.svn.sourceforge.net/sbml/?rev=12079&view=rev
Author: sarahkeating
Date: 2010-09-30 13:05:46 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
initial import of test cases for new event stuff
Note these are fairly basic
Added Paths:
-----------
trunk/test-suite/cases/semantic/00928/
trunk/test-suite/cases/semantic/00928/00928-model.m
trunk/test-suite/cases/semantic/00928/00928-results.csv
trunk/test-suite/cases/semantic/00928/00928-sbml-l3v1.xml
trunk/test-suite/cases/semantic/00928/00928-settings.txt
trunk/test-suite/cases/semantic/00929/
trunk/test-suite/cases/semantic/00929/00929-model.m
trunk/test-suite/cases/semantic/00929/00929-results.csv
trunk/test-suite/cases/semantic/00929/00929-sbml-l3v1.xml
trunk/test-suite/cases/semantic/00929/00929-settings.txt
Added: trunk/test-suite/cases/semantic/00928/00928-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00928/00928-model.m (rev 0)
+++ trunk/test-suite/cases/semantic/00928/00928-model.m 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,37 @@
+(*
+
+category: Test
+synopsis: Single forward reaction with two species in one compartment and an event
+componentTags: Compartment, Species, Reaction, Parameter, Event
+testTags: Amount, InitialValue
+testType: TimeCourse
+levels: 3.1
+generatedBy: Analytic
+
+The model contains one compartment called "compartment". There are two
+species called S1 and S2 and one parameter called k1. The model contains
+one reaction:
+
+[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
+| S1 -> S2 | $k1 * S1 * compartment$ |]
+
+The model contains one event that is triggered at t=0.
+
+The initial conditions are as follows:
+
+[{width:30em,margin-left:5em}| |*Value* |*Units* |
+|Initial amount of S1 |$1.5 \x 10^-4$ |mole |
+|Initial amount of S2 |$0$ |mole |
+|Value of parameter k1 |$1$ |second^-1^ |
+|Volume of compartment "compartment" |$1$ |litre |]
+
+The species' initial quantities are given in terms of substance units to
+make it easier to use the model in a discrete stochastic simulator, but (as
+per usual SBML principles) their symbols represent their values in
+concentration units where they appear in expressions.
+
+Note: The test data for this model was generated from an analytical
+solution of the system of equations.
+
+*)
+
Added: trunk/test-suite/cases/semantic/00928/00928-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00928/00928-results.csv (rev 0)
+++ trunk/test-suite/cases/semantic/00928/00928-results.csv 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,52 @@
+time,S1,S2
+0,0.00015,0
+0.1,0.0001357256127053939,1.427438729460607e-005
+0.2,0.0001228096129616973,2.719038703830272e-005
+0.3,0.0001111227331022577,3.887726689774233e-005
+0.4,0.0001005480069053459,4.945199309465411e-005
+0.5,9.097959895689501e-005,5.902040104310499e-005
+0.6,8.232174541410396e-005,6.767825458589604e-005
+0.7,7.448779556871142e-005,7.551220443128858e-005
+0.8,6.739934461758323e-005,8.260065538241677e-005
+0.9,6.098544896108986e-005,8.901455103891014e-005
+1,5.518191617571635e-005,9.481808382428365e-005
+1.1,4.993066255471193e-005,0.0001000693374452881
+1.2,4.517913178683031e-005,0.0001048208682131697
+1.3,4.087976895510189e-005,0.0001091202310448981
+1.4,3.698954459124097e-005,0.000113010455408759
+1.5,3.346952402226447e-005,0.0001165304759777355
+1.6,3.028447769919831e-005,0.0001197155223008017
+1.7,2.740252860791019e-005,0.0001225974713920898
+1.8,2.479483323323798e-005,0.000125205166766762
+1.9,2.243529288339526e-005,0.0001275647071166047
+2,2.03002924854919e-005,0.0001296997075145081
+2.1,1.836846423794729e-005,0.0001316315357620527
+2.2,1.662047375435008e-005,0.0001333795262456499
+2.3,1.503882655842056e-005,0.0001349611734415794
+2.4,1.360769299341187e-005,0.0001363923070065881
+2.5,1.231274979358482e-005,0.0001376872502064152
+2.6,1.114103673215008e-005,0.0001388589632678499
+2.7,1.008082691096246e-005,0.0001399191730890375
+2.8,9.121509393782692e-006,0.0001408784906062173
+2.9,8.253483008461082e-006,0.0001417465169915389
+3,7.468060255179591e-006,0.0001425319397448204
+3.1,6.757380359033671e-006,0.0001432426196409663
+3.2,6.114330596754931e-006,0.0001438856694032451
+3.3,5.532475110186e-006,0.000144467524889814
+3.4,5.00599049404891e-006,0.0001449940095059511
+3.5,4.529607513347775e-006,0.0001454703924866522
+3.6,4.098558367093884e-006,0.0001459014416329061
+3.7,3.708528970550908e-006,0.0001462914710294491
+3.8,3.355615778424839e-006,0.0001466443842215752
+3.9,3.036286716870657e-006,0.0001469637132831294
+4,2.747345833310127e-006,0.0001472526541666899
+4.1,2.485901310264186e-006,0.0001475140986897358
+4.2,2.249336523071655e-006,0.0001477506634769283
+4.3,2.03528385183014e-006,0.0001479647161481699
+4.4,1.841600985460266e-006,0.0001481583990145397
+4.5,1.666349480736346e-006,0.0001483336505192637
+4.6,1.507775361695036e-006,0.000148492224638305
+4.7,1.364291565254372e-006,0.0001486357084347456
+4.8,1.234462057353003e-006,0.000148765537942647
+4.9,1.116987460638651e-006,0.0001488830125393614
+5,1.01069204986282e-006,0.0001489893079501372
Added: trunk/test-suite/cases/semantic/00928/00928-sbml-l3v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00928/00928-sbml-l3v1.xml (rev 0)
+++ trunk/test-suite/cases/semantic/00928/00928-sbml-l3v1.xml 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model metaid="_case00928" id="case00928" name="case00928" timeUnits="second">
+ <listOfCompartments>
+ <compartment id="compartment" size="1" constant="true" spatialDimensions="3" units="litre"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S1" name="S1" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="k1" name="k1" value="1" constant="true"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> compartment </ci>
+ <ci> k1 </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <listOfEvents>
+ <event useValuesFromTriggerTime="true">
+ <trigger initialValue="false" persistent="true">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <geq/>
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+ <cn type="integer"> 0 </cn>
+ </apply>
+ </math>
+ </trigger>
+ <listOfEventAssignments>
+ <eventAssignment variable="S1">
+ <math xmlns="http://www.w3.org/1998/Math/MathML"
+ xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+ <apply>
+ <divide/>
+ <cn sbml:units="mole"> 0.00015 </cn>
+ <ci> compartment </ci>
+ </apply>
+ </math>
+ </eventAssignment>
+ </listOfEventAssignments>
+ </event>
+ </listOfEvents>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/semantic/00928/00928-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00928/00928-settings.txt (rev 0)
+++ trunk/test-suite/cases/semantic/00928/00928-settings.txt 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,9 @@
+start: 0
+duration: 5
+steps: 50
+variables: S1, S2
+absolute: 1.000000e-007
+relative: 0.0001
+amount: S1, S2
+concentration:
+
Added: trunk/test-suite/cases/semantic/00929/00929-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00929/00929-model.m (rev 0)
+++ trunk/test-suite/cases/semantic/00929/00929-model.m 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,37 @@
+(*
+
+category: Test
+synopsis: Single forward reaction with two species in one compartment and an event
+componentTags: Compartment, Species, Reaction, Parameter, Event
+testTags: Amount, InitialValue
+testType: TimeCourse
+levels: 3.1
+generatedBy: Analytic
+
+The model contains one compartment called "compartment". There are two
+species called S1 and S2 and one parameter called k1. The model contains
+one reaction:
+
+[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
+| S1 -> S2 | $k1 * S1 * compartment$ |]
+
+The model contains one event that is triggered at t=0.
+
+The initial conditions are as follows:
+
+[{width:30em,margin-left:5em}| |*Value* |*Units* |
+|Initial amount of S1 |$1.5 \x 10^-4$ |mole |
+|Initial amount of S2 |$0$ |mole |
+|Value of parameter k1 |$1$ |second^-1^ |
+|Volume of compartment "compartment" |$1$ |litre |]
+
+The species' initial quantities are given in terms of substance units to
+make it easier to use the model in a discrete stochastic simulator, but (as
+per usual SBML principles) their symbols represent their values in
+concentration units where they appear in expressions.
+
+Note: The test data for this model was generated from an analytical
+solution of the system of equations.
+
+*)
+
Added: trunk/test-suite/cases/semantic/00929/00929-results.csv
===================================================================
--- trunk/test-suite/cases/semantic/00929/00929-results.csv (rev 0)
+++ trunk/test-suite/cases/semantic/00929/00929-results.csv 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,52 @@
+time,S1,S2
+0,0.00015,0
+0.1,0.0001357256127053939,1.427438729460607e-005
+0.2,0.0001228096129616973,2.719038703830272e-005
+0.3,0.0001111227331022577,3.887726689774233e-005
+0.4,0.0001005480069053459,4.945199309465411e-005
+0.5,9.097959895689501e-005,5.902040104310499e-005
+0.6,8.232174541410396e-005,6.767825458589604e-005
+0.7,7.448779556871142e-005,7.551220443128858e-005
+0.8,6.739934461758323e-005,8.260065538241677e-005
+0.9,6.098544896108986e-005,8.901455103891014e-005
+1,5.518191617571635e-005,9.481808382428365e-005
+1.1,4.993066255471193e-005,0.0001000693374452881
+1.2,4.517913178683031e-005,0.0001048208682131697
+1.3,4.087976895510189e-005,0.0001091202310448981
+1.4,3.698954459124097e-005,0.000113010455408759
+1.5,3.346952402226447e-005,0.0001165304759777355
+1.6,3.028447769919831e-005,0.0001197155223008017
+1.7,2.740252860791019e-005,0.0001225974713920898
+1.8,2.479483323323798e-005,0.000125205166766762
+1.9,2.243529288339526e-005,0.0001275647071166047
+2,2.03002924854919e-005,0.0001296997075145081
+2.1,1.836846423794729e-005,0.0001316315357620527
+2.2,1.662047375435008e-005,0.0001333795262456499
+2.3,1.503882655842056e-005,0.0001349611734415794
+2.4,1.360769299341187e-005,0.0001363923070065881
+2.5,1.231274979358482e-005,0.0001376872502064152
+2.6,1.114103673215008e-005,0.0001388589632678499
+2.7,1.008082691096246e-005,0.0001399191730890375
+2.8,9.121509393782692e-006,0.0001408784906062173
+2.9,8.253483008461082e-006,0.0001417465169915389
+3,7.468060255179591e-006,0.0001425319397448204
+3.1,6.757380359033671e-006,0.0001432426196409663
+3.2,6.114330596754931e-006,0.0001438856694032451
+3.3,5.532475110186e-006,0.000144467524889814
+3.4,5.00599049404891e-006,0.0001449940095059511
+3.5,4.529607513347775e-006,0.0001454703924866522
+3.6,4.098558367093884e-006,0.0001459014416329061
+3.7,3.708528970550908e-006,0.0001462914710294491
+3.8,3.355615778424839e-006,0.0001466443842215752
+3.9,3.036286716870657e-006,0.0001469637132831294
+4,2.747345833310127e-006,0.0001472526541666899
+4.1,2.485901310264186e-006,0.0001475140986897358
+4.2,2.249336523071655e-006,0.0001477506634769283
+4.3,2.03528385183014e-006,0.0001479647161481699
+4.4,1.841600985460266e-006,0.0001481583990145397
+4.5,1.666349480736346e-006,0.0001483336505192637
+4.6,1.507775361695036e-006,0.000148492224638305
+4.7,1.364291565254372e-006,0.0001486357084347456
+4.8,1.234462057353003e-006,0.000148765537942647
+4.9,1.116987460638651e-006,0.0001488830125393614
+5,1.01069204986282e-006,0.0001489893079501372
Added: trunk/test-suite/cases/semantic/00929/00929-sbml-l3v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00929/00929-sbml-l3v1.xml (rev 0)
+++ trunk/test-suite/cases/semantic/00929/00929-sbml-l3v1.xml 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model metaid="_case00929" id="case00929" name="case00929" timeUnits="second">
+ <listOfCompartments>
+ <compartment id="compartment" size="1" constant="true" spatialDimensions="3" units="litre"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="k1" name="k1" value="1" constant="true"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="reaction1" name="reaction1" reversible="false" fast="false">
+ <listOfReactants>
+ <speciesReference species="S1" stoichiometry="1" constant="true"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="S2" stoichiometry="1" constant="true"/>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> compartment </ci>
+ <ci> k1 </ci>
+ <ci> S1 </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <listOfEvents>
+ <event useValuesFromTriggerTime="true">
+ <trigger initialValue="true" persistent="true">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <geq/>
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+ <cn type="integer"> 0 </cn>
+ </apply>
+ </math>
+ </trigger>
+ <listOfEventAssignments>
+ <eventAssignment variable="S1">
+ <math xmlns="http://www.w3.org/1998/Math/MathML"
+ xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
+ <apply>
+ <divide/>
+ <cn sbml:units="mole"> 1 </cn>
+ <ci> compartment </ci>
+ </apply>
+ </math>
+ </eventAssignment>
+ </listOfEventAssignments>
+ </event>
+ </listOfEvents>
+ </model>
+</sbml>
Added: trunk/test-suite/cases/semantic/00929/00929-settings.txt
===================================================================
--- trunk/test-suite/cases/semantic/00929/00929-settings.txt (rev 0)
+++ trunk/test-suite/cases/semantic/00929/00929-settings.txt 2010-09-30 13:05:46 UTC (rev 12079)
@@ -0,0 +1,9 @@
+start: 0
+duration: 5
+steps: 50
+variables: S1, S2
+absolute: 1.000000e-007
+relative: 0.0001
+amount: S1, S2
+concentration:
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-30 11:31:44
|
Revision: 12078
http://sbml.svn.sourceforge.net/sbml/?rev=12078&view=rev
Author: sarahkeating
Date: 2010-09-30 11:31:37 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
fixed unit checking bug reported by Rainer
Modified Paths:
--------------
branches/libsbml-5/NEWS.txt
branches/libsbml-5/src/units/UnitFormulaFormatter.cpp
Modified: branches/libsbml-5/NEWS.txt
===================================================================
--- branches/libsbml-5/NEWS.txt 2010-09-30 11:23:03 UTC (rev 12077)
+++ branches/libsbml-5/NEWS.txt 2010-09-30 11:31:37 UTC (rev 12078)
@@ -22,13 +22,16 @@
a new build system to facilitate the inclusion/exclusion of
packages.
-* Changes to dependencies on 3rd-party libraries:
-
- - The language bindings now require SWIG 2.0.0 or later.
-
+* Changes to dependencies on 3rd-party libraries:
+ - The language bindings now require SWIG 2.0.0 or later.
+* Known issues:
+ - The C API is not yet implemented.
+
+
+
======================================================================
Version 5.0.0-a0 (released 2010-01-18)
======================================================================
Modified: branches/libsbml-5/src/units/UnitFormulaFormatter.cpp
===================================================================
--- branches/libsbml-5/src/units/UnitFormulaFormatter.cpp 2010-09-30 11:23:03 UTC (rev 12077)
+++ branches/libsbml-5/src/units/UnitFormulaFormatter.cpp 2010-09-30 11:31:37 UTC (rev 12078)
@@ -1020,7 +1020,7 @@
{
for (n = 0; n < tempUd->getNumUnits(); n++)
{
- unit = const_cast<Unit*>(tempUd->getUnit(n));
+ unit = (const_cast<Unit*>(tempUd->getUnit(n)))->clone();
exponent = unit->getExponent();
unit->setExponent(exponent * -1);
ud->addUnit(unit);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-30 11:23:10
|
Revision: 12077
http://sbml.svn.sourceforge.net/sbml/?rev=12077&view=rev
Author: sarahkeating
Date: 2010-09-30 11:23:03 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
updated news
Modified Paths:
--------------
trunk/libsbml/NEWS.txt
Modified: trunk/libsbml/NEWS.txt
===================================================================
--- trunk/libsbml/NEWS.txt 2010-09-30 11:11:41 UTC (rev 12076)
+++ trunk/libsbml/NEWS.txt 2010-09-30 11:23:03 UTC (rev 12077)
@@ -53,6 +53,10 @@
in some places but not all. This is fixed. Thanks to Camille
Laibe for reporting this.
+ - There was a very subtle bug in the unit checking code involving
+ the id of a Reaction. This is now fixed. Thanks to Rainer
+ Machne for finding and reporting it.
+
- Converting a model to L3 was not setting all the required
attributes correctly. This has been corrected. Thanks to
Chris Myers for reporting this.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-30 11:11:47
|
Revision: 12076
http://sbml.svn.sourceforge.net/sbml/?rev=12076&view=rev
Author: sarahkeating
Date: 2010-09-30 11:11:41 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
fixed unit checking bug reported by Rainer
Modified Paths:
--------------
trunk/libsbml/src/units/UnitFormulaFormatter.cpp
Modified: trunk/libsbml/src/units/UnitFormulaFormatter.cpp
===================================================================
--- trunk/libsbml/src/units/UnitFormulaFormatter.cpp 2010-09-30 08:51:59 UTC (rev 12075)
+++ trunk/libsbml/src/units/UnitFormulaFormatter.cpp 2010-09-30 11:11:41 UTC (rev 12076)
@@ -1020,7 +1020,7 @@
{
for (n = 0; n < tempUd->getNumUnits(); n++)
{
- unit = const_cast<Unit*>(tempUd->getUnit(n));
+ unit = (const_cast<Unit*>(tempUd->getUnit(n)))->clone();
exponent = unit->getExponent();
unit->setExponent(exponent * -1);
ud->addUnit(unit);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-30 08:52:06
|
Revision: 12075
http://sbml.svn.sourceforge.net/sbml/?rev=12075&view=rev
Author: sarahkeating
Date: 2010-09-30 08:51:59 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
updated version to 4.2.0
Modified Paths:
--------------
trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win32.iss
trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win64.iss
Modified: trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win32.iss
===================================================================
--- trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win32.iss 2010-09-30 05:50:37 UTC (rev 12074)
+++ trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win32.iss 2010-09-30 08:51:59 UTC (rev 12075)
@@ -1,19 +1,19 @@
-; Version No is currently 4.1.0
+; Version No is currently 4.2.0
; Check before use
[Setup]
AppName=libSBML
-AppVerName=libSBML 4.1.0
+AppVerName=libSBML 4.2.0
AppPublisher=SBML Team
AppPublisherURL=http://sbml.org
AppSupportURL=http://sbml.org
AppUpdatesURL=http://sbml.org
-DefaultDirName={pf}\SBML\libSBML-4.1.0-libxml2-x86
+DefaultDirName={pf}\SBML\libSBML-4.2.0-libxml2-x86
DefaultGroupName=libSBML
DisableProgramGroupPage=yes
OutputDir=.\Output
-OutputBaseFilename=libSBML-4.1.0-win-libxml2-x86
+OutputBaseFilename=libSBML-4.2.0-win-libxml2-x86
WizardSmallImageFile=.\graphics\libsbml-installer-mini-logo.bmp
WizardImageFile=.\graphics\libsbml-installer-graphic.bmp
UsePreviousAppDir=no
@@ -40,7 +40,7 @@
Root: HKCU; Subkey: Software\SBML\libSBML; Flags: uninsdeletekey
Root: HKLM; Subkey: Software\SBML; Flags: uninsdeletekeyifempty
Root: HKLM; Subkey: Software\SBML\libSBML; Flags: uninsdeletekey
-Root: HKLM; Subkey: Software\SBML\libSBML; ValueType: string; ValueName: Version; ValueData: 4.1.0
+Root: HKLM; Subkey: Software\SBML\libSBML; ValueType: string; ValueName: Version; ValueData: 4.2.0
Root: HKLM; Subkey: Software\SBML\libSBML; ValueType: string; ValueName: InstallPath; ValueData: {app}
[Code]
@@ -220,7 +220,7 @@
Note: it includes a version number
**********************************************************************************************************}
- MsgBox('This setup installs the Windows version of libSBML 4.1.0 built using the libxml2 2.7.3 XML Parser library. All the necessary libraries are included. The source code is available as a separate download.', mbInformation, mb_Ok);
+ MsgBox('This setup installs the Windows version of libSBML 4.2.0 built using the libxml2 2.7.3 XML Parser library. All the necessary libraries are included. The source code is available as a separate download.', mbInformation, mb_Ok);
{ MsgBox('This setup installs the Windows release of libSBML 3.0.2 built using the Expat XML Parser libraries. All the necessary libraries are included. The source code is available as a seperate download.', mbInformation, mb_Ok); }
end;
@@ -237,7 +237,7 @@
begin
{get data from system}
PreviousInstalledVersion := GetVersion();
- ThisVersion := '4.1.0';
+ ThisVersion := '4.2.0';
MatlabRoot := GetMatlabRoot('');
GetPython25Dir('');
GetPython26Dir('');
Modified: trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win64.iss
===================================================================
--- trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win64.iss 2010-09-30 05:50:37 UTC (rev 12074)
+++ trunk/libsbml/dev/utilities/win_installer/install_libsbml_script_xml_win64.iss 2010-09-30 08:51:59 UTC (rev 12075)
@@ -1,19 +1,19 @@
-; Version No is currently 4.1.0
+; Version No is currently 4.2.0
; Check before use
[Setup]
AppName=libSBML
-AppVerName=libSBML 4.1.0
+AppVerName=libSBML 4.2.0
AppPublisher=SBML Team
AppPublisherURL=http://sbml.org
AppSupportURL=http://sbml.org
AppUpdatesURL=http://sbml.org
-DefaultDirName={pf}\SBML\libSBML-4.1.0-libxml2-x64
+DefaultDirName={pf}\SBML\libSBML-4.2.0-libxml2-x64
DefaultGroupName=libSBML
DisableProgramGroupPage=yes
OutputDir=.\Output
-OutputBaseFilename=libSBML-4.1.0-win-libxml2-x64
+OutputBaseFilename=libSBML-4.2.0-win-libxml2-x64
WizardSmallImageFile=.\graphics\libsbml-installer-mini-logo.bmp
WizardImageFile=.\graphics\libsbml-installer-graphic.bmp
UsePreviousAppDir=no
@@ -40,7 +40,7 @@
Root: HKCU; Subkey: Software\SBML\libSBML; Flags: uninsdeletekey
Root: HKLM; Subkey: Software\SBML; Flags: uninsdeletekeyifempty
Root: HKLM; Subkey: Software\SBML\libSBML; Flags: uninsdeletekey
-Root: HKLM; Subkey: Software\SBML\libSBML; ValueType: string; ValueName: Version; ValueData: 4.1.0
+Root: HKLM; Subkey: Software\SBML\libSBML; ValueType: string; ValueName: Version; ValueData: 4.2.0
Root: HKLM; Subkey: Software\SBML\libSBML; ValueType: string; ValueName: InstallPath; ValueData: {app}
[Code]
@@ -220,7 +220,7 @@
Note: it includes a version number
**********************************************************************************************************}
- MsgBox('This setup installs the Windows version of libSBML 4.1.0 built using the libxml2 2.7.3 XML Parser library. All the necessary libraries are included. The source code is available as a separate download.', mbInformation, mb_Ok);
+ MsgBox('This setup installs the Windows version of libSBML 4.2.0 built using the libxml2 2.7.3 XML Parser library. All the necessary libraries are included. The source code is available as a separate download.', mbInformation, mb_Ok);
{ MsgBox('This setup installs the Windows release of libSBML 3.0.2 built using the Expat XML Parser libraries. All the necessary libraries are included. The source code is available as a seperate download.', mbInformation, mb_Ok); }
end;
@@ -237,7 +237,7 @@
begin
{get data from system}
PreviousInstalledVersion := GetVersion();
- ThisVersion := '4.1.0';
+ ThisVersion := '4.2.0';
MatlabRoot := GetMatlabRoot('');
GetPython25Dir('');
GetPython26Dir('');
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2010-09-30 05:50:46
|
Revision: 12074
http://sbml.svn.sourceforge.net/sbml/?rev=12074&view=rev
Author: mhucka
Date: 2010-09-30 05:50:37 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
Bug fixes and other updates.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/introduction.doc
trunk/specifications/sbml-level-3/version-1/comp/introduction.pages
trunk/specifications/sbml-level-3/version-1/comp/introduction.pdf
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-1.graffle
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-1.pdf
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-1.svg
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-2.graffle
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-2.pdf
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-2.svg
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-3.graffle
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-3.pdf
trunk/specifications/sbml-level-3/version-1/comp/model-scenario-3.svg
Modified: trunk/specifications/sbml-level-3/version-1/comp/introduction.doc
===================================================================
(Binary files differ)
Modified: trunk/specifications/sbml-level-3/version-1/comp/introduction.pages
===================================================================
(Binary files differ)
Modified: trunk/specifications/sbml-level-3/version-1/comp/introduction.pdf
===================================================================
(Binary files differ)
Modified: trunk/specifications/sbml-level-3/version-1/comp/model-scenario-1.graffle
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/model-scenario-1.graffle 2010-09-30 00:12:06 UTC (rev 12073)
+++ trunk/specifications/sbml-level-3/version-1/comp/model-scenario-1.graffle 2010-09-30 05:50:37 UTC (rev 12074)
@@ -54,18 +54,18 @@
<string>LineGraphic</string>
<key>ControlPoints</key>
<array>
- <string>{-15.6668, -1.33296}</string>
- <string>{-5.5, 28}</string>
- <string>{5.50001, -28}</string>
+ <string>{-16.8829, -1.11246}</string>
+ <string>{-1.25, 1.25}</string>
+ <string>{1.25, -1.25}</string>
<string>{-9.48813, 7.17122}</string>
</array>
<key>ID</key>
- <integer>47</integer>
+ <integer>59</integer>
<key>Points</key>
<array>
- <string>{66.9152, 169.765}</string>
- <string>{47.5, 116}</string>
- <string>{78.6667, 50}</string>
+ <string>{66.75, 84}</string>
+ <string>{69.25, 64}</string>
+ <string>{95.5, 43.5}</string>
</array>
<key>Style</key>
<dict>
@@ -85,38 +85,24 @@
<real>0.5</real>
</dict>
</dict>
- <key>Tail</key>
- <dict>
- <key>ID</key>
- <integer>43</integer>
- <key>Info</key>
- <integer>8</integer>
- </dict>
</dict>
<dict>
<key>Class</key>
<string>LineGraphic</string>
<key>ControlPoints</key>
<array>
- <string>{-16.8829, -1.11246}</string>
- <string>{-5.66666, 18.3334}</string>
- <string>{5.66664, -18.3334}</string>
+ <string>{-15.6668, -1.33296}</string>
+ <string>{-5.25, 32.75}</string>
+ <string>{5.25002, -32.75}</string>
<string>{-9.48813, 7.17122}</string>
</array>
- <key>Head</key>
- <dict>
- <key>ID</key>
- <integer>39</integer>
- <key>Info</key>
- <integer>8</integer>
- </dict>
<key>ID</key>
- <integer>46</integer>
+ <integer>47</integer>
<key>Points</key>
<array>
- <string>{66.8829, 126.446}</string>
- <string>{47, 89}</string>
- <string>{78.6667, 44}</string>
+ <string>{66.9171, 169.764}</string>
+ <string>{43.5, 103.25}</string>
+ <string>{80, 42.25}</string>
</array>
<key>Style</key>
<dict>
@@ -139,7 +125,7 @@
<key>Tail</key>
<dict>
<key>ID</key>
- <integer>42</integer>
+ <integer>43</integer>
<key>Info</key>
<integer>8</integer>
</dict>
@@ -149,18 +135,18 @@
<string>LineGraphic</string>
<key>ControlPoints</key>
<array>
- <string>{-9.49339, 0.18029}</string>
- <string>{-4.00001, 10.6665}</string>
- <string>{4, -10.6665}</string>
- <string>{-4.00004, 2.66667}</string>
+ <string>{-16.8829, -1.11246}</string>
+ <string>{-8, 20.75}</string>
+ <string>{8, -20.75}</string>
+ <string>{-9.48813, 7.17122}</string>
</array>
<key>ID</key>
- <integer>45</integer>
+ <integer>46</integer>
<key>Points</key>
<array>
- <string>{66.8435, 83.1383}</string>
- <string>{52, 64.6665}</string>
- <string>{78.6667, 39.3333}</string>
+ <string>{66.9192, 126.43}</string>
+ <string>{52.5, 84.25}</string>
+ <string>{87.5, 43.75}</string>
</array>
<key>Style</key>
<dict>
@@ -183,7 +169,7 @@
<key>Tail</key>
<dict>
<key>ID</key>
- <integer>38</integer>
+ <integer>42</integer>
<key>Info</key>
<integer>8</integer>
</dict>
@@ -287,7 +273,7 @@
<string>{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural
\f0\fs18 \cf0 \expnd0\expndtw0\kerning0
instance 3 \
@@ -397,7 +383,7 @@
<string>{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural
\f0\fs18 \cf0 \expnd0\expndtw0\kerning0
instance 2 \
@@ -412,7 +398,7 @@
<key>AllowConnections</key>
<string>NO</string>
<key>Bounds</key>
- <string>{{78.6667, 30.3334}, {80.3334, 27.3333}}</string>
+ <string>{{78.6667, 16.0001}, {86.6666, 27.3333}}</string>
<key>Class</key>
<string>ShapedGraphic</string>
<key>FontInfo</key>
@@ -498,7 +484,7 @@
<string>{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural
\f0\fs18 \cf0 \expnd0\expndtw0\kerning0
model definition A}</string>
@@ -509,6 +495,8 @@
<integer>0</integer>
</dict>
<dict>
+ <key>AllowConnections</key>
+ <string>NO</string>
<key>Bounds</key>
<string>{{67.0001, 65.6665}, {92, 35.3333}}</string>
<key>Class</key>
@@ -607,7 +595,7 @@
<string>{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
{\colortbl;\red255\green255\blue255;}
-\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural
\f0\fs18 \cf0 \expnd0\expndtw0\kerning0
instance 1 \
@@ -622,7 +610,7 @@
<key>AllowConnections</key>
<string>NO</string>
<key>Bounds</key>
- <string>{{36.6667, 20.6667}, {134.667, 179.667}}</string>
+ <string>{{36.6667, 52}, {128.667, 142}}</string>
<key>Class</key>
<string>ShapedGraphic</string>
<key>FontInfo</key>
@@ -661,11 +649,11 @@
<key>Color</key>
<dict>
<key>b</key>
- <string>0.868803</string>
+ <string>0.929778</string>
<key>g</key>
- <string>0.943618</string>
+ <string>0.85594</string>
<key>r</key>
- <string>0.916106</string>
+ <string>0.841352</string>
</dict>
<key>FillType</key>
<integer>2</integer>
@@ -674,17 +662,19 @@
<key>GradientColor</key>
<dict>
<key>b</key>
- <string>0.73315</string>
+ <string>0.47449</string>
<key>g</key>
- <string>0.73315</string>
+ <string>0.311765</string>
<key>r</key>
- <string>0.73315</string>
+ <string>0.272095</string>
</dict>
<key>MiddleFraction</key>
- <real>0.67460322380065918</real>
+ <real>0.75396817922592163</real>
</dict>
<key>shadow</key>
<dict>
+ <key>Beneath</key>
+ <string>YES</string>
<key>Color</key>
<dict>
<key>a</key>
@@ -725,6 +715,113 @@
<key>TextPlacement</key>
<integer>0</integer>
</dict>
+ <dict>
+ <key>AllowConnections</key>
+ <string>NO</string>
+ <key>Bounds</key>
+ <string>{{29.3333, 8.66667}, {143.667, 192}}</string>
+ <key>Class</key>
+ <string>ShapedGraphic</string>
+ <key>FontInfo</key>
+ <dict>
+ <key>Color</key>
+ <dict>
+ <key>w</key>
+ <string>0</string>
+ </dict>
+ <key>Font</key>
+ <string>ArialMT</string>
+ <key>NSKern</key>
+ <real>0.0</real>
+ <key>Size</key>
+ <real>9</real>
+ </dict>
+ <key>ID</key>
+ <integer>58</integer>
+ <key>Magnets</key>
+ <array>
+ <string>{1, 0.5}</string>
+ <string>{1, -0.5}</string>
+ <string>{-1, 0.5}</string>
+ <string>{-1, -0.5}</string>
+ <string>{0.5, 1}</string>
+ <string>{-0.5, 1}</string>
+ <string>{0.5, -1}</string>
+ <string>{-0.5, -1}</string>
+ </array>
+ <key>Shape</key>
+ <string>Rectangle</string>
+ <key>Style</key>
+ <dict>
+ <key>fill</key>
+ <dict>
+ <key>Color</key>
+ <dict>
+ <key>b</key>
+ <string>0.816415</string>
+ <key>g</key>
+ <string>1</string>
+ <key>r</key>
+ <string>0.974914</string>
+ </dict>
+ <key>FillType</key>
+ <integer>2</integer>
+ <key>GradientAngle</key>
+ <real>90</real>
+ <key>GradientColor</key>
+ <dict>
+ <key>b</key>
+ <string>0.492612</string>
+ <key>g</key>
+ <string>0.556122</string>
+ <key>r</key>
+ <string>0.530412</string>
+ </dict>
+ <key>MiddleFraction</key>
+ <real>0.67460322380065918</real>
+ </dict>
+ <key>shadow</key>
+ <dict>
+ <key>Color</key>
+ <dict>
+ <key>a</key>
+ <string>0.75</string>
+ <key>b</key>
+ <string>0.361242</string>
+ <key>g</key>
+ <string>0.396597</string>
+ <key>r</key>
+ <string>0.384726</string>
+ </dict>
+ </dict>
+ <key>stroke</key>
+ <dict>
+ <key>CornerRadius</key>
+ <real>5</real>
+ <key>Width</key>
+ <real>0.5</real>
+ </dict>
+ </dict>
+ <key>Text</key>
+ <dict>
+ <key>Align</key>
+ <integer>0</integer>
+ <key>Pad</key>
+ <integer>3</integer>
+ <key>Text</key>
+ <string>{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
+{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
+{\colortbl;\red255\green255\blue255;}
+\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\ql\qnatural
+
+\f0\fs18 \cf0 \expnd0\expndtw0\kerning0
+<sbml>}</string>
+ <key>VerticalPad</key>
+ <integer>3</integer>
+ </dict>
+ <key>TextPlacement</key>
+ <integer>0</integer>
+ </dict>
</array>
<key>GridInfo</key>
<dict/>
@@ -773,7 +870,7 @@
<key>MasterSheets</key>
<array/>
<key>ModificationDate</key>
- <string>2010-09-29 06:07:13 +0200</string>
+ <string>2010-09-30 06:39:29 +0200</string>
<key>Modifier</key>
<string>Michael Hucka</string>
<key>NotesVisible</key>
@@ -817,1955 +914,2440 @@
<key>QuickLookPreview</key>
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[truncated message content] |
|
From: <fbe...@us...> - 2010-09-30 00:12:12
|
Revision: 12073
http://sbml.svn.sourceforge.net/sbml/?rev=12073&view=rev
Author: fbergmann
Date: 2010-09-30 00:12:06 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
- Updated package name generation
Modified Paths:
--------------
branches/libsbml-5/macosx/Makefile.in
Modified: branches/libsbml-5/macosx/Makefile.in
===================================================================
--- branches/libsbml-5/macosx/Makefile.in 2010-09-30 00:11:49 UTC (rev 12072)
+++ branches/libsbml-5/macosx/Makefile.in 2010-09-30 00:12:06 UTC (rev 12073)
@@ -34,21 +34,24 @@
include @top_srcdir@/config/makefile-common-vars.mk
+# -----------------------------------------------------------------------------
+# Determine Package name
+# -----------------------------------------------------------------------------
+PKGNAME=
OS=$(shell uname -s)
-ifeq "$OS" "Darwin"
-OSX_MAJOR_VER=$(shell sw_vers -productVersion | cut -d"." -f1)
-OSX_MINOR_VER=$(shell sw_vers -productVersion | cut -d"." -f2)
-ifeq "$(OSX_MAJOR_VER)" "10"
-ifeq "$(OSX_MINOR_VER)" "6"
-MACOS = "snowleopard"
-else
-MACOS = "leopard"
+ifeq "${OS}" "Darwin"
+ OSX_MAJOR_VER=$(shell sw_vers -productVersion | cut -d"." -f1)
+ OSX_MINOR_VER=$(shell sw_vers -productVersion | cut -d"." -f2)
+ ifeq "$(OSX_MAJOR_VER)" "10"
+ ifeq "$(OSX_MINOR_VER)" "6"
+ MACOS=snowleopard
+ else
+ MACOS=leopard
+ endif
+ endif
+ PKGNAME=libSBML-@PACKAGE_VERSION@-@XML_PARSER@-${MACOS}.pkg
endif
-endif
-endif
-PKGNAME = libSBML-@PACKAGE_VERSION@-@XML_PARSER@-${MACOS}.pkg
-
# `srcdir' points to the current directory, but should be set by configure.
# `subdir' must be set manually to the relative dir under srcdir. Don't
# set `subdir' to an absolute path, or some `make' actions will fail.
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|
|
From: <fbe...@us...> - 2010-09-30 00:11:55
|
Revision: 12072
http://sbml.svn.sourceforge.net/sbml/?rev=12072&view=rev
Author: fbergmann
Date: 2010-09-30 00:11:49 +0000 (Thu, 30 Sep 2010)
Log Message:
-----------
- Updated package name generation
Modified Paths:
--------------
trunk/libsbml/macosx/Makefile.in
Modified: trunk/libsbml/macosx/Makefile.in
===================================================================
--- trunk/libsbml/macosx/Makefile.in 2010-09-29 23:46:37 UTC (rev 12071)
+++ trunk/libsbml/macosx/Makefile.in 2010-09-30 00:11:49 UTC (rev 12072)
@@ -34,20 +34,24 @@
include @top_srcdir@/config/makefile-common-vars.mk
+# -----------------------------------------------------------------------------
+# Determine Package name
+# -----------------------------------------------------------------------------
+PKGNAME=
OS=$(shell uname -s)
-ifeq "$OS" "Darwin"
-OSX_MAJOR_VER=$(shell sw_vers -productVersion | cut -d"." -f1)
-OSX_MINOR_VER=$(shell sw_vers -productVersion | cut -d"." -f2)
-ifeq "$(OSX_MAJOR_VER)" "10"
-ifeq "$(OSX_MINOR_VER)" "6"
-MACOS = "snowleopard"
-else
-MACOS = "leopard"
+ifeq "${OS}" "Darwin"
+ OSX_MAJOR_VER=$(shell sw_vers -productVersion | cut -d"." -f1)
+ OSX_MINOR_VER=$(shell sw_vers -productVersion | cut -d"." -f2)
+ ifeq "$(OSX_MAJOR_VER)" "10"
+ ifeq "$(OSX_MINOR_VER)" "6"
+ MACOS=snowleopard
+ else
+ MACOS=leopard
+ endif
+ endif
+ PKGNAME=libSBML-@PACKAGE_VERSION@-@XML_PARSER@-${MACOS}.pkg
endif
-endif
-endif
-PKGNAME = libSBML-@PACKAGE_VERSION@-@XML_PARSER@-${MACOS}.pkg
# `srcdir' points to the current directory, but should be set by configure.
# `subdir' must be set manually to the relative dir under srcdir. Don't
@@ -129,7 +133,7 @@
&& $(MAKE) install DESTDIR=$(apath_thisdir)/$(staging)
create-pkg: create-dist pmdoc-files
- /Developer/usr/bin/packagemaker -v --doc libsbml-package.pmdoc --out $(PKGNAME)
+ /Developer/usr/bin/packagemaker -v --doc libsbml-package.pmdoc --out $(PKGNAME)
create-dmg: create-pkg build.sh
./build.sh
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|
|
From: <fbe...@us...> - 2010-09-29 23:46:43
|
Revision: 12071
http://sbml.svn.sourceforge.net/sbml/?rev=12071&view=rev
Author: fbergmann
Date: 2010-09-29 23:46:37 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
- only test for osx version on OSX
Modified Paths:
--------------
trunk/libsbml/macosx/Makefile.in
Modified: trunk/libsbml/macosx/Makefile.in
===================================================================
--- trunk/libsbml/macosx/Makefile.in 2010-09-29 23:46:17 UTC (rev 12070)
+++ trunk/libsbml/macosx/Makefile.in 2010-09-29 23:46:37 UTC (rev 12071)
@@ -34,7 +34,8 @@
include @top_srcdir@/config/makefile-common-vars.mk
-
+OS=$(shell uname -s)
+ifeq "$OS" "Darwin"
OSX_MAJOR_VER=$(shell sw_vers -productVersion | cut -d"." -f1)
OSX_MINOR_VER=$(shell sw_vers -productVersion | cut -d"." -f2)
ifeq "$(OSX_MAJOR_VER)" "10"
@@ -44,6 +45,7 @@
MACOS = "leopard"
endif
endif
+endif
PKGNAME = libSBML-@PACKAGE_VERSION@-@XML_PARSER@-${MACOS}.pkg
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|
|
From: <fbe...@us...> - 2010-09-29 23:46:23
|
Revision: 12070
http://sbml.svn.sourceforge.net/sbml/?rev=12070&view=rev
Author: fbergmann
Date: 2010-09-29 23:46:17 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
- only test for osx version on OSX
Modified Paths:
--------------
branches/libsbml-5/macosx/Makefile.in
Modified: branches/libsbml-5/macosx/Makefile.in
===================================================================
--- branches/libsbml-5/macosx/Makefile.in 2010-09-29 23:33:10 UTC (rev 12069)
+++ branches/libsbml-5/macosx/Makefile.in 2010-09-29 23:46:17 UTC (rev 12070)
@@ -34,7 +34,8 @@
include @top_srcdir@/config/makefile-common-vars.mk
-
+OS=$(shell uname -s)
+ifeq "$OS" "Darwin"
OSX_MAJOR_VER=$(shell sw_vers -productVersion | cut -d"." -f1)
OSX_MINOR_VER=$(shell sw_vers -productVersion | cut -d"." -f2)
ifeq "$(OSX_MAJOR_VER)" "10"
@@ -44,6 +45,7 @@
MACOS = "leopard"
endif
endif
+endif
PKGNAME = libSBML-@PACKAGE_VERSION@-@XML_PARSER@-${MACOS}.pkg
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|
|
From: <luc...@us...> - 2010-09-29 23:33:17
|
Revision: 12069
http://sbml.svn.sourceforge.net/sbml/?rev=12069&view=rev
Author: luciansmith
Date: 2010-09-29 23:33:10 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Small updates to the .xml files, mostly fixes.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 23:32:25 UTC (rev 12068)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 23:33:10 UTC (rev 12069)
@@ -25,8 +25,8 @@
</modelDefinition>
</listOfModelDefinitions>
- <model id="complexified">
- <listOfSubmodels xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <model id="complexified" xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <listOfSubmodels>
<submodel id="simple">
<modelRef model="simple" />
<listOfDeletions>
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml 2010-09-29 23:32:25 UTC (rev 12068)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml 2010-09-29 23:33:10 UTC (rev 12069)
@@ -3,7 +3,7 @@
xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
comp:required="true">
-<listOfModelDefinitions>
+<listOfModelDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
<modelDefinition id="simple" name="simple">
<listOfCompartments>
<compartment id="comp" size="1" constant="true" spatialDimensions="3" portid="comp"/>
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml 2010-09-29 23:32:25 UTC (rev 12068)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml 2010-09-29 23:33:10 UTC (rev 12069)
@@ -3,7 +3,7 @@
xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
comp:required="true">
- <model id="onespecies" xmlns:xlink="http://www.w3.org/1999/xlink">
+ <model id="onespecies" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
<listOfSubmodels>
<submodel id="A">
<modelRef xlink:href="enzyme_model.xml" model="enzyme" />
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|
|
From: <luc...@us...> - 2010-09-29 23:32:31
|
Revision: 12068
http://sbml.svn.sourceforge.net/sbml/?rev=12068&view=rev
Author: luciansmith
Date: 2010-09-29 23:32:25 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Slightly modified 'Use cases' to include the new versions of the .xml files, plus two new sections ('validation' and 'wrapup' which between the two of them should complete the proposal. Yay!
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/Use_cases.docx
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/comp/Validation.docx
trunk/specifications/sbml-level-3/version-1/comp/Wrapup.docx
Modified: trunk/specifications/sbml-level-3/version-1/comp/Use_cases.docx
===================================================================
(Binary files differ)
Added: trunk/specifications/sbml-level-3/version-1/comp/Validation.docx
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/comp/Validation.docx
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/specifications/sbml-level-3/version-1/comp/Wrapup.docx
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/comp/Wrapup.docx
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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|
|
From: <luc...@us...> - 2010-09-29 19:34:16
|
Revision: 12067
http://sbml.svn.sourceforge.net/sbml/?rev=12067&view=rev
Author: luciansmith
Date: 2010-09-29 19:34:06 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Updates to clean up the XML and incorporate Mike's suggested changes.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml 2010-09-29 18:40:53 UTC (rev 12066)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml 2010-09-29 19:34:06 UTC (rev 12067)
@@ -4,12 +4,7 @@
comp:required="true">
<listOfModelDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
- <model id="enzyme" name="enzyme">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p> Originally created by libAntimony v1.4 (using libSBML 4.1.0) </p>
- </body>
- </notes>
+ <modelDefinition id="enzyme" name="enzyme">
<listOfCompartments>
<compartment id="comp" size="1" constant="true" spatialDimensions="3"/>
</listOfCompartments>
@@ -39,7 +34,7 @@
</listOfProducts>
</reaction>
</listOfReactions>
- </model>
+ </modelDefinition>
</listOfModelDefinitions>
<model id="aggregate">
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 18:40:53 UTC (rev 12066)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 19:34:06 UTC (rev 12067)
@@ -9,8 +9,8 @@
<compartment id="comp" size="1" spatialDimensions="3" constant="true" portID="comp_port"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S" initialConcentration="5" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portID="S"/>
- <species id="D" initialConcentration="10" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portID="D"/>
+ <species id="S" initialConcentration="5" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portID="S_port"/>
+ <species id="D" initialConcentration="10" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portID="D_port"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="true" fast="false" portID="J0_port">
@@ -30,7 +30,7 @@
<submodel id="simple">
<modelRef model="simple" />
<listOfDeletions>
- <deletion id="oldrxn" port="J0_port">
+ <deletion id="oldrxn" port="J0_port" />
</listOfDeletions>
</submodel>
<submodel id="enzyme">
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml 2010-09-29 18:40:53 UTC (rev 12066)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml 2010-09-29 19:34:06 UTC (rev 12067)
@@ -1,16 +1,19 @@
<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
- <listOfModelDefinitions>
- <model id="simple" name="simple">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+ xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
+ comp:required="true">
+
+<listOfModelDefinitions>
+ <modelDefinition id="simple" name="simple">
<listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
+ <compartment id="comp" size="1" constant="true" spatialDimensions="3" portid="comp"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
- <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
+ <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S_port"/>
+ <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D_port"/>
</listOfSpecies>
<listOfReactions>
- <reaction id="J0" reversible="true" fast="false" portid="J0">
+ <reaction id="J0" reversible="true" fast="false" portid="J0_port">
<listOfReactants>
<speciesReference species="S" stoichiometry="1" constant="false"/>
</listOfReactants>
@@ -19,24 +22,19 @@
</listOfProducts>
</reaction>
</listOfReactions>
- </model>
- <model id="enzyme" name="enzyme">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p> Originally created by libAntimony v1.4 (using libSBML 4.1.0) </p>
- </body>
- </notes>
+ </modelDefinition>
+ <modelDefinition id="enzyme" name="enzyme">
<listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
+ <compartment id="comp" size="1" constant="true" spatialDimensions="3" portid="comp_port"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
- <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="E"/>
- <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
- <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="ES"/>
+ <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S_port"/>
+ <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="E_port"/>
+ <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D_port"/>
+ <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="ES_port"/>
</listOfSpecies>
<listOfReactions>
- <reaction id="J0" reversible="true" fast="false" portid="J0">
+ <reaction id="J0" reversible="true" fast="false" portid="J0_port">
<listOfReactants>
<speciesReference species="S" stoichiometry="1" constant="false"/>
<speciesReference species="E" stoichiometry="1" constant="false"/>
@@ -45,7 +43,7 @@
<speciesReference species="ES" stoichiometry="1" constant="false"/>
</listOfProducts>
</reaction>
- <reaction id="J1" reversible="true" fast="false" portid="J1">
+ <reaction id="J1" reversible="true" fast="false" portid="J1_port">
<listOfReactants>
<speciesReference species="ES" stoichiometry="1" constant="false"/>
</listOfReactants>
@@ -55,26 +53,26 @@
</listOfProducts>
</reaction>
</listOfReactions>
- </model>
+ </modelDefinition>
</listOfModelDefinitions>
<model id="complexified">
<listOfSubmodels>
<submodel id="simple">
- <modelRef modelID="simple" />
+ <modelRef model="simple" />
<listOfDeletions>
- <deletion id="oldrxn" port="J0">
+ <deletion id="oldrxn" port="J0_port" />
</listOfDeletions>
</submodel>
<submodel id="enzyme">
- <modelRef modelID="enzyme" />
+ <modelRef model="enzyme" />
</submodel>
</listOfSubmodels>
<listOfReactions>
<reaction id="J0" reversible="true" fast="false">
<replaces>
<subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="J0" identical="true" />
+ <subelement submodel="enzyme" port="J0_port" identical="true" />
</replaces>
<listOfReactants>
<speciesReference species="S" stoichiometry="1" constant="false"/>
@@ -87,7 +85,7 @@
<reaction id="J1" reversible="true" fast="false">
<replaces>
<subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="J1" identical="true" />
+ <subelement submodel="enzyme" port="J1_port" identical="true" />
</replaces>
<listOfReactants>
<speciesReference species="ES" stoichiometry="1" constant="false"/>
@@ -98,35 +96,36 @@
</reaction>
</listOfReactions>
<listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
+ <compartment id="comp" size="1" constant="true" spatialDimensions="3">
<replaces>
- <subelement submodel="simple" port="comp" identical="true" />
- <subelement submodel="enzyme" port="comp" identical="true" />
+ <subelement submodel="simple" port="comp_port" identical="true" />
+ <subelement submodel="enzyme" port="comp_port" identical="true" />
</replaces>
+ </compartment>
</listOfCompartments>
<listOfSpecies>
<species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<replaces>
- <subelement submodel="simple" port="S" identical="true" />
- <subelement submodel="enzyme" port="S" identical="false" />
+ <subelement submodel="simple" port="S_port" identical="true" />
+ <subelement submodel="enzyme" port="S_port" identical="false" />
</replaces>
</species>
<species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<replaces>
- <subelement submodel="simple" port="D" identical="true" />
- <subelement submodel="enzyme" port="D" identical="false" />
+ <subelement submodel="simple" port="D_port" identical="true" />
+ <subelement submodel="enzyme" port="D_port" identical="false" />
</replaces>
</species>
<species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<replaces>
<subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="E" identical="true" />
+ <subelement submodel="enzyme" port="E_port" identical="true" />
</replaces>
</species>
<species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<replaces>
<subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="ES" identical="true" />
+ <subelement submodel="enzyme" port="ES_port" identical="true" />
</replaces>
</species>
</listOfSpecies>
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml 2010-09-29 18:40:53 UTC (rev 12066)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml 2010-09-29 19:34:06 UTC (rev 12067)
@@ -1,26 +1,30 @@
<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+ xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
+ comp:required="true">
+
<model id="onespecies" xmlns:xlink="http://www.w3.org/1999/xlink">
<listOfSubmodels>
<submodel id="A">
- <modelRef xlink:href="enzyme_model.xml" modelID="enzyme" />
+ <modelRef xlink:href="enzyme_model.xml" model="enzyme" />
</submodel>
<submodel id="B">
- <modelRef xlink:href="enzyme_model.xml" modelID="enzyme" />
+ <modelRef xlink:href="enzyme_model.xml" model="enzyme" />
</submodel>
</listOfSubmodels>
<listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
+ <compartment id="comp" size="1" constant="true" spatialDimensions="3">
<replaces>
- <subelement submodel="A" idRef="comp" identical="true" />
- <subelement submodel="B" idRef="comp" identical="true" />
+ <subelement submodel="A" symbol="comp" identical="true" />
+ <subelement submodel="B" symbol="comp" identical="true" />
</replaces>
+ </compartment>
</listOfCompartments>
<listOfSpecies>
<species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<replaces>
- <subelement submodel="A" idRef="S" identical="true" />
- <subelement submodel="B" idRef="S" identical="true" />
+ <subelement submodel="A" symbol="S" identical="true" />
+ <subelement submodel="B" symbol="S" identical="true" />
</replaces>
</species>
</listOfSpecies>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2010-09-29 18:40:59
|
Revision: 12066
http://sbml.svn.sourceforge.net/sbml/?rev=12066&view=rev
Author: luciansmith
Date: 2010-09-29 18:40:53 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Deleted .txt files that were replaced by .xml files.
Removed Paths:
-------------
trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.txt
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.txt
Deleted: trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.txt
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.txt 2010-09-29 18:30:53 UTC (rev 12065)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.txt 2010-09-29 18:40:53 UTC (rev 12066)
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
- <listOfModelDefinitions>
- <model id="enzyme" name="enzyme">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p> Originally created by libAntimony v1.4 (using libSBML 4.1.0) </p>
- </body>
- </notes>
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="J0" reversible="true" fast="false">
- <listOfReactants>
- <speciesReference species="S" stoichiometry="1" constant="false"/>
- <speciesReference species="E" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="ES" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- <reaction id="J1" reversible="true" fast="false">
- <listOfReactants>
- <speciesReference species="ES" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="D" stoichiometry="1" constant="false"/>
- <speciesReference species="E" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- </listOfReactions>
- </model>
- </listOfModelDefinitions>
-
- <model id="aggregate">
- <listOfSubmodels>
- <submodel>
- <modelRef modelID="enzyme" />
- </submodel>
- <submodel>
- <modelRef modelID="enzyme" />
- </submodel>
- </listOfSubmodels>
- </model>
-</sbml>
Deleted: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.txt
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.txt 2010-09-29 18:30:53 UTC (rev 12065)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.txt 2010-09-29 18:40:53 UTC (rev 12066)
@@ -1,60 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
- <listOfModelDefinitions>
- <model id="simple" name="simple">
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" initialConcentration="5" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
- <species id="D" initialConcentration="10" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="J0" reversible="true" fast="false" portid="J0">
- <listOfReactants>
- <speciesReference species="S" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="D" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- </listOfReactions>
- </model>
- </listOfModelDefinitions>
-
- <model id="complexified">
- <listOfSubmodels>
- <submodel id="simple">
- <modelRef modelID="simple" />
- <listOfDeletions>
- <deletion id="oldrxn" port="J0">
- </listOfDeletions>
- </submodel>
- <submodel id="enzyme">
- <modelRef modelID="enzyme" />
- </submodel>
- </listOfSubmodels>
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
- <replaces>
- <subelement submodel="simple" port="comp" identical="true" />
- <subelement submodel="enzyme" idRef="comp" identical="true" />
- </replaces>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="simple" port="S" identical="true" />
- <subelement submodel="enzyme" idRef="S" identical="false" />
- </replaces>
- </species>
- <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="simple" port="D" identical="true" />
- <subelement submodel="enzyme" idRef="D" identical="false" />
- </replaces>
- </species>
- </listOfSpecies>
- </model>
-
-</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2010-09-29 18:30:59
|
Revision: 12065
http://sbml.svn.sourceforge.net/sbml/?rev=12065&view=rev
Author: luciansmith
Date: 2010-09-29 18:30:53 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Trying ONCE AGAIN to rename some files.
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml
Removed Paths:
-------------
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.txt
trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.txt
Deleted: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.txt
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.txt 2010-09-29 11:33:16 UTC (rev 12064)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.txt 2010-09-29 18:30:53 UTC (rev 12065)
@@ -1,135 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
- <listOfModelDefinitions>
- <model id="simple" name="simple">
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
- <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="J0" reversible="true" fast="false" portid="J0">
- <listOfReactants>
- <speciesReference species="S" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="D" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- </listOfReactions>
- </model>
- <model id="enzyme" name="enzyme">
- <notes>
- <body xmlns="http://www.w3.org/1999/xhtml">
- <p> Originally created by libAntimony v1.4 (using libSBML 4.1.0) </p>
- </body>
- </notes>
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
- <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="E"/>
- <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
- <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="ES"/>
- </listOfSpecies>
- <listOfReactions>
- <reaction id="J0" reversible="true" fast="false" portid="J0">
- <listOfReactants>
- <speciesReference species="S" stoichiometry="1" constant="false"/>
- <speciesReference species="E" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="ES" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- <reaction id="J1" reversible="true" fast="false" portid="J1">
- <listOfReactants>
- <speciesReference species="ES" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="D" stoichiometry="1" constant="false"/>
- <speciesReference species="E" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- </listOfReactions>
- </model>
- </listOfModelDefinitions>
-
- <model id="complexified">
- <listOfSubmodels>
- <submodel id="simple">
- <modelRef modelID="simple" />
- <listOfDeletions>
- <deletion id="oldrxn" port="J0">
- </listOfDeletions>
- </submodel>
- <submodel id="enzyme">
- <modelRef modelID="enzyme" />
- </submodel>
- </listOfSubmodels>
- <listOfReactions>
- <reaction id="J0" reversible="true" fast="false">
- <replaces>
- <subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="J0" identical="true" />
- </replaces>
- <listOfReactants>
- <speciesReference species="S" stoichiometry="1" constant="false"/>
- <speciesReference species="E" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="ES" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- <reaction id="J1" reversible="true" fast="false">
- <replaces>
- <subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="J1" identical="true" />
- </replaces>
- <listOfReactants>
- <speciesReference species="ES" stoichiometry="1" constant="false"/>
- </listOfReactants>
- <listOfProducts>
- <speciesReference species="D" stoichiometry="1" constant="false"/>
- </listOfProducts>
- </reaction>
- </listOfReactions>
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
- <replaces>
- <subelement submodel="simple" port="comp" identical="true" />
- <subelement submodel="enzyme" port="comp" identical="true" />
- </replaces>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="simple" port="S" identical="true" />
- <subelement submodel="enzyme" port="S" identical="false" />
- </replaces>
- </species>
- <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="simple" port="D" identical="true" />
- <subelement submodel="enzyme" port="D" identical="false" />
- </replaces>
- </species>
- <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="E" identical="true" />
- </replaces>
- </species>
- <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="simple" deletion="oldrxn" />
- <subelement submodel="enzyme" port="ES" identical="true" />
- </replaces>
- </species>
- </listOfSpecies>
- </model>
-
-</sbml>
Copied: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml (from rev 12064, trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.txt)
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex2.xml 2010-09-29 18:30:53 UTC (rev 12065)
@@ -0,0 +1,135 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <listOfModelDefinitions>
+ <model id="simple" name="simple">
+ <listOfCompartments>
+ <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
+ <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false" portid="J0">
+ <listOfReactants>
+ <speciesReference species="S" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="D" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+ <model id="enzyme" name="enzyme">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ <p> Originally created by libAntimony v1.4 (using libSBML 4.1.0) </p>
+ </body>
+ </notes>
+ <listOfCompartments>
+ <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410" portid="comp"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="S"/>
+ <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="E"/>
+ <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="D"/>
+ <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portid="ES"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false" portid="J0">
+ <listOfReactants>
+ <speciesReference species="S" stoichiometry="1" constant="false"/>
+ <speciesReference species="E" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="ES" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J1" reversible="true" fast="false" portid="J1">
+ <listOfReactants>
+ <speciesReference species="ES" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="D" stoichiometry="1" constant="false"/>
+ <speciesReference species="E" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+ </listOfModelDefinitions>
+
+ <model id="complexified">
+ <listOfSubmodels>
+ <submodel id="simple">
+ <modelRef modelID="simple" />
+ <listOfDeletions>
+ <deletion id="oldrxn" port="J0">
+ </listOfDeletions>
+ </submodel>
+ <submodel id="enzyme">
+ <modelRef modelID="enzyme" />
+ </submodel>
+ </listOfSubmodels>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <replaces>
+ <subelement submodel="simple" deletion="oldrxn" />
+ <subelement submodel="enzyme" port="J0" identical="true" />
+ </replaces>
+ <listOfReactants>
+ <speciesReference species="S" stoichiometry="1" constant="false"/>
+ <speciesReference species="E" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="ES" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J1" reversible="true" fast="false">
+ <replaces>
+ <subelement submodel="simple" deletion="oldrxn" />
+ <subelement submodel="enzyme" port="J1" identical="true" />
+ </replaces>
+ <listOfReactants>
+ <speciesReference species="ES" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="D" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ <listOfCompartments>
+ <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
+ <replaces>
+ <subelement submodel="simple" port="comp" identical="true" />
+ <subelement submodel="enzyme" port="comp" identical="true" />
+ </replaces>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <replaces>
+ <subelement submodel="simple" port="S" identical="true" />
+ <subelement submodel="enzyme" port="S" identical="false" />
+ </replaces>
+ </species>
+ <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <replaces>
+ <subelement submodel="simple" port="D" identical="true" />
+ <subelement submodel="enzyme" port="D" identical="false" />
+ </replaces>
+ </species>
+ <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <replaces>
+ <subelement submodel="simple" deletion="oldrxn" />
+ <subelement submodel="enzyme" port="E" identical="true" />
+ </replaces>
+ </species>
+ <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <replaces>
+ <subelement submodel="simple" deletion="oldrxn" />
+ <subelement submodel="enzyme" port="ES" identical="true" />
+ </replaces>
+ </species>
+ </listOfSpecies>
+ </model>
+
+</sbml>
Deleted: trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.txt
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.txt 2010-09-29 11:33:16 UTC (rev 12064)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.txt 2010-09-29 18:30:53 UTC (rev 12065)
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
- <model id="onespecies" xmlns:xlink="http://www.w3.org/1999/xlink">
- <listOfSubmodels>
- <submodel id="A">
- <modelRef xlink:href="enzyme_model.xml" modelID="enzyme" />
- </submodel>
- <submodel id="B">
- <modelRef xlink:href="enzyme_model.xml" modelID="enzyme" />
- </submodel>
- </listOfSubmodels>
- <listOfCompartments>
- <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
- <replaces>
- <subelement submodel="A" idRef="comp" identical="true" />
- <subelement submodel="B" idRef="comp" identical="true" />
- </replaces>
- </listOfCompartments>
- <listOfSpecies>
- <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
- <replaces>
- <subelement submodel="A" idRef="S" identical="true" />
- <subelement submodel="B" idRef="S" identical="true" />
- </replaces>
- </species>
- </listOfSpecies>
- </model>
-</sbml>
Copied: trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml (from rev 12064, trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.txt)
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_onespecies.xml 2010-09-29 18:30:53 UTC (rev 12065)
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+ <model id="onespecies" xmlns:xlink="http://www.w3.org/1999/xlink">
+ <listOfSubmodels>
+ <submodel id="A">
+ <modelRef xlink:href="enzyme_model.xml" modelID="enzyme" />
+ </submodel>
+ <submodel id="B">
+ <modelRef xlink:href="enzyme_model.xml" modelID="enzyme" />
+ </submodel>
+ </listOfSubmodels>
+ <listOfCompartments>
+ <compartment id="comp" size="1" constant="true" sboTerm="SBO:0000410"/>
+ <replaces>
+ <subelement submodel="A" idRef="comp" identical="true" />
+ <subelement submodel="B" idRef="comp" identical="true" />
+ </replaces>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <replaces>
+ <subelement submodel="A" idRef="S" identical="true" />
+ <subelement submodel="B" idRef="S" identical="true" />
+ </replaces>
+ </species>
+ </listOfSpecies>
+ </model>
+</sbml>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-29 11:33:28
|
Revision: 12064
http://sbml.svn.sourceforge.net/sbml/?rev=12064&view=rev
Author: sarahkeating
Date: 2010-09-29 11:33:16 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
updated version and files that use it
Modified Paths:
--------------
trunk/libsbml/VERSION.txt
trunk/libsbml/configure
trunk/libsbml/src/common/libsbml-namespace.h
trunk/libsbml/src/common/libsbml-package.h
trunk/libsbml/src/common/libsbml-version.h
Modified: trunk/libsbml/VERSION.txt
===================================================================
--- trunk/libsbml/VERSION.txt 2010-09-29 10:25:59 UTC (rev 12063)
+++ trunk/libsbml/VERSION.txt 2010-09-29 11:33:16 UTC (rev 12064)
@@ -1 +1 @@
-4.1.0
+4.2.0
\ No newline at end of file
Modified: trunk/libsbml/configure
===================================================================
--- trunk/libsbml/configure 2010-09-29 10:25:59 UTC (rev 12063)
+++ trunk/libsbml/configure 2010-09-29 11:33:16 UTC (rev 12064)
@@ -1,63 +1,86 @@
#! /bin/sh
-# From configure.ac Revision: 12053 .
+# From configure.ac Revision: 12054 .
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.61 for libSBML 4.1.0.
+# Generated by GNU Autoconf 2.67 for libSBML 4.2.0.
#
# Report bugs to <lib...@ca...>.
#
+#
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-# 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software
+# Foundation, Inc.
+#
+#
# This configure script is free software; the Free Software Foundation
# gives unlimited permission to copy, distribute and modify it.
-## --------------------- ##
-## M4sh Initialization. ##
-## --------------------- ##
+## -------------------- ##
+## M4sh Initialization. ##
+## -------------------- ##
# Be more Bourne compatible
DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
emulate sh
NULLCMD=:
- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
# is contrary to our usage. Disable this feature.
alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
+ case `(set -o) 2>/dev/null` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
esac
-
fi
-
-
-# PATH needs CR
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
-
-# The user is always right.
-if test "${PATH_SEPARATOR+set}" != set; then
- echo "#! /bin/sh" >conf$$.sh
- echo "exit 0" >>conf$$.sh
- chmod +x conf$$.sh
- if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
- PATH_SEPARATOR=';'
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+# Prefer a ksh shell builtin over an external printf program on Solaris,
+# but without wasting forks for bash or zsh.
+if test -z "$BASH_VERSION$ZSH_VERSION" \
+ && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='print -r --'
+ as_echo_n='print -rn --'
+elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
else
- PATH_SEPARATOR=:
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in #(
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
fi
- rm -f conf$$.sh
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
fi
-# Support unset when possible.
-if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
- as_unset=unset
-else
- as_unset=false
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
fi
@@ -66,20 +89,18 @@
# there to prevent editors from complaining about space-tab.
# (If _AS_PATH_WALK were called with IFS unset, it would disable word
# splitting by setting IFS to empty value.)
-as_nl='
-'
IFS=" "" $as_nl"
# Find who we are. Look in the path if we contain no directory separator.
-case $0 in
+case $0 in #((
*[\\/]* ) as_myself=$0 ;;
*) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
for as_dir in $PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
-done
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+ done
IFS=$as_save_IFS
;;
@@ -90,354 +111,322 @@
as_myself=$0
fi
if test ! -f "$as_myself"; then
- echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- { (exit 1); exit 1; }
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ exit 1
fi
-# Work around bugs in pre-3.0 UWIN ksh.
-for as_var in ENV MAIL MAILPATH
-do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+# Unset variables that we do not need and which cause bugs (e.g. in
+# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
+# suppresses any "Segmentation fault" message there. '((' could
+# trigger a bug in pdksh 5.2.14.
+for as_var in BASH_ENV ENV MAIL MAILPATH
+do eval test x\${$as_var+set} = xset \
+ && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
done
PS1='$ '
PS2='> '
PS4='+ '
# NLS nuisances.
-for as_var in \
- LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
- LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
- LC_TELEPHONE LC_TIME
-do
- if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
- eval $as_var=C; export $as_var
- else
- ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
- fi
-done
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
-# Required to use basename.
-if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-else
- as_expr=false
-fi
-
-if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
- as_basename=basename
-else
- as_basename=false
-fi
-
-
-# Name of the executable.
-as_me=`$as_basename -- "$0" ||
-$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
- X"$0" : 'X\(//\)$' \| \
- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-echo X/"$0" |
- sed '/^.*\/\([^/][^/]*\)\/*$/{
- s//\1/
- q
- }
- /^X\/\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\/\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
-
# CDPATH.
-$as_unset CDPATH
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
if test "x$CONFIG_SHELL" = x; then
- if (eval ":") 2>/dev/null; then
- as_have_required=yes
+ as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
else
- as_have_required=no
+ case \`(set -o) 2>/dev/null\` in #(
+ *posix*) :
+ set -o posix ;; #(
+ *) :
+ ;;
+esac
fi
+"
+ as_required="as_fn_return () { (exit \$1); }
+as_fn_success () { as_fn_return 0; }
+as_fn_failure () { as_fn_return 1; }
+as_fn_ret_success () { return 0; }
+as_fn_ret_failure () { return 1; }
- if test $as_have_required = yes && (eval ":
-(as_func_return () {
- (exit \$1)
-}
-as_func_success () {
- as_func_return 0
-}
-as_func_failure () {
- as_func_return 1
-}
-as_func_ret_success () {
- return 0
-}
-as_func_ret_failure () {
- return 1
-}
-
exitcode=0
-if as_func_success; then
- :
-else
- exitcode=1
- echo as_func_success failed.
-fi
+as_fn_success || { exitcode=1; echo as_fn_success failed.; }
+as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
+as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
+as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
+if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
-if as_func_failure; then
- exitcode=1
- echo as_func_failure succeeded.
-fi
-
-if as_func_ret_success; then
- :
else
- exitcode=1
- echo as_func_ret_success failed.
+ exitcode=1; echo positional parameters were not saved.
fi
-
-if as_func_ret_failure; then
- exitcode=1
- echo as_func_ret_failure succeeded.
-fi
-
-if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
- :
+test x\$exitcode = x0 || exit 1"
+ as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
+ as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
+ eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
+ test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
+test \$(( 1 + 1 )) = 2 || exit 1"
+ if (eval "$as_required") 2>/dev/null; then :
+ as_have_required=yes
else
- exitcode=1
- echo positional parameters were not saved.
+ as_have_required=no
fi
+ if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
-test \$exitcode = 0) || { (exit 1); exit 1; }
-
-(
- as_lineno_1=\$LINENO
- as_lineno_2=\$LINENO
- test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
- test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
-") 2> /dev/null; then
- :
else
- as_candidate_shells=
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+as_found=false
for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
do
IFS=$as_save_IFS
test -z "$as_dir" && as_dir=.
- case $as_dir in
+ as_found=:
+ case $as_dir in #(
/*)
for as_base in sh bash ksh sh5; do
- as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
+ # Try only shells that exist, to save several forks.
+ as_shell=$as_dir/$as_base
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ CONFIG_SHELL=$as_shell as_have_required=yes
+ if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
+ break 2
+fi
+fi
done;;
esac
+ as_found=false
done
+$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
+ { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
+ CONFIG_SHELL=$SHELL as_have_required=yes
+fi; }
IFS=$as_save_IFS
- for as_shell in $as_candidate_shells $SHELL; do
- # Try only shells that exist, to save several forks.
- if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
- { ("$as_shell") 2> /dev/null <<\_ASEOF
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
- emulate sh
- NULLCMD=:
- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
-else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
-esac
-
+ if test "x$CONFIG_SHELL" != x; then :
+ # We cannot yet assume a decent shell, so we have to provide a
+ # neutralization value for shells without unset; and this also
+ # works around shells that cannot unset nonexistent variables.
+ BASH_ENV=/dev/null
+ ENV=/dev/null
+ (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
fi
-
-:
-_ASEOF
-}; then
- CONFIG_SHELL=$as_shell
- as_have_required=yes
- if { "$as_shell" 2> /dev/null <<\_ASEOF
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
- emulate sh
- NULLCMD=:
- # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
-else
- case `(set -o) 2>/dev/null` in
- *posix*) set -o posix ;;
-esac
-
+ if test x$as_have_required = xno; then :
+ $as_echo "$0: This script requires a shell more modern than all"
+ $as_echo "$0: the shells that I found on your system."
+ if test x${ZSH_VERSION+set} = xset ; then
+ $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
+ $as_echo "$0: be upgraded to zsh 4.3.4 or later."
+ else
+ $as_echo "$0: Please tell bug...@gn... and
+$0: lib...@ca... about your system, including
+$0: any error possibly output before this message. Then
+$0: install a modern shell, or manually run the script
+$0: under such a shell if you do have one."
+ fi
+ exit 1
fi
-
-
-:
-(as_func_return () {
- (exit $1)
-}
-as_func_success () {
- as_func_return 0
-}
-as_func_failure () {
- as_func_return 1
-}
-as_func_ret_success () {
- return 0
-}
-as_func_ret_failure () {
- return 1
-}
-
-exitcode=0
-if as_func_success; then
- :
-else
- exitcode=1
- echo as_func_success failed.
fi
-
-if as_func_failure; then
- exitcode=1
- echo as_func_failure succeeded.
fi
+SHELL=${CONFIG_SHELL-/bin/sh}
+export SHELL
+# Unset more variables known to interfere with behavior of common tools.
+CLICOLOR_FORCE= GREP_OPTIONS=
+unset CLICOLOR_FORCE GREP_OPTIONS
-if as_func_ret_success; then
- :
-else
- exitcode=1
- echo as_func_ret_success failed.
-fi
+## --------------------- ##
+## M4sh Shell Functions. ##
+## --------------------- ##
+# as_fn_unset VAR
+# ---------------
+# Portably unset VAR.
+as_fn_unset ()
+{
+ { eval $1=; unset $1;}
+}
+as_unset=as_fn_unset
-if as_func_ret_failure; then
- exitcode=1
- echo as_func_ret_failure succeeded.
-fi
+# as_fn_set_status STATUS
+# -----------------------
+# Set $? to STATUS, without forking.
+as_fn_set_status ()
+{
+ return $1
+} # as_fn_set_status
-if ( set x; as_func_ret_success y && test x = "$1" ); then
- :
-else
- exitcode=1
- echo positional parameters were not saved.
-fi
+# as_fn_exit STATUS
+# -----------------
+# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
+as_fn_exit ()
+{
+ set +e
+ as_fn_set_status $1
+ exit $1
+} # as_fn_exit
-test $exitcode = 0) || { (exit 1); exit 1; }
+# as_fn_mkdir_p
+# -------------
+# Create "$as_dir" as a directory, including parents if necessary.
+as_fn_mkdir_p ()
+{
-(
- as_lineno_1=$LINENO
- as_lineno_2=$LINENO
- test "x$as_lineno_1" != "x$as_lineno_2" &&
- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
+ case $as_dir in #(
+ -*) as_dir=./$as_dir;;
+ esac
+ test -d "$as_dir" || eval $as_mkdir_p || {
+ as_dirs=
+ while :; do
+ case $as_dir in #(
+ *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ test -d "$as_dir" && break
+ done
+ test -z "$as_dirs" || eval "mkdir $as_dirs"
+ } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-_ASEOF
-}; then
- break
-fi
-fi
+} # as_fn_mkdir_p
+# as_fn_append VAR VALUE
+# ----------------------
+# Append the text in VALUE to the end of the definition contained in VAR. Take
+# advantage of any shell optimizations that allow amortized linear growth over
+# repeated appends, instead of the typical quadratic growth present in naive
+# implementations.
+if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
+ eval 'as_fn_append ()
+ {
+ eval $1+=\$2
+ }'
+else
+ as_fn_append ()
+ {
+ eval $1=\$$1\$2
+ }
+fi # as_fn_append
- done
+# as_fn_arith ARG...
+# ------------------
+# Perform arithmetic evaluation on the ARGs, and store the result in the
+# global $as_val. Take advantage of shells that can avoid forks. The arguments
+# must be portable across $(()) and expr.
+if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
+ eval 'as_fn_arith ()
+ {
+ as_val=$(( $* ))
+ }'
+else
+ as_fn_arith ()
+ {
+ as_val=`expr "$@" || test $? -eq 1`
+ }
+fi # as_fn_arith
- if test "x$CONFIG_SHELL" != x; then
- for as_var in BASH_ENV ENV
- do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
- done
- export CONFIG_SHELL
- exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
-fi
+# as_fn_error STATUS ERROR [LINENO LOG_FD]
+# ----------------------------------------
+# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
+# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
+# script with STATUS, using 1 if that was 0.
+as_fn_error ()
+{
+ as_status=$1; test $as_status -eq 0 && as_status=1
+ if test "$4"; then
+ as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
+ fi
+ $as_echo "$as_me: error: $2" >&2
+ as_fn_exit $as_status
+} # as_fn_error
- if test $as_have_required = no; then
- echo This script requires a shell more modern than all the
- echo shells that I found on your system. Please install a
- echo modern shell, or manually run the script under such a
- echo shell if you do have one.
- { (exit 1); exit 1; }
-fi
-
-
-fi
-
-fi
-
-
-
-(eval "as_func_return () {
- (exit \$1)
-}
-as_func_success () {
- as_func_return 0
-}
-as_func_failure () {
- as_func_return 1
-}
-as_func_ret_success () {
- return 0
-}
-as_func_ret_failure () {
- return 1
-}
-
-exitcode=0
-if as_func_success; then
- :
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
else
- exitcode=1
- echo as_func_success failed.
+ as_expr=false
fi
-if as_func_failure; then
- exitcode=1
- echo as_func_failure succeeded.
-fi
-
-if as_func_ret_success; then
- :
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
else
- exitcode=1
- echo as_func_ret_success failed.
+ as_basename=false
fi
-if as_func_ret_failure; then
- exitcode=1
- echo as_func_ret_failure succeeded.
-fi
-
-if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
- :
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
else
- exitcode=1
- echo positional parameters were not saved.
+ as_dirname=false
fi
-test \$exitcode = 0") || {
- echo No shell found that supports shell functions.
- echo Please tell aut...@gn... about your system,
- echo including any error possibly output before this
- echo message
-}
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
- as_lineno_1=$LINENO
- as_lineno_2=$LINENO
- test "x$as_lineno_1" != "x$as_lineno_2" &&
- test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
-
- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
- # uniformly replaced by the line number. The first 'sed' inserts a
- # line-number line after each line using $LINENO; the second 'sed'
- # does the real work. The second script uses 'N' to pair each
- # line-number line with the line containing $LINENO, and appends
- # trailing '-' during substitution so that $LINENO is not a special
- # case at line end.
- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
- # scripts with optimization help from Paolo Bonzini. Blame Lee
- # E. McMahon (1931-1989) for sed's syntax. :-)
+ as_lineno_1=$LINENO as_lineno_1a=$LINENO
+ as_lineno_2=$LINENO as_lineno_2a=$LINENO
+ eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
+ test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
+ # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
sed -n '
p
/[$]LINENO/=
@@ -454,8 +443,7 @@
s/-\n.*//
' >$as_me.lineno &&
chmod +x "$as_me.lineno" ||
- { echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
- { (exit 1); exit 1; }; }
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
# Don't try to exec as it changes $[0], causing all sort of problems
# (the dirname of $[0] is not the place where we might find the
@@ -465,49 +453,40 @@
exit
}
-
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
- as_dirname=dirname
-else
- as_dirname=false
-fi
-
ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in
+case `echo -n x` in #(((((
-n*)
- case `echo 'x\c'` in
+ case `echo 'xy\c'` in
*c*) ECHO_T=' ';; # ECHO_T is single tab character.
- *) ECHO_C='\c';;
+ xy) ECHO_C='\c';;
+ *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
+ ECHO_T=' ';;
esac;;
*)
ECHO_N='-n';;
esac
-if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-else
- as_expr=false
-fi
-
rm -f conf$$ conf$$.exe conf$$.file
if test -d conf$$.dir; then
rm -f conf$$.dir/conf$$.file
else
rm -f conf$$.dir
- mkdir conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
fi
-echo >conf$$.file
-if ln -s conf$$.file conf$$ 2>/dev/null; then
- as_ln_s='ln -s'
- # ... but there are two gotchas:
- # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
- # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -p'.
- ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
as_ln_s='cp -p'
-elif ln conf$$.file conf$$ 2>/dev/null; then
- as_ln_s=ln
+ fi
else
as_ln_s='cp -p'
fi
@@ -515,7 +494,7 @@
rmdir conf$$.dir 2>/dev/null
if mkdir -p . 2>/dev/null; then
- as_mkdir_p=:
+ as_mkdir_p='mkdir -p "$as_dir"'
else
test -d ./-p && rmdir ./-p
as_mkdir_p=false
@@ -532,12 +511,12 @@
as_test_x='
eval sh -c '\''
if test -d "$1"; then
- test -d "$1/.";
+ test -d "$1/.";
else
- case $1 in
- -*)set "./$1";;
+ case $1 in #(
+ -*)set "./$1";;
esac;
- case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #((
???[sx]*):;;*)false;;esac;fi
'\'' sh
'
@@ -552,7 +531,6 @@
-
# Check that we are running under the correct shell.
SHELL=${CONFIG_SHELL-/bin/sh}
@@ -706,10 +684,11 @@
tagnames=${tagnames+${tagnames},}F77
-exec 7<&0 </dev/null 6>&1
+test -n "$DJDIR" || exec 7<&0 </dev/null
+exec 6>&1
# Name of the host.
-# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
# so uname gets run too.
ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
@@ -724,14 +703,14 @@
subdirs=
MFLAGS=
MAKEFLAGS=
-SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='libSBML'
PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='4.1.0'
-PACKAGE_STRING='libSBML 4.1.0'
+PACKAGE_VERSION='4.2.0'
+PACKAGE_STRING='libSBML 4.2.0'
PACKAGE_BUGREPORT='lib...@ca...'
+PACKAGE_URL=''
ac_unique_file="src/Makefile.in"
# Factoring default headers for most tests.
@@ -770,197 +749,233 @@
# include <unistd.h>
#endif"
-ac_subst_vars='SHELL
-PATH_SEPARATOR
-PACKAGE_NAME
-PACKAGE_TARNAME
-PACKAGE_VERSION
-PACKAGE_STRING
-PACKAGE_BUGREPORT
-exec_prefix
-prefix
-program_transform_name
-bindir
-sbindir
-libexecdir
-datarootdir
-datadir
-sysconfdir
-sharedstatedir
-localstatedir
-includedir
-oldincludedir
-docdir
-infodir
-htmldir
-dvidir
-pdfdir
-psdir
-libdir
-localedir
-mandir
-DEFS
-ECHO_C
-ECHO_N
-ECHO_T
-LIBS
-build_alias
-host_alias
-target_alias
-LIBSBML_VERSION_NUMERIC
-LIBSBML_MAJOR_VERSION
-LIBSBML_MINOR_VERSION
-LIBSBML_REVISION_VERSION
-LIBSBML_BETA_VERSION
-USE_LAYOUT
-USE_COMPRESSION
-build
-build_cpu
-build_vendor
-build_os
-host
-host_cpu
-host_vendor
-host_os
-USE_UNIVBINARY
-SHAREDLIBEXT
-HOST_TYPE
-LIBSUFFIX
-RUN_LDPATH
-CXX
-CXXFLAGS
-LDFLAGS
-CPPFLAGS
-ac_ct_CXX
-EXEEXT
-OBJEXT
-CC
-CFLAGS
-ac_ct_CC
-CPP
-INSTALL_PROGRAM
-INSTALL_SCRIPT
-INSTALL_DATA
-SET_MAKE
-AUTOCONF
-ACLOCAL
-HAS_GCC_WNO_LONG_DOUBLE
-PYTHON
-USE_PYTHON
-PYTHON_CPPFLAGS
-PYTHON_LDFLAGS
-PYTHON_LIBS
-PYTHON_EXT
-PERL
-USE_PERL
-PERL_CPPFLAGS
-PERL_LDFLAGS
-PERL_LIBS
-JAVA
-JAVAC
-JAR
-USE_JAVA
-JAVA_CPPFLAGS
-JAVA_LDFLAGS
-JNIEXT
-JNIBASENAME
-JAVADOC_JAR
-MEX
-MATLAB
-USE_MATLAB
-MATLAB_CPPFLAGS
-MATLAB_LDFLAGS
-MATLAB_LIBS
-MEX_FLAGS
-MEX_ARCH
-MEXEXT
-MATLABROOT
-OCTAVE
-MKOCTFILE
-OCTAVE_CONFIG
-USE_OCTAVE
-MKOCTFILE_FLAGS
-OCTAVEEXT
-LOCALOCTFILEDIR
-RUBY
-USE_RUBY
-RUBY_CPPFLAGS
-RUBY_LDFLAGS
-RUBY_LIBS
-CSHARP_COMPILER
-CSHARP_CILINTERPRETER
-SN
-GACUTIL
-USE_CSHARP
-CSHARP_CPPFLAGS
-CSHARP_LDFLAGS
-CSHARP_SWIGFLAGS
-CSHARP_EXT
-SWIG_CONFIG_OPT
-SWIG
-USE_SWIG
-SWIGLIB
-SWIGFLAGS
-SWIG_CPPFLAGS
-SWIG_LDFLAGS
-SWIG_LIBS
-SWIGNEEDVERSION
-DOXYGEN_CONFIG_OPT
-DOXYGEN
-USE_DOXYGEN
-SED
-GREP
-EGREP
-LN_S
-ECHO
-AR
-RANLIB
-STRIP
-DSYMUTIL
-NMEDIT
-DLLTOOL
-AS
-OBJDUMP
-CXXCPP
-F77
-FFLAGS
-ac_ct_F77
-LIBTOOL
-DOLT_BASH
-LTCOMPILE
-LTCXXCOMPILE
-USE_EXPAT
-EXPAT_CPPFLAGS
-EXPAT_LDFLAGS
-EXPAT_LIBS
-XML_PARSER
-USE_XERCES
-XERCES_CPPFLAGS
-XERCES_LDFLAGS
-XERCES_LIBS
-XML2_CONFIG
-USE_LIBXML
-LIBXML_CPPFLAGS
-LIBXML_LDFLAGS
-LIBXML_LIBS
-BUGGY_APPLE_LIBXML
-USE_LIBCHECK
-LIBCHECK_CPPFLAGS
-LIBCHECK_LDFLAGS
-LIBCHECK_LIBS
-USE_ZLIB
-ZLIB_CPPFLAGS
-ZLIB_LDFLAGS
-ZLIB_LIBS
-USE_BZ2
-BZ2_CPPFLAGS
-BZ2_LDFLAGS
-BZ2_LIBS
-USE_SUN_CC
-LIBSBML_OPTIONS
+ac_subst_vars='LTLIBOBJS
LIBOBJS
-LTLIBOBJS'
+LIBSBML_OPTIONS
+USE_SUN_CC
+BZ2_LIBS
+BZ2_LDFLAGS
+BZ2_CPPFLAGS
+USE_BZ2
+ZLIB_LIBS
+ZLIB_LDFLAGS
+ZLIB_CPPFLAGS
+USE_ZLIB
+LIBCHECK_LIBS
+LIBCHECK_LDFLAGS
+LIBCHECK_CPPFLAGS
+USE_LIBCHECK
+BUGGY_APPLE_LIBXML
+LIBXML_LIBS
+LIBXML_LDFLAGS
+LIBXML_CPPFLAGS
+USE_LIBXML
+XML2_CONFIG
+XERCES_LIBS
+XERCES_LDFLAGS
+XERCES_CPPFLAGS
+USE_XERCES
+XML_PARSER
+EXPAT_LIBS
+EXPAT_LDFLAGS
+EXPAT_CPPFLAGS
+USE_EXPAT
+LTCXXCOMPILE
+LTCOMPILE
+DOLT_BASH
+LIBTOOL
+ac_ct_F77
+FFLAGS
+F77
+CXXCPP
+OBJDUMP
+AS
+DLLTOOL
+NMEDIT
+DSYMUTIL
+STRIP
+RANLIB
+AR
+ECHO
+LN_S
+EGREP
+GREP
+SED
+USE_DOXYGEN
+DOXYGEN
+DOXYGEN_CONFIG_OPT
+SWIGNEEDVERSION
+SWIG_LIBS
+SWIG_LDFLAGS
+SWIG_CPPFLAGS
+SWIGFLAGS
+SWIGLIB
+USE_SWIG
+SWIG
+SWIG_CONFIG_OPT
+CSHARP_EXT
+CSHARP_SWIGFLAGS
+CSHARP_LDFLAGS
+CSHARP_CPPFLAGS
+USE_CSHARP
+GACUTIL
+SN
+CSHARP_CILINTERPRETER
+CSHARP_COMPILER
+RUBY_LIBS
+RUBY_LDFLAGS
+RUBY_CPPFLAGS
+USE_RUBY
+RUBY
+LOCALOCTFILEDIR
+OCTAVEEXT
+MKOCTFILE_FLAGS
+USE_OCTAVE
+OCTAVE_CONFIG
+MKOCTFILE
+OCTAVE
+MATLABROOT
+MEXEXT
+MEX_ARCH
+MEX_FLAGS
+MATLAB_LIBS
+MATLAB_LDFLAGS
+MATLAB_CPPFLAGS
+USE_MATLAB
+MATLAB
+MEX
+JAVADOC_JAR
+JNIBASENAME
+JNIEXT
+JAVA_LDFLAGS
+JAVA_CPPFLAGS
+USE_JAVA
+JAR
+JAVAC
+JAVA
+PERL_LIBS
+PERL_LDFLAGS
+PERL_CPPFLAGS
+USE_PERL
+PERL
+PYTHON_EXT
+PYTHON_LIBS
+PYTHON_LDFLAGS
+PYTHON_CPPFLAGS
+USE_PYTHON
+PYTHON
+HAS_GCC_WNO_LONG_DOUBLE
+ACLOCAL
+AUTOCONF
+SET_MAKE
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+CPP
+ac_ct_CC
+CFLAGS
+CC
+OBJEXT
+EXEEXT
+ac_ct_CXX
+CPPFLAGS
+LDFLAGS
+CXXFLAGS
+CXX
+RUN_LDPATH
+LIBSUFFIX
+HOST_TYPE
+SHAREDLIBEXT
+USE_UNIVBINARY
+host_os
+host_vendor
+host_cpu
+host
+build_os
+build_vendor
+build_cpu
+build
+USE_COMPRESSION
+USE_LAYOUT
+LIBSBML_BETA_VERSION
+LIBSBML_REVISION_VERSION
+LIBSBML_MINOR_VERSION
+LIBSBML_MAJOR_VERSION
+LIBSBML_VERSION_NUMERIC
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_URL
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
ac_subst_files=''
+ac_user_opts='
+enable_option_checking
+enable_cpp_namespace
+enable_layout
+enable_compression
+enable_m32
+enable_m64
+enable_universal_binary
+with_python
+with_perl
+with_java
+with_java_bin_check
+with_matlab
+with_octave
+with_ruby
+with_csharp
+with_cil_interpreter
+with_csharp_compiler
+with_swig
+with_doxygen
+enable_shared
+enable_static
+enable_fast_install
+with_gnu_ld
+enable_libtool_lock
+with_pic
+with_tags
+with_expat
+with_xerces
+with_libxml
+with_check
+with_zlib
+with_zlib_version_check
+with_bzip2
+'
ac_precious_vars='build_alias
host_alias
target_alias
@@ -984,6 +999,8 @@
# Initialize some variables set by options.
ac_init_help=
ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
# The variables have the same names as the options, with
# dashes changed to underlines.
cache_file=/dev/null
@@ -1039,8 +1056,9 @@
fi
case $ac_option in
- *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
- *) ac_optarg=yes ;;
+ *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *=) ac_optarg= ;;
+ *) ac_optarg=yes ;;
esac
# Accept the important Cygnus configure options, so we can diagnose typos.
@@ -1082,13 +1100,20 @@
datarootdir=$ac_optarg ;;
-disable-* | --disable-*)
- ac_feature=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
# Reject names that are not valid shell variable names.
- expr "x$ac_feature" : ".*[^-._$as_cr_alnum]" >/dev/null &&
- { echo "$as_me: error: invalid feature name: $ac_feature" >&2
- { (exit 1); exit 1; }; }
- ac_feature=`echo $ac_feature | sed 's/[-.]/_/g'`
- eval enable_$ac_feature=no ;;
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
-docdir | --docdir | --docdi | --doc | --do)
ac_prev=docdir ;;
@@ -1101,13 +1126,20 @@
dvidir=$ac_optarg ;;
-enable-* | --enable-*)
- ac_feature=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
# Reject names that are not valid shell variable names.
- expr "x$ac_feature" : ".*[^-._$as_cr_alnum]" >/dev/null &&
- { echo "$as_me: error: invalid feature name: $ac_feature" >&2
- { (exit 1); exit 1; }; }
- ac_feature=`echo $ac_feature | sed 's/[-.]/_/g'`
- eval enable_$ac_feature=\$ac_optarg ;;
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid feature name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--enable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=\$ac_optarg ;;
-exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
| --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
@@ -1298,22 +1330,36 @@
ac_init_version=: ;;
-with-* | --with-*)
- ac_package=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
+ ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
# Reject names that are not valid shell variable names.
- expr "x$ac_package" : ".*[^-._$as_cr_alnum]" >/dev/null &&
- { echo "$as_me: error: invalid package name: $ac_package" >&2
- { (exit 1); exit 1; }; }
- ac_package=`echo $ac_package | sed 's/[-.]/_/g'`
- eval with_$ac_package=\$ac_optarg ;;
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid package name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--with-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=\$ac_optarg ;;
-without-* | --without-*)
- ac_package=`expr "x$ac_option" : 'x-*without-\(.*\)'`
+ ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
# Reject names that are not valid shell variable names.
- expr "x$ac_package" : ".*[^-._$as_cr_alnum]" >/dev/null &&
- { echo "$as_me: error: invalid package name: $ac_package" >&2
- { (exit 1); exit 1; }; }
- ac_package=`echo $ac_package | sed 's/[-.]/_/g'`
- eval with_$ac_package=no ;;
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ as_fn_error $? "invalid package name: $ac_useropt"
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"with_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval with_$ac_useropt=no ;;
--x)
# Obsolete; use --with-x.
@@ -1333,25 +1379,25 @@
| --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
x_libraries=$ac_optarg ;;
- -*) { echo "$as_me: error: unrecognized option: $ac_option
-Try \`$0 --help' for more information." >&2
- { (exit 1); exit 1; }; }
+ -*) as_fn_error $? "unrecognized option: \`$ac_option'
+Try \`$0 --help' for more information"
;;
*=*)
ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
# Reject names that are not valid shell variable names.
- expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null &&
- { echo "$as_me: error: invalid variable name: $ac_envvar" >&2
- { (exit 1); exit 1; }; }
+ case $ac_envvar in #(
+ '' | [0-9]* | *[!_$as_cr_alnum]* )
+ as_fn_error $? "invalid variable name: \`$ac_envvar'" ;;
+ esac
eval $ac_envvar=\$ac_optarg
export $ac_envvar ;;
*)
# FIXME: should be removed in autoconf 3.0.
- echo "$as_me: WARNING: you should use --build, --host, --target" >&2
+ $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
- echo "$as_me: WARNING: invalid host type: $ac_option" >&2
+ $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2
: ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
;;
@@ -1360,23 +1406,36 @@
if test -n "$ac_prev"; then
ac_option=--`echo $ac_prev | sed 's/_/-/g'`
- { echo "$as_me: error: missing argument to $ac_option" >&2
- { (exit 1); exit 1; }; }
+ as_fn_error $? "missing argument to $ac_option"
fi
-# Be sure to have absolute directory names.
+if test -n "$ac_unrecognized_opts"; then
+ case $enable_option_checking in
+ no) ;;
+ fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;;
+ *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
+ esac
+fi
+
+# Check all directory arguments for consistency.
for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
datadir sysconfdir sharedstatedir localstatedir includedir \
oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
libdir localedir mandir
do
eval ac_val=\$$ac_var
+ # Remove trailing slashes.
case $ac_val in
+ */ )
+ ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
+ eval $ac_var=\$ac_val;;
+ esac
+ # Be sure to have absolute directory names.
+ case $ac_val in
[\\/$]* | ?:[\\/]* ) continue;;
NONE | '' ) case $ac_var in *prefix ) continue;; esac;;
esac
- { echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2
- { (exit 1); exit 1; }; }
+ as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val"
done
# There might be people who depend on the old broken behavior: `$host'
@@ -1390,8 +1449,8 @@
if test "x$host_alias" != x; then
if test "x$build_alias" = x; then
cross_compiling=maybe
- echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
- If a cross compiler is detected then cross compile mode will be used." >&2
+ $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host.
+ If a cross compiler is detected then cross compile mode will be used" >&2
elif test "x$build_alias" != "x$host_alias"; then
cross_compiling=yes
fi
@@ -1406,23 +1465,21 @@
ac_pwd=`pwd` && test -n "$ac_pwd" &&
ac_ls_di=`ls -di .` &&
ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
- { echo "$as_me: error: Working directory cannot be determined" >&2
- { (exit 1); exit 1; }; }
+ as_fn_error $? "working directory cannot be determined"
test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
- { echo "$as_me: error: pwd does not report name of working directory" >&2
- { (exit 1); exit 1; }; }
+ as_fn_error $? "pwd does not report name of working directory"
# Find the source files, if location was not specified.
if test -z "$srcdir"; then
ac_srcdir_defaulted=yes
# Try the directory containing this script, then the parent directory.
- ac_confdir=`$as_dirname -- "$0" ||
-$as_expr X"$0" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$0" : 'X\(//\)[^/]' \| \
- X"$0" : 'X\(//\)$' \| \
- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-echo X"$0" |
+ ac_confdir=`$as_dirname -- "$as_myself" ||
+$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_myself" : 'X\(//\)[^/]' \| \
+ X"$as_myself" : 'X\(//\)$' \| \
+ X"$as_myself" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$as_myself" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
@@ -1449,13 +1506,11 @@
fi
if test ! -r "$srcdir/$ac_unique_file"; then
test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
- { echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
- { (exit 1); exit 1; }; }
+ as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir"
fi
ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
ac_abs_confdir=`(
- cd "$srcdir" && test -r "./$ac_unique_file" || { echo "$as_me: error: $ac_msg" >&2
- { (exit 1); exit 1; }; }
+ cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg"
pwd)`
# When building in place, set srcdir=.
if test "$ac_abs_confdir" = "$ac_pwd"; then
@@ -1481,7 +1536,7 @@
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures libSBML 4.1.0 to adapt to many kinds of systems.
+\`configure' configures libSBML 4.2.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1495,7 +1550,7 @@
--help=short display options specific to this package
--help=recursive display the short help of all the included packages
-V, --version display version information and exit
- -q, --quiet, --silent do not print \`checking...' messages
+ -q, --quiet, --silent do not print \`checking ...' messages
--cache-file=FILE cache test results in FILE [disabled]
-C, --config-cache alias for \`--cache-file=config.cache'
-n, --no-create do not create output files
@@ -1503,9 +1558,9 @@
Installation directories:
--prefix=PREFIX install architecture-independent files in PREFIX
- [$ac_default_prefix]
+ [$ac_default_prefix]
--exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
- [PREFIX]
+ [PREFIX]
By default, \`make install' will install all the files in
\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
@@ -1515,25 +1570,25 @@
For better control, use the options below.
Fine tuning of the installation directories:
- --bindir=DIR user executables [EPREFIX/bin]
- --sbindir=DIR system admin executables [EPREFIX/sbin]
- --libexecdir=DIR program executables [EPREFIX/libexec]
- --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
- --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
- --localstatedir=DIR modifiable single-machine data [PREFIX/var]
- --libdir=DIR object code libraries [EPREFIX/lib]
- --includedir=DIR C header files [PREFIX/include]
- --oldincludedir=DIR C header files for non-gcc [/usr/include]
- --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
- --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
- --infodir=DIR info documentation [DATAROOTDIR/info]
- --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
- --mandir=DIR man documentation [DATAROOTDIR/man]
- --docdir=DIR documentation root [DATAROOTDIR/doc/libsbml]
- --htmldir=DIR html documentation [DOCDIR]
- --dvidir=DIR dvi documentation [DOCDIR]
- --pdfdir=DIR pdf documentation [DOCDIR]
- --psdir=DIR ps documentation [DOCDIR]
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
+ --mandir=DIR man documentation [DATAROOTDIR/man]
+ --docdir=DIR documentation root [DATAROOTDIR/doc/libsbml]
+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
_ACEOF
cat <<\_ACEOF
@@ -1546,11 +1601,12 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of libSBML 4.1.0:";;
+ short | recursive ) echo "Configuration of libSBML 4.2.0:";;
esac
cat <<\_ACEOF
Optional Features:
+ --disable-option-checking ignore unrecognized --enable/--with options
--disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
--enable-FEATURE[=ARG] include FEATURE [ARG=yes]
--enable-cpp-namespace[=ARG]
@@ -1606,7 +1662,7 @@
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
- CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
+ CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CC C compiler command
CFLAGS C compiler flags
@@ -1629,15 +1685,17 @@
if test "$ac_init_help" = "recursive"; then
# If there are subdirs, report their specific --help.
for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
- test -d "$ac_dir" || continue
+ test -d "$ac_dir" ||
+ { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
+ continue
ac_builddir=.
case "$ac_dir" in
.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
*)
- ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
# A ".." for each directory in $ac_dir_suffix.
- ac_top_builddir_sub=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,/..,g;s,/,,'`
+ ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
case $ac_top_builddir_sub in
"") ac_top_builddir_sub=. ac_top_build_prefix= ;;
*) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
@@ -1673,7 +1731,7 @@
echo &&
$SHELL "$ac_srcdir/configure" --help=recursive
else
- echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
fi || ac_status=$?
cd "$ac_pwd" || { ac_status=$?; break; }
done
@@ -1682,22 +1740,727 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-libSBML configure 4.1.0
-generated by GNU Autoconf 2.61
+libSBML configure 4.2.0
+generated by GNU Autoconf 2.67
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
-2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+Copyright (C) 2010 Free Software Foundation, Inc.
This configure script is free software; the Free Software Foundation
gives unlimited permission to copy, distribute and modify it.
_ACEOF
exit
fi
+
+## ------------------------ ##
+## Autoconf initialization. ##
+## ------------------------ ##
+
+# ac_fn_cxx_try_compile LINENO
+# ----------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_cxx_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_cxx_try_compile
+
+# ac_fn_c_try_compile LINENO
+# --------------------------
+# Try to compile conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext
+ if { { ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_compile") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_compile
+
+# ac_fn_c_try_cpp LINENO
+# ----------------------
+# Try to preprocess conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_cpp ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } > conftest.i && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_cpp
+
+# ac_fn_c_try_link LINENO
+# -----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded.
+ac_fn_c_try_link ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ rm -f conftest.$ac_objext conftest$ac_exeext
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>conftest.err
+ ac_status=$?
+ if test -s conftest.err; then
+ grep -v '^ *+' conftest.err >conftest.er1
+ cat conftest.er1 >&5
+ mv -f conftest.er1 conftest.err
+ fi
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=1
+fi
+ # Delete the IPA/IPO (Inter Procedural Analysis/Optimization) information
+ # created by the PGI compiler (conftest_ipa8_conftest.oo), as it would
+ # interfere with the next link command; also delete a directory that is
+ # left behind by Apple's compiler. We do this before executing the actions.
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_link
+
+# ac_fn_c_check_header_mongrel LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists, giving a warning if it cannot be compiled using
+# the include files in INCLUDES and setting the cache variable VAR
+# accordingly.
+ac_fn_c_check_header_mongrel ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if eval "test \"\${$3+set}\"" = set; then :
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 usability" >&5
+$as_echo_n "checking $2 usability... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ac_header_compiler=yes
+else
+ ac_header_compiler=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking $2 presence" >&5
+$as_echo_n "checking $2 presence... " >&6; }
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <$2>
+_ACEOF
+if ac_fn_c_try_cpp "$LINENO"; then :
+ ac_header_preproc=yes
+else
+ ac_header_preproc=no
+fi
+rm -f conftest.err conftest.i conftest.$ac_ext
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in #((
+ yes:no: )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $2: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $2: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $2: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $2: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $2: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $2: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;}
+( $as_echo "## --------------------------------------- ##
+## Report this to lib...@ca... ##
+## --------------------------------------- ##"
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ eval "$3=\$ac_header_compiler"
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+fi
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_header_mongrel
+
+# ac_fn_c_try_run LINENO
+# ----------------------
+# Try to link conftest.$ac_ext, and return whether this succeeded. Assumes
+# that executables *can* be run.
+ac_fn_c_try_run ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ if { { ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; } && { ac_try='./conftest$ac_exeext'
+ { { case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+ test $ac_status = 0; }; }; then :
+ ac_retval=0
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_retval=$ac_status
+fi
+ rm -rf conftest.dSYM conftest_ipa8_conftest.oo
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+ as_fn_set_status $ac_retval
+
+} # ac_fn_c_try_run
+
+# ac_fn_c_check_header_compile LINENO HEADER VAR INCLUDES
+# -------------------------------------------------------
+# Tests whether HEADER exists and can be compiled using the include files in
+# INCLUDES, setting the cache variable VAR accordingly.
+ac_fn_c_check_header_compile ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+$4
+#include <$2>
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+ eval $as_lineno_stack; test "x$as_lineno_stack" = x && { as_lineno=; unset as_lineno;}
+
+} # ac_fn_c_check_header_compile
+
+# ac_fn_c_check_func LINENO FUNC VAR
+# ----------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_c_check_func ()
+{
+ as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+$as_echo_n "checking for $2... " >&6; }
+if eval "test \"\${$3+set}\"" = set; then :
+ $as_echo_n "(cached) " >&6
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $2 (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main ()
+{
+return $2 ();
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_link "$LINENO"; then :
+ eval "$3=yes"
+else
+ eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext \
+ ...
[truncated message content] |
|
From: <sar...@us...> - 2010-09-29 10:26:05
|
Revision: 12063
http://sbml.svn.sourceforge.net/sbml/?rev=12063&view=rev
Author: sarahkeating
Date: 2010-09-29 10:25:59 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
updated
Modified Paths:
--------------
trunk/libsbml/NEWS.txt
Modified: trunk/libsbml/NEWS.txt
===================================================================
--- trunk/libsbml/NEWS.txt 2010-09-29 10:17:38 UTC (rev 12062)
+++ trunk/libsbml/NEWS.txt 2010-09-29 10:25:59 UTC (rev 12063)
@@ -1,11 +1,16 @@
libSBML NEWS -- History of user-visible changes
======================================================================
-Current development
+Version 4.2.0 (Released 2010-10-05)
======================================================================
* New features
+ - A number of new helper functions have been added to the XMLNode
+ class.
+
+ - Basic conversion of an L3 model to earlier levels is now supported.
+
- There is an additional validation rule that will be logged during
a 'read' that warns the user that they are reading an L3 model that
contains information from a required L3 package. Since this version
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-29 10:17:45
|
Revision: 12062
http://sbml.svn.sourceforge.net/sbml/?rev=12062&view=rev
Author: sarahkeating
Date: 2010-09-29 10:17:38 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
updated
Modified Paths:
--------------
branches/libsbml-5/NEWS.txt
Modified: branches/libsbml-5/NEWS.txt
===================================================================
--- branches/libsbml-5/NEWS.txt 2010-09-29 10:02:47 UTC (rev 12061)
+++ branches/libsbml-5/NEWS.txt 2010-09-29 10:17:38 UTC (rev 12062)
@@ -1,6 +1,35 @@
libSBML NEWS -- History of user-visible changes
======================================================================
+Version 5.0.0-a1 (released 2010-10-05)
+======================================================================
+
+This is the next alpha release of libSBML-5.
+
+This includes full support for SBML Level 3 Core; as found in
+libSBML-4.2.0.
+
+It also includes mechanisms for support of a 'layout' and a 'groups'
+extension. This support extends to all language bindings with the
+exception of matlab/octave. Note these are dummy packages based on
+proposals for the layout and groups packages. They do not represent
+fully approved L3 packages.
+
+There have been no API changes from the pre-alpha release.
+
+It is anticipated that the next release (beta) will rearrange the
+directory structure for contributed package code and provide
+a new build system to facilitate the inclusion/exclusion of
+packages.
+
+* Changes to dependencies on 3rd-party libraries:
+
+ - The language bindings now require SWIG 2.0.0 or later.
+
+
+
+
+======================================================================
Version 5.0.0-a0 (released 2010-01-18)
======================================================================
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2010-09-29 10:02:54
|
Revision: 12061
http://sbml.svn.sourceforge.net/sbml/?rev=12061&view=rev
Author: sarahkeating
Date: 2010-09-29 10:02:47 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
took out the class-id-style code for now
Actually I just commented it out using #if (0) so it is still there when we can spend time on it
Modified Paths:
--------------
branches/libsbml-5/src/math/ASTNode.cpp
branches/libsbml-5/src/math/ASTNode.h
branches/libsbml-5/src/math/MathML.cpp
branches/libsbml-5/src/math/test/TestASTNode.c
branches/libsbml-5/src/math/test/TestReadMathML.cpp
branches/libsbml-5/src/math/test/TestWriteMathML.cpp
Modified: branches/libsbml-5/src/math/ASTNode.cpp
===================================================================
--- branches/libsbml-5/src/math/ASTNode.cpp 2010-09-29 10:00:47 UTC (rev 12060)
+++ branches/libsbml-5/src/math/ASTNode.cpp 2010-09-29 10:02:47 UTC (rev 12061)
@@ -177,9 +177,11 @@
mDenominator = 1;
mParentSBMLObject = NULL;
mUnits = "";
+#if (0)
mId = "";
mClass = "";
mStyle = "";
+#endif
mUserData = NULL;
setType(type);
@@ -208,9 +210,11 @@
mDenominator = 1;
mParentSBMLObject = NULL;
mUnits = "";
+#if (0)
mId = "";
mClass = "";
mStyle = "";
+#endif
mUserData = NULL;
mChildren = new List;
@@ -238,7 +242,7 @@
}
}
-/**
+/*
*
* Copy constructor; Creates a deep copy of the given ASTNode
*
@@ -258,9 +262,11 @@
,mSemanticsAnnotations ( new List() )
,mParentSBMLObject ( orig.mParentSBMLObject )
,mUnits ( orig.mUnits)
+#if (0)
,mId ( orig.mId)
,mClass ( orig.mClass)
,mStyle ( orig.mStyle)
+#endif
,mUserData ( orig.mUserData )
{
if (orig.mName)
@@ -279,7 +285,7 @@
}
}
-/**
+/*
*
* assignment operator
*
@@ -298,9 +304,11 @@
hasSemantics = rhs.hasSemantics;
mParentSBMLObject = rhs.mParentSBMLObject;
mUnits = rhs.mUnits;
+#if (0)
mId = rhs.mId;
mClass = rhs.mClass;
mStyle = rhs.mStyle;
+#endif
mUserData = rhs.mUserData;
if (rhs.mName)
{
@@ -1161,6 +1169,7 @@
return mType;
}
+#if (0)
LIBSBML_EXTERN
std::string
ASTNode::getId() const
@@ -1181,6 +1190,7 @@
{
return mStyle;
}
+#endif
LIBSBML_EXTERN
std::string
@@ -1497,6 +1507,7 @@
}
+#if (0)
LIBSBML_EXTERN
bool
ASTNode::isSetId() const
@@ -1517,6 +1528,7 @@
{
return (mStyle.empty() == false);
}
+#endif
LIBSBML_EXTERN
bool
@@ -1736,6 +1748,7 @@
}
}
+#if (0)
LIBSBML_EXTERN
int
ASTNode::setId (std::string id)
@@ -1759,6 +1772,7 @@
mStyle = style;
return LIBSBML_OPERATION_SUCCESS;
}
+#endif
@@ -1784,15 +1798,16 @@
int
ASTNode::swapChildren (ASTNode *that)
{
- List* temp;
+ if (that == NULL)
+ return LIBSBML_OPERATION_FAILED;
-
- temp = this->mChildren;
+ List *temp = this->mChildren;
this->mChildren = that->mChildren;
that->mChildren = temp;
return LIBSBML_OPERATION_SUCCESS;
}
+#if (0)
LIBSBML_EXTERN
int
ASTNode::unsetId ()
@@ -1841,6 +1856,7 @@
return LIBSBML_OPERATION_FAILED;
}
}
+#endif
LIBSBML_EXTERN
int
@@ -2172,7 +2188,7 @@
}
-/**
+/*
* gets the definitionURL attributes
*/
LIBSBML_EXTERN
@@ -2568,6 +2584,7 @@
return static_cast<const ASTNode*>(node)->getType();
}
+#if (0)
/**
* Get the mathml id of this ASTNode.
*
@@ -2605,6 +2622,7 @@
}
+#endif
/**
* Get the units of this ASTNode.
@@ -2885,6 +2903,7 @@
}
+#if (0)
/**
* @return true (non-zero) if this ASTNode has a mathml id, false
* (0) otherwise.
@@ -2917,6 +2936,7 @@
{
return static_cast<int>(node->isSetStyle());
}
+#endif
/**
* Predicate returning true (non-zero) if this node has sbml:units.
@@ -3083,6 +3103,7 @@
}
+#if (0)
/**
* Sets the mathml id of this ASTNode to id.
*
@@ -3133,6 +3154,7 @@
{
return static_cast<ASTNode*>(node)->setStyle(style);
}
+#endif
/**
* Sets the units of this ASTNode to units.
@@ -3178,6 +3200,7 @@
->swapChildren( static_cast<ASTNode*>(that) );
}
+#if (0)
/**
* Unsets the mathml id of this ASTNode.
@@ -3223,6 +3246,7 @@
{
return static_cast<ASTNode*>(node)->unsetStyle();
}
+#endif
/**
* Unsets the units of this ASTNode.
Modified: branches/libsbml-5/src/math/ASTNode.h
===================================================================
--- branches/libsbml-5/src/math/ASTNode.h 2010-09-29 10:00:47 UTC (rev 12060)
+++ branches/libsbml-5/src/math/ASTNode.h 2010-09-29 10:02:47 UTC (rev 12061)
@@ -756,6 +756,7 @@
LIBSBML_EXTERN
char getCharacter () const;
+#if (0)
/**
* Get the id of this ASTNode.
*
@@ -779,6 +780,7 @@
*/
LIBSBML_EXTERN
std::string getStyle () const;
+#endif
/**
* Get the value of this node as an integer. This function should be
@@ -1148,6 +1150,7 @@
LIBSBML_EXTERN
bool isUnknown () const;
+#if (0)
/**
* Predicate returning @c true (non-zero) if this node has the mathml attribute
* <code>id</code>.
@@ -1174,6 +1177,7 @@
*/
LIBSBML_EXTERN
bool isSetStyle() const;
+#endif
/**
* Predicate returning @c true (non-zero) if this node has the attribute
@@ -1214,6 +1218,7 @@
LIBSBML_EXTERN
int setCharacter (char value);
+#if (0)
/**
* Sets the mathml id of this ASTNode to id.
*
@@ -1249,6 +1254,7 @@
*/
LIBSBML_EXTERN
int setStyle (std::string style);
+#endif
/**
* Sets the value of this ASTNode to the given name.
@@ -1415,6 +1421,7 @@
LIBSBML_EXTERN
int unsetUnits ();
+#if (0)
/**
* Unsets the mathml id of this ASTNode.
*
@@ -1447,6 +1454,7 @@
*/
LIBSBML_EXTERN
int unsetStyle ();
+#endif
/** @cond doxygen-libsbml-internal */
@@ -1645,10 +1653,12 @@
std::string mUnits;
void *mUserData;
+#if (0)
// additional MathML attributes
std::string mId;
std::string mClass;
std::string mStyle;
+#endif
friend class MathMLFormatter;
friend class MathMLHandler;
@@ -1923,6 +1933,7 @@
ASTNode_getType (const ASTNode_t *node);
+#if (0)
LIBSBML_EXTERN
const char *
ASTNode_getId(const ASTNode_t * node);
@@ -1934,6 +1945,7 @@
LIBSBML_EXTERN
const char *
ASTNode_getStyle(const ASTNode_t * node);
+#endif
LIBSBML_EXTERN
const char *
@@ -2125,6 +2137,7 @@
int
ASTNode_isUnknown (const ASTNode_t *node);
+#if (0)
LIBSBML_EXTERN
int
ASTNode_isSetId (const ASTNode_t *node);
@@ -2136,6 +2149,7 @@
LIBSBML_EXTERN
int
ASTNode_isSetStyle (const ASTNode_t *node);
+#endif
LIBSBML_EXTERN
@@ -2213,6 +2227,7 @@
int
ASTNode_setType (ASTNode_t *node, ASTNodeType_t type);
+#if (0)
LIBSBML_EXTERN
int
ASTNode_setId (ASTNode_t *node, const char *id);
@@ -2224,6 +2239,7 @@
LIBSBML_EXTERN
int
ASTNode_setStyle (ASTNode_t *node, const char *style);
+#endif
LIBSBML_EXTERN
int
@@ -2236,6 +2252,7 @@
int
ASTNode_swapChildren (ASTNode_t *node, ASTNode_t *that);
+#if (0)
LIBSBML_EXTERN
int
@@ -2248,6 +2265,7 @@
LIBSBML_EXTERN
int
ASTNode_unsetStyle (ASTNode_t *node);
+#endif
LIBSBML_EXTERN
int
Modified: branches/libsbml-5/src/math/MathML.cpp
===================================================================
--- branches/libsbml-5/src/math/MathML.cpp 2010-09-29 10:00:47 UTC (rev 12060)
+++ branches/libsbml-5/src/math/MathML.cpp 2010-09-29 10:02:47 UTC (rev 12061)
@@ -612,14 +612,17 @@
string type;
string url;
string units;
+#if (0)
string id;
string className;
string style;
+#endif
elem.getAttributes().readInto( "encoding" , encoding );
elem.getAttributes().readInto( "type" , type );
elem.getAttributes().readInto( "definitionURL", url );
elem.getAttributes().readInto( "units" , units );
+#if (0)
elem.getAttributes().readInto( "id" , id );
elem.getAttributes().readInto( "class" , className );
elem.getAttributes().readInto( "style" , style );
@@ -632,6 +635,7 @@
if (!style.empty())
node.setStyle(style);
+#endif
if ( !type.empty() && name != "cn")
{
@@ -884,12 +888,14 @@
static void
writeAttributes(const ASTNode& node, XMLOutputStream& stream)
{
+#if (0)
if (node.isSetId())
stream.writeAttribute("id", node.getId());
if (node.isSetClass())
stream.writeAttribute("class", node.getClass());
if (node.isSetStyle())
stream.writeAttribute("style", node.getStyle());
+#endif
}
/**
@@ -909,7 +915,9 @@
{
stream.startElement("ci");
stream.setAutoIndent(false);
+#if (0)
writeAttributes(node, stream);
+#endif
if (node.getDefinitionURL())
stream.writeAttribute("definitionURL",
node.getDefinitionURL()->getValue(0));
@@ -954,7 +962,9 @@
else
{
stream.startElement("cn");
+#if (0)
writeAttributes(node, stream);
+#endif
if (!node.getUnits().empty())
{
stream.writeAttribute("sbml:units", node.getUnits());
@@ -1031,7 +1041,9 @@
stream.startElement("csymbol");
stream.setAutoIndent(false);
+#if (0)
writeAttributes(node, stream);
+#endif
static const string text = "text";
stream.writeAttribute( "encoding" , text );
stream.writeAttribute( "definitionURL", url );
@@ -1372,7 +1384,9 @@
{
inSemantics = true;
stream.startElement("semantics");
+#if (0)
writeAttributes(node, stream);
+#endif
if (node.getDefinitionURL())
stream.writeAttribute("definitionURL",
node.getDefinitionURL()->getValue(0));
Modified: branches/libsbml-5/src/math/test/TestASTNode.c
===================================================================
--- branches/libsbml-5/src/math/test/TestASTNode.c 2010-09-29 10:00:47 UTC (rev 12060)
+++ branches/libsbml-5/src/math/test/TestASTNode.c 2010-09-29 10:02:47 UTC (rev 12061)
@@ -2124,7 +2124,7 @@
}
END_TEST
-
+#if (0)
START_TEST (test_ASTNode_id)
{
int i;
@@ -2187,6 +2187,7 @@
ASTNode_free(n);
}
END_TEST
+#endif
START_TEST (test_ASTNode_avogadro)
{
@@ -2265,9 +2266,11 @@
tcase_add_test( tcase, test_ASTNode_freeName );
tcase_add_test( tcase, test_ASTNode_addSemanticsAnnotation );
tcase_add_test( tcase, test_ASTNode_units );
+#if (0)
tcase_add_test( tcase, test_ASTNode_id );
tcase_add_test( tcase, test_ASTNode_class );
tcase_add_test( tcase, test_ASTNode_style );
+#endif
tcase_add_test( tcase, test_ASTNode_avogadro );
suite_add_tcase(suite, tcase);
Modified: branches/libsbml-5/src/math/test/TestReadMathML.cpp
===================================================================
--- branches/libsbml-5/src/math/test/TestReadMathML.cpp 2010-09-29 10:00:47 UTC (rev 12060)
+++ branches/libsbml-5/src/math/test/TestReadMathML.cpp 2010-09-29 10:02:47 UTC (rev 12061)
@@ -1805,6 +1805,7 @@
}
END_TEST
+#if (0)
START_TEST (test_element_cn_id)
{
const char* s = wrapMathML("<cn id=\"test\"> 12345.7 </cn>");
@@ -1849,6 +1850,7 @@
fail_unless( N->getNumChildren() == 0 );
}
END_TEST
+#endif
START_TEST (test_element_ci_definitionURL)
@@ -1992,9 +1994,11 @@
tcase_add_test( tcase, test_element_invalid_mathml );
tcase_add_test( tcase, test_element_cn_units );
+#if (0)
tcase_add_test( tcase, test_element_cn_id );
tcase_add_test( tcase, test_element_cn_class );
tcase_add_test( tcase, test_element_cn_style );
+#endif
// this fails while default level/version is 2/4
// but other validation fails if I change it to 3/1
Modified: branches/libsbml-5/src/math/test/TestWriteMathML.cpp
===================================================================
--- branches/libsbml-5/src/math/test/TestWriteMathML.cpp 2010-09-29 10:00:47 UTC (rev 12060)
+++ branches/libsbml-5/src/math/test/TestWriteMathML.cpp 2010-09-29 10:02:47 UTC (rev 12061)
@@ -988,6 +988,7 @@
}
END_TEST
+#if (0)
START_TEST (test_MathMLFormatter_ci_id)
{
const char* expected = wrapMathML(" <ci id=\"test\"> foo </ci>\n");
@@ -1023,6 +1024,7 @@
fail_unless( equals(expected, S) );
}
END_TEST
+#endif
Suite *
@@ -1084,9 +1086,11 @@
tcase_add_test( tcase, test_MathMLFormatter_csymbol_avogadro );
tcase_add_test( tcase, test_MathMLFormatter_ci_definitionURL );
+#if (0)
tcase_add_test( tcase, test_MathMLFormatter_ci_id );
tcase_add_test( tcase, test_MathMLFormatter_ci_class );
tcase_add_test( tcase, test_MathMLFormatter_ci_style );
+#endif
suite_add_tcase(suite, tcase);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2010-09-29 10:00:53
|
Revision: 12060
http://sbml.svn.sourceforge.net/sbml/?rev=12060&view=rev
Author: mhucka
Date: 2010-09-29 10:00:47 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Added missing spatialDimensions attribute on compartment, for more completeness.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 09:59:33 UTC (rev 12059)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 10:00:47 UTC (rev 12060)
@@ -38,7 +38,7 @@
</submodel>
</listOfSubmodels>
<listOfCompartments>
- <compartment id="comp" size="1" constant="true">
+ <compartment id="comp" size="1" constant="true" spatialDimensions="3">
<listOfReplacements xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
<replace submodel="simple" port="comp_port" identical="true" />
<replace submodel="enzyme" symbol="comp" identical="true" />
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2010-09-29 09:59:40
|
Revision: 12059
http://sbml.svn.sourceforge.net/sbml/?rev=12059&view=rev
Author: mhucka
Date: 2010-09-29 09:59:33 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Goofed on a prior edit: spatialDimensions belongs on compartment, not species.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml
Modified: trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml 2010-09-29 06:13:04 UTC (rev 12058)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml 2010-09-29 09:59:33 UTC (rev 12059)
@@ -11,13 +11,13 @@
</body>
</notes>
<listOfCompartments>
- <compartment id="comp" size="1" constant="true"/>
+ <compartment id="comp" size="1" constant="true" spatialDimensions="3"/>
</listOfCompartments>
<listOfSpecies>
- <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
- <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
- <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
- <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
+ <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+ <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="J0" reversible="true" fast="false">
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From: <mh...@us...> - 2010-09-29 06:13:14
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Revision: 12058
http://sbml.svn.sourceforge.net/sbml/?rev=12058&view=rev
Author: mhucka
Date: 2010-09-29 06:13:04 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Some attempts at updating the XML -- not finished, though.
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml
trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
Added: trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_aggregate.xml 2010-09-29 06:13:04 UTC (rev 12058)
@@ -0,0 +1,55 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+ xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
+ comp:required="true">
+
+ <listOfModelDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <model id="enzyme" name="enzyme">
+ <notes>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ <p> Originally created by libAntimony v1.4 (using libSBML 4.1.0) </p>
+ </body>
+ </notes>
+ <listOfCompartments>
+ <compartment id="comp" size="1" constant="true"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
+ <species id="E" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
+ <species id="D" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
+ <species id="ES" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatialDimensions="3"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference species="S" stoichiometry="1" constant="false"/>
+ <speciesReference species="E" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="ES" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ <reaction id="J1" reversible="true" fast="false">
+ <listOfReactants>
+ <speciesReference species="ES" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="D" stoichiometry="1" constant="false"/>
+ <speciesReference species="E" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </model>
+ </listOfModelDefinitions>
+
+ <model id="aggregate">
+ <listOfSubmodels xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <submodel>
+ <modelRef model="enzyme" />
+ </submodel>
+ <submodel>
+ <modelRef model="enzyme" />
+ </submodel>
+ </listOfSubmodels>
+ </model>
+</sbml>
Added: trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/comp/ex1_complex.xml 2010-09-29 06:13:04 UTC (rev 12058)
@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1"
+ xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1"
+ comp:required="true">
+
+ <listOfModelDefinitions xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <modelDefinition id="simple" name="simple">
+ <listOfCompartments>
+ <compartment id="comp" size="1" spatialDimensions="3" constant="true" portID="comp_port"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" initialConcentration="5" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portID="S"/>
+ <species id="D" initialConcentration="10" compartment="comp" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" portID="D"/>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="J0" reversible="true" fast="false" portID="J0_port">
+ <listOfReactants>
+ <speciesReference species="S" stoichiometry="1" constant="false"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="D" stoichiometry="1" constant="false"/>
+ </listOfProducts>
+ </reaction>
+ </listOfReactions>
+ </modelDefinition>
+ </listOfModelDefinitions>
+
+ <model id="complexified">
+ <listOfSubmodels xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <submodel id="simple">
+ <modelRef model="simple" />
+ <listOfDeletions>
+ <deletion id="oldrxn" port="J0_port">
+ </listOfDeletions>
+ </submodel>
+ <submodel id="enzyme">
+ <modelRef model="enzyme" />
+ </submodel>
+ </listOfSubmodels>
+ <listOfCompartments>
+ <compartment id="comp" size="1" constant="true">
+ <listOfReplacements xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <replace submodel="simple" port="comp_port" identical="true" />
+ <replace submodel="enzyme" symbol="comp" identical="true" />
+ </listOfReplacements>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="S" compartment="comp" initialConcentration="5" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <listOfReplacements xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <replace submodel="simple" port="S_port" identical="true" />
+ <replace submodel="enzyme" symbol="S" identical="false" />
+ </listOfReplacements>
+ </species>
+ <species id="D" compartment="comp" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+ <listOfReplacements xmlns="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <replace submodel="simple" port="D_port" identical="true" />
+ <replace submodel="enzyme" symbol="D" identical="false" />
+ </listOfReplacements>
+ </species>
+ </listOfSpecies>
+ </model>
+
+</sbml>
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|
|
From: <mh...@us...> - 2010-09-29 06:12:48
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Revision: 12057
http://sbml.svn.sourceforge.net/sbml/?rev=12057&view=rev
Author: mhucka
Date: 2010-09-29 06:12:42 +0000 (Wed, 29 Sep 2010)
Log Message:
-----------
Updated PDF.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/introduction.pdf
Modified: trunk/specifications/sbml-level-3/version-1/comp/introduction.pdf
===================================================================
(Binary files differ)
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