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From: <sar...@us...> - 2012-08-30 17:18:59
|
Revision: 16264
http://sbml.svn.sourceforge.net/sbml/?rev=16264&view=rev
Author: sarahkeating
Date: 2012-08-30 17:18:41 +0000 (Thu, 30 Aug 2012)
Log Message:
-----------
reverted my attempts to merge with trunk as it had not worked fully
Modified Paths:
--------------
branches/L3Parser/Makefile.in
branches/L3Parser/configure
branches/L3Parser/layout-package.cmake
branches/L3Parser/src/CMakeLists.txt
branches/L3Parser/src/bindings/CMakeLists.txt
branches/L3Parser/src/bindings/Makefile.in
branches/L3Parser/src/bindings/csharp/CMakeLists.txt
branches/L3Parser/src/bindings/csharp/Makefile.in
branches/L3Parser/src/bindings/csharp/Properties/AssemblyInfo.cs
branches/L3Parser/src/bindings/csharp/Properties/AssemblyInfo.cs.in
branches/L3Parser/src/bindings/csharp/Properties/AssemblyInfoTR.cs
branches/L3Parser/src/bindings/csharp/TestRW.cs
branches/L3Parser/src/bindings/csharp/TestRunner.cs
branches/L3Parser/src/bindings/csharp/local-packages-layout.i
branches/L3Parser/src/bindings/csharp/test/annotation/TestCVTerms_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestDate_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestModelCreator_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestModelHistory_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestRDFAnnotation.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestCompartmentType_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestCompartment_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestEvent_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestL3KineticLaw.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestL3Species.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestModel.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestModel_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestParameter_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReaction_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReadFromFile6.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReadFromFile7.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReadFromFile8.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestRequiredAttributes.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestRequiredElements.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSBMLConvertStrict.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSpeciesReference_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSpeciesType_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSpecies_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestUnitDefinition_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestUnit_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/xml/TestXMLNode_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/xml/TestXMLToken.cs
branches/L3Parser/src/bindings/csharp/test/xml/TestXMLToken_newSetters.cs
branches/L3Parser/src/bindings/java/CMakeLists.txt
branches/L3Parser/src/bindings/java/Makefile.in
branches/L3Parser/src/bindings/java/local-packages-layout.i
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotation.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartmentType_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartment_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestEvent_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3KineticLaw.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3LocalParameter.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Trigger.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestParameter_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReaction_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile6.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile7.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile8.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestRequiredAttributes.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestRequiredElements.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSpeciesReference_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSpeciesType_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSpecies_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSyntaxChecker.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestUnitDefinition_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestUnit_newSetters.java
branches/L3Parser/src/bindings/matlab/ConvertFormulaToMathML.m
branches/L3Parser/src/bindings/matlab/FindMatlab.cmake
branches/L3Parser/src/bindings/matlab/Makefile.in
branches/L3Parser/src/bindings/matlab/OutputSBML.c
branches/L3Parser/src/bindings/matlab/buildSBML.m
branches/L3Parser/src/bindings/matlab/installSBML.m
branches/L3Parser/src/bindings/matlab/isoctave.m
branches/L3Parser/src/bindings/matlab/test/Makefile.in
branches/L3Parser/src/bindings/matlab/test/testIsSBMLModel.m
branches/L3Parser/src/bindings/matlab/test/testReadFlags.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile1.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile10.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile11.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile12.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile13.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile14.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile15.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile2.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile3.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile4.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile5.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile6.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile7.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile8.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile9.m
branches/L3Parser/src/bindings/octave/.svnignore
branches/L3Parser/src/bindings/octave/Makefile.in
branches/L3Parser/src/bindings/octave/test/Makefile.in
branches/L3Parser/src/bindings/perl/CMakeLists.txt
branches/L3Parser/src/bindings/perl/Makefile.in
branches/L3Parser/src/bindings/perl/local-downcast-packages-layout.cpp
branches/L3Parser/src/bindings/perl/local-layout.i
branches/L3Parser/src/bindings/perl/local-packages.i.in
branches/L3Parser/src/bindings/perl/local.i
branches/L3Parser/src/bindings/perl/t/02__ReadFromFileL3.t
branches/L3Parser/src/bindings/perl/t/03__DowncastSBase.t
branches/L3Parser/src/bindings/perl/t/04__ListOf.t
branches/L3Parser/src/bindings/perl/t/05__AssignmentRule.t
branches/L3Parser/src/bindings/perl/t/05__Compartment.t
branches/L3Parser/src/bindings/perl/t/05__Event.t
branches/L3Parser/src/bindings/perl/t/05__KineticLaw.t
branches/L3Parser/src/bindings/perl/t/05__Model.t
branches/L3Parser/src/bindings/perl/t/05__ModelL3.t
branches/L3Parser/src/bindings/perl/t/05__Parameter.t
branches/L3Parser/src/bindings/perl/t/06__TestReadSBML.t
branches/L3Parser/src/bindings/perl/t/06__TestReadSBMLL3.t
branches/L3Parser/src/bindings/perl/t/06__TestWriteSBML.t
branches/L3Parser/src/bindings/perl/t/06__TestWriteSBMLL3.t
branches/L3Parser/src/bindings/python/.svnignore
branches/L3Parser/src/bindings/python/CMakeLists.txt
branches/L3Parser/src/bindings/python/Makefile.in
branches/L3Parser/src/bindings/python/doc-converter/README.txt
branches/L3Parser/src/bindings/python/doc-converter/argparse.py
branches/L3Parser/src/bindings/python/doc-converter/rewrite_pydoc.py
branches/L3Parser/src/bindings/python/local-downcast-packages-layout.cpp
branches/L3Parser/src/bindings/python/local-layout.i
branches/L3Parser/src/bindings/python/local-packages.i.in
branches/L3Parser/src/bindings/python/local.cpp
branches/L3Parser/src/bindings/python/local.i
branches/L3Parser/src/bindings/python/setup.py.in
branches/L3Parser/src/bindings/python/test/annotation/TestRDFAnnotation.py
branches/L3Parser/src/bindings/python/test/sbml/.svnignore
branches/L3Parser/src/bindings/python/test/sbml/TestCompartmentType_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestCompartment_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestEvent_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestInternalConsistencyChecks.py
branches/L3Parser/src/bindings/python/test/sbml/TestL3KineticLaw.py
branches/L3Parser/src/bindings/python/test/sbml/TestL3LocalParameter.py
branches/L3Parser/src/bindings/python/test/sbml/TestL3Trigger.py
branches/L3Parser/src/bindings/python/test/sbml/TestModel_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestParameter_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestReaction_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestReadFromFile6.py
branches/L3Parser/src/bindings/python/test/sbml/TestReadFromFile7.py
branches/L3Parser/src/bindings/python/test/sbml/TestReadFromFile8.py
branches/L3Parser/src/bindings/python/test/sbml/TestRequiredAttributes.py
branches/L3Parser/src/bindings/python/test/sbml/TestRequiredElements.py
branches/L3Parser/src/bindings/python/test/sbml/TestSBase_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSpeciesReference_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSpeciesType_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSpecies_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSyntaxChecker.py
branches/L3Parser/src/bindings/python/test/sbml/TestUnitDefinition_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestUnit_newSetters.py
branches/L3Parser/src/bindings/python/test.py
branches/L3Parser/src/bindings/ruby/CMakeLists.txt
branches/L3Parser/src/bindings/ruby/Makefile.in
branches/L3Parser/src/bindings/ruby/local-downcast-packages-layout.cpp
branches/L3Parser/src/bindings/ruby/local-layout.i
branches/L3Parser/src/bindings/ruby/local-packages.i.in
branches/L3Parser/src/bindings/ruby/test/annotation/TestRDFAnnotation.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestAlgebraicRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestAssignmentRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestCompartment.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestCompartmentType.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestCompartmentVolumeRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestConstraint.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestEvent.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestEventAssignment.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestFunctionDefinition.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestInitialAssignment.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestInternalConsistencyChecks.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestKineticLaw.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestL3KineticLaw.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestL3LocalParameter.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestL3Trigger.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestListOf.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestModel.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestModifierSpeciesReference.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestParameter.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestParameterRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRateRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReaction.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile1.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile2.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile3.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile4.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile6.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile7.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile8.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRequiredAttributes.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRequiredElements.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSBMLConvert.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSBMLDocument.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpecies.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpeciesConcentrationRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpeciesReference.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpeciesType.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestUnit.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestUnitDefinition.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestUnitKind.rb
branches/L3Parser/src/bindings/swig/OStream.h
branches/L3Parser/src/bindings/swig/layout-package.h
branches/L3Parser/src/bindings/swig/layout-package.i
branches/L3Parser/src/bindings/swig/libsbml.h
branches/L3Parser/src/bindings/swig/libsbml.i
branches/L3Parser/src/bindings/swig/std_set.i
branches/L3Parser/src/bindings/swig/swigdoc.py
branches/L3Parser/src/layout-package.cmake
branches/L3Parser/src/sbml/AlgebraicRule.cpp
branches/L3Parser/src/sbml/AlgebraicRule.h
branches/L3Parser/src/sbml/AssignmentRule.cpp
branches/L3Parser/src/sbml/AssignmentRule.h
branches/L3Parser/src/sbml/CMakeLists.txt
branches/L3Parser/src/sbml/Compartment.cpp
branches/L3Parser/src/sbml/Compartment.h
branches/L3Parser/src/sbml/CompartmentType.cpp
branches/L3Parser/src/sbml/CompartmentType.h
branches/L3Parser/src/sbml/Constraint.cpp
branches/L3Parser/src/sbml/Constraint.h
branches/L3Parser/src/sbml/Delay.cpp
branches/L3Parser/src/sbml/Delay.h
branches/L3Parser/src/sbml/Event.cpp
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-03.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-09.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10523-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10523-fail-01-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/xml-parser-constraints/01006-fail-01-13.xml
branches/L3Parser/src/sbml/xml/ExpatAttributes.h
branches/L3Parser/src/sbml/xml/ExpatParser.h
branches/L3Parser/src/sbml/xml/LibXMLParser.h
branches/L3Parser/src/sbml/xml/XMLAttributes.cpp
branches/L3Parser/src/sbml/xml/XMLAttributes.h
branches/L3Parser/src/sbml/xml/XMLConstructorException.cpp
branches/L3Parser/src/sbml/xml/XMLConstructorException.h
branches/L3Parser/src/sbml/xml/XMLError.cpp
branches/L3Parser/src/sbml/xml/XMLError.h
branches/L3Parser/src/sbml/xml/XMLErrorLog.h
branches/L3Parser/src/sbml/xml/XMLExtern.h
branches/L3Parser/src/sbml/xml/XMLHandler.h
branches/L3Parser/src/sbml/xml/XMLInputStream.h
branches/L3Parser/src/sbml/xml/XMLNamespaces.cpp
branches/L3Parser/src/sbml/xml/XMLNamespaces.h
branches/L3Parser/src/sbml/xml/XMLNode.cpp
branches/L3Parser/src/sbml/xml/XMLNode.h
branches/L3Parser/src/sbml/xml/XMLOutputStream.h
branches/L3Parser/src/sbml/xml/XMLParser.h
branches/L3Pars...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-30 12:16:54
|
Revision: 16263
http://sbml.svn.sourceforge.net/sbml/?rev=16263&view=rev
Author: sarahkeating
Date: 2012-08-30 12:16:45 +0000 (Thu, 30 Aug 2012)
Log Message:
-----------
added missing bib
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
===================================================================
(Binary files differ)
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib 2012-08-30 11:54:15 UTC (rev 16262)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib 2012-08-30 12:16:45 UTC (rev 16263)
@@ -201,6 +201,14 @@
Volume = {153},
Year = {1991}}
+@article{batt05,
+Author = {G. Batt and D. Ropers and H. de Jong and J. Geiselmann and R. Mateescu and M. Page and D. Schneider},
+ Journal = {Bioinformatics},
+ Number = {1},
+ Pages = {i19-i28},
+ Title = {Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli},
+ Volume = {21},
+ Year = {2005}}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2012-08-30 11:54:21
|
Revision: 16262
http://sbml.svn.sourceforge.net/sbml/?rev=16262&view=rev
Author: sarahkeating
Date: 2012-08-30 11:54:15 +0000 (Thu, 30 Aug 2012)
Log Message:
-----------
adding edits by Claudine
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/qual/spec/acknowledgments.tex
trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex
trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/acknowledgments.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/acknowledgments.tex 2012-08-30 11:15:59 UTC (rev 16261)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/acknowledgments.tex 2012-08-30 11:54:15 UTC (rev 16262)
@@ -4,4 +4,4 @@
\label{sec:acknowledgements}
\label{sec:acknowledgments}
- The development of the qual SBML package has been made possible through the organization of three meetings. These were mainly supported by the EMBL-EBI, Cambridge, UK and by the IGC, Portugal. It has been boosted by the Path2models projects sponsored by ??? Finally T. Helikar, A. von Kamp, S. Klamt, N. Le Nov\xE8re, N. Rodriguez, J. Saez-Rodriguez have also collaborated to this proposal.
+ The development of the qual SBML package has been made possible through the organization of three meetings. These were mainly supported by the EMBL-EBI, Cambridge, UK and by the IGC, Portugal. It has been boosted by the path2models projects sponsored by EMBL-EBI. Finally the authors would like to thank the members of the \textit{sbml-qual} Package Working Group and in particular T. Helikar, A. von Kamp, S. Klamt, N. Le Nov�re, N. Rodriguez and J. Saez-Rodriguez who have also collaborated in this proposal.
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex 2012-08-30 11:15:59 UTC (rev 16261)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex 2012-08-30 11:54:15 UTC (rev 16262)
@@ -22,11 +22,10 @@
reactive systems, which dynamics are represented by means of state
transition graphs (or other Kripke structures representing, in the form
of a graph, which node are the reachable states and the edges are the
-state transitions). In this context, logical regulatory networks
+state transitions). In this context, logical regulatory networksp
(Boolean or multi-valued) \cite{kauffman69,thomas91} and standard Petri
nets \cite{chaouiya07} are the two formalisms mostly used in biology
-that give rise to such behaviours. Published models using these approaches cover, far from exhaustiveness, gene regulatory networks and signalling pathways (e.g. \cite{thieffry95,sanchez03,albert03,faure06,mendoza06,helikar08,naldi10,calzone10})
-}), metabolic pathways (see review in \cite{chaouiya07}).
+that give rise to such behaviours. Published models using these approaches cover, far from exhaustiveness, gene regulatory networks and signalling pathways (e.g. \cite{thieffry95,sanchez03,albert03,faure06,mendoza06,helikar08,naldi10,calzone10}), metabolic pathways (see review in \cite{chaouiya07}).
Finally, because their dynamics can be abstracted by Kripke
structures, models expressed as systems of piece-wide linear
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2012-08-30 11:16:06
|
Revision: 16261
http://sbml.svn.sourceforge.net/sbml/?rev=16261&view=rev
Author: sarahkeating
Date: 2012-08-30 11:15:59 +0000 (Thu, 30 Aug 2012)
Log Message:
-----------
added further intro bits from Claudine
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex
trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex 2012-08-24 19:34:46 UTC (rev 16260)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/intro.tex 2012-08-30 11:15:59 UTC (rev 16261)
@@ -4,10 +4,40 @@
\label{intro}
\subsection{Motivation}
-Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as gene expression data coming from functional genomic experiments.
-The qualitative models contemplated in this package are essentially based on the definition of \emph{regulatory} or \emph{influence graph}. The components of these models differ from species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. Boolean networks, logical models and some Petri nets are the most used qualitative formalisms in biology. Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.
+Quantitative methods for modelling biological networks require an
+in-depth knowledge of the biochemical reactions and their stoichiometric
+and kinetic parameters. In many practical cases, this knowledge is
+missing. This has led to the development of several qualitative
+modelling methods using information such as gene expression data coming
+from functional genomic experiments.
+The qualitative models contemplated in this package are essentially
+based on the definition of \emph{regulatory} or \emph{influence
+ graph}. The components of these models differ from species and
+reactions used in current SBML models. For example, qualitative models
+typically associate discrete levels of activities with entity pools; the
+processes involving them cannot be described as reactions per se but
+rather as transitions between states. These systems can be viewed as
+reactive systems, which dynamics are represented by means of state
+transition graphs (or other Kripke structures representing, in the form
+of a graph, which node are the reachable states and the edges are the
+state transitions). In this context, logical regulatory networks
+(Boolean or multi-valued) \cite{kauffman69,thomas91} and standard Petri
+nets \cite{chaouiya07} are the two formalisms mostly used in biology
+that give rise to such behaviours. Published models using these approaches cover, far from exhaustiveness, gene regulatory networks and signalling pathways (e.g. \cite{thieffry95,sanchez03,albert03,faure06,mendoza06,helikar08,naldi10,calzone10})
+}), metabolic pathways (see review in \cite{chaouiya07}).
+
+Finally, because their dynamics can be abstracted by Kripke
+structures, models expressed as systems of piece-wide linear
+differential equations \cite{batt05}, may be covered by this package, provided some extension (see \ref{apdx-future}).
+
+
+ Despite differences from traditional SBML models, it is desirable to
+ bring these classes of models under a common format scheme. The purpose
+ of this Qualitative Models package for SBML Level 3 is to support
+ encoding qualitative models in SBML.
+
\subsection{Package dependencies}
The QualitativeModels package has no dependencies on other
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib 2012-08-24 19:34:46 UTC (rev 16260)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/qual.bib 2012-08-30 11:15:59 UTC (rev 16261)
@@ -77,5 +77,130 @@
}
+@article{thieffry95,
+ Author = {D. Thieffry and R. Thomas},
+ Journal = {Bul. Math. Biol.},
+ Number = {2},
+ Pages = {277-297},
+ Title = {Dynamical Behaviour of Biological Regulatory Networks, II. Immunity Control in Bacteriophage Lambda.},
+ Volume = {57},
+ Year = {1995}}
+@article{sanchez03,
+ Author = {S\'anchez, L and Thieffry, D},
+ Journal = {J. Theor. Biol.},
+ Number = {4},
+ Pages = {517-537},
+ Title = {Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module},
+ Volume = {224},
+ Year = {2003}}
+
+
+@article{albert03,
+ Author = {R.~Albert and H.~G. Othmer},
+ Date-Added = {2009-03-04 23:32:09 +0000},
+ Date-Modified = {2009-03-04 23:33:31 +0000},
+ Journal = {J. Theor. Biol.},
+ Keywords = {Drosophila segmentation},
+ Number = {1},
+ Pages = {1--18},
+ Title = {The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in drosophila melanogaster.},
+ Volume = {223},
+ Year = {2003}}
+
+
+
+@article{faure06,
+ Author = {A. Faur\'e and A. Naldi and {C. Chaouiya} and D. Thieffry},
+ Journal = {Bioinformatics},
+ Number = {14},
+ Pages = {124-131},
+ Title = {Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle},
+ Volume = {22},
+ Year = {2006}}
+
+
+@article{naldi10,
+ Author = {Naldi, Aur{\'e}lien and Carneiro, Jorge and Chaouiya, Claudine and Thieffry, Denis},
+ Journal = {PLoS Comput Biol},
+ Number = {9},
+ Pages = {e1000912},
+ Title = {Diversity and plasticity of Th cell types predicted from regulatory network modelling},
+ Volume = {6},
+ Year = {2010}}
+
+
+@article{saez07,
+ Author = {J. Saez-Rodriguez and L. Simeoni and JA. Lindquist and R. Hemenway and U. Bommhardt and B. Arndt and U-U. Haus and R. Weismantel and ED. Gilles and S. Klamt and B. Schraven},
+ Journal = {PLoS Comput Biol},
+ Number = {8},
+ Pages = {e163},
+ Title = {A logical model provides insights into {T} cell receptor signaling.},
+ Volume = {3},
+ Year = {2007 Aug}}
+
+@article{helikar08,
+ Author = {Helikar, T and Konvalina, J and Heidel, J and Rogers, J A},
+ Journal = {Proc Natl Acad Sci U S A},
+ Month = {Feb},
+ Number = {6},
+ Pages = {1913-8},
+ Title = {Emergent decision-making in biological signal transduction networks},
+ Volume = {105},
+ Year = {2008}}
+
+@article{calzone10,
+ Author = {Calzone, Laurence and Tournier, Laurent and Fourquet, Simon and Thieffry, Denis and Zhivotovsky, Boris and Barillot, Emmanuel and Zinovyev, Andrei},
+ Journal = {PLoS Comput Biol},
+ Month = {Mar},
+ Number = {3},
+ Pages = {e1000702},
+ Title = {Mathematical modelling of cell-fate decision in response to death receptor engagement},
+ Volume = {6},
+ Year = {2010}}
+
+@article{sackmann06,
+ Author = {A. Sackmann and M. Heiner and I. Koch},
+ Journal = {BMC Bioinformatics},
+ Title = {Application of Petri net based analysis techniques to signal transduction pathways},
+ Year = {2006}}
+
+
+@article{chaouiya07,
+ Author = {C. Chaouiya},
+ Journal = {Briefings in Bioinformatics},
+ Pages = {210-9},
+ Title = {Petri net modelling of biological networks},
+ Volume = {8},
+ Year = {2007}}
+
+
+@article{mendoza06,
+ Author = {Luis Mendoza and Ioannis Xenarios},
+ Journal = {Theor Biol Med Model},
+ Pages = {13},
+ Title = {A method for the generation of standardized qualitative dynamical systems of regulatory networks.},
+ Volume = {3},
+ Year = {2006}}
+
+
+@article{kauffman69,
+ Author = {S Kauffman},
+ Journal = {J. Theor. Biol.},
+ Pages = {437--67.},
+ Title = {Metabolic stability and epigenesis in randomly constructed genetics nets.},
+ Volume = {22},
+ Year = {1969}}
+
+@article{thomas91,
+ Author = {R. Thomas},
+ Journal = {J. Theor. Biol.},
+ Pages = {1-23},
+ Title = {Regulatory networks seen as asynchronous automata: A logical description},
+ Volume = {153},
+ Year = {1991}}
+
+
+
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2012-08-24 19:34:55
|
Revision: 16260
http://sbml.svn.sourceforge.net/sbml/?rev=16260&view=rev
Author: luciansmith
Date: 2012-08-24 19:34:46 +0000 (Fri, 24 Aug 2012)
Log Message:
-----------
Mentioned in .m files of tests where the l3 version was removed that the l3 version was removed.
Fixed the name of 931 to be 'case00931' (instead of 930).
Gave a real 'synopsis' for model 1121.
No math or results are changed in this update.
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00068/00068-model.m
trunk/test-suite/cases/semantic/00069/00069-model.m
trunk/test-suite/cases/semantic/00070/00070-model.m
trunk/test-suite/cases/semantic/00129/00129-model.m
trunk/test-suite/cases/semantic/00130/00130-model.m
trunk/test-suite/cases/semantic/00131/00131-model.m
trunk/test-suite/cases/semantic/00388/00388-model.m
trunk/test-suite/cases/semantic/00391/00391-model.m
trunk/test-suite/cases/semantic/00394/00394-model.m
trunk/test-suite/cases/semantic/00445/00445-model.m
trunk/test-suite/cases/semantic/00448/00448-model.m
trunk/test-suite/cases/semantic/00451/00451-model.m
trunk/test-suite/cases/semantic/00516/00516-model.m
trunk/test-suite/cases/semantic/00517/00517-model.m
trunk/test-suite/cases/semantic/00518/00518-model.m
trunk/test-suite/cases/semantic/00519/00519-model.m
trunk/test-suite/cases/semantic/00520/00520-model.m
trunk/test-suite/cases/semantic/00521/00521-model.m
trunk/test-suite/cases/semantic/00561/00561-model.m
trunk/test-suite/cases/semantic/00562/00562-model.m
trunk/test-suite/cases/semantic/00563/00563-model.m
trunk/test-suite/cases/semantic/00564/00564-model.m
trunk/test-suite/cases/semantic/00609/00609-model.m
trunk/test-suite/cases/semantic/00610/00610-model.m
trunk/test-suite/cases/semantic/00725/00725-model.m
trunk/test-suite/cases/semantic/00726/00726-model.m
trunk/test-suite/cases/semantic/00727/00727-model.m
trunk/test-suite/cases/semantic/00728/00728-model.m
trunk/test-suite/cases/semantic/00729/00729-model.m
trunk/test-suite/cases/semantic/00730/00730-model.m
trunk/test-suite/cases/semantic/00731/00731-model.m
trunk/test-suite/cases/semantic/00827/00827-model.m
trunk/test-suite/cases/semantic/00828/00828-model.m
trunk/test-suite/cases/semantic/00829/00829-model.m
trunk/test-suite/cases/semantic/00898/00898-model.m
trunk/test-suite/cases/semantic/00899/00899-model.m
trunk/test-suite/cases/semantic/00900/00900-model.m
trunk/test-suite/cases/semantic/00931/00931-sbml-l3v1.xml
trunk/test-suite/cases/semantic/00968/00968-model.m
trunk/test-suite/cases/semantic/00973/00973-model.m
trunk/test-suite/cases/semantic/00989/00989-model.m
trunk/test-suite/cases/semantic/00990/00990-model.m
trunk/test-suite/cases/semantic/00991/00991-model.m
trunk/test-suite/cases/semantic/00992/00992-model.m
trunk/test-suite/cases/semantic/00993/00993-model.m
trunk/test-suite/cases/semantic/00994/00994-model.m
trunk/test-suite/cases/semantic/01027/01027-model.m
trunk/test-suite/cases/semantic/01028/01028-model.m
trunk/test-suite/cases/semantic/01029/01029-model.m
trunk/test-suite/cases/semantic/01121/01121-model.m
Modified: trunk/test-suite/cases/semantic/00068/00068-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00068/00068-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00068/00068-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Analytic
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called "compartment". There are two
species named S1 and S2 and two parameters named k1 and p1. The model
contains one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00069/00069-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00069/00069-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00069/00069-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called "compartment". There are three
species named S1, S2 and S3 and three parameters named k1, k2 and p1. The
model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00070/00070-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00070/00070-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00070/00070-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called "compartment". There are three
species named S1, S2 and S3 and three parameters named k1, k2 and p1. The
model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00129/00129-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00129/00129-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00129/00129-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -1,5 +1,4 @@
(*
-
category: Test
synopsis: Basic single forward reaction involving two species and a
stoichiometryMath element that uses a functionDefinition.
@@ -9,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called "compartment". There are two
species named S1 and S2 and two parameters named k1 and p1. The model
contains one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00130/00130-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00130/00130-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00130/00130-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -1,61 +1,127 @@
(*
+
+
category: Test
+
synopsis: Basic reactions with three species in a compartment
+
involving a stoichiometryMath element that uses a functionDefinition.
+
componentTags: StoichiometryMath, Compartment, Species, Reaction, Parameter, FunctionDefinition
+
testTags: Amount, AssignedConstantStoichiometry, NonUnityStoichiometry
+
testType: TimeCourse
+
levels: 2.1, 2.2, 2.3, 2.4
+
generatedBy: Numeric
+
+
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
+
The model contains one compartment called "compartment". There are three
+
species named S1, S2 and S3 and three parameters named k1, k2 and p1. The
+
model contains two reactions defined as:
+
+
[{width:30em,margin-left:5em}| *Reaction* | *Rate* |
+
| S1 + S2 -> S3 | $k1 * S1 * S2 * compartment$ |
+
| multiply(2, p1)S3 -> S1 + S2 | $k2 * S3 * compartment$ |]
+
+
+
The model contains one functionDefinition defined as:
+
+
[{width:30em,margin-left:5em}| *Id* | *Arguments* | *Formula* |
+
| multiply | x, y | $x * y$ |]
+
+
+
The initial conditions are as follows:
+
+
[{width:30em,margin-left:5em}| |*Value* |*Units* |
+
|Initial amount of S1 |$1.0 \x 10^-4$ |mole |
+
|Initial amount of S2 |$2.0 \x 10^-4$ |mole |
+
|Initial amount of S3 |$1.0 \x 10^-4$ |mole |
+
|Value of parameter k1 |$ 1.7 \x 10^2$ |litre mole^-1^ second^-1^ |
+
|Value of parameter k2 |$ 0.3$ |second^-1^ |
+
|Value of parameter p1 |$ 1$ |dimensionless |
+
|Volume of compartment "compartment" |$ 1$ |litre |]
+
+
The species values are given as amounts of substance 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.
+
+
*)
+
+
newcase[ "00130" ];
+
+
addFunction[ multiply, arguments -> {x, y}, math -> x * y];
+
addCompartment[ compartment, size -> 1 ];
+
addSpecies[ S1, initialAmount -> 1.0 10^-4];
+
addSpecies[ S2, initialAmount -> 2.0 10^-4];
+
addSpecies[ S3, initialAmount -> 1.0 10^-4];
+
addParameter[ k1, value -> 1.7 10^2 ];
+
addParameter[ k2, value -> 0.3 ];
+
addParameter[ p1, value -> 1 ];
+
addReaction[ S1 + S2 -> S3, reversible -> False,
+
kineticLaw -> k1 * S1 * S2 * compartment ];
+
addReaction[ reactants->{S3}, products->{S1, S2},
+
reactantStoichiometry->{multiply[2,p1]}, reversible -> False,
+
kineticLaw -> k2 * S3 * compartment ];
+
+
makemodel[]
+
Modified: trunk/test-suite/cases/semantic/00131/00131-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00131/00131-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00131/00131-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -1,5 +1,4 @@
(*
-
category: Test
synopsis: Basic reactions with three species in a compartment
involving a stoichiometryMath element that uses a functionDefinition.
@@ -9,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called "compartment". There are three
species named S1, S2 and S3 and three parameters named k1, k2 and p1. The
model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00388/00388-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00388/00388-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00388/00388-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species
called S1, S2 and S3 and two parameters called k1 and k2. The model
contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00391/00391-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00391/00391-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00391/00391-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four species called
S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains
two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00394/00394-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00394/00394-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00394/00394-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species
called S1, S2 and S3 and two parameters called k1 and k2. The model
contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00445/00445-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00445/00445-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00445/00445-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species
called S1, S2 and S3 and two parameters called k1 and k2. The model
contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00448/00448-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00448/00448-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00448/00448-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four species called
S1, S2, S3 and S4 and two parameters called k1 and k2. The model contains
two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00451/00451-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00451/00451-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00451/00451-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species
called S1, S2 and S3 and two parameters called k1 and k2. The model
contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00516/00516-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00516/00516-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00516/00516-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Analytic
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are two
species called S1 and S2 and three parameters called k1, k2 and p1. The model contains
one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00517/00517-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00517/00517-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00517/00517-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Analytic
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are two
species called S1 and S2 and three parameters called k1, k2 and p1. The model contains
one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00518/00518-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00518/00518-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00518/00518-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Analytic
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are two
species called S1 and S2 and three parameters called k1, k2 and p1. The model contains
one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00519/00519-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00519/00519-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00519/00519-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains
two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00520/00520-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00520/00520-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00520/00520-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains
two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00521/00521-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00521/00521-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00521/00521-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and four parameters called k1, k2, p1 and p2. The model contains
two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00561/00561-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00561/00561-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00561/00561-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called X0, X1, T and S1 and four parameters called k1, k2, k3 and p1.
Species X0 is labeled as an SBML boundary species. The model
Modified: trunk/test-suite/cases/semantic/00562/00562-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00562/00562-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00562/00562-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called X0, X1, T and S1 and four parameters called k1, k2, k3 and p1.
Species X0 is labeled as an SBML boundary species. The model
Modified: trunk/test-suite/cases/semantic/00563/00563-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00563/00563-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00563/00563-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.
Species S3 is labeled as an SBML boundary species. The model
Modified: trunk/test-suite/cases/semantic/00564/00564-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00564/00564-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00564/00564-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1.
Species S3 is labeled as an SBML boundary species. The model
Modified: trunk/test-suite/cases/semantic/00609/00609-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00609/00609-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00609/00609-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three
species called S1, S2 and S3 and three parameters called k1, k2 and p1. The model
contains one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00610/00610-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00610/00610-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00610/00610-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S and four parameters called k1, k2, k3 and p1.
The model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00725/00725-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00725/00725-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00725/00725-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The
model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00726/00726-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00726/00726-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00726/00726-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The
model contains one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00727/00727-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00727/00727-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00727/00727-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The
model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00728/00728-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00728/00728-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00728/00728-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S and four parameters called k1, k2, k3 and p1.
The model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00729/00729-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00729/00729-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00729/00729-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and four parameters called k1, k2, p1 and p2. The
model contains one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00730/00730-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00730/00730-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00730/00730-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The
model contains one reaction defined as:
Modified: trunk/test-suite/cases/semantic/00731/00731-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00731/00731-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00731/00731-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. The
model contains two reactions defined as:
Modified: trunk/test-suite/cases/semantic/00827/00827-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00827/00827-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00827/00827-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are two species called
S1 and S2 and three parameters called kf, kr and p1. The model contains one reaction
defined as:
Modified: trunk/test-suite/cases/semantic/00828/00828-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00828/00828-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00828/00828-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction
defined as:
Modified: trunk/test-suite/cases/semantic/00829/00829-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00829/00829-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00829/00829-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction
defined as:
Modified: trunk/test-suite/cases/semantic/00898/00898-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00898/00898-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00898/00898-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Analytic
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are two
species called S1 and S2 and two parameters called k1 and p1. The model contains
one reaction:
Modified: trunk/test-suite/cases/semantic/00899/00899-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00899/00899-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00899/00899-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species named S1, S2, S3 and S4 and four parameters named k1, k2, k3 and p1.
The model contains three reactions defined as:
Modified: trunk/test-suite/cases/semantic/00900/00900-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00900/00900-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00900/00900-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -9,6 +9,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The model contains one compartment called C. There are four
species called S1, S2, S3 and S4 and two parameters called k1 and p1.
The model contains three reactions defined as:
Modified: trunk/test-suite/cases/semantic/00931/00931-sbml-l3v1.xml
===================================================================
--- trunk/test-suite/cases/semantic/00931/00931-sbml-l3v1.xml 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00931/00931-sbml-l3v1.xml 2012-08-24 19:34:46 UTC (rev 16260)
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v1.4 on 2011-02-09 22:26 with libSBML version 5.0.0-b1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
- <model id="case00930" name="case00930">
+ <model id="case00931" name="case00931">
<listOfCompartments>
<compartment id="C" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
Modified: trunk/test-suite/cases/semantic/00968/00968-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00968/00968-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00968/00968-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,8 +8,12 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Analytic
-The speciesReference ('Xref') is set with an initialAssignment of 3 for the L3 model, and with stoichiometryMath in the L2 models. No 'stoichiometry' value is provided in the speciesReference in the reaction itself.
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+The speciesReference ('Xref') is set with stoichiometryMath in the L2 models. No 'stoichiometry' value is provided in the speciesReference in the reaction itself.
+
The model contains:
* 1 species (X)
* 1 parameter (k1)
Modified: trunk/test-suite/cases/semantic/00973/00973-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00973/00973-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00973/00973-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,8 +8,12 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Analytic
-Over the course of the simulation, the stoichiometry 'Xref' changes at a rate of 0.01/time, so the effective rate of synthesis increases as well, identically to the same model with k1 changing instead of Xref. The Level 2 versions of this test create a new parameter 'parameterId_0' which functions identically to 'Xref' in the Level 3 version of the model.
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+Over the course of the simulation, the stoichiometry 'Xref' changes at a rate of 0.01/time, so the effective rate of synthesis increases as well, identically to the same model with k1 changing instead of Xref. The Level 2 versions of this test create a new parameter 'parameterId_0'.
+
The model contains:
* 1 species (X)
* 1 parameter (k1)
Modified: trunk/test-suite/cases/semantic/00989/00989-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00989/00989-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00989/00989-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,7 +8,11 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
- This model contains two reactions that do the same thing, one by having a kinetic law that varies with the produced species, and the other by having a variable stoichiometry set to equal the produced species, for a sort of auto-catalytic reaction.
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
+This model contains two reactions that do the same thing, one by having a kinetic law that varies with the produced species, and the other by having a variable stoichiometry set to equal the produced species, for a sort of auto-catalytic reaction.
The model contains:
Modified: trunk/test-suite/cases/semantic/00990/00990-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00990/00990-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00990/00990-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -8,6 +8,10 @@
levels: 2.1, 2.2, 2.3, 2.4
generatedBy: Numeric
+Note: earlier versions of the test suite contained a 3.1 version of this test.
+That model was moved to its own test, because it did not have the 'StoichiometryMath'
+component.
+
The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that starts at 1 and increases at a rate of 1.
The model contains:
Modified: trunk/test-suite/cases/semantic/00991/00991-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00991/00991-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00991/00991-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -10,6 +10,9 @@
The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that starts at 1 and switches to 2 due to an event.
+The equivalent model using Level 3 constructs is present as
+test 1106.
+
The model contains:
* 1 species (X)
* 2 parameters (p1, k1)
Modified: trunk/test-suite/cases/semantic/00992/00992-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00992/00992-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00992/00992-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -10,6 +10,9 @@
The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that is set by an assignment rule to be equal to X.
+The equivalent model using Level 3 constructs is present as
+test 1107.
+
The model contains:
* 1 species (X)
* 2 parameters (p1, k1)
Modified: trunk/test-suite/cases/semantic/00993/00993-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00993/00993-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00993/00993-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -10,6 +10,9 @@
The stoichiometry of the reaction '-> nX' is set to be equal to p1, a parameter that is set by an algebraic rule to be equal to X.
+The equivalent model using Level 3 constructs is present as
+test 1108.
+
The model contains:
* 1 species (X)
* 2 parameters (p1, k1)
Modified: trunk/test-suite/cases/semantic/00994/00994-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00994/00994-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/00994/00994-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -10,6 +10,9 @@
Variable stoichiometry: the stoichiometry is literally 'time'.
+The equivalent model using Level 3 constructs is present as
+test 1109.
+
The model contains:
* 1 species (X)
* 1 parameter (k1)
Modified: trunk/test-suite/cases/semantic/01027/01027-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01027/01027-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/01027/01027-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -13,6 +13,9 @@
the kinetic law actually goes negative (a requirement for reversibe reactions).
The reaction listed below is therfore equivalent to the one in the file, but reversed from it.
+The version of this model using Level 3 constructs is present
+as test 1110.
+
The model contains one compartment called C. There are two species called
S1 and S2 and three parameters called kf, kr and p1. The model contains one reaction
defined as:
Modified: trunk/test-suite/cases/semantic/01028/01028-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01028/01028-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/01028/01028-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -13,6 +13,9 @@
the kinetic law actually goes negative (a requirement for reversibe reactions).
The reaction listed below is therfore equivalent to the one in the file, but reversed from it.
+The version of this model using Level 3 constructs is present
+as test 1111.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction
defined as:
Modified: trunk/test-suite/cases/semantic/01029/01029-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01029/01029-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/01029/01029-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -1,4 +1,4 @@
-(*
+\(*
category: Test
synopsis: Single reversible reaction.
@@ -13,6 +13,9 @@
the kinetic law actually goes negative (a requirement for reversibe reactions).
The reaction listed below is therfore equivalent to the one in the file, but reversed from it.
+The version of this model using Level 3 constructs is present
+as test 1064.
+
The model contains one compartment called C. There are three species called
S1, S2 and S3 and three parameters called kf, kr and p1. The model contains one reaction
defined as:
Modified: trunk/test-suite/cases/semantic/01121/01121-model.m
===================================================================
--- trunk/test-suite/cases/semantic/01121/01121-model.m 2012-08-23 14:53:18 UTC (rev 16259)
+++ trunk/test-suite/cases/semantic/01121/01121-model.m 2012-08-24 19:34:46 UTC (rev 16260)
@@ -1,7 +1,7 @@
(*
category: Test
-synopsis: [[Write description here.]]
+synopsis: A combination test of almost everything but events.
componentTags: AssignmentRule, CSymbolAvogadro, CSymbolTime, Compartment, FunctionDefinition, InitialAssignment, Parameter, RateRule, Reaction, Species
testTags: Amount, AssignedConstantStoichiometry, AssignedVariableStoichiometry, BoundaryCondition, ConstantSpecies, ConversionFactors, HasOnlySubstanceUnits, InitialValueReassigned, LocalParameters, MultiCompartment, NonConstantCompartment, NonConstantParameter, NonUnityCompartment, NonUnityStoichiometry, SpeciesReferenceInMath
testType: TimeCourse
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2012-08-23 14:53:25
|
Revision: 16259
http://sbml.svn.sourceforge.net/sbml/?rev=16259&view=rev
Author: sarahkeating
Date: 2012-08-23 14:53:18 +0000 (Thu, 23 Aug 2012)
Log Message:
-----------
changing documentation comments
Modified Paths:
--------------
branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.cpp
branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.h
Modified: branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.cpp
===================================================================
--- branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.cpp 2012-08-22 20:09:34 UTC (rev 16258)
+++ branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.cpp 2012-08-23 14:53:18 UTC (rev 16259)
@@ -172,7 +172,7 @@
/*
- * Returns the value of the "boolean" attribute of this QualitativeSpecies.
+ * Returns the value of the "constant" attribute of this QualitativeSpecies.
*/
const bool
QualitativeSpecies::getConstant() const
@@ -232,7 +232,7 @@
/*
- * Returns true/false if boolean is set.
+ * Returns true/false if constant is set.
*/
bool
QualitativeSpecies::isSetConstant() const
@@ -304,12 +304,12 @@
/*
- * Sets boolean and returns value indicating success.
+ * Sets constant and returns value indicating success.
*/
int
-QualitativeSpecies::setConstant(bool boolean)
+QualitativeSpecies::setConstant(bool constant)
{
- mConstant = boolean;
+ mConstant = constant;
mIsSetConstant = true;
return LIBSBML_OPERATION_SUCCESS;
}
@@ -396,7 +396,7 @@
/*
- * Unsets boolean and returns value indicating success.
+ * Unsets constant and returns value indicating success.
*/
int
QualitativeSpecies::unsetConstant()
@@ -992,7 +992,7 @@
* write comments
*/
LIBSBML_EXTERN
-const char *
+char *
QualitativeSpecies_getName(QualitativeSpecies_t * qs)
{
if (qs == NULL)
@@ -1117,9 +1117,9 @@
*/
LIBSBML_EXTERN
int
-QualitativeSpecies_setConstant(QualitativeSpecies_t * qs, int boolean)
+QualitativeSpecies_setConstant(QualitativeSpecies_t * qs, int constant)
{
- return (qs != NULL) ? qs->setConstant(boolean) : LIBSBML_INVALID_OBJECT;
+ return (qs != NULL) ? qs->setConstant(constant) : LIBSBML_INVALID_OBJECT;
}
Modified: branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.h
===================================================================
--- branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.h 2012-08-22 20:09:34 UTC (rev 16258)
+++ branches/libsbml-packages/qual/src/sbml/QualitativeSpecies.h 2012-08-23 14:53:18 UTC (rev 16259)
@@ -138,9 +138,9 @@
/**
- * Returns the value of the "Constant" attribute of this QualitativeSpecies.
+ * Returns the value of the "constant" attribute of this QualitativeSpecies.
*
- * @return the value of the "Constant" attribute of this QualitativeSpecies as a Constant.
+ * @return the value of the "constant" attribute of this QualitativeSpecies as a boolean.
*/
virtual const bool getConstant() const;
@@ -191,9 +191,9 @@
/**
* Predicate returning @c true or @c false depending on whether this
- * QualitativeSpecies's "Constant" attribute has been set.
+ * QualitativeSpecies's "constant" attribute has been set.
*
- * @return @c true if this QualitativeSpecies's "Constant" attribute has been set,
+ * @return @c true if this QualitativeSpecies's "constant" attribute has been set,
* otherwise @c false is returned.
*/
virtual bool isSetConstant() const;
@@ -260,9 +260,9 @@
/**
- * Sets the value of the "Constant" attribute of this QualitativeSpecies.
+ * Sets the value of the "constant" attribute of this QualitativeSpecies.
*
- * @param Constant; bool value of the "Constant" attribute to be set
+ * @param constant; bool value of the "constant" attribute to be set
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
@@ -271,7 +271,7 @@
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
*/
- virtual int setConstant(bool Constant);
+ virtual int setConstant(bool constant);
/**
@@ -346,7 +346,7 @@
/**
- * Unsets the value of the "Constant" attribute of this QualitativeSpecies.
+ * Unsets the value of the "constant" attribute of this QualitativeSpecies.
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
@@ -446,9 +446,9 @@
* @note The required attributes for a QualitativeSpecies object are:
* @li "id"
* @li "compartment"
- * @li "Constant"
+ * @li "constant"
*
- * @return a Constant value indicating whether all the required
+ * @return a boolean value indicating whether all the required
* attributes for this object have been defined.
*/
virtual bool hasRequiredAttributes() const;
@@ -808,7 +808,7 @@
LIBSBML_EXTERN
-const char *
+char *
QualitativeSpecies_getName(QualitativeSpecies_t * qs);
@@ -864,7 +864,7 @@
LIBSBML_EXTERN
int
-QualitativeSpecies_setConstant(QualitativeSpecies_t * qs, int Constant);
+QualitativeSpecies_setConstant(QualitativeSpecies_t * qs, int constant);
LIBSBML_EXTERN
@@ -935,3 +935,4 @@
#endif /* !SWIG */
#endif /* QualitativeSpecies_H__ */
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <luc...@us...> - 2012-08-22 20:09:45
|
Revision: 16258
http://sbml.svn.sourceforge.net/sbml/?rev=16258&view=rev
Author: luciansmith
Date: 2012-08-22 20:09:34 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
Commented back in the md5 attribute.
Modified Paths:
--------------
branches/libsbml-packages/comp/examples/c++/example1.cpp
branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp
branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.h
branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/test/TestSBaseObjects.cpp
Modified: branches/libsbml-packages/comp/examples/c++/example1.cpp
===================================================================
--- branches/libsbml-packages/comp/examples/c++/example1.cpp 2012-08-22 17:55:41 UTC (rev 16257)
+++ branches/libsbml-packages/comp/examples/c++/example1.cpp 2012-08-22 20:09:34 UTC (rev 16258)
@@ -120,7 +120,7 @@
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
- //extmod2.setMd5("406022s908ge74sklj");
+ extmod2.setMd5("406022s908ge74sklj");
compdoc->addExternalModelDefinition(&extmod2);
// Create submodels
Modified: branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp
===================================================================
--- branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp 2012-08-22 17:55:41 UTC (rev 16257)
+++ branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.cpp 2012-08-22 20:09:34 UTC (rev 16258)
@@ -40,7 +40,7 @@
, mName("")
, mSource("")
, mModelRef("")
- //, mMd5("")
+ , mMd5("")
{
// set an SBMLNamespaces derived object (CompPkgNamespaces) of this package.
setSBMLNamespacesAndOwn(new CompPkgNamespaces(level,version,pkgVersion));
@@ -54,7 +54,7 @@
, mName("")
, mSource("")
, mModelRef("")
- //, mMd5("")
+ , mMd5("")
{
// set the element namespace of this object
setElementNamespace(compns->getURI());
@@ -73,7 +73,7 @@
mName=source.mName;
mSource=source.mSource;
mModelRef=source.mModelRef;
- //mMd5=source.mMd5;
+ mMd5=source.mMd5;
// connect child elements to this element.
connectToChild();
@@ -88,7 +88,7 @@
mName=source.mName;
mSource=source.mSource;
mModelRef=source.mModelRef;
- //mMd5=source.mMd5;
+ mMd5=source.mMd5;
// connect child elements to this element.
connectToChild();
@@ -260,54 +260,54 @@
/*
* Sets the md5 of this SBML object to a copy of md5.
*/
-//int
-//ExternalModelDefinition::setMd5 (const std::string& md5)
-//{
-// //LS DEBUG: Check format of md5 to ensure validity?
-// mMd5 = md5;
-// return LIBSBML_OPERATION_SUCCESS;
-//}
+int
+ExternalModelDefinition::setMd5 (const std::string& md5)
+{
+ //LS DEBUG: Check format of md5 to ensure validity?
+ mMd5 = md5;
+ return LIBSBML_OPERATION_SUCCESS;
+}
/*
* @return the md5 of this SBML object.
*/
-//const string&
-//ExternalModelDefinition::getMd5 () const
-//{
-// return mMd5;
-//}
+const string&
+ExternalModelDefinition::getMd5 () const
+{
+ return mMd5;
+}
/*
* @return true if the md5 of this SBML object has been set, false
* otherwise.
*/
-//bool
-//ExternalModelDefinition::isSetMd5 () const
-//{
-// return (mMd5.empty() == false);
-//}
+bool
+ExternalModelDefinition::isSetMd5 () const
+{
+ return (mMd5.empty() == false);
+}
/*
* Unsets the md5 of this SBML object.
*/
-//int
-//ExternalModelDefinition::unsetMd5 ()
-//{
-// mMd5.erase();
-//
-// if (mMd5.empty())
-// {
-// return LIBSBML_OPERATION_SUCCESS;
-// }
-// else
-// {
-// return LIBSBML_OPERATION_FAILED;
-// }
-//}
+int
+ExternalModelDefinition::unsetMd5 ()
+{
+ mMd5.erase();
+ if (mMd5.empty())
+ {
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+ else
+ {
+ return LIBSBML_OPERATION_FAILED;
+ }
+}
+
/*
* Sets the source of this SBML object to a copy of source.
*/
@@ -382,7 +382,7 @@
attributes.add("name");
attributes.add("source");
attributes.add("modelRef");
- //attributes.add("md5");
+ attributes.add("md5");
}
@@ -418,10 +418,10 @@
logInvalidId("comp:modelRef", mModelRef);
}
}
- //XMLTriple tripleMd5("md5", mURI, getPrefix());
- //if (attributes.readInto(tripleMd5, mMd5, getErrorLog(), false, getLine(), getColumn())) {
- // //LS DEBUG: md5 syntax checking here.
- //}
+ XMLTriple tripleMd5("md5", mURI, getPrefix());
+ if (attributes.readInto(tripleMd5, mMd5, getErrorLog(), false, getLine(), getColumn())) {
+ //LS DEBUG: md5 syntax checking here.
+ }
}
}
@@ -443,9 +443,9 @@
if (isSetModelRef()) {
stream.writeAttribute("modelRef", getPrefix(), mModelRef);
}
- //if (isSetMd5()) {
- // stream.writeAttribute("md5", getPrefix(), mMd5);
- //}
+ if (isSetMd5()) {
+ stream.writeAttribute("md5", getPrefix(), mMd5);
+ }
ExternalModelDefinition::writeExtensionAttributes(stream);
}
Modified: branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.h
===================================================================
--- branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.h 2012-08-22 17:55:41 UTC (rev 16257)
+++ branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/ExternalModelDefinition.h 2012-08-22 20:09:34 UTC (rev 16258)
@@ -45,7 +45,7 @@
std::string mName;
std::string mSource;
std::string mModelRef;
- //std::string mMd5;
+ std::string mMd5;
public:
@@ -243,7 +243,7 @@
*
* @return the value of the "md5" attribute of this ExternalModelDefinition.
*/
- //virtual const std::string& getMd5 () const;
+ virtual const std::string& getMd5 () const;
/**
@@ -253,7 +253,7 @@
* @return @c true if this ExternalModelDefinition's "md5" attribute has been set,
* otherwise @c false is returned.
*/
- //virtual bool isSetMd5 () const;
+ virtual bool isSetMd5 () const;
/**
@@ -266,7 +266,7 @@
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE @endlink
*/
- //virtual int setMd5 (const std::string& id);
+ virtual int setMd5 (const std::string& id);
/**
@@ -279,7 +279,7 @@
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
- //virtual int unsetMd5 ();
+ virtual int unsetMd5 ();
/**
Modified: branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/test/TestSBaseObjects.cpp
===================================================================
--- branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/test/TestSBaseObjects.cpp 2012-08-22 17:55:41 UTC (rev 16257)
+++ branches/libsbml-packages/comp/src/sbml/packages/comp/sbml/test/TestSBaseObjects.cpp 2012-08-22 20:09:34 UTC (rev 16258)
@@ -145,13 +145,13 @@
fail_unless(emd.unsetModelRef()==LIBSBML_OPERATION_SUCCESS);
fail_unless(emd.isSetModelRef()==false);
- //fail_unless(emd.isSetMd5()==false);
- //fail_unless(emd.setMd5("1&d")==LIBSBML_OPERATION_SUCCESS);
- //fail_unless(emd.setMd5("ID1")==LIBSBML_OPERATION_SUCCESS);
- //fail_unless(emd.getMd5()=="ID1");
- //fail_unless(emd.isSetMd5()==true);
- //fail_unless(emd.unsetMd5()==LIBSBML_OPERATION_SUCCESS);
- //fail_unless(emd.isSetMd5()==false);
+ fail_unless(emd.isSetMd5()==false);
+ fail_unless(emd.setMd5("1&d")==LIBSBML_OPERATION_SUCCESS);
+ fail_unless(emd.setMd5("ID1")==LIBSBML_OPERATION_SUCCESS);
+ fail_unless(emd.getMd5()=="ID1");
+ fail_unless(emd.isSetMd5()==true);
+ fail_unless(emd.unsetMd5()==LIBSBML_OPERATION_SUCCESS);
+ fail_unless(emd.isSetMd5()==false);
fail_unless(emd.isSetSource()==false);
fail_unless(emd.setSource("1&d")==LIBSBML_OPERATION_SUCCESS);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2012-08-22 17:55:48
|
Revision: 16257
http://sbml.svn.sourceforge.net/sbml/?rev=16257&view=rev
Author: sarahkeating
Date: 2012-08-22 17:55:41 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/L3Parser/src/sbml/math/test/TestL3FormulaParser.cpp
branches/L3Parser/src/sbml/math/test/TestL3FormulaParserC.c
Modified: branches/L3Parser/src/sbml/math/test/TestL3FormulaParser.cpp
===================================================================
--- branches/L3Parser/src/sbml/math/test/TestL3FormulaParser.cpp 2012-08-22 17:46:07 UTC (rev 16256)
+++ branches/L3Parser/src/sbml/math/test/TestL3FormulaParser.cpp 2012-08-22 17:55:41 UTC (rev 16257)
@@ -27,16 +27,19 @@
#include <sbml/common/common.h>
#include <sbml/math/L3Parser.h>
+#include <sbml/math/L3ParserSettings.h>
+#include <sbml/Model.h>
#include <check.h>
#if __cplusplus
+LIBSBML_CPP_NAMESPACE_USE
CK_CPPSTART
#endif
START_TEST (test_SBML_parseL3Formula_1)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1");
+ ASTNode_t *r = SBML_parseL3Formula("1");
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
@@ -50,7 +53,7 @@
START_TEST (test_SBML_parseL3Formula_2)
{
- ASTNode_t *r = L3Parser::parseL3Formula("2.1");
+ ASTNode_t *r = SBML_parseL3Formula("2.1");
fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
@@ -64,7 +67,7 @@
START_TEST (test_SBML_parseL3Formula_3)
{
- ASTNode_t *r = L3Parser::parseL3Formula("2.1e5");
+ ASTNode_t *r = SBML_parseL3Formula("2.1e5");
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
@@ -79,7 +82,7 @@
START_TEST (test_SBML_parseL3Formula_4)
{
- ASTNode_t *r = L3Parser::parseL3Formula("foo");
+ ASTNode_t *r = SBML_parseL3Formula("foo");
fail_unless( ASTNode_getType(r) == AST_NAME , NULL );
@@ -93,7 +96,7 @@
START_TEST (test_SBML_parseL3Formula_5)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 + foo");
+ ASTNode_t *r = SBML_parseL3Formula("1 + foo");
ASTNode_t *c;
@@ -121,7 +124,7 @@
START_TEST (test_SBML_parseL3Formula_6)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 + 2");
+ ASTNode_t *r = SBML_parseL3Formula("1 + 2");
ASTNode_t *c;
@@ -149,7 +152,7 @@
START_TEST (test_SBML_parseL3Formula_7)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 + 2 * 3");
+ ASTNode_t *r = SBML_parseL3Formula("1 + 2 * 3");
ASTNode_t *c;
@@ -189,7 +192,7 @@
START_TEST (test_SBML_parseL3Formula_8)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(1 - 2) * 3");
+ ASTNode_t *r = SBML_parseL3Formula("(1 - 2) * 3");
ASTNode_t *c;
@@ -228,7 +231,7 @@
START_TEST (test_SBML_parseL3Formula_9)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 + -2 / 3");
+ ASTNode_t *r = SBML_parseL3Formula("1 + -2 / 3");
ASTNode_t *c;
@@ -273,7 +276,7 @@
START_TEST (test_SBML_parseL3Formula_10)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 + -2e100 / 3");
+ ASTNode_t *r = SBML_parseL3Formula("1 + -2e100 / 3");
ASTNode_t *c;
@@ -319,7 +322,7 @@
START_TEST (test_SBML_parseL3Formula_11)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 - -foo / 3");
+ ASTNode_t *r = SBML_parseL3Formula("1 - -foo / 3");
ASTNode_t *c;
@@ -365,7 +368,7 @@
START_TEST (test_SBML_parseL3Formula_12)
{
- ASTNode_t *r = L3Parser::parseL3Formula("2 * foo^bar + 3.0");
+ ASTNode_t *r = SBML_parseL3Formula("2 * foo^bar + 3.0");
ASTNode_t *c;
@@ -416,7 +419,7 @@
START_TEST (test_SBML_parseL3Formula_13)
{
- ASTNode_t *r = L3Parser::parseL3Formula("foo()");
+ ASTNode_t *r = SBML_parseL3Formula("foo()");
fail_unless( ASTNode_getType(r) == AST_FUNCTION , NULL );
@@ -430,7 +433,7 @@
START_TEST (test_SBML_parseL3Formula_14)
{
- ASTNode_t *r = L3Parser::parseL3Formula("foo(1)");
+ ASTNode_t *r = SBML_parseL3Formula("foo(1)");
ASTNode_t *c;
@@ -451,7 +454,7 @@
START_TEST (test_SBML_parseL3Formula_15)
{
- ASTNode_t *r = L3Parser::parseL3Formula("foo(1, bar)");
+ ASTNode_t *r = SBML_parseL3Formula("foo(1, bar)");
ASTNode_t *c;
@@ -478,7 +481,7 @@
START_TEST (test_SBML_parseL3Formula_16)
{
- ASTNode_t *r = L3Parser::parseL3Formula("foo(1, bar, 2^-3)");
+ ASTNode_t *r = SBML_parseL3Formula("foo(1, bar, 2^-3)");
ASTNode_t *c;
@@ -529,27 +532,27 @@
START_TEST (test_SBML_parseL3Formula_17)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1//1");
+ ASTNode_t *r = SBML_parseL3Formula("1//1");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input '1//1' at position 3: syntax error, unexpected '/'"), NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '1//1' at position 3: syntax error, unexpected '/'"), NULL);
}
END_TEST
START_TEST (test_SBML_parseL3Formula_18)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1+2*3 4");
+ ASTNode_t *r = SBML_parseL3Formula("1+2*3 4");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input '1+2*3 4' at position 7: syntax error, unexpected integer"), NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '1+2*3 4' at position 7: syntax error, unexpected integer"), NULL);
}
END_TEST
START_TEST (test_SBML_parseL3Formula_negInf)
{
- ASTNode_t *r = L3Parser::parseL3Formula("-inf");
+ ASTNode_t *r = SBML_parseL3Formula("-inf");
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getCharacter (r) == '-', NULL );
@@ -569,7 +572,7 @@
START_TEST (test_SBML_parseL3Formula_negZero)
{
- ASTNode_t *r = L3Parser::parseL3Formula("-0.0");
+ ASTNode_t *r = SBML_parseL3Formula("-0.0");
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getCharacter (r) == '-', NULL );
@@ -588,7 +591,7 @@
START_TEST (test_SBML_parseL3Formula_e1)
{
- ASTNode_t *r = L3Parser::parseL3Formula("2.001e+5");
+ ASTNode_t *r = SBML_parseL3Formula("2.001e+5");
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
@@ -603,7 +606,7 @@
START_TEST (test_SBML_parseL3Formula_e2)
{
- ASTNode_t *r = L3Parser::parseL3Formula(".001e+5");
+ ASTNode_t *r = SBML_parseL3Formula(".001e+5");
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
@@ -618,7 +621,7 @@
START_TEST (test_SBML_parseL3Formula_e3)
{
- ASTNode_t *r = L3Parser::parseL3Formula(".001e-5");
+ ASTNode_t *r = SBML_parseL3Formula(".001e-5");
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
@@ -633,7 +636,7 @@
START_TEST (test_SBML_parseL3Formula_e4)
{
- ASTNode_t *r = L3Parser::parseL3Formula("2.e-005");
+ ASTNode_t *r = SBML_parseL3Formula("2.e-005");
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
@@ -648,10 +651,10 @@
START_TEST (test_SBML_parseL3Formula_e5)
{
- ASTNode_t *r = L3Parser::parseL3Formula(".e+5");
+ ASTNode_t *r = SBML_parseL3Formula(".e+5");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input '.e+5' at position 1: syntax error, unexpected $undefined"), NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '.e+5' at position 1: syntax error, unexpected $undefined"), NULL);
ASTNode_free(r);
}
@@ -660,7 +663,7 @@
START_TEST (test_SBML_parseL3Formula_rational1)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(3/4)");
+ ASTNode_t *r = SBML_parseL3Formula("(3/4)");
fail_unless( ASTNode_getType (r) == AST_RATIONAL, NULL );
fail_unless( ASTNode_getNumerator (r) == 3, NULL );
@@ -674,7 +677,7 @@
START_TEST (test_SBML_parseL3Formula_rational2)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(3/4) mL");
+ ASTNode_t *r = SBML_parseL3Formula("(3/4) mL");
fail_unless( ASTNode_getType (r) == AST_RATIONAL, NULL );
fail_unless( ASTNode_getNumerator (r) == 3, NULL );
@@ -689,7 +692,7 @@
START_TEST (test_SBML_parseL3Formula_rational3)
{
- ASTNode_t *r = L3Parser::parseL3Formula("3/4");
+ ASTNode_t *r = SBML_parseL3Formula("3/4");
fail_unless( ASTNode_getType (r) == AST_DIVIDE, NULL );
fail_unless( ASTNode_getCharacter (r) == '/', NULL );
@@ -714,7 +717,7 @@
START_TEST (test_SBML_parseL3Formula_rational4)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(3/x)");
+ ASTNode_t *r = SBML_parseL3Formula("(3/x)");
fail_unless( ASTNode_getType (r) == AST_DIVIDE, NULL );
fail_unless( ASTNode_getCharacter (r) == '/', NULL );
@@ -739,7 +742,7 @@
START_TEST (test_SBML_parseL3Formula_rational5)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(3/4.4)");
+ ASTNode_t *r = SBML_parseL3Formula("(3/4.4)");
fail_unless( ASTNode_getType (r) == AST_DIVIDE, NULL );
fail_unless( ASTNode_getCharacter (r) == '/', NULL );
@@ -764,7 +767,7 @@
START_TEST (test_SBML_parseL3Formula_rational6)
{
- ASTNode_t *r = L3Parser::parseL3Formula("3/4 ml");
+ ASTNode_t *r = SBML_parseL3Formula("3/4 ml");
fail_unless( ASTNode_getType (r) == AST_DIVIDE, NULL );
fail_unless( ASTNode_getCharacter (r) == '/', NULL );
@@ -791,17 +794,17 @@
START_TEST (test_SBML_parseL3Formula_rational7)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(3/4.4) ml");
+ ASTNode_t *r = SBML_parseL3Formula("(3/4.4) ml");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input '(3/4.4) ml' at position 10: syntax error, unexpected element name"), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '(3/4.4) ml' at position 10: syntax error, unexpected element name"), NULL );
}
END_TEST
START_TEST (test_SBML_parseL3Formula_constants1)
{
- ASTNode_t *r = L3Parser::parseL3Formula("true");
+ ASTNode_t *r = SBML_parseL3Formula("true");
fail_unless( ASTNode_getType (r) == AST_CONSTANT_TRUE, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
@@ -811,7 +814,7 @@
START_TEST (test_SBML_parseL3Formula_constants2)
{
- ASTNode_t *r = L3Parser::parseL3Formula("false");
+ ASTNode_t *r = SBML_parseL3Formula("false");
fail_unless( ASTNode_getType (r) == AST_CONSTANT_FALSE, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
@@ -821,7 +824,7 @@
START_TEST (test_SBML_parseL3Formula_constants3)
{
- ASTNode_t *r = L3Parser::parseL3Formula("pi");
+ ASTNode_t *r = SBML_parseL3Formula("pi");
fail_unless( ASTNode_getType (r) == AST_CONSTANT_PI, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
@@ -831,7 +834,7 @@
START_TEST (test_SBML_parseL3Formula_constants4)
{
- ASTNode_t *r = L3Parser::parseL3Formula("exponentiale");
+ ASTNode_t *r = SBML_parseL3Formula("exponentiale");
fail_unless( ASTNode_getType (r) == AST_CONSTANT_E, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
@@ -841,7 +844,7 @@
START_TEST (test_SBML_parseL3Formula_constants5)
{
- ASTNode_t *r = L3Parser::parseL3Formula("avogadro");
+ ASTNode_t *r = SBML_parseL3Formula("avogadro");
fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
@@ -851,7 +854,7 @@
START_TEST (test_SBML_parseL3Formula_constants6)
{
- ASTNode_t *r = L3Parser::parseL3Formula("time");
+ ASTNode_t *r = SBML_parseL3Formula("time");
fail_unless( ASTNode_getType (r) == AST_NAME_TIME, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
@@ -861,7 +864,7 @@
START_TEST (test_SBML_parseL3Formula_constants7)
{
- ASTNode_t *r = L3Parser::parseL3Formula("inf");
+ ASTNode_t *r = SBML_parseL3Formula("inf");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( util_isInf(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -872,7 +875,7 @@
START_TEST (test_SBML_parseL3Formula_constants8)
{
- ASTNode_t *r = L3Parser::parseL3Formula("infinity");
+ ASTNode_t *r = SBML_parseL3Formula("infinity");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( util_isInf(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -883,7 +886,7 @@
START_TEST (test_SBML_parseL3Formula_constants9)
{
- ASTNode_t *r = L3Parser::parseL3Formula("INF");
+ ASTNode_t *r = SBML_parseL3Formula("INF");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( util_isInf(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -897,7 +900,7 @@
#ifdef _MSC_VER
# define isnan(d) _isnan(d)
#endif
- ASTNode_t *r = L3Parser::parseL3Formula("notanumber");
+ ASTNode_t *r = SBML_parseL3Formula("notanumber");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( isnan(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -908,7 +911,7 @@
START_TEST (test_SBML_parseL3Formula_constants11)
{
- ASTNode_t *r = L3Parser::parseL3Formula("nan");
+ ASTNode_t *r = SBML_parseL3Formula("nan");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( isnan(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -919,7 +922,7 @@
START_TEST (test_SBML_parseL3Formula_constants12)
{
- ASTNode_t *r = L3Parser::parseL3Formula("NaN");
+ ASTNode_t *r = SBML_parseL3Formula("NaN");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( isnan(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -930,7 +933,7 @@
START_TEST (test_SBML_parseL3Formula_modulo)
{
- ASTNode_t *r = L3Parser::parseL3Formula("x % y");
+ ASTNode_t *r = SBML_parseL3Formula("x % y");
//Instead of trying to go through everything individually, we'll just test the round-tripping:
fail_unless( !strcmp(SBML_formulaToString(r), "piecewise(x - y * ceil(x / y), xor(lt(x, 0), lt(y, 0)), x - y * floor(x / y))"), NULL );
ASTNode_free(r);
@@ -940,7 +943,7 @@
START_TEST (test_SBML_parseL3Formula_oddMathML1)
{
- ASTNode_t *r = L3Parser::parseL3Formula("sqrt(3)");
+ ASTNode_t *r = SBML_parseL3Formula("sqrt(3)");
fail_unless( ASTNode_getType (r) == AST_FUNCTION_ROOT, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -964,7 +967,7 @@
START_TEST (test_SBML_parseL3Formula_oddMathML2)
{
- ASTNode_t *r = L3Parser::parseL3Formula("sqr(3)");
+ ASTNode_t *r = SBML_parseL3Formula("sqr(3)");
fail_unless( ASTNode_getType (r) == AST_FUNCTION_POWER, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -988,7 +991,7 @@
START_TEST (test_SBML_parseL3Formula_oddMathML3)
{
- ASTNode_t *r = L3Parser::parseL3Formula("log10(3)");
+ ASTNode_t *r = SBML_parseL3Formula("log10(3)");
fail_unless( ASTNode_getType (r) == AST_FUNCTION_LOG, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1012,7 +1015,7 @@
START_TEST (test_SBML_parseL3Formula_oddMathML4)
{
- ASTNode_t *r = L3Parser::parseL3Formula("log(4.4, 3)");
+ ASTNode_t *r = SBML_parseL3Formula("log(4.4, 3)");
fail_unless( ASTNode_getType (r) == AST_FUNCTION_LOG, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1036,7 +1039,7 @@
START_TEST (test_SBML_parseL3Formula_oddMathML5)
{
- ASTNode_t *r = L3Parser::parseL3Formula("root(1.1, 3)");
+ ASTNode_t *r = SBML_parseL3Formula("root(1.1, 3)");
fail_unless( ASTNode_getType (r) == AST_FUNCTION_ROOT, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1063,7 +1066,7 @@
Model_t *model = Model_create(3,1);
Parameter *p = Model_createParameter(model);
Parameter_setId(p, "infinity");
- ASTNode_t *r = L3Parser::parseL3Formula("infinity", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("infinity", model);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "infinity") , NULL );
@@ -1079,7 +1082,7 @@
Model_t *model = Model_create(3,1);
Species *p = Model_createSpecies(model);
Species_setId(p, "true");
- ASTNode_t *r = L3Parser::parseL3Formula("true", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("true", model);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "true") , NULL );
@@ -1095,7 +1098,7 @@
Model_t *model = Model_create(3,1);
Compartment *p = Model_createCompartment(model);
Compartment_setId(p, "NaN");
- ASTNode_t *r = L3Parser::parseL3Formula("NaN", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("NaN", model);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "NaN") , NULL );
@@ -1111,7 +1114,7 @@
Model_t *model = Model_create(3,1);
Reaction *p = Model_createReaction(model);
Reaction_setId(p, "pi");
- ASTNode_t *r = L3Parser::parseL3Formula("pi", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("pi", model);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "pi") , NULL );
@@ -1128,7 +1131,7 @@
Reaction *p = Model_createReaction(model);
SpeciesReference_t* sr = Reaction_createProduct(p);
SpeciesReference_setId(sr, "avogadro");
- ASTNode_t *r = L3Parser::parseL3Formula("avogadro", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("avogadro", model);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "avogadro") , NULL );
@@ -1145,7 +1148,7 @@
Reaction *p = Model_createReaction(model);
SpeciesReference_t* sr = Reaction_createProduct(p);
SpeciesReference_setId(sr, "AVOGADRO");
- ASTNode_t *r = L3Parser::parseL3Formula("avogadro", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("avogadro", model);
fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "avogadro") , NULL );
@@ -1161,7 +1164,7 @@
Model_t *model = Model_create(3,1);
FunctionDefinition *p = Model_createFunctionDefinition(model);
FunctionDefinition_setId(p, "sin");
- ASTNode_t *r = L3Parser::parseL3Formula("sin(x, y)", model);
+ ASTNode_t *r = SBML_parseL3FormulaWithModel("sin(x, y)", model);
fail_unless( ASTNode_getType (r) == AST_FUNCTION, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "sin") , NULL );
@@ -1174,40 +1177,40 @@
START_TEST (test_SBML_parseL3Formula_arguments)
{
- ASTNode_t *r = L3Parser::parseL3Formula("sin(x,y)");
+ ASTNode_t *r = SBML_parseL3Formula("sin(x,y)");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'sin(x,y)' at position 8: The function 'sin' takes exactly one argument, but 2 were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'sin(x,y)' at position 8: The function 'sin' takes exactly one argument, but 2 were found."), NULL );
- r = L3Parser::parseL3Formula("delay(x)");
+ r = SBML_parseL3Formula("delay(x)");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'delay(x)' at position 8: The function 'delay' takes exactly two arguments, but 1 were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'delay(x)' at position 8: The function 'delay' takes exactly two arguments, but 1 were found."), NULL );
- r = L3Parser::parseL3Formula("piecewise()");
+ r = SBML_parseL3Formula("piecewise()");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'piecewise()' at position 11: The function 'piecewise' takes at least one argument, but none were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'piecewise()' at position 11: The function 'piecewise' takes at least one argument, but none were found."), NULL );
- r = L3Parser::parseL3Formula("gt(x)");
+ r = SBML_parseL3Formula("gt(x)");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'gt(x)' at position 5: The function 'gt' takes at least two arguments, but 1 were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'gt(x)' at position 5: The function 'gt' takes at least two arguments, but 1 were found."), NULL );
- r = L3Parser::parseL3Formula("minus()");
+ r = SBML_parseL3Formula("minus()");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'minus()' at position 7: The function 'minus' takes exactly one or two arguments, but 0 were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'minus()' at position 7: The function 'minus' takes exactly one or two arguments, but 0 were found."), NULL );
- r = L3Parser::parseL3Formula("root(x, y, z)");
+ r = SBML_parseL3Formula("root(x, y, z)");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'root(x, y, z)' at position 13: The function 'root' takes exactly one or two arguments, but 3 were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'root(x, y, z)' at position 13: The function 'root' takes exactly one or two arguments, but 3 were found."), NULL );
- r = L3Parser::parseL3Formula("power()");
+ r = SBML_parseL3Formula("power()");
fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'power()' at position 7: The function 'power' takes exactly two arguments, but 0 were found."), NULL );
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'power()' at position 7: The function 'power' takes exactly two arguments, but 0 were found."), NULL );
}
END_TEST
START_TEST (test_SBML_parseL3Formula_logic1)
{
- ASTNode_t *r = L3Parser::parseL3Formula("1 && 2 == 3");
+ ASTNode_t *r = SBML_parseL3Formula("1 && 2 == 3");
ASTNode_t *c;
@@ -1247,7 +1250,7 @@
START_TEST (test_SBML_parseL3Formula_logic2)
{
- ASTNode_t *r = L3Parser::parseL3Formula("(1 && 2) == 3");
+ ASTNode_t *r = SBML_parseL3Formula("(1 && 2) == 3");
ASTNode_t *c;
@@ -1286,7 +1289,7 @@
START_TEST (test_SBML_parseL3Formula_precedence)
{
- ASTNode_t *root = L3Parser::parseL3Formula("a && b == !c - d * e^-f ");
+ ASTNode_t *root = SBML_parseL3Formula("a && b == !c - d * e^-f ");
ASTNode_t *left;
ASTNode_t *right;
@@ -1374,7 +1377,7 @@
START_TEST (test_SBML_parseL3Formula_parselogsettings)
{
//Default:
- ASTNode_t *r = L3Parser::parseL3Formula("log(4.4)");
+ ASTNode_t *r = SBML_parseL3Formula("log(4.4)");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_FUNCTION_LOG, NULL );
@@ -1395,7 +1398,7 @@
//Explicit parsing as ln
settings.setParseLog(L3P_PARSE_LOG_AS_LN);
- r = L3Parser::parseL3Formula("log(4.4)", settings);
+ r = SBML_parseL3FormulaWithSettings("log(4.4)", &settings);
fail_unless( ASTNode_getType (r) == AST_FUNCTION_LN, NULL );
fail_unless( ASTNode_getNumChildren(r) == 1 , NULL );
@@ -1409,7 +1412,7 @@
//Explicit parsing as log10
settings.setParseLog(L3P_PARSE_LOG_AS_LOG10);
- r = L3Parser::parseL3Formula("log(4.4)", settings);
+ r = SBML_parseL3FormulaWithSettings("log(4.4)", &settings);
fail_unless( ASTNode_getType (r) == AST_FUNCTION_LOG, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1427,10 +1430,10 @@
//Explicit setting as error
settings.setParseLog(L3P_PARSE_LOG_AS_ERROR);
- r = L3Parser::parseL3Formula("log(4.4)", settings);
+ r = SBML_parseL3FormulaWithSettings("log(4.4)", &settings);
fail_unless( r == NULL, NULL );
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input 'log(4.4)' at position 8: Writing a function as 'log(x)' was legal in the L1 parser, but translated as the natural log, not the base-10 log. This construct is disallowed entirely as being ambiguous, and you are encouraged instead to use 'ln(x)', 'log10(x)', or 'log(base, x)'."), NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'log(4.4)' at position 8: Writing a function as 'log(x)' was legal in the L1 parser, but translated as the natural log, not the base-10 log. This construct is disallowed entirely as being ambiguous, and you are encouraged instead to use 'ln(x)', 'log10(x)', or 'log(base, x)'."), NULL);
}
END_TEST
@@ -1438,7 +1441,7 @@
START_TEST (test_SBML_parseL3Formula_collapseminussettings1)
{
//Default:
- ASTNode_t *r = L3Parser::parseL3Formula("--4.4");
+ ASTNode_t *r = SBML_parseL3Formula("--4.4");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
@@ -1457,8 +1460,8 @@
L3ParserSettings settings;
//Explicit parsing to collapse the minuses
- settings.setCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
- r = L3Parser::parseL3Formula("--4.4", settings);
+ settings.setParseCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("--4.4", &settings);
fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
fail_unless( ASTNode_getReal (r) == 4.4, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -1466,8 +1469,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- settings.setCollapseMinus(L3P_EXPAND_UNARY_MINUS);
- r = L3Parser::parseL3Formula("--4.4");
+ settings.setParseCollapseMinus(L3P_EXPAND_UNARY_MINUS);
+ r = SBML_parseL3Formula("--4.4");
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getNumChildren(r) == 1 , NULL );
@@ -1489,7 +1492,7 @@
START_TEST (test_SBML_parseL3Formula_collapseminussettings2)
{
//Default:
- ASTNode_t *r = L3Parser::parseL3Formula("--x");
+ ASTNode_t *r = SBML_parseL3Formula("--x");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
@@ -1508,8 +1511,8 @@
L3ParserSettings settings;
//Explicit parsing to collapse the minuses
- settings.setCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
- r = L3Parser::parseL3Formula("--x", settings);
+ settings.setParseCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("--x", &settings);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "x"), NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -1517,8 +1520,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- settings.setCollapseMinus(L3P_EXPAND_UNARY_MINUS);
- r = L3Parser::parseL3Formula("--x", settings);
+ settings.setParseCollapseMinus(L3P_EXPAND_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("--x", &settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getNumChildren(r) == 1 , NULL );
@@ -1540,7 +1543,7 @@
START_TEST (test_SBML_parseL3Formula_collapseminussettings3)
{
//Default:
- ASTNode_t *r = L3Parser::parseL3Formula("x---4.4");
+ ASTNode_t *r = SBML_parseL3Formula("x---4.4");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
@@ -1568,8 +1571,8 @@
L3ParserSettings settings;
//Explicit parsing to collapse the minuses
- settings.setCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
- r = L3Parser::parseL3Formula("x---4.4", settings);
+ settings.setParseCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("x---4.4", &settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1586,8 +1589,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- settings.setCollapseMinus(L3P_EXPAND_UNARY_MINUS);
- r = L3Parser::parseL3Formula("x---4.4", settings);
+ settings.setParseCollapseMinus(L3P_EXPAND_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("x---4.4", &settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1618,7 +1621,7 @@
START_TEST (test_SBML_parseL3Formula_collapseminussettings4)
{
//Default:
- ASTNode_t *r = L3Parser::parseL3Formula("x---y");
+ ASTNode_t *r = SBML_parseL3Formula("x---y");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
@@ -1646,8 +1649,8 @@
L3ParserSettings settings;
//Explicit parsing to collapse the minuses
- settings.setCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
- r = L3Parser::parseL3Formula("x---y", settings);
+ settings.setParseCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("x---y", &settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1664,8 +1667,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- settings.setCollapseMinus(L3P_EXPAND_UNARY_MINUS);
- r = L3Parser::parseL3Formula("x---y", settings);
+ settings.setParseCollapseMinus(L3P_EXPAND_UNARY_MINUS);
+ r = SBML_parseL3FormulaWithSettings("x---y", &settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
@@ -1697,41 +1700,41 @@
{
//Explicit parsing to collapse the minuses
L3ParserSettings settings;
- settings.setCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
- ASTNode_t* r = L3Parser::parseL3Formula("---4", settings);
+ settings.setParseCollapseMinus(L3P_COLLAPSE_UNARY_MINUS);
+ ASTNode_t* r = SBML_parseL3FormulaWithSettings("---4", &settings);
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (r) == -4, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- r = L3Parser::parseL3Formula("---(3/8)", settings);
+ r = SBML_parseL3FormulaWithSettings("---(3/8)", &settings);
fail_unless( ASTNode_getType (r) == AST_RATIONAL, NULL );
fail_unless( ASTNode_getNumerator (r) == -3, NULL );
fail_unless( ASTNode_getDenominator(r) == 8, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- r = L3Parser::parseL3Formula("---(-3/8)", settings);
+ r = SBML_parseL3FormulaWithSettings("---(-3/8)", &settings);
fail_unless( ASTNode_getType (r) == AST_RATIONAL, NULL );
fail_unless( ASTNode_getNumerator (r) == 3, NULL );
fail_unless( ASTNode_getDenominator(r) == 8, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- r = L3Parser::parseL3Formula("---4.4", settings);
+ r = SBML_parseL3FormulaWithSettings("---4.4", &settings);
fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
fail_unless( ASTNode_getReal (r) == -4.4, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- r = L3Parser::parseL3Formula("---4e-3", settings);
+ r = SBML_parseL3FormulaWithSettings("---4e-3", &settings);
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
fail_unless( ASTNode_getMantissa (r) == -4, NULL );
fail_unless( ASTNode_getExponent (r) == -3, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- r = L3Parser::parseL3Formula("---.4", settings);
+ r = SBML_parseL3FormulaWithSettings("---.4", &settings);
fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
fail_unless( ASTNode_getReal (r) == -.4, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
@@ -1741,111 +1744,418 @@
END_TEST
-START_TEST (test_SBML_parseL3Formula_targetl2settings)
+START_TEST (test_SBML_parseL3Formula_avogadrosettings)
{
- ASTNode_t *r = L3Parser::parseL3Formula("4 mL");
-
- fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
- fail_unless( ASTNode_getInteger (r) == 4, NULL );
- fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
- ASTNode_free(r);
-
- r = L3Parser::parseL3Formula("avogadro");
+ ASTNode_t *r = SBML_parseL3Formula("avogadro");
fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
L3ParserSettings settings;
- settings.targetL2();
- r = L3Parser::parseL3Formula("4 mL", settings);
- fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input '4 mL' at position 4: The ability to associate units with numbers has been disabled in this software."), NULL );
+ settings.setParseAvogadroCsymbol(L3P_AVOGADRO_IS_NAME);
- r = L3Parser::parseL3Formula("avogadro", settings);
+ r = SBML_parseL3FormulaWithSettings("avogadro", &settings);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
fail_unless( !strcmp(ASTNode_getName(r), "avogadro") , NULL );
fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
ASTNode_free(r);
- settings.targetL3();
- r = L3Parser::parseL3Formula("4 mL", settings);
+ settings.setParseAvogadroCsymbol(L3P_AVOGADRO_IS_CSYMBOL);
+
+ r = SBML_parseL3FormulaWithSettings("avogadro", &settings);
+ fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+ ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_unitssettings)
+{
+ ASTNode_t *r = SBML_parseL3Formula("4 mL");
+
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (r) == 4, NULL );
fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- r = L3Parser::parseL3Formula("avogadro", settings);
- fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
+ L3ParserSettings settings;
+ settings.setParseUnits(L3P_NO_UNITS);
+ r = SBML_parseL3FormulaWithSettings("4 mL", &settings);
+ fail_unless(r == NULL, NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '4 mL' at position 4: The ability to associate units with numbers has been disabled."), NULL );
+
+ settings.setParseUnits(L3P_PARSE_UNITS);
+ r = SBML_parseL3FormulaWithSettings("4 mL", &settings);
+ fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
+ fail_unless( ASTNode_getInteger (r) == 4, NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
+
}
END_TEST
-START_TEST (test_SBML_parseL3Formula_avogadrosettings)
+START_TEST (test_SBML_parseL3Formula_power)
{
- ASTNode_t *r = L3Parser::parseL3Formula("avogadro");
- fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+ ASTNode_t *r = SBML_parseL3Formula("pow(1.1, 3)");
+
+ fail_unless( ASTNode_getType (r) == AST_POWER, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
+
+ ASTNode_t *c = ASTNode_getLeftChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (c) == 1.1, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+ c = ASTNode_getRightChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
+ fail_unless( ASTNode_getInteger (c) == 3, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
ASTNode_free(r);
- L3ParserSettings settings;
- settings.setAvogadroCsymbol(L3P_AVOGADRO_IS_NAME);
- fail_unless(settings.getTargetL2() == false, NULL);
- fail_unless(settings.getTargetL3() == false, NULL);
+ r = SBML_parseL3Formula("Power(1.1, 3)");
- r = L3Parser::parseL3Formula("avogadro", settings);
- fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
- fail_unless( !strcmp(ASTNode_getName(r), "avogadro") , NULL );
+ fail_unless( ASTNode_getType (r) == AST_POWER, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
+
+ c = ASTNode_getLeftChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (c) == 1.1, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+ c = ASTNode_getRightChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
+ fail_unless( ASTNode_getInteger (c) == 3, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longint)
+{
+ ASTNode_t *r = SBML_parseL3Formula("166112956810631");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 166112956810631.0, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+
ASTNode_free(r);
- settings.setAvogadroCsymbol(L3P_AVOGADRO_IS_CSYMBOL);
- fail_unless(settings.getTargetL2() == false, NULL);
- fail_unless(settings.getTargetL3() == true, NULL);
+}
+END_TEST
- r = L3Parser::parseL3Formula("avogadro", settings);
- fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+
+START_TEST (test_SBML_parseL3Formula_longdecimal)
+{
+ ASTNode_t *r = SBML_parseL3Formula("0.00166112956810631");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 0.00166112956810631, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+
ASTNode_free(r);
+
}
END_TEST
-START_TEST (test_SBML_parseL3Formula_unitssettings)
+START_TEST (test_SBML_parseL3Formula_longnumberparen)
{
- ASTNode_t *r = L3Parser::parseL3Formula("4 mL");
+ ASTNode_t *r = SBML_parseL3Formula("(0.00166112956810631)");
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 0.00166112956810631, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_crazylong)
+{
+ ASTNode_t *r = SBML_parseL3Formula("(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890)");
+
+ if (r==NULL) {
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890)' at position 312: syntax error, unexpected end of string"), NULL);
+ }
+ else {
+ fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
+ fail_unless( util_isInf(ASTNode_getReal(r)) == 1, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+
+ ASTNode_free(r);
+ }
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_easunit)
+{
+ ASTNode_t *r = SBML_parseL3Formula("1.01e");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 1.01, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "e"), NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_easunitparen)
+{
+ ASTNode_t *r = SBML_parseL3Formula("(1.01e)");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 1.01, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "e"), NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_easunitint)
+{
+ ASTNode_t *r = SBML_parseL3Formula("101e");
+
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
- fail_unless( ASTNode_getInteger (r) == 4, NULL );
- fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+ fail_unless( ASTNode_getInteger (r) == 101, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "e"), NULL );
+
ASTNode_free(r);
- L3ParserSettings settings;
- settings.setParseUnits(L3P_NO_UNITS);
- fail_unless(settings.getTargetL2() == false, NULL);
- fail_unless(settings.getTargetL3() == false, NULL);
- r = L3Parser::parseL3Formula("4 mL", settings);
- fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(L3Parser::getLastParseL3Error(), "Error when parsing input '4 mL' at position 4: The ability to associate units with numbers has been disabled in this software."), NULL );
+}
+END_TEST
- settings.setParseUnits(L3P_PARSE_UNITS);
- fail_unless(settings.getTargetL2() == false, NULL);
- fail_unless(settings.getTargetL3() == true, NULL);
- r = L3Parser::parseL3Formula("4 mL", settings);
+
+START_TEST (test_SBML_parseL3Formula_ergunit)
+{
+ ASTNode_t *r = SBML_parseL3Formula("101erg");
+
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
- fail_unless( ASTNode_getInteger (r) == 4, NULL );
- fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+ fail_unless( ASTNode_getInteger (r) == 101, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
ASTNode_free(r);
}
END_TEST
+START_TEST (test_SBML_parseL3Formula_longinterg)
+{
+ ASTNode_t *r = SBML_parseL3Formula("166112956810631erg");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 166112956810631.0, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longdecimalerg)
+{
+ ASTNode_t *r = SBML_parseL3Formula("0.00166112956810631erg");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 0.00166112956810631, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longnumberparenerg)
+{
+ ASTNode_t *r = SBML_parseL3Formula("(0.00166112956810631erg)");
+
+ fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (r) == 0.00166112956810631, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+ ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_crazylongerg)
+{
+ ASTNode_t *r = SBML_parseL3Formula("(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890erg)");
+
+ if (r==NULL) {
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890erg)' at position 311: syntax error, unexpected end of string"), NULL);
+ }
+ else {
+ fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
+ fail_unless( util_isInf(ASTNode_getReal(r)) == 1, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
+ fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+ ASTNode_free(r);
+ }
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_wrongnum)
+{
+ ASTNode_t *r = SBML_parseL3Formula("1.2.4");
+
+ fail_unless(r == NULL, NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '1.2.4' at position 5: syntax error, unexpected number"), NULL);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_wrongnum2)
+{
+ ASTNode_t *r = SBML_parseL3Formula("1.2.");
+
+ fail_unless(r == NULL, NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '1.2.' at position 4: syntax error, unexpected $undefined"), NULL);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambda1)
+{
+ ASTNode_t *r = SBML_parseL3Formula("lambda(3.3)");
+
+ fail_unless( ASTNode_getType (r) == AST_LAMBDA, NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 1 , NULL );
+
+ ASTNode_t *c = ASTNode_getLeftChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_REAL, NULL );
+ fail_unless( ASTNode_getReal (c) == 3.3, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+ ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambda2)
+{
+ ASTNode_t *r = SBML_parseL3Formula("lambda(x,x^3)");
+ ASTNode_t *c;
+
+
+ fail_unless( ASTNode_getType(r) == AST_LAMBDA , NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
+
+ c = ASTNode_getLeftChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_NAME, NULL );
+ fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
+
+ c = ASTNode_getRightChild(r);
+
+ fail_unless( ASTNode_getType (c) == AST_POWER, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 2 , NULL );
+
+ c = ASTNode_getLeftChild(c);
+
+ fail_unless( ASTNode_getType (c) == AST_NAME, NULL );
+ fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
+
+ c = ASTNode_getRightChild(r->getRightChild());
+
+ fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
+ fail_unless( ASTNode_getInteger (c) == 3, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+
+ ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambda3)
+{
+ ASTNode_t *r = SBML_parseL3Formula("lambda(x, y, x+y)");
+ ASTNode_t *c;
+
+
+ fail_unless( ASTNode_getType(r) == AST_LAMBDA , NULL );
+ fail_unless( ASTNode_getNumChildren(r) == 3 , NULL );
+
+ c = ASTNode_getChild(r, 0);
+
+ fail_unless( ASTNode_getType (c) == AST_NAME, NULL );
+ fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
+
+ c = ASTNode_getChild(r, 1);
+
+ fail_unless( ASTNode_getType (c) == AST_NAME, NULL );
+ fail_unless( !strcmp(ASTNode_getName(c), "y") , NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
+
+ c = ASTNode_getChild(r, 2);
+
+ fail_unless( ASTNode_getType (c) == AST_PLUS, NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 2 , NULL );
+
+ c = ASTNode_getLeftChild(c);
+
+ fail_unless( ASTNode_getType (c) == AST_NAME, NULL );
+ fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
+
+ c = ASTNode_getRightChild(r->getChild(2));
+
+ fail_unless( ASTNode_getType (c) == AST_NAME, NULL );
+ fail_unless( !strcmp(ASTNode_getName(c), "y") , NULL );
+ fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+
+ ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambdaerr)
+{
+ ASTNode_t *r = SBML_parseL3Formula("lambda()");
+
+ fail_unless(r == NULL, NULL);
+ fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'lambda()' at position 8: The function 'lambda' takes at least one argument, but none were found."), NULL);
+}
+END_TEST
+
+
Suite *
create_suite_L3FormulaParser (void)
{
@@ -1883,6 +2193,7 @@
tcase_add_test( tcase, test_SBML_parseL3Formula_rational4);
tcase_add_test( tcase, test_SBML_parseL3Formula_rational5);
tcase_add_test( tcase, test_SBML_parseL3Formula_rational6);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_rational7);
tcase_add_test( tcase, test_SBML_parseL3Formula_constants1);
tcase_add_test( tcase, test_SBML_parseL3Formula_constants2);
tcase_add_test( tcase, test_SBML_parseL3Formula_constants3);
@@ -1918,10 +2229,27 @@
tcase_add_test( tcase, test_SBML_parseL3Formula_collapseminussettings3);
tcase_add_test( tcase, test_SBML_parseL3Formula_collapseminussettings4);
tcase_add_test( tcase, test_SBML_parseL3Formula_collapseminussettings5);
- tcase_add_test( tcase, test_SBML_parseL3Formula_targetl2settings);
tcase_add_test( tcase, test_SBML_parseL3Formula_avogadrosettings);
tcase_add_test( tcase, test_SBML_parseL3Formula_unitssettings);
-
+ tcase_add_test( tcase, test_SBML_parseL3Formula_power);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_longint);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_longdecimal);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_longnumberparen);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_crazylong);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_easunit);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_easunitparen);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_easunitint);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_ergunit);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_longinterg);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_longdecimalerg);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_longnumberparenerg);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_crazylongerg);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_wrongnum);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_wrongnum2);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_lambda1);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_lambda2);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_lambda3);
+ tcase_add_test( tcase, test_SBML_parseL3Formula_lambdaerr);
suite_add_tcase(suite, tcase);
return suite;
Modified: branches/L3Parser/src/sbml/math/test/TestL3FormulaParserC.c
===================================================================
--- branches/L3Parser/src/sbml/math/test/TestL3FormulaParserC.c 2012-08-22 17:46:07 UTC (rev 16256)
+++ branches/L3Parser/src/sbml/math/test/TestL3FormulaParserC.c 2012-08-22 17:55:41 UTC (rev 16257)
@@ -26,12 +26,20 @@
* ---------------------------------------------------------------------- -->*/
#include <sbml/common/common.h>
-#include <sbml/math/L3Parser.h>
+#include <sbml/math/L3Parser.h>
+#include <sbml/math/L3ParserSettings.h>
+#include <sbml/Model.h>
#include <sbml/Reaction.h>
+#include <sbml/Species.h>
+#include <sbml/Parameter.h>
+#include <sbml/Compartment.h>
+#include <sbml/SpeciesReference.h>
+#include <sbml/FunctionDefinition.h>
#include <check.h>
#if __cplusplus
+LIBSBML_CPP_NAMESPACE_USE
CK_CPPSTART
#endif
@@ -1145,7 +1153,7 @@
Model_t *model = Model_create(3,1);
Reaction_t *p = Model_createReaction(model);
SpeciesReference_t* sr = Reaction_createProduct(p);
- SpeciesReference_setId(sr, "AVOGADRO");
+ SpeciesReference_setId(sr, "AVOGADRO");
ASTNode_t *r = SBML_parseL3FormulaWithModel("avogadro", model);
fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
@@ -1463,11 +1471,11 @@
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
- L3ParserSettings_t *settings = L3ParserSettings_create();
+ L3ParserSettings_t *settings = SBML_getDefaultL3ParserSettings();
//Explicit parsing to collapse the minuses
- L3ParserSettings_setCollapseMinus(settings, 1);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 1);
+ L3ParserSettings_setParseCollapseMinus(settings, 1);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 1);
r = SBML_parseL3FormulaWithSettings("--4.4", settings);
fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
@@ -1477,8 +1485,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- L3ParserSettings_setCollapseMinus(settings, 0);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 0);
+ L3ParserSettings_setParseCollapseMinus(settings, 0);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 0);
r = SBML_parseL3FormulaWithSettings("--4.4", settings);
@@ -1519,11 +1527,11 @@
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
- L3ParserSettings_t *settings = L3ParserSettings_create();
+ L3ParserSettings_t *settings = SBML_getDefaultL3ParserSettings();
//Explicit parsing to collapse the minuses
- L3ParserSettings_setCollapseMinus(settings, 1);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 1);
+ L3ParserSettings_setParseCollapseMinus(settings, 1);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 1);
r = SBML_parseL3FormulaWithSettings("--x", settings);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
@@ -1533,8 +1541,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- L3ParserSettings_setCollapseMinus(settings, 0);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 0);
+ L3ParserSettings_setParseCollapseMinus(settings, 0);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 0);
r = SBML_parseL3FormulaWithSettings("--x", settings);
@@ -1584,11 +1592,11 @@
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
- L3ParserSettings_t *settings = L3ParserSettings_create();
+ L3ParserSettings_t *settings = SBML_getDefaultL3ParserSettings();
//Explicit parsing to collapse the minuses
- L3ParserSettings_setCollapseMinus(settings, 1);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 1);
+ L3ParserSettings_setParseCollapseMinus(settings, 1);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 1);
r = SBML_parseL3FormulaWithSettings("x---4.4", settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
@@ -1607,8 +1615,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- L3ParserSettings_setCollapseMinus(settings, 0);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 0);
+ L3ParserSettings_setParseCollapseMinus(settings, 0);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 0);
r = SBML_parseL3FormulaWithSettings("x---4.4", settings);
@@ -1667,11 +1675,11 @@
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
- L3ParserSettings_t *settings = L3ParserSettings_create();
+ L3ParserSettings_t *settings = SBML_getDefaultL3ParserSettings();
//Explicit parsing to collapse the minuses
- L3ParserSettings_setCollapseMinus(settings, 1);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 1);
+ L3ParserSettings_setParseCollapseMinus(settings, 1);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 1);
r = SBML_parseL3FormulaWithSettings("x---y", settings);
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
@@ -1690,8 +1698,8 @@
ASTNode_free(r);
//Explicit parsing to expand the minuses
- L3ParserSettings_setCollapseMinus(settings, 0);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 0);
+ L3ParserSettings_setParseCollapseMinus(settings, 0);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 0);
r = SBML_parseL3FormulaWithSettings("x---y", settings);
@@ -1725,9 +1733,9 @@
START_TEST (test_SBML_C_parseL3Formula_collapseminussettings5)
{
////Explicit parsing to collapse the minuses
- L3ParserSettings_t *settings = L3ParserSettings_create();
- L3ParserSettings_setCollapseMinus(settings, 1);
- fail_unless(L3ParserSettings_getCollapseMinus(settings) == 1);
+ L3ParserSettings_t *settings = SBML_getDefaultL3ParserSettings();
+ L3ParserSettings_setParseCollapseMinus(settings, 1);
+ fail_unless(L3ParserSettings_getParseCollapseMinus(settings) == 1);
ASTNode_t* r = SBML_parseL3FormulaWithSettings("---4", settings);
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
@@ -1773,56 +1781,6 @@
END_TEST
-START_TEST (test_SBML_C_parseL3Formula_targetl2settings)
-{
- ASTNode_t *r = SBML_parseL3Formula("4 mL");
-
- fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
- fail_unless( ASTNode_getInteger (r) == 4, NULL );
- fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
- ASTNode_free(r);
-
- r = SBML_parseL3Formula("avogadro");
- fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
- ASTNode_free(r);
-
- L3ParserSettings_t *settings = L3ParserSettings_create();
- L3ParserSettings_setTargetL2(settings);
- fail_unless(L3ParserSettings_getTargetL2(settings) == 1);
- fail_unless(L3ParserSettings_getTargetL3(settings) == 0);
-
- r = SBML_parseL3FormulaWithSettings("4 mL", settings);
- fail_unless(r == NULL, NULL);
- fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '4 mL' at position 4: The ability to associate units with numbers has been disabled in this software."), NULL );
-
- r = SBML_parseL3FormulaWithSettings("avogadro", settings);
- fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
- fail_unless( !strcmp(ASTNode_getName(r), "avogadro") , NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
- ASTNode_free(r);
-
- L3ParserSettings_setTargetL3(settings);
- fail_unless(L3ParserSettings_getTargetL2(settings) == 0);
- fail_unless(L3ParserSettings_getTargetL3(settings) == 1);
-
- r = SBML_parseL3FormulaWithSettings("4 mL", settings);
- fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
- fail_unless( ASTNode_getInteger (r) == 4, NULL );
- fail_unless( !strcmp(ASTNode_getUnits(r), "mL"), NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
- ASTNode_free(r);
-
- r = SBML_parseL3FormulaWithSettings("avogadro", settings);
- fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
- fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
- ASTNode_free(r);
- L3ParserSettings_free(settings);
-}
-END_TEST
-
-
START_TEST (test_SBML_C_parseL3Formula_avogadrosettings)
{
ASTNode_t *r = SBML_parseL3Formula("avogadro");
@@ -1830,11 +1788,9 @@
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- L3ParserSettings_t *settings = L3ParserSettings_create();
- L3ParserSettings_setAvogadroCsymbol(settings, 0);
- fail_unless(L3ParserSettings_getAvogadroCsymbol(settings) == 0);
- fail_unless(L3ParserSettings_getTargetL2(settings) == 0);
- fail_unless(L3ParserSettings_getTargetL3(settings) == 0);
+ L3ParserSettings_t *settings = SBML_getDefaultL3ParserSettings();
+ L3ParserSettings_setParseAvogadroCsymbol(settings, 0);
+ fail_unless(L3ParserSettings_getParseAvogadroCsymbol(settings) == 0);
r = SBML_parseL3FormulaWithSettings("avogadro", settings);
fail_unless( ASTNode_getType (r) == AST_NAME, NULL );
@@ -1842,10 +1798,8 @@
fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
ASTNode_free(r);
- L3ParserSettings_setAvogadroCsymbol(settings, 1);
- fail_unless(L3ParserSettings_getAvogadroCsymbol(settings) == 1);
- fail_unless(L3ParserSettings_getTargetL2(settings) == 0);
- fail_unless(L3ParserSettings_getTargetL3(settings) == 1);
+ L3ParserSettings_setParseAvogadroCsymbol(settings, 1);
+ fail_unless(L3ParserSettings_getParseAvogadroCsymbol(settings) == 1);
r = SBML_parseL3FormulaWithSettings("avogadro", settings);
fail_unless( ASTNode_getType (r) == AST_NAME_AVOGADRO, NULL );
@@ -1866,20 +1820,16 @@
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
- L3ParserSettings_t *settings = L3ParserSettings_create();
+ L3ParserSettings_t *settings = SBML_g...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-22 17:46:20
|
Revision: 16256
http://sbml.svn.sourceforge.net/sbml/?rev=16256&view=rev
Author: sarahkeating
Date: 2012-08-22 17:46:07 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/L3Parser/src/sbml/math/ASTNode.cpp
branches/L3Parser/src/sbml/math/ASTNode.h
branches/L3Parser/src/sbml/math/FormulaFormatter.c
branches/L3Parser/src/sbml/math/FormulaFormatter.h
branches/L3Parser/src/sbml/math/FormulaParser.c
branches/L3Parser/src/sbml/math/FormulaParser.h
branches/L3Parser/src/sbml/math/FormulaTokenizer.h
branches/L3Parser/src/sbml/math/L3Parser.h
branches/L3Parser/src/sbml/math/L3Parser.ypp
branches/L3Parser/src/sbml/math/L3ParserSettings.cpp
branches/L3Parser/src/sbml/math/L3ParserSettings.h
branches/L3Parser/src/sbml/math/Makefile.in
branches/L3Parser/src/sbml/math/test/CMakeLists.txt
branches/L3Parser/src/sbml/math/test/TestASTNode.c
branches/L3Parser/src/sbml/math/test/TestFormulaFormatter.c
branches/L3Parser/src/sbml/math/test/TestFormulaParser.c
branches/L3Parser/src/sbml/math/test/TestFormulaTokenizer.c
branches/L3Parser/src/sbml/math/test/TestRunner.c
branches/L3Parser/src/sbml/math/test/TestWriteMathMLFromAST.cpp
Added Paths:
-----------
branches/L3Parser/src/sbml/math/L3Parser.cpp
Removed Paths:
-------------
branches/L3Parser/src/sbml/math/L3Parser.tab.cpp
Modified: branches/L3Parser/src/sbml/math/ASTNode.cpp
===================================================================
--- branches/L3Parser/src/sbml/math/ASTNode.cpp 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/ASTNode.cpp 2012-08-22 17:46:07 UTC (rev 16256)
@@ -703,7 +703,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -731,7 +731,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -1976,7 +1976,7 @@
for (unsigned int i=0; i<getNumChildren(); i++) {
ASTNode* child = getChild(i);
if (child->getType() == AST_NAME &&
- child->getId() == id) {
+ child->getName() == id) {
replaceChild(i, function->deepCopy());
}
else {
@@ -2474,7 +2474,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_UNEXPECTED_ATTRIBUTE
@@ -2531,7 +2531,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2553,7 +2553,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -3283,7 +3283,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3307,7 +3307,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3327,7 +3327,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3347,7 +3347,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3371,7 +3371,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3391,7 +3391,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3410,7 +3410,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -3487,7 +3487,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_UNEXPECTED_ATTRIBUTE
@@ -3510,7 +3510,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -3575,7 +3575,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_UNEXPECTED_ATTRIBUTE
@@ -3648,7 +3648,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -3675,7 +3675,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -3701,7 +3701,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -3726,7 +3726,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -3782,7 +3782,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
Modified: branches/L3Parser/src/sbml/math/ASTNode.h
===================================================================
--- branches/L3Parser/src/sbml/math/ASTNode.h 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/ASTNode.h 2012-08-22 17:46:07 UTC (rev 16256)
@@ -78,22 +78,25 @@
*
* @if clike <h3><a class="anchor" name="ASTNodeType_t">
* ASTNodeType_t</a></h3> @else <h3><a class="anchor"
- * name="ASTNodeType_t">The set of possible %ASTNode types</a></h3> @endif
+ * name="ASTNodeType_t">The set of possible %ASTNode types</a></h3> @endif@~
*
- * @if clike Every ASTNode has an associated type code to indicate,
+ * Every ASTNode has an associated type code to indicate,
* for example, whether it holds a number or stands for an arithmetic
- * operator. The type is recorded as a value drawn from the enumeration
- * @link ASTNode.h::ASTNodeType_t ASTNodeType_t@endlink. The list of
- * possible types is quite long, because it covers all the mathematical
- * functions that are permitted in SBML. The values are shown in the
- * following table: @else Every ASTNode has an associated
- * type code to indicate, for example, whether it holds a number or stands for
- * an arithmetic operator. The type is recorded as a value drawn from a
+ * operator.
+ * @if clike The type is recorded as a value drawn from the enumeration
+ * @link ASTNode.h::ASTNodeType_t ASTNodeType_t@endlink.@endif
+ * @if java The type is recorded as a value drawn from a
* set of static integer constants defined in the class {@link
- * libsbmlConstants}. Their names begin with the characters @c AST_. The
- * list of possible types is quite long, because it covers all the
- * mathematical functions that are permitted in SBML. The values are shown
- * in the following table: @endif
+ * libsbmlConstants}. Their names begin with the characters @c AST_.@endif
+ * @if python The type is recorded as a value drawn from a
+ * set of static integer constants defined in the class {@link
+ * libsbml}. Their names begin with the characters @c AST_.@endif
+ * @if csharp The type is recorded as a value drawn from a
+ * set of static integer constants defined in the class {@link
+ * libsbml}. Their names begin with the characters @c AST_.@endif
+ * The list of possible types is quite long, because it covers all the
+ * mathematical functions that are permitted in SBML. The values are shown
+ * in the following table:
*
* @htmlinclude astnode-types.html
*
@@ -139,11 +142,13 @@
*
* <h3><a class="anchor" name="math-convert">Converting between ASTs and text strings</a></h3>
*
- * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@if csharp SBML_formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
- * read by @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
- * are simple C-inspired infix notation taken from SBML Level 1. A
+ * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@if csharp SBML_formulaToString()@endif@if python libsbml.formulaToString()@endif@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~ and
+ * read by @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
+ * and
+ * @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * are in a simple C-inspired infix notation. A
* formula in this text-string form can be handed to a program that
- * understands SBML Level 1 mathematical expressions, or used as part
+ * understands SBML mathematical expressions, or used as part
* of a translation system. The libSBML distribution comes with an example
* program in the @c "examples" subdirectory called @c translateMath that
* implements an interactive command-line demonstration of translating
@@ -200,6 +205,15 @@
* @htmlinclude math-functions.html
*
* @warning @htmlinclude L1-math-syntax-warning.html
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * @if clike @see SBML_parseFormula()@endif@~
+ * @if csharp @see SBML_parseFormula()@endif@~
+ * @if python @see libsbml.parseFormula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseFormula(String formula)">libsbml.parseFormula(String formula)</a></code>@endif@~
*/
#ifndef ASTNode_h
@@ -386,10 +400,10 @@
* @if clike setType()@else ASTNode::setType(int)@endif.
*
* @param type an optional
- * @if clike @link #ASTNodeType_t ASTNodeType_t@endlink@else type@endif
+ * @if clike @link #ASTNodeType_t ASTNodeType_t@endlink@else type@endif@~
* code indicating the type of node to create.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
LIBSBML_EXTERN
ASTNode (ASTNodeType_t type = AST_UNKNOWN);
@@ -500,7 +514,7 @@
* render the representation invalid. Callers need to be careful to use
* this method in the context of other operations to create complete and
* correct formulas. The method
- * @if clike isWellFormedASTNode()@else ASTNode::isWellFormedASTNode()@endif
+ * @if clike isWellFormedASTNode()@else ASTNode::isWellFormedASTNode()@endif@~
* may also be useful for checking the results of node modifications.
*
* @see prependChild(ASTNode* child)
@@ -628,7 +642,7 @@
*
* @return the nth child of this ASTNode or @c NULL if this node has no nth
* child (<code>n > </code>
- * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
+ * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif@~
* <code>- 1</code>).
*/
LIBSBML_EXTERN
@@ -639,7 +653,7 @@
* Get the left child of this node.
*
* @return the left child of this ASTNode. This is equivalent to calling
- * @if clike getChild()@else ASTNode::getChild(unsigned int)@endif
+ * @if clike getChild()@else ASTNode::getChild(unsigned int)@endif@~
* with an argument of @c 0.
*/
LIBSBML_EXTERN
@@ -651,7 +665,7 @@
*
* @return the right child of this ASTNode, or @c NULL if this node has no
* right child. If
- * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
+ * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif@~
* <code>> 1</code>, then this is equivalent to:
* @code
* getChild( getNumChildren() - 1 );
@@ -718,7 +732,7 @@
*
* @return the nth annotation of this ASTNode, or @c NULL if this node has
* no nth annotation (<code>n ></code>
- * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
+ * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif@~
* <code>- 1</code>).
*
* @see ASTNode::addSemanticsAnnotation(XMLNode* sAnnotation)
@@ -733,14 +747,14 @@
* <code>predicate(node)</code> returns @c true (non-zero).
*
* For portability between different programming languages, the predicate
- * is passed in as a pointer to a function. The function definition must
- * have the type @link ASTNode.h::ASTNodePredicate ASTNodePredicate
- * @endlink, which is defined as
+ * is passed in as a pointer to a function. @if clike The function
+ * definition must have the type @link ASTNode::ASTNodePredicate
+ * ASTNodePredicate @endlink, which is defined as
* @code
* int (*ASTNodePredicate) (const ASTNode_t *node);
* @endcode
* where a return value of non-zero represents @c true and zero
- * represents @c false.
+ * represents @c false. @endif
*
* @param predicate the predicate to use
*
@@ -786,7 +800,7 @@
/**
* Get the value of this node as a single character. This function
* should be called only when
- * @if clike getType()@else ASTNode::getType()@endif returns
+ * @if clike getType()@else ASTNode::getType()@endif@~ returns
* @link ASTNodeType_t#AST_PLUS AST_PLUS@endlink,
* @link ASTNodeType_t#AST_MINUS AST_MINUS@endlink,
* @link ASTNodeType_t#AST_TIMES AST_TIMES@endlink,
@@ -798,6 +812,7 @@
LIBSBML_EXTERN
char getCharacter () const;
+
/**
* Get the id of this ASTNode.
*
@@ -806,6 +821,7 @@
LIBSBML_EXTERN
std::string getId () const;
+
/**
* Get the class of this ASTNode.
*
@@ -814,6 +830,7 @@
LIBSBML_EXTERN
std::string getClass () const;
+
/**
* Get the style of this ASTNode.
*
@@ -822,10 +839,11 @@
LIBSBML_EXTERN
std::string getStyle () const;
+
/**
* Get the value of this node as an integer. This function should be
* called only when
- * @if clike getType()@else ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif@~
* <code>== @link ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink</code>.
*
* @return the value of this ASTNode as a (<code>long</code>) integer.
@@ -837,9 +855,9 @@
/**
* Get the value of this node as a string. This function may be called
* on nodes that (1) are not operators, i.e., nodes for which
- * @if clike isOperator()@else ASTNode::isOperator()@endif
+ * @if clike isOperator()@else ASTNode::isOperator()@endif@~
* returns @c false, and (2) are not numbers, i.e.,
- * @if clike isNumber()@else ASTNode::isNumber()@endif returns @c false.
+ * @if clike isNumber()@else ASTNode::isNumber()@endif@~ returns @c false.
*
* @return the value of this ASTNode as a string.
*/
@@ -850,7 +868,7 @@
/**
* Get the value of this operator node as a string. This function may be called
* on nodes that are operators, i.e., nodes for which
- * @if clike isOperator()@else ASTNode::isOperator()@endif
+ * @if clike isOperator()@else ASTNode::isOperator()@endif@~
* returns @c true.
*
* @return the name of this operator ASTNode as a string (or NULL if not an operator).
@@ -862,7 +880,7 @@
/**
* Get the value of the numerator of this node. This function should be
* called only when
- * @if clike getType()@else ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif@~
* <code>== @link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink</code>.
*
* @return the value of the numerator of this ASTNode.
@@ -874,7 +892,7 @@
/**
* Get the value of the denominator of this node. This function should
* be called only when
- * @if clike getType()@else ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif@~
* <code>== @link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink</code>.
*
* @return the value of the denominator of this ASTNode.
@@ -886,7 +904,7 @@
/**
* Get the real-numbered value of this node. This function
* should be called only when
- * @if clike isReal()@else ASTNode::isReal()@endif
+ * @if clike isReal()@else ASTNode::isReal()@endif@~
* <code>== true</code>.
*
* This function performs the necessary arithmetic if the node type is
@@ -902,10 +920,10 @@
/**
* Get the mantissa value of this node. This function should be called
- * only when @if clike getType()@else ASTNode::getType()@endif
+ * only when @if clike getType()@else ASTNode::getType()@endif@~
* returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink
* or @link ASTNodeType_t#AST_REAL AST_REAL@endlink.
- * If @if clike getType()@else ASTNode::getType()@endif
+ * If @if clike getType()@else ASTNode::getType()@endif@~
* returns @link ASTNodeType_t#AST_REAL AST_REAL@endlink,
* this method is identical to
* @if clike getReal()@else ASTNode::getReal()@endif.
@@ -919,7 +937,7 @@
/**
* Get the exponent value of this ASTNode. This function should be
* called only when
- * @if clike getType()@else ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif@~
* returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink
* or @link ASTNodeType_t#AST_REAL AST_REAL@endlink.
*
@@ -963,6 +981,10 @@
* @note The <code>sbml:units</code> attribute is only available in SBML
* Level 3. It may not be used in Levels 1–2 of SBML.
*
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
*/
LIBSBML_EXTERN
std::string getUnits () const;
@@ -973,6 +995,11 @@
* symbol @c avogadro. The predicate returns @c false (zero) otherwise.
*
* @return @c true if this ASTNode is the special symbol avogadro.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
*/
LIBSBML_EXTERN
bool isAvogadro () const;
@@ -1076,6 +1103,11 @@
*
* @return @c true if the given ASTNode represents a log10() function, @c
* false otherwise.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
*/
LIBSBML_EXTERN
bool isLog10 () const;
@@ -1220,16 +1252,25 @@
*
* For numbers, unary minus nodes can be "collapsed" by negating the
* number. In fact,
- * @if clike SBML_parseFormula() @endif@if csharp SBML_parseFormula() @else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif does this during its parsing process.
- * However, unary minus nodes for symbols
+ * @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
+ * does this during its parsing process, and
+ * @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * has a configuration option that allows this behavior to be turned
+ * on or off. However, unary minus nodes for symbols
* (@link ASTNodeType_t#AST_NAME AST_NAME@endlink) cannot
* be "collapsed", so this predicate function is necessary.
*
* @return @c true if this ASTNode is a unary minus, @c false otherwise.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
*/
LIBSBML_EXTERN
bool isUMinus () const;
+
/**
* Predicate returning @c true (non-zero) if this node is a unary plus
* operator, @c false (zero) otherwise. A node is defined as a unary
@@ -1241,6 +1282,7 @@
LIBSBML_EXTERN
bool isUPlus () const;
+
/**
* Predicate returning @c true (non-zero) if this node has an unknown type.
*
@@ -1259,6 +1301,7 @@
LIBSBML_EXTERN
bool isUnknown () const;
+
/**
* Predicate returning @c true (non-zero) if this node has the mathml attribute
* <code>id</code>.
@@ -1267,6 +1310,7 @@
*/
LIBSBML_EXTERN
bool isSetId() const;
+
/**
* Predicate returning @c true (non-zero) if this node has the mathml attribute
@@ -1277,6 +1321,7 @@
LIBSBML_EXTERN
bool isSetClass() const;
+
/**
* Predicate returning @c true (non-zero) if this node has the mathml attribute
* <code>style</code>.
@@ -1285,6 +1330,7 @@
*/
LIBSBML_EXTERN
bool isSetStyle() const;
+
/**
* Predicate returning @c true (non-zero) if this node has the attribute
@@ -1375,9 +1421,9 @@
* As a side-effect, this ASTNode object's type will be reset to
* @link ASTNodeType_t#AST_NAME AST_NAME@endlink if (and <em>only
* if</em>) the ASTNode was previously an operator (
- * @if clike isOperator()@else ASTNode::isOperator()@endif
+ * @if clike isOperator()@else ASTNode::isOperator()@endif@~
* <code>== true</code>), number (
- * @if clike isNumber()@else ASTNode::isNumber()@endif
+ * @if clike isNumber()@else ASTNode::isNumber()@endif@~
* <code>== true</code>), or unknown.
* This allows names to be set for @link ASTNodeType_t#AST_FUNCTION
* AST_FUNCTION@endlink nodes and the like.
@@ -1496,7 +1542,7 @@
* The units will be set @em only if this ASTNode object represents a
* MathML <code><cn></code> element, i.e., represents a number.
* Callers may use
- * @if clike isNumber()@else ASTNode::isNumber()@endif
+ * @if clike isNumber()@else ASTNode::isNumber()@endif@~
* to inquire whether the node is of that type.
*
* @htmlinclude about-sbml-units-attrib.html
@@ -1556,6 +1602,7 @@
virtual void replaceIDWithFunction(const std::string& id, const ASTNode* function);
/** @endcond */
+
/** @cond doxygen-libsbml-internal */
/**
* Replaces any 'AST_NAME_TIME' nodes with a node that multiplies time by the given function.
@@ -1589,6 +1636,7 @@
LIBSBML_EXTERN
int unsetId ();
+
/**
* Unsets the mathml class of this ASTNode.
*
@@ -1600,6 +1648,7 @@
LIBSBML_EXTERN
int unsetClass ();
+
/**
* Unsets the mathml style of this ASTNode.
*
@@ -1611,6 +1660,7 @@
LIBSBML_EXTERN
int unsetStyle ();
+
/** @cond doxygen-libsbml-internal */
/**
@@ -1746,7 +1796,7 @@
*
* @if clike
* @see ASTNode::setUserData
- * @endif
+ * @endif@~
*/
LIBSBML_EXTERN
void *getUserData() const;
@@ -2204,6 +2254,11 @@
*
* More precisley, the node type is @c AST_FUNCTION_LOG with two children
* the first of which is an @c AST_INTEGER equal to 10.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
*/
LIBSBML_EXTERN
int
@@ -2314,12 +2369,20 @@
* otherwise.
*
* For numbers, unary minus nodes can be "collapsed" by negating the
- * number. In fact, SBML_parseFormula() does this during its parse.
- * However, unary minus nodes for symbols (@c AST_NAMES) cannot be
- * "collapsed", so this predicate function is necessary.
+ * number. In fact, @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
+ * does this during its parse, and
+ * @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * has a configuration option that allows this behavior to be turned
+ * on or off. However, unary minus nodes for symbols (@c AST_NAMES)
+ * cannot be "collapsed", so this predicate function is necessary.
*
* A node is defined as a unary minus node if it is of type @c AST_MINUS
* and has exactly one child.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
*/
LIBSBML_EXTERN
int
Modified: branches/L3Parser/src/sbml/math/FormulaFormatter.c
===================================================================
--- branches/L3Parser/src/sbml/math/FormulaFormatter.c 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/FormulaFormatter.c 2012-08-22 17:46:07 UTC (rev 16256)
@@ -34,26 +34,29 @@
# define isnan(d) _isnan(d)
#endif
+
+/** @cond doxygen-c-only */
/**
- * @if doxygen-c-only
* Converts an AST to a string representation of a formula using a syntax
* basically derived from SBML Level 1.
*
* @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level 1. A formula in
+ * SBML_formulaToString() and read by SBML_parseFormula() and SBML_parseL3Formula()
+ * are in a C-inspired infix notation. A formula in
* this text-string form therefore can be handed to a program that
- * understands SBML Level 1 mathematical expressions, or used as part
+ * understands SBML mathematical expressions, or used as part
* of a formula translation system. The syntax is described in detail in
* the documentation for ASTNode. @endif@if java The text-string form of
* mathematical formulas produced by <code><a
* href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">
* libsbml.formulaToString()</a></code> and read by
* <code><a href="libsbml.html#parseFormula(java.lang.String)">
- * libsbml.parseFormula()</a></code> are
- * simple C-inspired infix notation taken from SBML Level 1. A
+ * libsbml.parseFormula()</a></code> and
+ * <code><a href="libsbml.html#parseL3Formula(java.lang.String)">
+ * libsbml.parseL3Formula()</a></code> are in a
+ * simple C-inspired infix notation. A
* formula in this text-string form therefore can be handed to a program
- * that understands SBML Level 1 mathematical expressions, or used as
+ * that understands SBML mathematical expressions, or used as
* part of a formula translation system. The syntax is described in detail
* in the documentation for ASTNode. @endif
*
@@ -110,8 +113,8 @@
* mathematical formula. The caller owns the returned string and is
* responsible for freeing it when it is no longer needed.
*
- * SBML_parseFormula()
- * @endif
+ * @see SBML_parseFormula()
+ * @see SBML_parseL3Formula()
*/
LIBSBML_EXTERN
char *
@@ -133,6 +136,7 @@
}
return s;
}
+/** @endcond */
/**
Modified: branches/L3Parser/src/sbml/math/FormulaFormatter.h
===================================================================
--- branches/L3Parser/src/sbml/math/FormulaFormatter.h 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/FormulaFormatter.h 2012-08-22 17:46:07 UTC (rev 16256)
@@ -42,29 +42,14 @@
* Converts an AST to a string representation of a formula using a syntax
* basically derived from SBML Level 1.
*
- * @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level 1. A formula in
- * this text-string form therefore can be handed to a program that
- * understands SBML Level 1 mathematical expressions, or used as part
- * of a formula translation system. The syntax is described in detail in
- * the documentation for ASTNode. @endif@if csharp The text-string form of
- * mathematical formulas produced by SBML_formulaToString() and read by
- * SBML_parseFormula() are simple C-inspired infix notation taken from SBML
- * Level 1. A formula in this text-string form therefore can be
- * handed to a program that understands SBML Level 1 mathematical
- * expressions, or used as part of a formula translation system. The
- * syntax is described in detail in the documentation for
- * ASTNode. @else The text-string form of mathematical formulas produced by <code><a
- * href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">
- * libsbml.formulaToString()</a></code> and read by <code><a
- * href="libsbml.html#parseFormula(java.lang.String)">
- * libsbml.parseFormula()</a></code> are simple C-inspired infix notation
- * taken from SBML Level 1. A formula in this text-string form
- * therefore can be handed to a program that understands SBML Level 1
- * mathematical expressions, or used as part of a formula translation
- * system. The syntax is described in detail in the documentation for
- * ASTNode. @endif
+ * The text-string form of mathematical formulas produced by
+ * @if clike SBML_formulaToString()@endif@if csharp SBML_formulaToString()@endif@if python libsbml.formulaToString()@endif@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString(ASTNode tree)</a></code>@endif@~
+ * and read by @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
+ * use a simple C-inspired infix notation taken from SBML Level 1. A
+ * formula in this text-string form therefore can be handed to a program
+ * that understands SBML Level 1 mathematical expressions, or used as
+ * part of a formula translation system. The syntax is described in detail
+ * in the documentation for ASTNode.
*
* Note that this facility is provided as a convenience by libSBML—the
* MathML standard does not actually define a "string-form" equivalent to
@@ -119,9 +104,34 @@
* mathematical formula. The caller owns the returned string and is
* responsible for freeing it when it is no longer needed.
*
- * @if clike @see SBML_parseFormula()@endif
- * @if csharp @see SBML_parseFormula()@endif
- * @if java @see parseFormula(java.lang.String)@endif
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
*/
LIBSBML_EXTERN
char *
Modified: branches/L3Parser/src/sbml/math/FormulaParser.c
===================================================================
--- branches/L3Parser/src/sbml/math/FormulaParser.c 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/FormulaParser.c 2012-08-22 17:46:07 UTC (rev 16256)
@@ -293,24 +293,25 @@
/** @endcond */
+/** @cond doxygen-c-only */
/**
- * @if doxygen-c-only
* Parses the given SBML formula and returns a representation of it as an
* Abstract Syntax Tree (AST).
*
* @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level 1. A formula in
+ * SBML_formulaToString() and read by SBML_parseFormula() and SBML_parseL3Formula()
+ * are in a simple C-inspired infix notation. A formula in
* this text-string form therefore can be handed to a program that
- * understands SBML Level 1 mathematical expressions, or used as part
+ * understands SBML mathematical expressions, or used as part
* of a formula translation system. The syntax is described in detail in
* the documentation for ASTNode. @endif@if java The text-string form of
* mathematical formulas produced by <code><a
* href="libsbml.html">libsbml.formulaToString()</a></code> and read by
- * <code><a href="libsbml.html">libsbml.parseFormula()</a></code> are
- * simple C-inspired infix notation taken from SBML Level 1. A
+ * <code><a href="libsbml.html">libsbml.parseFormula()</a></code> and
+ * <code><a href="libsbml.html">libsbml.parseL3Formula()</a></code>
+ * are in a simple C-inspired infix notation. A
* formula in this text-string form therefore can be handed to a program
- * that understands SBML Level 1 mathematical expressions, or used as
+ * that understands SBML mathematical expressions, or used as
* part of a formula translation system. The syntax is described in detail
* in the documentation for ASTNode. @endif
*
@@ -370,7 +371,10 @@
* parsing the formula
*
* @see SBML_formulaToString()
- * @endif
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
*/
LIBSBML_EXTERN
ASTNode_t *
@@ -451,11 +455,11 @@
return node;
}
+/** @endcond */
/** @cond doxygen-libsbml-internal */
-
/**
* @return the action for the current state and token.
*
Modified: branches/L3Parser/src/sbml/math/FormulaParser.h
===================================================================
--- branches/L3Parser/src/sbml/math/FormulaParser.h 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/FormulaParser.h 2012-08-22 17:46:07 UTC (rev 16256)
@@ -43,27 +43,16 @@
* Parses the given SBML formula and returns a representation of it as an
* Abstract Syntax Tree (AST).
*
- * @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level 1. A formula in
- * this text-string form therefore can be handed to a program that
- * understands SBML Level 1 mathematical expressions, or used as part
- * of a formula translation system. The syntax is described in detail in
- * the documentation for ASTNode. @endif@if csharp The text-string form of
- * mathematical formulas produced by SBML_formulaToString() and read by
- * SBML_parseFormula() are simple C-inspired infix notation taken from SBML
- * Level 1. A formula in this text-string form therefore can be
- * handed to a program that understands SBML Level 1 mathematical
- * expressions, or used as part of a formula translation system. The
- * syntax is described in detail in the documentation for
- * ASTNode. @else The text-string form of mathematical formulas produced by <code><a
- * href="libsbml.html">libsbml.formulaToString()</a></code> and read by
- * <code><a href="libsbml.html">libsbml.parseFormula()</a></code> are
- * simple C-inspired infix notation taken from SBML Level 1. A
+ * The text-string form of mathematical formulas produced by
+ * @if clike SBML_formulaToString()@endif@if csharp SBML_formulaToString()@endif@if python libsbml.formulaToString()@endif@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString(ASTNode tree)</a></code>@endif@~
+ * and read by @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
+ * and
+ * @if clike SBML_parseL3Formula()@endif@if csharp SBML_parseL3Formula()@endif@if python libsbml.parseL3Formula()@endif@if java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * use a simple C-inspired infix notation. A
* formula in this text-string form therefore can be handed to a program
- * that understands SBML Level 1 mathematical expressions, or used as
+ * that understands SBML mathematical expressions, or used as
* part of a formula translation system. The syntax is described in detail
- * in the documentation for ASTNode. @endif
+ * in the documentation for ASTNode.
*
* This returns the root node of the AST corresponding to the formula. If
* the formula contains a syntax error, @c NULL is returned instead.
@@ -120,9 +109,34 @@
* @return the root node of the AST, or NULL if an error occurred in
* parsing the formula
*
- * @if clike @see SBML_formulaToString()@endif
- * @if csharp @see SBML_formulaToString()@endif
- * @if java @see formulaToString(ASTNode tree)@endif
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
*/
LIBSBML_EXTERN
ASTNode_t *
Modified: branches/L3Parser/src/sbml/math/FormulaTokenizer.h
===================================================================
--- branches/L3Parser/src/sbml/math/FormulaTokenizer.h 2012-08-22 17:40:10 UTC (rev 16255)
+++ branches/L3Parser/src/sbml/math/FormulaTokenizer.h 2012-08-22 17:46:07 UTC (rev 16256)
@@ -76,8 +76,9 @@
* Levels 2 and 3. LibSBML implements a parser and converter to
* translate formulas between this text-string representation and MathML.
* The principal entry points to the translation system are
- * @if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@else SBML_formulaToString()@endif
- * and @if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@else SBML_parseFormula()@endif.
+ * @if clike SBML_formulaToString()@endif@if csharp SBML_formulaToString()@endif@if python libsbml.formulaToString()@endif@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * and
+ * @if clike SBML_parseFormula()@endif@if csharp SBML_parseFormula()@endif@if python libsbml.parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~.
*
* LibSBML also provides a lower-level interface to the formula parser.
* This takes the form of the C functions
Copied: branches/L3Parser/src/sbml/math/L3Parser.cpp (from rev 16253, trunk/libsbml/src/sbml/math/L3Parser.cpp)
===================================================================
--- branches/L3Parser/src/sbml/math/L3Parser.cpp (rev 0)
+++ branches/L3Parser/src/sbml/math/L3Parser.cpp 2012-08-22 17:46:07 UTC (rev 16256)
@@ -0,0 +1,3214 @@
+/* A Bison parser, made by GNU Bison 2.4.2. */
+
+/* Skeleton implementation for Bison's Yacc-like parsers in C
+
+ Copyright (C) 1984, 1989-1990, 2000-2006, 2009-2010 Free Software
+ Foundation, Inc.
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>. */
+
+/* As a special exception, you may create a larger work that contains
+ part or all of the Bison parser skeleton and distribute that work
+ under terms of your choice, so long as that work isn't itself a
+ parser generator using the skeleton or a modified version thereof
+ as a parser skeleton. Alternatively, if you modify or redistribute
+ the parser skeleton itself, you may (at your option) remove this
+ special exception, which will cause the skeleton and the resulting
+ Bison output files to be licensed under the GNU General Public
+ License without this special exception.
+
+ This special exception was added by the Free Software Foundation in
+ version 2.2 of Bison. */
+
+/* C LALR(1) parser skeleton written by Richard Stallman, by
+ simplifying the original so-called "semantic" parser. */
+
+/* All symbols defined below should begin with yy or YY, to avoid
+ infringing on user name space. This should be done even for local
+ variables, as they might otherwise be expanded by user macros.
+ There are some unavoidable exceptions within include files to
+ define necessary library symbols; they are noted "INFRINGES ON
+ USER NAME SPACE" below. */
+
+/* Identify Bison output. */
+#define YYBISON 1
+
+/* Bison version. */
+#define YYBISON_VERSION "2.4.2"
+
+/* Skeleton name. */
+#define YYSKELETON_NAME "yacc.c"
+
+/* Pure parsers. */
+#define YYPURE 0
+
+/* Push parsers. */
+#define YYPUSH 0
+
+/* Pull parsers. */
+#define YYPULL 1
+
+/* Using locations. */
+#define YYLSP_NEEDED 0
+
+/* "%code top" blocks. */
+
+/* Line 171 of yacc.c */
+#line 52 "L3Parser.ypp"
+
+
+ /** @cond doxygen-libsbml-internal */
+
+
+
+/* Line 171 of yacc.c */
+#line 77 "L3Parser.cpp"
+/* Substitute the variable and function names. */
+#define yyparse sbml_yyparse
+#define yylex sbml_yylex
+#define yyerror sbml_yyerror
+#define yylval sbml_yylval
+#define yychar sbml_yychar
+#define yydebug sbml_yydebug
+#define yynerrs sbml_yynerrs
+
+
+/* Copy the first part of user declarations. */
+
+/* Line 189 of yacc.c */
+#line 57 "L3Parser.ypp"
+
+/**
+ *
+ * This file is AUTOMATICALLY GENERATED by the 'bison' program and
+ * should not be modified directly. It is created with the command
+ *
+ * bison -v L3Parser.ypp -o L3Parser.cpp
+ *
+ * from the L3Parser.ypp file. Any modifications should be performed on
+ * that file directly.
+ *
+ * This file defines an entire class, 'L3Parser', that does not appear
+ * in any header file, as it is only useful in the context of the C functions
+ * generated by the bison program. Future versions of this parser may
+ * use a version of bison that generates a parser object instead of C
+ * functions, but for now, the only interface with the library is defined
+ * in the L3Parser.h file.
+ */
+
+#include <sbml/common/libsbml-namespace.h>
+#include <sbml/math/L3Parser.h>
+#include <sbml/Model.h>
+#include <sbml/math/L3ParserSettings.h>
+
+#include <sstream>
+
+LIBSBML_CPP_NAMESPACE_USE
+LIBSBML_CPP_NAMESPACE_BEGIN
+class SBMLVisitor;
+class FormulaUnitsData;
+
+#ifndef SWIG //Hide the entire class from SWIG
+/**
+ * @class L3Parser
+ * @brief Class providing functionality for the bison-generated parser.
+ *
+ * The L3Parser class is an internal class designed to hold the guts of the bison parser, plus
+ * the lexer. It is designed to be a global singleton object, because that's the cleanest way
+ * I could find to incorporate functions into the bison framework.
+ *
+ * The functions declared in this file are defined in the file L3Parser.ypp, which
+ * must be compiled by bison to create L3Parser.cpp, the file included in
+ * libsbml. For more details, see the L3Parser.ypp file.
+ *
+ * Within the various 'sbml_yylex*' functions that bison creates, functions
+ * from the global 'l3p' object (of the L3Parser class) are used to calculate
+ * necessary information for the parsing of the string, and to determine appropriate
+ * error messages when things go wrong.
+ * @internal
+ */
+class LIBSBML_EXTERN L3Parser
+{
+public:
+
+ std::stringstream input;
+ ASTNode* outputNode;
+ std::string error;
+ std::map<std::string, std::string*> words;
+ long exponent;
+ long denominator;
+
+ //settings:
+ L3ParserSettings defaultL3ParserSettings;
+ const Model* model;
+ ParseLogType_t parselog;
+ bool collapseminus;
+ bool parseunits;
+ bool avocsymbol;
+
+ L3Parser();
+ ~L3Parser();
+
+ //Functions needed for the parser and the lexer:
+ /**
+ * Compares 'name' against a list of known constants, and returns the particular
+ * constant type (AST_CONSTANT_TRUE, AST_CONSTANT_PI, AST_NAME_TIME) associated
+ * with that string (with case ignored). For the mathematical constants
+ * infinity and notanumber, AST_REAL is returned, and the parser must then
+ * examine the string again to discover what to do with the ASTNode.
+ */
+ ASTNodeType_t getSymbolFor(std::string name) const;
+ /**
+ * Compares 'name' against a list of known functions allowed in the MathML
+ * of SBML Level 2 and 3. Multiple mappings of string->type are present,
+ * so that (for example) both the strings 'acos' and 'arccos' return the
+ * type AST_FUNCTION_ARCCOS. "log" returns AST_FUNCTION_LOG, so when
+ * user preference is taken into consideration, 'name' must once again
+ * be checked.
+ */
+ ASTNodeType_t getFunctionFor(std::string name) const;
+ /**
+ * This function creates an ASTNode that is a 'piecewise' function that
+ * mimics the 'modulo' function 'x % y'. It was modified from the
+ * function of the same name in Copasi in its CEvaluationNodeOperator
+ * class, which itself had modifications submitted by Frank Bergmann.
+ */
+ ASTNode* createModuloTree(ASTNode* x, ASTNode* y) const;
+ /**
+ * Sets the member variable 'collapseminus' to the provided boolean value. Used in parsing
+ * unary minuses.
+ */
+ void setCollapseMinus(bool collapse);
+ /**
+ * Sets the member variable 'parselog' to the provided enum. Used in parsing
+ * strings with the function "log" with a single argument.
+ */
+ void setParseLog(ParseLogType_t parseas);
+ /**
+ * Sets the member variable 'parseunits' to the provided boolean. Used in
+ * deciding whether strings that assign units to numbers (like "10 mL")
+ * are parsed correctly, or as errors.
+ */
+ void setParseUnits(bool units);
+ /**
+ * Sets the member variable 'avocsymbol' to the provided boolean. Used in
+ * deciding whether to parse the string 'avogadro' as an ASTNode of type
+ * AST_NAME_AVOGADRO or AST_NAME with the name 'avogadro'.
+ */
+ void setAvoCsymbol(bool avo);
+ /**
+ * Compares the two strings, and returns 'true' if they are equivalent,
+ * ignoring case. Used in the parser and in the 'getSymbolFor' and
+ * 'getFunctionFor' functions.
+ */
+ bool caselessStrCmp(const std::string& lhs, const std::string& rhs) const;
+ /**
+ * Sets the input string to be parsed, copied to the 'input' stringstream
+ * member variable.
+ */
+ void setInput(const char* c);
+ /**
+ * Sets the error string so that it can be retrieved by the function
+ * 'SBML_getLastParseL3Error'.
+ */
+ void setError(const char* c);
+ /**
+ * Sets the error string so that it can be retrieved by the function
+ * 'SBML_getLastParseL3Error'.
+ */
+ void setError(std::string c);
+ /**
+ * Resets the L3Parser object, removing any error or input strings,
+ * setting the output ASTNode to NULL, and resetting all parser settings
+ * to that stored in the 'defaultL3ParserSettings' member variable.
+ */
+ void clear();
+ /**
+ * Returns the 'error' member variable, which is either empty or contains
+ * the error message set from a 'setError' function.
+ */
+ std::string getError();
+
+ /**
+ * The bison parser needs string pointers to pass around from function to
+ * function. In order to not create too many of these objects, and to
+ * ensure that they are properly deleted, the lexer calls this function
+ * when it encounters a valid ID string to get a stable pointer that can
+ * be passed to the parser functions.
+ *
+ * In this function, 'word' is looked up in a hash map of strings to
+ * string pointers; if it is not found, a new string pointer containing
+ * the string is created, added to the hash, and returned. If it is
+ * found, the previously-created pointer is returned.
+ */
+ std::string* addWord(const std::string& word);
+
+ /**
+ * This function checks the provided ASTNode function to see if it is a
+ * known function with the wrong number of arguments. If so, an error is set
+ * (using the 'setError' function) and 'true' is returned. If the
+ * correct number of arguments is provided, 'false' is returned.
+ */
+ bool checkNumArguments(const ASTNode* function);
+
+ /**
+ * Provides a copy of the default parser settings member variable.
+ */
+ L3ParserSettings getDefaultL3ParserSettings();
+
+ /*
+ * Change the default settings for this parser to the settings provided. All subsequent
+ * calls to parseL3Formula with no 'settings' argument will use these settings
+ * instead of the defaults.
+ */
+ void setDefaultSettings(L3ParserSettings settings);
+
+ /**
+ * If the either versions of the function @see SBML_parseL3Formula() returns NULL, an error
+ * is set internally which is accessible via this function. The returned error will
+ * report the string it was trying to parse, which character it had parsed when it
+ * encountered the error, and what the error was.
+ *
+ */
+ static char* getLastParseL3Error();
+};
+#endif //The entire class should be invisible to SWIG, too.
+
+LIBSBML_CPP_NAMESPACE_END
+
+ using namespace std;
+
+ int sbml_yylex(void);
+ L3Parser* l3p = NULL;
+ void sbml_yyerror(char const *);
+ int sbml_yylloc_first_position = 1;
+ int sbml_yylloc_last_position = 1;
+
+
+/* Line 189 of yacc.c */
+#line 301 "L3Parser.cpp"
+
+/* Enabling traces. */
+#ifndef YYDEBUG
+# define YYDEBUG 1
+#endif
+
+/* Enabling verbose error messages. */
+#ifdef YYERROR_VERBOSE
+# undef YYERROR_VERBOSE
+# define YYERROR_VERBOSE 1
+#else
+# define YYERROR_VERBOSE 1
+#endif
+
+/* Enabling the token table. */
+#ifndef YYTOKEN_TABLE
+# define YYTOKEN_TABLE 0
+#endif
+
+
+/* Tokens. */
+#ifndef YYTOKENTYPE
+# define YYTOKENTYPE
+ /* Put the tokens into the symbol table, so that GDB and other debuggers
+ know about them. */
+ enum yytokentype {
+ YYEOF = 0,
+ NOT = 258,
+ NEG = 259,
+ DOUBLE = 260,
+ INTEGER = 261,
+ E_NOTATION = 262,
+ RATIONAL = 263,
+ SYMBOL = 264
+ };
+#endif
+
+
+
+#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
+typedef union YYSTYPE
+{
+
+/* Line 214 of yacc.c */
+#line 266 "L3Parser.ypp"
+
+ ASTNode* astnode;
+ char character;
+ const string* word;
+ double numdouble;
+ long numlong;
+ double mantissa;
+ long rational;
+
+
+
+/* Line 214 of yacc.c */
+#line 359 "L3Parser.cpp"
+} YYSTYPE;
+# define YYSTYPE_IS_TRIVIAL 1
+# define yystype YYSTYPE /* obsolescent; will be withdrawn */
+# define YYSTYPE_IS_DECLARED 1
+#endif
+
+
+/* Copy the second part of user declarations. */
+
+
+/* Line 264 of yacc.c */
+#line 371 "L3Parser.cpp"
+
+#ifdef short
+# undef short
+#endif
+
+#ifdef YYTYPE_UINT8
+typedef YYTYPE_UINT8 yytype_uint8;
+#else
+typedef unsigned char yytype_uint8;
+#endif
+
+#ifdef YYTYPE_INT8
+typedef YYTYPE_INT8 yytype_int8;
+#elif (defined __STDC__ || defined __C99__FUNC__ \
+ || defined __cplusplus || defined _MSC_VER)
+typedef signed char yytype_int8;
+#else
+typedef short int yytype_int8;
+#endif
+
+#ifdef YYTYPE_UINT16
+typedef YYTYPE_UINT16 yytype_uint16;
+#else
+typedef unsigned short int yytype_uint16;
+#endif
+
+#ifdef YYTYPE_INT16
+typedef YYTYPE_INT16 yytype_int16;
+#else
+typedef short int yytype_int16;
+#endif
+
+#ifndef YYSIZE_T
+# ifdef __SIZE_TYPE__
+# define YYSIZE_T __SIZE_TYPE__
+# elif defined size_t
+# define YYSIZE_T size_t
+# elif ! defined YYSIZE_T && (defined __STDC__ || defined __C99__FUNC__ \
+ || defined __cplusplus || defined _MSC_VER)
+# include <stddef.h> /* INFRINGES ON USER NAME SPACE */
+# define YYSIZE_T size_t
+# else
+# define YYSIZE_T unsigned int
+# endif
+#endif
+
+#define YYSIZE_MAXIMUM ((YYSIZE_T) -1)
+
+#ifndef YY_
+# if defined YYENABLE_NLS && YYENABLE_NLS
+# if E...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-22 17:40:24
|
Revision: 16255
http://sbml.svn.sourceforge.net/sbml/?rev=16255&view=rev
Author: sarahkeating
Date: 2012-08-22 17:40:10 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/L3Parser/src/sbml/AlgebraicRule.h
branches/L3Parser/src/sbml/AssignmentRule.cpp
branches/L3Parser/src/sbml/AssignmentRule.h
branches/L3Parser/src/sbml/CMakeLists.txt
branches/L3Parser/src/sbml/Compartment.cpp
branches/L3Parser/src/sbml/Compartment.h
branches/L3Parser/src/sbml/CompartmentType.cpp
branches/L3Parser/src/sbml/CompartmentType.h
branches/L3Parser/src/sbml/Constraint.cpp
branches/L3Parser/src/sbml/Constraint.h
branches/L3Parser/src/sbml/Delay.cpp
branches/L3Parser/src/sbml/Event.cpp
branches/L3Parser/src/sbml/Event.h
branches/L3Parser/src/sbml/EventAssignment.cpp
branches/L3Parser/src/sbml/EventAssignment.h
branches/L3Parser/src/sbml/FunctionDefinition.h
branches/L3Parser/src/sbml/InitialAssignment.cpp
branches/L3Parser/src/sbml/InitialAssignment.h
branches/L3Parser/src/sbml/KineticLaw.cpp
branches/L3Parser/src/sbml/KineticLaw.h
branches/L3Parser/src/sbml/ListOf.h
branches/L3Parser/src/sbml/LocalParameter.cpp
branches/L3Parser/src/sbml/LocalParameter.h
branches/L3Parser/src/sbml/Model.cpp
branches/L3Parser/src/sbml/Model.h
branches/L3Parser/src/sbml/ModifierSpeciesReference.h
branches/L3Parser/src/sbml/Parameter.cpp
branches/L3Parser/src/sbml/Parameter.h
branches/L3Parser/src/sbml/Priority.cpp
branches/L3Parser/src/sbml/Priority.h
branches/L3Parser/src/sbml/RateRule.cpp
branches/L3Parser/src/sbml/RateRule.h
branches/L3Parser/src/sbml/Reaction.cpp
branches/L3Parser/src/sbml/Reaction.h
branches/L3Parser/src/sbml/Rule.cpp
branches/L3Parser/src/sbml/Rule.h
branches/L3Parser/src/sbml/SBMLConvert.cpp
branches/L3Parser/src/sbml/SBMLDocument.cpp
branches/L3Parser/src/sbml/SBMLDocument.h
branches/L3Parser/src/sbml/SBMLError.cpp
branches/L3Parser/src/sbml/SBMLError.h
branches/L3Parser/src/sbml/SBMLErrorLog.h
branches/L3Parser/src/sbml/SBMLErrorTable.h
branches/L3Parser/src/sbml/SBMLNamespaces.cpp
branches/L3Parser/src/sbml/SBMLNamespaces.h
branches/L3Parser/src/sbml/SBMLReader.h
branches/L3Parser/src/sbml/SBMLTypeCodes.h
branches/L3Parser/src/sbml/SBMLTypes.h
branches/L3Parser/src/sbml/SBMLVisitor.cpp
branches/L3Parser/src/sbml/SBMLVisitor.h
branches/L3Parser/src/sbml/SBMLWriter.cpp
branches/L3Parser/src/sbml/SBMLWriter.h
branches/L3Parser/src/sbml/SBO.cpp
branches/L3Parser/src/sbml/SBO.h
branches/L3Parser/src/sbml/SBase.cpp
branches/L3Parser/src/sbml/SimpleSpeciesReference.h
branches/L3Parser/src/sbml/Species.cpp
branches/L3Parser/src/sbml/Species.h
branches/L3Parser/src/sbml/SpeciesReference.cpp
branches/L3Parser/src/sbml/SpeciesReference.h
branches/L3Parser/src/sbml/SpeciesType.cpp
branches/L3Parser/src/sbml/SpeciesType.h
branches/L3Parser/src/sbml/StoichiometryMath.cpp
branches/L3Parser/src/sbml/StoichiometryMath.h
branches/L3Parser/src/sbml/SyntaxChecker.cpp
branches/L3Parser/src/sbml/SyntaxChecker.h
branches/L3Parser/src/sbml/Trigger.h
branches/L3Parser/src/sbml/Unit.cpp
branches/L3Parser/src/sbml/Unit.h
branches/L3Parser/src/sbml/UnitDefinition.cpp
branches/L3Parser/src/sbml/UnitDefinition.h
branches/L3Parser/src/sbml/UnitKind.h
branches/L3Parser/src/sbml/packages/layout/common/LayoutExtensionTypes.h
branches/L3Parser/src/sbml/packages/layout/common/layoutfwd.h
branches/L3Parser/src/sbml/packages/layout/extension/LayoutExtension.cpp
branches/L3Parser/src/sbml/packages/layout/extension/LayoutExtension.h
branches/L3Parser/src/sbml/packages/layout/extension/LayoutModelPlugin.cpp
branches/L3Parser/src/sbml/packages/layout/extension/LayoutModelPlugin.h
branches/L3Parser/src/sbml/packages/layout/extension/Makefile.in
branches/L3Parser/src/sbml/packages/layout/sbml/Curve.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/GraphicalObject.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/GraphicalObject.h
branches/L3Parser/src/sbml/packages/layout/sbml/Layout.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/Layout.h
branches/L3Parser/src/sbml/packages/layout/sbml/Makefile.in
branches/L3Parser/src/sbml/packages/layout/sbml/ReactionGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/CMakeLists.txt
branches/L3Parser/src/sbml/packages/layout/sbml/test/Makefile.in
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestBoundingBox.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestCompartmentGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestCubicBezier.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestCurve.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestDimensions.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestGraphicalObject.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestLayout.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestLayoutCreation.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestLayoutFormatter.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestLayoutWriting.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestLineSegment.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestPoint.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestReactionGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestRunner.c
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestSBMLHandler.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestSpeciesGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestSpeciesReferenceGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestTextGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/utility.cpp
branches/L3Parser/src/sbml/packages/layout/util/LayoutUtilities.cpp
branches/L3Parser/src/sbml/packages/layout/util/LayoutUtilities.h
branches/L3Parser/src/sbml/test/CMakeLists.txt
branches/L3Parser/src/sbml/test/TestAlgebraicRule.c
branches/L3Parser/src/sbml/test/TestAssignmentRule.c
branches/L3Parser/src/sbml/test/TestCompartment.c
branches/L3Parser/src/sbml/test/TestCompartmentType.c
branches/L3Parser/src/sbml/test/TestCompartmentType_newSetters.c
branches/L3Parser/src/sbml/test/TestCompartmentVolumeRule.c
branches/L3Parser/src/sbml/test/TestCompartment_newSetters.c
branches/L3Parser/src/sbml/test/TestConstraint.c
branches/L3Parser/src/sbml/test/TestConstraint_newSetters.c
branches/L3Parser/src/sbml/test/TestDelay.c
branches/L3Parser/src/sbml/test/TestEvent.c
branches/L3Parser/src/sbml/test/TestEventAssignment.c
branches/L3Parser/src/sbml/test/TestEventAssignment_newSetters.c
branches/L3Parser/src/sbml/test/TestEvent_newSetters.c
branches/L3Parser/src/sbml/test/TestFunctionDefinition.c
branches/L3Parser/src/sbml/test/TestFunctionDefinition_newSetters.c
branches/L3Parser/src/sbml/test/TestInitialAssignment.c
branches/L3Parser/src/sbml/test/TestInitialAssignment_newSetters.c
branches/L3Parser/src/sbml/test/TestKineticLaw.c
branches/L3Parser/src/sbml/test/TestKineticLaw_newSetters.c
branches/L3Parser/src/sbml/test/TestL3Compartment.c
branches/L3Parser/src/sbml/test/TestL3Event.c
branches/L3Parser/src/sbml/test/TestL3KineticLaw.c
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Added Paths:
-----------
branches/L3Parser/src/sbml/packages/layout/sbml/GeneralGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/GeneralGlyph.h
branches/L3Parser/src/sbml/packages/layout/sbml/ReferenceGlyph.cpp
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branches/L3Parser/src/sbml/packages/layout/sbml/test/TestGeneralGlyph.cpp
branches/L3Parser/src/sbml/packages/layout/sbml/test/TestReferenceGlyph.cpp
Removed Paths:
-------------
branches/L3Parser/src/sbml/packages/layout/extension/LayoutSBMLDocumentPlugin.cpp
branches/L3Parser/src/sbml/packages/layout/extension/LayoutSBMLDocumentPlugin.h
Property Changed:
----------------
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branches/L3Parser/src/sbml/validator/test/test-data/libsbml-constraints/99129-pass-00-07.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-17.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-19.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-27.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-01.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-12.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-17.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-20.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-17.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-21.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-22.xml
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branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-24.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-25.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-17.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10514-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10514-fail-01-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10514-fail-01-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10514-pass-00-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-17.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-21.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-25.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-17.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-21.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-22.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-23.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-24.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-25.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-26.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-29.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-04.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-08.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-13.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10523-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10523-fail-01-02.xml
Modified: branches/L3Parser/src/sbml/AlgebraicRule.h
===================================================================
--- branches/L3Parser/src/sbml/AlgebraicRule.h 2012-08-22 17:21:02 UTC (rev 16254)
+++ branches/L3Parser/src/sbml/AlgebraicRule.h 2012-08-22 17:40:10 UTC (rev 16255)
@@ -81,14 +81,12 @@
* distinguishing rules; specifically, it uses an attribute whose value is
* drawn from an enumeration of 3 values. LibSBML supports this using methods
* that work @if clike a libSBML enumeration type, RuleType_t, whose values
- * are @else with the enumeration values @endif listed below.
+ * are @else with the enumeration values @endif@~ listed below.
*
* @li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@endlink: Indicates
* the rule is a "rate" rule.
- *
* @li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@endlink:
* Indicates the rule is a "scalar" rule.
- *
* @li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@endlink:
* Indicates the rule type is unknown or not yet set.
*
Modified: branches/L3Parser/src/sbml/AssignmentRule.cpp
===================================================================
--- branches/L3Parser/src/sbml/AssignmentRule.cpp 2012-08-22 17:21:02 UTC (rev 16254)
+++ branches/L3Parser/src/sbml/AssignmentRule.cpp 2012-08-22 17:40:10 UTC (rev 16255)
@@ -130,5 +130,4 @@
}
}
-/** @endcond */
LIBSBML_CPP_NAMESPACE_END
Modified: branches/L3Parser/src/sbml/AssignmentRule.h
===================================================================
--- branches/L3Parser/src/sbml/AssignmentRule.h 2012-08-22 17:21:02 UTC (rev 16254)
+++ branches/L3Parser/src/sbml/AssignmentRule.h 2012-08-22 17:40:10 UTC (rev 16255)
@@ -127,14 +127,12 @@
* distinguishing rules; specifically, it uses an attribute whose value is
* drawn from an enumeration of 3 values. LibSBML supports this using methods
* that work @if clike a libSBML enumeration type, RuleType_t, whose values
- * are @else with the enumeration values @endif listed below.
+ * are @else with the enumeration values @endif@~ listed below.
*
* @li @link RuleType_t#RULE_TYPE_RATE RULE_TYPE_RATE@endlink: Indicates
* the rule is a "rate" rule.
- *
* @li @link RuleType_t#RULE_TYPE_SCALAR RULE_TYPE_SCALAR@endlink:
* Indicates the rule is a "scalar" rule.
- *
* @li @link RuleType_t#RULE_TYPE_INVALID RULE_TYPE_INVALID@endlink:
* Indicates the rule type is unknown or not yet set.
*
@@ -176,7 +174,7 @@
* @param version an unsigned int, the SBML Version to assign to this
* AssignmentRule
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
@@ -208,7 +206,7 @@
*
* @param sbmlns an SBMLNamespaces object.
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
Modified: branches/L3Parser/src/sbml/CMakeLists.txt
===================================================================
--- branches/L3Parser/src/sbml/CMakeLists.txt 2012-08-22 17:21:02 UTC (rev 16254)
+++ branches/L3Parser/src/sbml/CMakeLists.txt 2012-08-22 17:40:10 UTC (rev 16255)
@@ -1,48 +1,48 @@
-###############################################################################
-#
+###############################################################################
+#
#
-#
-# Description : CMake build script for the native libsbml tests
-# Original author(s): Frank Bergmann <fbe...@ca...>
-# Organization : California Institute of Technology
-#
-# This file is part of libSBML. Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2009-2012 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-# Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-# 1. California Institute of Technology, Pasadena, CA, USA
-# 2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation. A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-#
-###############################################################################
-
-###############################################################################
-#
-# Build test files and add tests
-#
-if(WITH_CHECK)
-
- add_subdirectory(annotation/test)
- add_subdirectory(conversion/test)
- add_subdirectory(extension/test)
- add_subdirectory(math/test)
- add_subdirectory(test)
- add_subdirectory(units/test)
- add_subdirectory(util/test)
- add_subdirectory(validator/test)
- add_subdirectory(xml/test)
-
-endif()
-
+#
+# Description : CMake build script for the native libsbml tests
+# Original author(s): Frank Bergmann <fbe...@ca...>
+# Organization : California Institute of Technology
+#
+# This file is part of libSBML. Please visit http://sbml.org for more
+# information about SBML, and the latest version of libSBML.
+#
+# Copyright (C) 2009-2012 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+#
+# Copyright (C) 2006-2008 by the California Institute of Technology,
+# Pasadena, CA, USA
+#
+# Copyright (C) 2002-2005 jointly by the following organizations:
+# 1. California Institute of Technology, Pasadena, CA, USA
+# 2. Japan Science and Technology Agency, Japan
+#
+# This library is free software; you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation. A copy of the license agreement is provided
+# in the file named "LICENSE.txt" included with this software distribution
+# and also available online as http://sbml.org/software/libsbml/license.html
+#
+###############################################################################
+
+###############################################################################
+#
+# Build test files and add tests
+#
+if(WITH_CHECK)
+
+ add_subdirectory(annotation/test)
+ add_subdirectory(conversion/test)
+ add_subdirectory(extension/test)
+ add_subdirectory(math/test)
+ add_subdirectory(test)
+ add_subdirectory(units/test)
+ add_subdirectory(util/test)
+ add_subdirectory(validator/test)
+ add_subdirectory(xml/test)
+
+endif()
+
Modified: branches/L3Parser/src/sbml/Compartment.cpp
===================================================================
--- branches/L3Parser/src/sbml/Compartment.cpp 2012-08-22 17:21:02 UTC (rev 16254)
+++ branches/L3Parser/src/sbml/Compartment.cpp 2012-08-22 17:40:10 UTC (rev 16255)
@@ -1180,7 +1180,7 @@
// default="3" } (L2v1 ->)
mExplicitlySetSpatialDimensions = attributes.readInto("spatialDimensions",
mSpatialDimensions, getErrorLog(), false, getLine(), getColumn());
- if (mSpatialDimensions < 0 || mSpatialDimensions > 3)
+ if (/*mSpatialDimensions < 0 ||*/ mSpatialDimensions > 3)
{
std::string message = "The spatialDimensions attribute on ";
message += "a <compartment> may only have values 0, 1, 2 or 3.";
@@ -1330,7 +1330,7 @@
if (level == 2)
{
unsigned int sd = mSpatialDimensions;
- if (sd >= 0 && sd <= 2)
+ if (/*sd >= 0 &&*/ sd <= 2)
{
stream.writeAttribute("spatialDimensions", sd);
}
@@ -2102,7 +2102,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2134,7 +2134,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2166,7 +2166,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2202,7 +2202,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2229,7 +2229,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2259,7 +2259,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
*/
@@ -2288,7 +2288,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
*/
@@ -2313,7 +2313,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2342,7 +2342,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -2371,7 +2371,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_UNEXPECTED_ATTRIBUTE
@@ -2394,7 +2394,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2418,7 +2418,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2442,7 +2442,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
*/
@@ -2470,7 +2470,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
*/
@@ -2493,7 +2493,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2517,7 +2517,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2541,7 +2541,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
Modified: branches/L3Parser/src/sbml/Compartment.h
===================================================================
--- branches/L3Parser/src/sbml/Compartment.h 2012-08-22 17:21:02 UTC (rev 16254)
+++ branches/L3Parser/src/sbml/Compartment.h 2012-08-22 17:40:10 UTC (rev 16255)
@@ -345,7 +345,7 @@
* @param version an unsigned int, the SBML Version to assign to this
* Compartment
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
@@ -384,7 +384,7 @@
*
* @param sbmlns an SBMLNamespaces object.
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the given @p level and @p version combination, or this kind
* of SBML object, are either invalid or mismatched with respect to the
* parent SBMLDocument object.
@@ -414,7 +414,7 @@
*
* @param orig the Compartment instance to copy.
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
Compartment(const Compartment& orig);
@@ -426,7 +426,7 @@
* @param rhs The object whose values are used as the basis of the
* assignment.
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
Compartment& operator=(const Compartment& rhs);
@@ -545,8 +545,8 @@
* compartments may be other than three-dimensional and therefore the
* "volume" attribute is named "size" in Level 2. LibSBML provides
* both
- * @if java Compartment::getSize()@else getSize()@endif and
- * @if java Compartment::getVolume()@else getVolume()@endif for
+ * @if java Compartment::getSize()@else getSize()@endif@~ and
+ * @if java Compartment::getVolume()@else getVolume()@endif@~ for
* easier compatibility between SBML Levels.
*
* @return the value of the "size" attribute ("volume" in Level 1) of
@@ -568,8 +568,8 @@
* compartments may be other than three-dimensional and therefore the
* "volume" attribute is named "size" in Level 2. LibSBML provides
* both
- * @if java Compartment::getSize()@else getSize()@endif and
- * @if java Compartment::getVolume()@else getVolume()@endif
+ * @if java Compartment::getSize()@else getSize()@endif@~ and
+ * @if java Compartment::getVolume()@else getVolume()@endif@~
* for easier compatibility between SBML Levels.
*
* @return the value of the "volume" attribute ("size" in Level 2) of
@@ -598,7 +598,7 @@
* @note @htmlinclude unassigned-units-are-not-a-default.html
*
* @see isSetUnits()
- * @see @if java Compartment::setUnits(String sid)@else setUnits()@endif
+ * @see @if java Compartment::setUnits(String sid)@else setUnits()@endif@~
* @see getSize()
*/
const std::string& getUnits () const;
@@ -666,8 +666,8 @@
* This method is similar but not identical to
* @if java Compartment::isSetVolume()@else isSetVolume()@endif. The latter
* should be used in the context of SBML Level 1 models instead of
- * @if java Compartment::isSetSize()@else isSetSize()@endif
- * because @if java Compartment::isSetVolume()@else isSetVolume()@endif
+ * @if java Compartment::isSetSize()@else isSetSize()@endif@~
+ * because @if java Compartment::isSetVolume()@else isSetVolume()@endif@~
* performs extra processing to take into account the difference in
* default values between SBML Levels 1 and 2.
*
@@ -702,7 +702,7 @@
* therefore may or may not be set.
*
* @see isSetSize()
- * @see @if java Compartment::setVolume(double value)@else setVolume()@endif
+ * @see @if java Compartment::setVolume(double value)@else setVolume()@endif@~
*/
bool isSetVolume () const;
@@ -846,7 +846,7 @@
* Compartment.
*
* This method is identical to
- * @if java Compartment::setVolume(double value)@else setVolume()@endif
+ * @if java Compartment::setVolume(double value)@else setVolume()@endif@~
* and is provided for compatibility between
* SBML Level 1 and Level 2.
*
@@ -870,7 +870,7 @@
* Compartment.
*
* This method is identical to
- * @if java Compartment::setVolume(double value)@else setVolume()@endif
+ * @if java Compartment::setVolume(double value)@else setVolume()@endif@~
* and is provided for compatibility between SBML Level 1 and
* Level 2.
*
@@ -1163,7 +1163,7 @@
* codes</em>. In the C# language interface for libSBML, the type codes
* are defined as static integer constants in the interface class @link
* libsbmlcs.libsbml@endlink. The names of the type codes all begin with
- * the characters @c SBML_. @endif
+ * the characters @c SBML_. @endif@~
*
* @return the SBML type code for this object, or
* @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
@@ -1351,7 +1351,7 @@
* codes</em>. In the C# language interface for libSBML, the type codes
* are defined as static integer constants in the interface class @link
* libsbmlcs.libsbml@endlink. The names of the type codes all begin with
- * the characters @c SBML_. @endif
+ * the characters @c SBML_. @endif@~
*
* @return the SBML type code for this object, or @link SBMLTypeCode_t#SBML_UNKNOWN SBML_UNKNOWN@endlink (default).
*
@@ -1384,7 +1384,7 @@
* codes</em>. In the C# language interface for libSBML, the type codes
* are defined as static integer constants in the interface class @link
* libsbmlcs.libsbml@endlink. The names of the type codes all begin with
- ...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-22 17:21:12
|
Revision: 16254
http://sbml.svn.sourceforge.net/sbml/?rev=16254&view=rev
Author: sarahkeating
Date: 2012-08-22 17:21:02 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/L3Parser/src/sbml/annotation/CVTerm.cpp
branches/L3Parser/src/sbml/annotation/CVTerm.h
branches/L3Parser/src/sbml/annotation/Date.cpp
branches/L3Parser/src/sbml/annotation/Date.h
branches/L3Parser/src/sbml/annotation/ModelCreator.cpp
branches/L3Parser/src/sbml/annotation/ModelCreator.h
branches/L3Parser/src/sbml/annotation/ModelHistory.cpp
branches/L3Parser/src/sbml/annotation/ModelHistory.h
branches/L3Parser/src/sbml/annotation/RDFAnnotation.h
branches/L3Parser/src/sbml/annotation/RDFAnnotationParser.cpp
branches/L3Parser/src/sbml/annotation/RDFAnnotationParser.h
branches/L3Parser/src/sbml/annotation/test/CMakeLists.txt
branches/L3Parser/src/sbml/annotation/test/Makefile.in
branches/L3Parser/src/sbml/annotation/test/TestCVTerms.c
branches/L3Parser/src/sbml/annotation/test/TestCVTerms_newSetters.c
branches/L3Parser/src/sbml/annotation/test/TestDate_newSetters.c
branches/L3Parser/src/sbml/annotation/test/TestL3ModelHistory.cpp
branches/L3Parser/src/sbml/annotation/test/TestModelCreator_newSetters.c
branches/L3Parser/src/sbml/annotation/test/TestModelHistory.c
branches/L3Parser/src/sbml/annotation/test/TestModelHistory_newSetters.c
branches/L3Parser/src/sbml/annotation/test/TestRDFAnnotation.cpp
branches/L3Parser/src/sbml/annotation/test/TestRDFAnnotationC.c
branches/L3Parser/src/sbml/annotation/test/TestRunner.c
branches/L3Parser/src/sbml/annotation/test/TestSyncAnnotation.cpp
branches/L3Parser/src/sbml/common/.svnignore
branches/L3Parser/src/sbml/common/extern.h
branches/L3Parser/src/sbml/common/libsbml-config-common.h.cmake
branches/L3Parser/src/sbml/common/libsbml-config-common.h.in
branches/L3Parser/src/sbml/common/libsbml-package.h
branches/L3Parser/src/sbml/common/libsbml-version.h
branches/L3Parser/src/sbml/common/operationReturnValues.h
branches/L3Parser/src/sbml/compress/ioapi.h
branches/L3Parser/src/sbml/compress/unzip.c
branches/L3Parser/src/sbml/compress/zfstream.cpp
branches/L3Parser/src/sbml/compress/zip.c
branches/L3Parser/src/sbml/compress/zipfstream.cpp
branches/L3Parser/src/sbml/conversion/ConversionOption.h
branches/L3Parser/src/sbml/conversion/ConversionProperties.h
branches/L3Parser/src/sbml/conversion/SBMLConverter.h
branches/L3Parser/src/sbml/conversion/SBMLConverterRegistry.cpp
branches/L3Parser/src/sbml/conversion/SBMLConverterRegistry.h
branches/L3Parser/src/sbml/conversion/SBMLFunctionDefinitionConverter.cpp
branches/L3Parser/src/sbml/conversion/SBMLFunctionDefinitionConverter.h
branches/L3Parser/src/sbml/conversion/SBMLInitialAssignmentConverter.cpp
branches/L3Parser/src/sbml/conversion/SBMLInitialAssignmentConverter.h
branches/L3Parser/src/sbml/conversion/SBMLLevelVersionConverter.cpp
branches/L3Parser/src/sbml/conversion/SBMLLevelVersionConverter.h
branches/L3Parser/src/sbml/conversion/SBMLRuleConverter.cpp
branches/L3Parser/src/sbml/conversion/SBMLRuleConverter.h
branches/L3Parser/src/sbml/conversion/SBMLStripPackageConverter.cpp
branches/L3Parser/src/sbml/conversion/SBMLStripPackageConverter.h
branches/L3Parser/src/sbml/conversion/SBMLUnitsConverter.cpp
branches/L3Parser/src/sbml/conversion/SBMLUnitsConverter.h
branches/L3Parser/src/sbml/conversion/test/CMakeLists.txt
branches/L3Parser/src/sbml/conversion/test/TestRunner.c
branches/L3Parser/src/sbml/extension/Makefile.in
branches/L3Parser/src/sbml/extension/SBMLDocumentPlugin.cpp
branches/L3Parser/src/sbml/extension/SBMLDocumentPlugin.h
branches/L3Parser/src/sbml/extension/SBMLExtension.cpp
branches/L3Parser/src/sbml/extension/SBMLExtension.h
branches/L3Parser/src/sbml/extension/SBMLExtensionNamespaces.cpp
branches/L3Parser/src/sbml/extension/SBaseExtensionPoint.cpp
branches/L3Parser/src/sbml/extension/SBasePlugin.cpp
branches/L3Parser/src/sbml/extension/SBasePlugin.h
branches/L3Parser/src/sbml/extension/test/CMakeLists.txt
branches/L3Parser/src/sbml/extension/test/TestPackage.cpp
branches/L3Parser/src/sbml/extension/test/TestPackage.h
branches/L3Parser/src/sbml/extension/test/TestSBasePluginCreator.cpp
Added Paths:
-----------
branches/L3Parser/src/sbml/annotation/test/TestRDFAnnotationMetaid.cpp
branches/L3Parser/src/sbml/annotation/test/test-data/annotationL3_3.xml
branches/L3Parser/src/sbml/extension/SBMLDocumentPluginNotRequired.cpp
branches/L3Parser/src/sbml/extension/SBMLDocumentPluginNotRequired.h
Modified: branches/L3Parser/src/sbml/annotation/CVTerm.cpp
===================================================================
--- branches/L3Parser/src/sbml/annotation/CVTerm.cpp 2012-08-22 16:29:46 UTC (rev 16253)
+++ branches/L3Parser/src/sbml/annotation/CVTerm.cpp 2012-08-22 17:21:02 UTC (rev 16254)
@@ -638,7 +638,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -660,7 +660,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -686,7 +686,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -711,7 +711,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -740,7 +740,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
@@ -769,7 +769,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -794,7 +794,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_ATTRIBUTE_VALUE
Modified: branches/L3Parser/src/sbml/annotation/CVTerm.h
===================================================================
--- branches/L3Parser/src/sbml/annotation/CVTerm.h 2012-08-22 16:29:46 UTC (rev 16253)
+++ branches/L3Parser/src/sbml/annotation/CVTerm.h 2012-08-22 17:21:02 UTC (rev 16254)
@@ -52,34 +52,34 @@
* such as Species, Compartment, etc. The following template illustrates
* the different parts of SBML annotations in XML form:
*
- <div class="fragment">
- <<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid="<span style="border-bottom: 1px solid black">meta id</span>" <span style="background-color: #d0eed0">+++</span>><br>
- <span style="background-color: #d0eed0">+++</span><br>
- <annotation><br>
- <span style="background-color: #d0eed0">+++</span><br>
- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br>
- xmlns:dc="http://purl.org/dc/elements/1.1/"<br>
- xmlns:dcterm="http://purl.org/dc/terms/"<br>
- xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"<br>
- xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"<br>
- xmlns:bqmodel="http://biomodels.net/model-qualifiers/" ><br>
- <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>"><br>
- <span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span><br>
- <<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <rdf:Bag><br>
- <rdf:li rdf:resource="<span style="background-color: #d0d0ee">URI</span>" /><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Bag><br>
- </<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Description><br>
- <span style="background-color: #d0eed0">+++</span><br>
- </rdf:RDF><br>
- <span style="background-color: #d0eed0">+++</span><br>
- </annotation><br>
- <span style="background-color: #d0eed0">+++</span><br>
- </<span style="background-color: #bbb">SBML_ELEMENT</span>><br>
- </div>
+ <pre class="fragment">
+ <<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid="<span style="border-bottom: 1px solid black">meta id</span>" <span style="background-color: #d0eed0">+++</span>>
+ <span style="background-color: #d0eed0">+++</span>
+ <annotation>
+ <span style="background-color: #d0eed0">+++</span>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:dcterm="http://purl.org/dc/terms/"
+ xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"
+ xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
+ xmlns:bqmodel="http://biomodels.net/model-qualifiers/" >
+ <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>">
+ <span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
+ <<span style="background-color: #bbb">RELATION_ELEMENT</span>>
+ <rdf:Bag>
+ <rdf:li rdf:resource="<span style="background-color: #d0d0ee">URI</span>" />
+ <span style="background-color: #edd">...</span>
+ </rdf:Bag>
+ </<span style="background-color: #bbb">RELATION_ELEMENT</span>>
+ <span style="background-color: #edd">...</span>
+ </rdf:Description>
+ <span style="background-color: #d0eed0">+++</span>
+ </rdf:RDF>
+ <span style="background-color: #d0eed0">+++</span>
+ </annotation>
+ <span style="background-color: #d0eed0">+++</span>
+ </<span style="background-color: #bbb">SBML_ELEMENT</span>>
+ </pre>
*
* In the template above, the placeholder
* <span class="code" style="background-color: #bbb">SBML_ELEMENT</span> stands for
@@ -222,8 +222,7 @@
public:
/**
- * Creates an empty CVTerm, optionally with the given
- * @if clike #QualifierType_t value@else qualifier@endif @p type.
+ * Creates an empty CVTerm, optionally with the given @if clike #QualifierType_t value@else qualifier@endif@~ @p type.
*
* The SBML Level 2 and Level 3 specifications define a simple
* format for annotating models when (a) referring to controlled
@@ -248,8 +247,7 @@
* QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink. If
* an explicit value for @p type is not given, this method defaults to
* using @link QualifierType_t#UNKNOWN_QUALIFIER
- * UNKNOWN_QUALIFIER@endlink. The
- * @if clike #QualifierType_t value@else qualifier type@endif
+ * UNKNOWN_QUALIFIER@endlink. The @if clike #QualifierType_t value@else qualifier type@endif@~
* can be set later using the
* CVTerm::setQualifierType(@if java int type@endif) method.
*
@@ -259,9 +257,9 @@
* qualifiers web page</a> for an explanation of the meaning of these
* different qualifiers.
*
- * @param type a @if clike #QualifierType_t value@else qualifier type@endif
+ * @param type a @if clike #QualifierType_t value@else qualifier type@endif@~
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
CVTerm(QualifierType_t type = UNKNOWN_QUALIFIER);
@@ -315,7 +313,7 @@
*
* @param orig the CVTerm instance to copy.
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
CVTerm(const CVTerm& orig);
@@ -327,7 +325,7 @@
* @param rhs The object whose values are used as the basis of the
* assignment.
*
- * @throws @if python ValueError @else SBMLConstructorException @endif
+ * @throws @if python ValueError @else SBMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
CVTerm& operator=(const CVTerm& rhs);
@@ -346,8 +344,8 @@
*
* @htmlinclude cvterm-common-description-text.html
*
- * The placeholder <span class="code" style="background-color:
- * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier
+ * The placeholder <span class="code" style="background-color: #bbb">
+ * RELATION_ELEMENT</span> refers to a BioModels.net qualifier
* element name. This is an element in either the XML namespace
* <code>"http://biomodels.net/model-qualifiers"</code> (for model
* qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
@@ -368,7 +366,7 @@
* the @em other two methods to call to find out the specific
* relationship.
*
- * @return the @if clike #QualifierType_t value@else qualifier type@endif
+ * @return the @if clike #QualifierType_t value@else qualifier type@endif@~
* of this object or @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
* (the default).
*
@@ -384,8 +382,8 @@
*
* @htmlinclude cvterm-common-description-text.html
*
- * The placeholder <span class="code" style="background-color:
- * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier
+ * The placeholder <span class="code" style="background-color: #bbb">
+ * RELATION_ELEMENT</span> refers to a BioModels.net qualifier
* element name. This is an element in either the XML namespace
* <code>"http://biomodels.net/model-qualifiers"</code> (for model
* qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
@@ -404,7 +402,7 @@
* unknown by libSBML and reported as
* @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink.
*
- * @return the @if clike #ModelQualifierType_t value@else model qualifier type@endif
+ * @return the @if clike #ModelQualifierType_t value@else model qualifier type@endif@~
* of this object or @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink
* (the default).
*/
@@ -416,8 +414,8 @@
*
* @htmlinclude cvterm-common-description-text.html
*
- * The placeholder <span class="code" style="background-color:
- * #bbb">RELATION_ELEMENT</span> refers to a BioModels.net qualifier
+ * The placeholder <span class="code" style="background-color: #bbb">
+ * RELATION_ELEMENT</span> refers to a BioModels.net qualifier
* element name. This is an element in either the XML namespace
* <code>"http://biomodels.net/model-qualifiers"</code> (for model
* qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
@@ -445,7 +443,7 @@
* unknown by libSBML and reported as
* @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
*
- * @return the @if clike #BiolQualifierType_t value@else biology qualifier type@endif
+ * @return the @if clike #BiolQualifierType_t value@else biology qualifier type@endif@~
* of this object or @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink
* (the default).
*/
@@ -462,8 +460,8 @@
* CVTerm objects using an XMLAttributes object. Each attribute stored
* inside the XMLAttributes will have the same name (specifically,
* "<code>rdf:resource</code>") but a different value, and the
- * value will be a <span class="code" style="background-color:
- * #d0d0ee">resource URI</span> shown in the XML template above.
+ * value will be a <span class="code" style="background-color: #d0d0ee">
+ * resource URI</span> shown in the XML template above.
*
* A valid CVTerm entity must always have at least one resource and
* a value for the relationship qualifier.
@@ -487,8 +485,8 @@
* CVTerm objects using an XMLAttributes object. Each attribute stored
* inside the XMLAttributes will have the same name (specifically,
* "<code>rdf:resource</code>") but a different value, and the
- * value will be a <span class="code" style="background-color:
- * #d0d0ee">resource URI</span> shown in the XML template above.
+ * value will be a <span class="code" style="background-color: #d0d0ee">
+ * resource URI</span> shown in the XML template above.
*
* A valid CVTerm entity must always have at least one resource and
* a value for the relationship qualifier.
@@ -550,7 +548,7 @@
/**
- * Sets the @if clike #QualifierType_t@else qualifier code@endif of this
+ * Sets the @if clike #QualifierType_t@else qualifier code@endif@~ of this
* CVTerm object.
*
* @param type the @if clike #QualifierType_t value@else qualifier type@endif.
@@ -563,10 +561,10 @@
/**
- * Sets the @if clike #ModelQualifierType_t value@else model qualifier type@endif
+ * Sets the @if clike #ModelQualifierType_t value@else model qualifier type@endif@~
* of this CVTerm object.
*
- * @param type the @if clike #ModelQualifierType_t value@else model qualifier type@endif
+ * @param type the @if clike #ModelQualifierType_t value@else model qualifier type@endif@~
*
* @return integer value indicating success/failure of the
* function. The possible values returned by this function are:
@@ -585,7 +583,7 @@
/**
- * Sets the @if clike #BiolQualifierType_t value@else biology qualifier type@endif
+ * Sets the @if clike #BiolQualifierType_t value@else biology qualifier type@endif@~
* of this CVTerm object.
*
* @param type the @if clike #BiolQualifierType_t value@else biology qualifier type@endif.
@@ -597,7 +595,7 @@
*
* @note If the Qualifier Type of this object is not
* @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink,
- * then the @if clike #BiolQualifierType_t value@else biology qualifier type@endif will default
+ * then the @if clike #BiolQualifierType_t value@else biology qualifier type@endif@~ will default
* to @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
*
* @see getQualifierType()
@@ -607,7 +605,7 @@
/**
- * Sets the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif value of this CVTerm object.
+ * Sets the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif@~ value of this CVTerm object.
*
* @param qualifier the string representing a model qualifier
*
@@ -629,7 +627,7 @@
/**
- * Sets the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif of this CVTerm object.
+ * Sets the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif@~ of this CVTerm object.
*
* @param qualifier the string representing a biology qualifier
*
@@ -641,7 +639,7 @@
*
* @note If the Qualifier Type of this object is not
* @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink,
- * then the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif value will default
+ * then the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif@~ value will default
* to @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
*
* @see getQualifierType()
@@ -669,30 +667,30 @@
* together identified uniquely using a URI. The following template
* illustrates the structure:
*
- <DIV class="fragment">
- <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>"><br>
- <span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span><br>
- <<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <rdf:Bag><br>
- <rdf:li rdf:resource="<span style="background-color: #d0d0ee">resource URI</span>" /><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Bag><br>
- </<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Description><br>
- </div>
+ <pre class="fragment">
+ <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>">
+ <span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
+ <<span style="background-color: #bbb">RELATION_ELEMENT</span>>
+ <rdf:Bag>
+ <rdf:li rdf:resource="<span style="background-color: #d0d0ee">resource URI</span>" />
+ <span style="background-color: #edd">...</span>
+ </rdf:Bag>
+ </<span style="background-color: #bbb">RELATION_ELEMENT</span>>
+ <span style="background-color: #edd">...</span>
+ </rdf:Description>
+ </pre>
*
* In the template above, the placeholder <span class="code"
* style="border-bottom: 1px solid black">meta id</span> stands for the
* element's meta identifier, which is a field available on all SBML
* components derived from the SBase base object class. The <span
* style="border-bottom: 2px dotted #888">dotted</span> portions are
- * optional, and the ellipses <span class="code" style="background-color:
- * #edd">...</span> are placeholders for zero or more elements of the
- * same form as the immediately preceding element. The placeholder <span
- * class="code" style="background-color: #bbb">RELATION_ELEMENT</span>
- * refers to a BioModels.net qualifier element name. This is an element
- * in either the XML namespace
+ * optional, and the ellipses <span class="code"
+ * style="background-color: #edd">...</span> are placeholders for zero or
+ * more elements of the same form as the immediately preceding element.
+ * The placeholder <span class="code" style="background-color: #bbb">
+ * RELATION_ELEMENT</span> refers to a BioModels.net qualifier element
+ * name. This is an element in either the XML namespace
* <code>"http://biomodels.net/model-qualifiers"</code> (for model
* qualifiers) or <code>"http://biomodels.net/biology-qualifiers"</code>
* (for biological qualifier).
Modified: branches/L3Parser/src/sbml/annotation/Date.cpp
===================================================================
--- branches/L3Parser/src/sbml/annotation/Date.cpp 2012-08-22 16:29:46 UTC (rev 16253)
+++ branches/L3Parser/src/sbml/annotation/Date.cpp 2012-08-22 17:21:02 UTC (rev 16254)
@@ -1,1159 +1,1159 @@
-/**
- * @file Date.cpp
- * @brief Date I/O
- * @author Sarah Keating
- *
- * Copyright (C) 2009-2012 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
- *
- * Copyright (C) 2006-2008 by the California Institute of Technology,
- * Pasadena, CA, USA
- *
- * Copyright (C) 2002-2005 jointly by the following organizations:
- * 1. California Institute of Technology, Pasadena, CA, USA
- * 2. Japan Science and Technology Agency, Japan
- *
- * This library is free software; you can redistribute it and/or modify it
- * under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation. A copy of the license agreement is
- * provided in the file named "LICENSE.txt" included with this software
- * distribution. It is also available online at
- * http://sbml.org/software/libsbml/license.html
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this library; if not, write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-
-#include <sbml/annotation/Date.h>
-#include <sbml/common/common.h>
-#include <sbml/SBase.h>
-#include <cstdio>
-
-/** @cond doxygen-ignored */
-
-using namespace std;
-
-/** @endcond */
-
-LIBSBML_CPP_NAMESPACE_BEGIN
-
-/*
- * creates a date from the individual fields entered as numbers
- */
-Date::Date(unsigned int year, unsigned int month,
- unsigned int day, unsigned int hour,
- unsigned int minute, unsigned int second,
- unsigned int sign, unsigned int hoursOffset,
- unsigned int minutesOffset) :
- mHasBeenModified (false)
-{
- mYear = year;
- mMonth = month;
- mDay = day;
- mHour = hour;
- mMinute = minute;
- mSecond = second;
-
- mSignOffset = sign;
- mHoursOffset = hoursOffset;
- mMinutesOffset = minutesOffset;;
-
- parseDateNumbersToString();
-}
-
-
-/*
- * creates a date from a string
- */
-Date::Date (const std::string& date) :
- mHasBeenModified (false)
-{
- if (&(date) == NULL)
- mDate = "";
- else
- mDate = date;
-
- parseDateStringToNumbers();
- parseDateNumbersToString();
-}
-
-Date::~Date() {}
-
-/*
- * Copy constructor.
- */
-Date::Date(const Date& orig)
-{
- if (&orig == NULL)
- {
- throw SBMLConstructorException("Null argument to copy constructor");
- }
- else
- {
- mYear = orig.mYear;
- mMonth = orig.mMonth;
- mDay = orig.mDay;
- mHour = orig.mHour;
- mMinute = orig.mMinute;
- mSecond = orig.mSecond;
-
- mSignOffset = orig.mSignOffset;
- mHoursOffset = orig.mHoursOffset;
- mMinutesOffset = orig.mMinutesOffset;;
-
- mDate = orig.mDate;
-
- mHasBeenModified = orig.mHasBeenModified;
- }
-}
-
-/*
- * Assignment operator
- */
-Date& Date::operator=(const Date& rhs)
-{
- if (&rhs == NULL)
- {
- throw SBMLConstructorException("Null argument to assignment operator");
- }
- else if(&rhs!=this)
- {
- mYear = rhs.mYear;
- mMonth = rhs.mMonth;
- mDay = rhs.mDay;
- mHour = rhs.mHour;
- mMinute = rhs.mMinute;
- mSecond = rhs.mSecond;
-
- mSignOffset = rhs.mSignOffset;
- mHoursOffset = rhs.mHoursOffset;
- mMinutesOffset = rhs.mMinutesOffset;;
-
- mDate = rhs.mDate;
-
- mHasBeenModified = rhs.mHasBeenModified;
- }
-
- return *this;
-}
-
-/*
- * @return a (deep) copy of this Date.
- */
-Date* Date::clone () const
-{
- return new Date(*this);
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setYear (unsigned int year)
-{
- if (year <1000 || year > 9999)
- {
- mYear = 2000;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mYear = year;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setMonth (unsigned int month)
-{
- if (month < 1 || month > 12)
- {
- mMonth = 1;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mMonth = month;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setDay (unsigned int day)
-{
- bool validDay = true;
- if (day < 1 || day > 31)
- {
- validDay = false;
- }
- else
- {
- switch (mMonth)
- {
- case 4:
- case 6:
- case 9:
- case 11:
- if (day > 30) validDay = false;
- break;
- case 2:
- if (mYear % 4 == 0)
- {
- if (day > 29) validDay = false;
- }
- else
- {
- if (day > 28) validDay = false;
- }
- break;
- case 1:
- case 3:
- case 5:
- case 7:
- case 8:
- case 10:
- case 12:
- default:
- break;
- }
- }
-
- if (!validDay)
- {
- mDay = 1;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mDay = day;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setHour (unsigned int hour)
-{
- if (hour < 0 || hour > 23)
- {
- mHour = 0;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mHour = hour;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setMinute (unsigned int minute)
-{
- if (minute < 0 || minute > 59)
- {
- mMinute = 0;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mMinute = minute;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setSecond (unsigned int second)
-{
- if (second < 0 || second > 59)
- {
- mSecond = 0;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mSecond = second;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setSignOffset (unsigned int sign)
-{
- if (sign < 0 || sign > 1)
- {
- mSignOffset = 0;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mSignOffset = sign;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setHoursOffset (unsigned int hour)
-{
- if (hour < 0 || hour > 12)
- {
- mHoursOffset = 0;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mHoursOffset = hour;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the year checking appropriateness
- */
-int
-Date::setMinutesOffset (unsigned int minute)
-{
- if (minute < 0 || minute > 59)
- {
- mMinutesOffset = 0;
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- mMinutesOffset = minute;
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-/*
- * sets the value of the date string checking appropriateness
- */
-int
-Date::setDateAsString (const std::string& date)
-{
- /* if date is NULL consider this as resetting
- * the date completely
- */
-
- if (&(date) == NULL)
- {
- mDate = "";
- // revert to default numbers
- // rewrite date string to reflect the defaults
- parseDateStringToNumbers();
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else if (date.empty())
- {
- mDate = "";
- // revert to default numbers
- // rewrite date string to reflect the defaults
- parseDateStringToNumbers();
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-
- /* Date must be: YYYY-MM-DDThh:mm:ssTZD
- * where TZD is either Z or +/-HH:MM
- */
- mDate = date;
-
- if (!representsValidDate())
- {
- mDate = "";
- parseDateNumbersToString();
- return LIBSBML_INVALID_ATTRIBUTE_VALUE;
- }
- else
- {
- parseDateStringToNumbers();
- parseDateNumbersToString();
- mHasBeenModified = true;
- return LIBSBML_OPERATION_SUCCESS;
- }
-}
-
-
-
-/** @cond doxygen-libsbml-internal */
-/*
- * returns the date in numbers as a W3CDTF string
- */
-void
-Date::parseDateNumbersToString()
-{
- char cdate[10];
-
- if (mMonth < 10)
- sprintf(cdate, "%u-0%u-", mYear, mMonth);
- else
- sprintf(cdate, "%u-%u-", mYear, mMonth);
- mDate = cdate;
-
- if (mDay < 10)
- sprintf(cdate, "0%uT", mDay);
- else
- sprintf(cdate, "%uT", mDay);
- mDate.append(cdate);
-
- if (mHour < 10)
- sprintf(cdate, "0%u:", mHour);
- else
- sprintf(cdate, "%u:", mHour);
- mDate.append(cdate);
-
- if (mMinute < 10)
- sprintf(cdate, "0%u:", mMinute);
- else
- sprintf(cdate, "%u:", mMinute);
- mDate.append(cdate);
-
- if (mSecond < 10)
- sprintf(cdate, "0%u", mSecond);
- else
- sprintf(cdate, "%u", mSecond);
- mDate.append(cdate);
-
- if (mHoursOffset == 0 && mMinutesOffset == 0)
- {
- sprintf(cdate, "Z");
- mDate.append(cdate);
- }
- else
- {
- if (mSignOffset == 0)
- sprintf(cdate, "-");
- else
- sprintf(cdate, "+");
- mDate.append(cdate);
-
- if (mHoursOffset < 10)
- sprintf(cdate, "0%u:", mHoursOffset);
- else
- sprintf(cdate, "%u:", mHoursOffset);
- mDate.append(cdate);
-
- if (mMinutesOffset < 10)
- sprintf(cdate, "0%u", mMinutesOffset);
- else
- sprintf(cdate, "%u", mMinutesOffset);
- mDate.append(cdate);
- }
-
-}
-/** @endcond */
-
-
-/** @cond doxygen-libsbml-internal */
-void
-Date::parseDateStringToNumbers()
-{
- if (mDate.length() == 0)
- {
- mYear = 2000;
- mMonth = 1;
- mDay = 1;
- mHour = 0;
- mMinute = 0;
- mSecond = 0;
-
- mSignOffset = 0;
- mHoursOffset = 0;
- mMinutesOffset = 0;
- }
- else
- {
- const char * cdate = mDate.c_str();
- char year[5];
- year[4] = '\0';
- char block[3];
- block[2] = '\0';
-
- year[0] = cdate[0];
- year[1] = cdate[1];
- year[2] = cdate[2];
- year[3] = cdate[3];
-
- mYear = strtol(year, NULL, 10);
-
- block[0] = cdate[5];
- block[1] = cdate[6];
-
- mMonth = strtol(block, NULL, 10);
-
- block[0] = cdate[8];
- block[1] = cdate[9];
-
- mDay = strtol(block, NULL, 10);
-
- block[0] = cdate[11];
- block[1] = cdate[12];
-
- mHour = strtol(block, NULL, 10);
-
- block[0] = cdate[14];
- block[1] = cdate[15];
-
- mMinute = strtol(block, NULL, 10);
-
- block[0] = cdate[17];
- block[1] = cdate[18];
-
- mSecond = strtol(block, NULL, 10);
-
- if (cdate[19] == '+')
- {
- mSignOffset = 1;
- block[0] = cdate[20];
- block[1] = cdate[21];
- mHoursOffset = strtol(block, NULL, 10);
-
- block[0] = cdate[23];
- block[1] = cdate[24];
- mMinutesOffset = strtol(block, NULL, 10);
- }
- else if (cdate[19] == '-')
- {
- mSignOffset = 0;
- block[0] = cdate[20];
- block[1] = cdate[21];
- mHoursOffset = strtol(block, NULL, 10);
-
- block[0] = cdate[23];
- block[1] = cdate[24];
- mMinutesOffset = strtol(block, NULL, 10);
- }
- else
- {
- mSignOffset = 0;
- mHoursOffset = 0;
- mMinutesOffset = 0;
- }
- }
-}
-
-bool
-Date::representsValidDate()
-{
- bool valid = true;
-// parseDateNumbersToString();
- const char * cdate = mDate.c_str();
-
- if (mDate.length() != 20 && mDate.length() != 25)
- {
- valid = false;
- }
- else if (cdate[4] != '-' ||
- cdate[7] != '-' ||
- cdate[10] != 'T' ||
- cdate[13] != ':' ||
- cdate[16] != ':')
- {
- valid = false;
- }
- else if (cdate[19] != 'Z' &&
- cdate[19] != '+' &&
- cdate[19] != '-')
- {
- valid = false;
- }
- else if (cdate[19] != 'Z' &&
- cdate[22] != ':')
- {
- valid = false;
- }
-
-
- if (getMonth() > 12 ||
- getDay() > 31 ||
- getHour() > 23 ||
- getMinute() > 59 ||
- getSecond() > 59 ||
- getSignOffset() > 1 ||
- getHoursOffset() > 11 ||
- getMinutesOffset() > 59)
- {
- valid = false;
- }
- else
- {
- switch(getMonth())
- {
- case 4:
- case 6:
- case 9:
- case 11:
- if (getDay() > 30)
- valid = false;
- break;
- case 2:
- if (getYear() % 4 == 0)
- {
- if (getDay() > 29)
- valid = false;
- }
- else
- {
- if (getDay() > 28)
- valid = false;
- }
- break;
- default:
- break;
- }
- }
-
- return valid;
-}
-
-bool
-Date::hasBeenModified()
-{
- return mHasBeenModified;
-}
-
-void
-Date::resetModifiedFlags()
-{
- mHasBeenModified = false;
-}
-
-
-
-/** @endcond */
-
-
-/**
- * Creates a date optionally from the individual fields entered as numbers.
- *
- * @param year an unsigned int representing the year.
- * @param month an unsigned int representing the month.
- * @param day an unsigned int representing the day.
- * @param hour an unsigned int representing the hour.
- * @param minute an unsigned int representing the minute.
- * @param second an unsigned int representing the second.
- * @param sign an unsigned int representing the sign of the offset
- * (0/1 equivalent to +/-).
- * @param hoursOffset an unsigned int representing the hoursOffset.
- * @param minutesOffset an unsigned int representing the minutesOffset.
- *
- * @return pointer to the newly created Date_t structure.
- */
-LIBSBML_EXTERN
-Date_t *
-Date_createFromValues(unsigned int year, unsigned int month,
- unsigned int day, unsigned int hour,
- unsigned int minute, unsigned int second,
- unsigned int sign, unsigned int hoursOffset,
- unsigned int minutesOffset)
-{
- return new(nothrow) Date(year, month, day, hour, minute,
- second, sign, hoursOffset, minutesOffset);
-}
-
-
-/**
- * Creates a date from a string.
- *
- * @param date a string representing the date.
- *
- * @return pointer to the newly created Date_t structure.
- *
- * @note the string should be in W3CDTF format
- * YYYY-MM-DDThh:mm:ssTZD (eg 1997-07-16T19:20:30+01:00)
- * where TZD is the time zone designator.
- */
-LIBSBML_EXTERN
-Date_t *
-Date_createFromString (const char * date)
-{
- if (date == NULL ) return NULL;
- return new(nothrow) Date(date);
-}
-
-
-/**
- * Destroys this Date.
- *
- * @param date Date_t structure to be freed.
- */
-LIBSBML_EXTERN
-void
-Date_free(Date_t * date)
-{
- delete static_cast<Date*>(date);
-}
-
-
-/**
- * Creates a deep copy of the given Date_t structure
- *
- * @param date the Date_t structure to be copied
- *
- * @return a (deep) copy of the given Date_t structure.
- */
-LIBSBML_EXTERN
-Date_t *
-Date_clone (const Date_t* date)
-{
- if (date == NULL ) return NULL;
- return static_cast<Date*>( date->clone() );
-}
-
-
-/**
- * Returns the Date as a string.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the date as a string.
- */
-LIBSBML_EXTERN
-const char *
-Date_getDateAsString(Date_t * date)
-{
- if (date == NULL) return NULL;
- return date->getDateAsString().c_str();
-}
-
-
-/**
- * Returns the year from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the year from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getYear(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getYear();
-}
-
-
-/**
- * Returns the month from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the month from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getMonth(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getMonth();
-}
-
-
-/**
- * Returns the day from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the day from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getDay(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getDay();
-}
-
-
-/**
- * Returns the hour from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the hour from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getHour(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getHour();
-}
-
-
-/**
- * Returns the minute from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the minute from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getMinute(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getMinute();
-}
-
-
-/**
- * Returns the seconds from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the seconds from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getSecond(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getSecond();
-}
-
-
-/**
- * Returns the sign of the offset from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the sign of the offset from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getSignOffset(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getSignOffset();
-}
-
-
-/**
- * Returns the hours of the offset from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the hours of the offset from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getHoursOffset(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getHoursOffset();
-}
-
-
-/**
- * Returns the minutes of the offset from this Date.
- *
- * @param date the Date_t structure to be queried
- *
- * @return the minutes of the offset from this Date.
- */
-LIBSBML_EXTERN
-unsigned int
-Date_getMinutesOffset(Date_t * date)
-{
- if (date == NULL) return SBML_INT_MAX;
- return date->getMinutesOffset();
-}
-
-
-/**
- * Sets the value of the year checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the year to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setYear(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setYear(value);
-}
-
-
-/**
- * Sets the value of the month checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the month to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setMonth(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setMonth(value);
-}
-
-
-/**
- * Sets the value of the day checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the day to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setDay(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setDay(value);
-}
-
-
-/**
- * Sets the value of the hour checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the hour to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT;
- */
-LIBSBML_EXTERN
-int
-Date_setHour(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setHour(value);
-}
-
-
-/**
- * Sets the value of the minute checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the minute to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setMinute(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setMinute(value);
-}
-
-
-/**
- * Sets the value of the second checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the second to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setSecond(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setSecond(value);
-}
-
-
-/**
- * Sets the value of the offset sign checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the sign of the
- * offset to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setSignOffset(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setSignOffset(value);
-}
-
-
-/**
- * Sets the value of the offset hour checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the hours of the
- * offset to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setHoursOffset(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setHoursOffset(value);
-}
-
-
-/**
- * Sets the value of the offset minutes checking appropriateness.
- *
- * @param date the Date_t structure to be set
- * @param value an unsigned int representing the minutes of the
- * offset to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setMinutesOffset(Date_t * date, unsigned int value)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return date->setMinutesOffset(value);
-}
-
-/**
- * Sets the value of the date from a string.
- *
- * @param date the Date_t structure to be set
- * @param str string representing the date to set.
- *
- * @return integer value indicating success/failure of the
- * function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
- * returned by this function are:
- * @li LIBSBML_OPERATION_SUCCESS
- * @li LIBSBML_INVALID_ATTRIBUTE_VALUE
- * @li LIBSBML_INVALID_OBJECT
- */
-LIBSBML_EXTERN
-int
-Date_setDateAsString(Date_t * date, const char *str)
-{
- if (date == NULL) return LIBSBML_INVALID_OBJECT;
- return (str == NULL) ? date->setDateAsString("") :
- date->setDateAsString(str);
-}
-
-
-LIBSBML_EXTERN
-int
-Date_representsValidDate(Date_t *date)
-{
- if (date == NULL) return (int)false;
- return static_cast<int> (date->representsValidDate());
-}
-
-
-LIBSBML_CPP_NAMESPACE_END
-
+/**
+ * @file Date.cpp
+ * @brief Date I/O
+ * @author Sarah Keating
+ *
+ * Copyright (C) 2009-2012 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is
+ * provided in the file named "LICENSE.txt" included with this software
+ * distribution. It is also available online at
+ * http://sbml.org/software/libsbml/license.html
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this library; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ */
+
+
+#include <sbml/annotation/Date.h>
+#include <sbml/common/common.h>
+#include <sbml/SBase.h>
+#include <cstdio>
+
+/** @cond doxygen-ignored */
+
+using namespace std;
+
+/** @endcond */
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+/*
+ * creates a date from the individual fields entered as numbers
+ */
+Date::Date(unsigned int year, unsigned int month,
+ unsigned int day, unsigned int hour,
+ unsigned int minute, unsigned int second,
+ unsigned int sign, unsigned int hoursOffset,
+ unsigned int minutesOffset) :
+ mHasBeenModified (false)
+{
+ mYear = year;
+ mMonth = month;
+ mDay = day;
+ mHour = hour;
+ mMinute = minute;
+ mSecond = second;
+
+ mSignOffset = sign;
+ mHoursOffset = hoursOffset;
+ mMinutesOffset = minutesOffset;;
+
+ parseDateNumbersToString();
+}
+
+
+/*
+ * creates a date from a string
+ */
+Date::Date (const std::string& date) :
+ mHasBeenModified (false)
+{
+ if (&(date) == NULL)
+ mDate = "";
+ else
+ mDate = date;
+
+ parseDateStringToNumbers();
+ parseDateNumbersToString();
+}
+
+Date::~Date() {}
+
+/*
+ * Copy constructor.
+ */
+Date::Date(const Date& orig)
+{
+ if (&orig == NULL)
+ {
+ throw SBMLConstructorException("Null argument to copy constructor");
+ }
+ else
+ {
+ mYear = orig.mYear;
+ mMonth = orig.mMonth;
+ mDay = orig.mDay;
+ mHour = orig.mHour;
+ mMinute = orig.mMinute;
+ mSecond = orig.mSecond;
+
+ mSignOffset = orig.mSignOffset;
+ mHoursOffset = orig.mHoursOffset;
+ mMinutesOffset = orig.mMinutesOffset;;
+
+ mDate = orig.mDate;
+
+ mHasBeenModified = orig.mHasBeenModified;
+ }
+}
+
+/*
+ * Assignment operator
+ */
+Date& Date::operator=(const Date& rhs)
+{
+ if (&rhs == NULL)
+ {
+ throw SBMLConstructorException("Null argument to assignment operator");
+ }
+ else if(&rhs!=this)
+ {
+ mYear = rhs.mYear;
+ mMonth = rhs.mMonth;
+ mDay = rhs.mDay;
+ mHour = rhs.mHour;
+ mMinute = rhs.mMinute;
+ mSecond = rhs.mSecond;
+
+ mSignOffset = rhs.mSignOffset;
+ mHoursOffset = rhs.mHoursOffset;
+ mMinutesOffset = rhs.mMinutesOffset;;
+
+ mDate = rhs.mDate;
+
+ mHasBeenModified = rhs.mHasBeenModified;
+ }
+
+ return *this;
+}
+
+/*
+ * @return a (deep) copy of this Date.
+ */
+Date* Date::clone () const
+{
+ return new Date(*this);
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setYear (unsigned int year)
+{
+ if (year <1000 || year > 9999)
+ {
+ mYear = 2000;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mYear = year;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setMonth (unsigned int month)
+{
+ if (month < 1 || month > 12)
+ {
+ mMonth = 1;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mMonth = month;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setDay (unsigned int day)
+{
+ bool validDay = true;
+ if (day < 1 || day > 31)
+ {
+ validDay = false;
+ }
+ else
+ {
+ switch (mMonth)
+ {
+ case 4:
+ case 6:
+ case 9:
+ case 11:
+ if (day > 30) validDay = false;
+ break;
+ case 2:
+ if (mYear % 4 == 0)
+ {
+ if (day > 29) validDay = false;
+ }
+ else
+ {
+ if (day > 28) validDay = false;
+ }
+ break;
+ case 1:
+ case 3:
+ case 5:
+ case 7:
+ case 8:
+ case 10:
+ case 12:
+ default:
+ break;
+ }
+ }
+
+ if (!validDay)
+ {
+ mDay = 1;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mDay = day;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setHour (unsigned int hour)
+{
+ if (/*hour < 0 ||*/ hour > 23)
+ {
+ mHour = 0;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mHour = hour;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setMinute (unsigned int minute)
+{
+ if (/*minute < 0 ||*/ minute > 59)
+ {
+ mMinute = 0;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mMinute = minute;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setSecond (unsigned int second)
+{
+ if (/*second < 0 ||*/ second > 59)
+ {
+ mSecond = 0;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mSecond = second;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setSignOffset (unsigned int sign)
+{
+ if (/*sign < 0 ||*/ sign > 1)
+ {
+ mSignOffset = 0;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mSignOffset = sign;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setHoursOffset (unsigned int hour)
+{
+ if (/*hour < 0 ||*/ hour > 12)
+ {
+ mHoursOffset = 0;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mHoursOffset = hour;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the year checking appropriateness
+ */
+int
+Date::setMinutesOffset (unsigned int minute)
+{
+ if (/*minute < 0 ||*/ minute > 59)
+ {
+ mMinutesOffset = 0;
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ mMinutesOffset = minute;
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+/*
+ * sets the value of the date string checking appropriateness
+ */
+int
+Date::setDateAsString (const std::string& date)
+{
+ /* if date is NULL consider this as resetting
+ * the date completely
+ */
+
+ if (&(date) == NULL)
+ {
+ mDate = "";
+ // revert to default numbers
+ // rewrite date string to reflect the defaults
+ parseDateStringToNumbers();
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else if (date.empty())
+ {
+ mDate = "";
+ // revert to default numbers
+ // rewrite date string to reflect the defaults
+ parseDateStringToNumbers();
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+
+ /* Date must be: YYYY-MM-DDThh:mm:ssTZD
+ * where TZD is either Z or +/-HH:MM
+ */
+ mDate = date;
+
+ if (!representsValidDate())
+ {
+ mDate = "";
+ parseDateNumbersToString();
+ return LIBSBML_INVALID_ATTRIBUTE_VALUE;
+ }
+ else
+ {
+ parseDateStringToNumbers();
+ parseDateNumbersToString();
+ mHasBeenModified = true;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+}
+
+
+
+/** @cond doxygen-libsbml-internal */
+/*
+ * returns the date in numbers as a W3CDTF string
+ */
+void
+Date::parseDateNumbersToString()
+{
+ char cdate[10];
+
+ if (mMonth < 10)
+ sprintf(cdate, "%u-0%u-", mYear, mMonth);
+ else
+ sprintf(cdate, "%u-%u-", mYear, mMonth);
+ mDate = cdate;
+
+ if (mDay < 10)
+ sprintf(cdate, "0%uT", mDay);
+ else
+ sprint...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-22 16:29:54
|
Revision: 16253
http://sbml.svn.sourceforge.net/sbml/?rev=16253&view=rev
Author: sarahkeating
Date: 2012-08-22 16:29:46 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/L3Parser/src/sbml/xml/ExpatAttributes.h
branches/L3Parser/src/sbml/xml/ExpatParser.h
branches/L3Parser/src/sbml/xml/LibXMLParser.h
branches/L3Parser/src/sbml/xml/XMLAttributes.cpp
branches/L3Parser/src/sbml/xml/XMLAttributes.h
branches/L3Parser/src/sbml/xml/XMLConstructorException.cpp
branches/L3Parser/src/sbml/xml/XMLConstructorException.h
branches/L3Parser/src/sbml/xml/XMLError.cpp
branches/L3Parser/src/sbml/xml/XMLError.h
branches/L3Parser/src/sbml/xml/XMLErrorLog.h
branches/L3Parser/src/sbml/xml/XMLExtern.h
branches/L3Parser/src/sbml/xml/XMLHandler.h
branches/L3Parser/src/sbml/xml/XMLInputStream.h
branches/L3Parser/src/sbml/xml/XMLNamespaces.cpp
branches/L3Parser/src/sbml/xml/XMLNamespaces.h
branches/L3Parser/src/sbml/xml/XMLNode.cpp
branches/L3Parser/src/sbml/xml/XMLNode.h
branches/L3Parser/src/sbml/xml/XMLOutputStream.h
branches/L3Parser/src/sbml/xml/XMLParser.h
branches/L3Parser/src/sbml/xml/XMLToken.cpp
branches/L3Parser/src/sbml/xml/XMLToken.h
branches/L3Parser/src/sbml/xml/XMLTokenizer.h
branches/L3Parser/src/sbml/xml/XMLTriple.h
branches/L3Parser/src/sbml/xml/XercesParser.h
branches/L3Parser/src/sbml/xml/test/Makefile.in
branches/L3Parser/src/sbml/xml/test/TestXMLAttributesC.c
branches/L3Parser/src/sbml/xml/test/TestXMLErrorC.c
branches/L3Parser/src/sbml/xml/test/TestXMLErrorLog.c
branches/L3Parser/src/sbml/xml/test/TestXMLInputStream.c
branches/L3Parser/src/sbml/xml/test/TestXMLNamespaces.c
branches/L3Parser/src/sbml/xml/test/TestXMLNode_newSetters.c
branches/L3Parser/src/sbml/xml/test/TestXMLOutputStream.c
branches/L3Parser/src/sbml/xml/test/TestXMLToken.c
branches/L3Parser/src/sbml/xml/test/TestXMLToken_newSetters.c
branches/L3Parser/src/sbml/xml/test/TestXMLTriple.c
Property Changed:
----------------
branches/L3Parser/src/sbml/xml/
Property changes on: branches/L3Parser/src/sbml/xml
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/libsbml-4/src/sbml/xml:9056-10118
/branches/libsbml-5-conversion/src/sbml/xml:14155-14227
/trunk/libsbml/src/sbml/xml:15528-16252
Modified: branches/L3Parser/src/sbml/xml/ExpatAttributes.h
===================================================================
--- branches/L3Parser/src/sbml/xml/ExpatAttributes.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/ExpatAttributes.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -48,7 +48,7 @@
* The Expat attribute names are assumed to be in namespace triplet form
* separated by sepchar.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
ExpatAttributes (const XML_Char** attrs,
const XML_Char* elementName,
Modified: branches/L3Parser/src/sbml/xml/ExpatParser.h
===================================================================
--- branches/L3Parser/src/sbml/xml/ExpatParser.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/ExpatParser.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -140,7 +140,7 @@
/**
* Log or otherwise report the given error.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
void reportError ( const XMLErrorCode_t code
, const std::string& extraMsg = ""
Modified: branches/L3Parser/src/sbml/xml/LibXMLParser.h
===================================================================
--- branches/L3Parser/src/sbml/xml/LibXMLParser.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/LibXMLParser.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -141,7 +141,7 @@
/**
* Log or otherwise report the given error.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
void reportError ( const XMLErrorCode_t code
Modified: branches/L3Parser/src/sbml/xml/XMLAttributes.cpp
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLAttributes.cpp 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLAttributes.cpp 2012-08-22 16:29:46 UTC (rev 16253)
@@ -1332,7 +1332,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -1363,7 +1363,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -1393,7 +1393,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -1438,7 +1438,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -1461,7 +1461,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -1484,7 +1484,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -1514,7 +1514,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -1538,7 +1538,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -1560,7 +1560,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
Modified: branches/L3Parser/src/sbml/xml/XMLAttributes.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLAttributes.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLAttributes.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -45,7 +45,7 @@
* callers, those classes will throw an XMLConstructorException. @if cpp
* Callers can use the standard C++ <code>std::exception</code> method
* <code>what()</code> to extract the diagnostic message stored with the
- * exception.@endif
+ * exception.@endif@~
* <p>
* In languages that don't have an exception mechanism (e.g., C), the
* constructors generally try to return an error code instead of throwing
@@ -100,7 +100,7 @@
*
* @p orig the XMLAttributes object to copy.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
XMLAttributes(const XMLAttributes& orig);
@@ -112,7 +112,7 @@
* @param rhs The XMLAttributes object whose values are used as the basis
* of the assignment.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
XMLAttributes& operator=(const XMLAttributes& rhs);
@@ -143,7 +143,7 @@
* @note if local name with the same namespace URI already exists in this
* attribute set, its value and prefix will be replaced.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
int add ( const std::string& name
, const std::string& value
@@ -522,7 +522,7 @@
* be used to read a value for an attribute name with a prefix and
* namespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const std::string& name
, bool& value
@@ -554,7 +554,7 @@
*
* @returns @c true if the attribute was read into value, @c false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const XMLTriple& triple
, bool& value
@@ -592,7 +592,7 @@
* should be used to read a value for an attribute name with a prefix and
* namespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const std::string& name
, double& value
@@ -624,7 +624,7 @@
*
* @returns @c true if the attribute was read into value, @c false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const XMLTriple& triple
, double& value
@@ -661,7 +661,7 @@
* be used to read a value for an attribute name with a prefix and
* namespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const std::string& name
, long& value
@@ -693,7 +693,7 @@
*
* @returns @c true if the attribute was read into value, @c false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const XMLTriple& triple
, long& value
@@ -730,7 +730,7 @@
* be used to read a value for an attribute name with a prefix and
* namespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const std::string& name
, int& value
@@ -762,7 +762,7 @@
*
* @returns @c true if the attribute was read into value, @c false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const XMLTriple& triple
, int& value
@@ -799,7 +799,7 @@
* ...) const should be used to read a value for an attribute name with a
* prefix and namespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const std::string& name
, unsigned int& value
@@ -831,7 +831,7 @@
*
* @returns @c true if the attribute was read into value, @c false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const XMLTriple& triple
, unsigned int& value
@@ -862,7 +862,7 @@
* should be used to read a value for an attribute name with a prefix and
* namespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const std::string& name
, std::string& value
@@ -888,7 +888,7 @@
*
* @returns @c true if the attribute was read into value, @c false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool readInto ( const XMLTriple& triple
, std::string& value
Modified: branches/L3Parser/src/sbml/xml/XMLConstructorException.cpp
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLConstructorException.cpp 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLConstructorException.cpp 2012-08-22 16:29:46 UTC (rev 16253)
@@ -48,7 +48,3 @@
/** @endcond */
LIBSBML_CPP_NAMESPACE_END
-
-
-/** @endcond */
-
Modified: branches/L3Parser/src/sbml/xml/XMLConstructorException.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLConstructorException.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLConstructorException.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -1,6 +1,6 @@
/**
- * @file XMLConstuctorException.h
- * @brief XMLConstuctorException an exception thrown by XML classes
+ * @file XMLConstructorException.h
+ * @brief XMLConstructorException an exception thrown by XML classes
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
@@ -37,7 +37,7 @@
* callers, those classes will throw an XMLConstructorException. @if cpp
* Callers can use the standard C++ <code>std::exception</code> method
* <code>what()</code> to extract the diagnostic message stored with the
- * exception.@endif
+ * exception.@endif@~
* <p>
* In languages that don't have an exception mechanism (e.g., C), the
* constructors generally try to return an error code instead of throwing
Modified: branches/L3Parser/src/sbml/xml/XMLError.cpp
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLError.cpp 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLError.cpp 2012-08-22 16:29:46 UTC (rev 16253)
@@ -486,7 +486,7 @@
/*
* @return the id of this XMLError.
*/
-const unsigned int
+unsigned int
XMLError::getErrorId () const
{
return mErrorId;
Modified: branches/L3Parser/src/sbml/xml/XMLError.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLError.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLError.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -53,7 +53,7 @@
* changing their behavior if desired. @else This
* error identifier is one of the constants listed in the next section below.
* Applications can use the error identifiers as a means of recognizing the
- * error encountered and changing their behavior if desired. @endif
+ * error encountered and changing their behavior if desired. @endif@~
*
* Integer error codes are useful for software, but not so much for telling
* humans what happened. For this reason, XMLError also provides two text
@@ -67,7 +67,7 @@
* Each XMLError object also contains a category code; its value may be
* retrieved using the method XMLError::getCategory(). Category values
* are drawn from @if clike the enumeration <a class="el" href="#XMLErrorCategory_t">XMLErrorCategory_t</a> described below.@else a
- * set of constants whose names begin with the characters @c LIBSBML_CAT_, described below.@endif Categories
+ * set of constants whose names begin with the characters @c LIBSBML_CAT_, described below.@endif@~ Categories
* are used by libSBML to provide more information to calling programs about
* the nature of a given error.
*
@@ -122,7 +122,7 @@
* The error and warning codes returned by the XML layer in libSBML are
* listed in the table below. In the libSBML C# language interface,
* these error identifiers are currently implemented as static integer
- * constants defined in the interface class @link libsbmlcs.libsbml@endlink.@endif
+ * constants defined in the interface class @link libsbmlcs.libsbml@endlink.@endif@~
*
* <center>
* <table cellspacing="1" cellpadding="1" border="0" class="text-table width80 normal-font alt-row-colors">
@@ -225,7 +225,7 @@
* As is the case with the error codes, in the libSBML C# language
* interface, the category identifiers are currently implemented as static
* integer constants defined in the interface
- * class @link libsbmlcs.libsbml@endlink. @endif
+ * class @link libsbmlcs.libsbml@endlink. @endif@~
*
* <center>
* <table width="90%" cellspacing="1" cellpadding="1" border="0" class="text-table width80 normal-font alt-row-colors">
@@ -291,7 +291,7 @@
* As is the case with the category codes, in the libSBML C# language
* interface, these severity codes are currently
* implemented as static integer constants defined in the interface class
- * @link libsbmlcs.libsbml@endlink.@endif
+ * @link libsbmlcs.libsbml@endlink.@endif@~
*
* <center>
* <table width="90%" cellspacing="1" cellpadding="1" border="0" class="text-table width80 normal-font alt-row-colors">
@@ -552,7 +552,7 @@
* integer constants in the file
* "libsbmlConstants.java". See the <a class="el"
* href="#XMLErrorCode_t">top of this documentation</a> for a table
- * listing the possible values and their meanings. @endif The argument @p
+ * listing the possible values and their meanings. @endif@~ The argument @p
* errorId to this constructor @em can be (but does not have to be) a
* value from this @if clike enumeration. If it is a value
* from <a class="el" href="#XMLErrorCode_t">XMLErrorCode_t</a>, the
@@ -571,7 +571,7 @@
* passed in the argument @p details to this constructor. In addition,
* all the predefined error identifiers have associated values for the @p
* severity and @p category codes, and these fields are filled-in as
- * well. @endif
+ * well. @endif@~
*
* If the error identifier @p errorId is a number greater than 9999, this
* constructor assumes that the error was generated from another part of
@@ -608,7 +608,7 @@
* codes, callers do not need to fill in @p severity and @p category in a
* call to this constructor. Conversely, if @p errorId is not an existing
* XML-level error code, callers can use other values for @p severity and
- * @p category. @endif
+ * @p category. @endif@~
*
* @param errorId an unsigned int, the identification number of the error.
*
@@ -627,7 +627,7 @@
* @param category an integer indicating the category to which the error
* belongs.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLError
(
@@ -645,7 +645,7 @@
*
* @p orig the XMLError object to copy.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
XMLError(const XMLError& orig);
@@ -657,7 +657,7 @@
* @param rhs The XMLError object whose values are used as the basis
* of the assignment.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
XMLError& operator=(const XMLError& rhs);
@@ -679,7 +679,7 @@
* @see getCategory()
* @see getSeverity()
*/
- const unsigned int getErrorId () const;
+ unsigned int getErrorId () const;
/**
@@ -854,7 +854,7 @@
* object (via XMLError::getSeverity()) and then comparing it to the
* value @link XMLErrorSeverity_t#LIBSBML_SEV_INFO LIBSBML_SEV_INFO@endlink from the
* @if clike enumeration #XMLErrorSeverity_t. @else set of predefined
- * severity codes.@endif
+ * severity codes.@endif@~
*
* @return @c true if this XMLError is for informational purposes only,
* @c false otherwise.
@@ -874,7 +874,7 @@
* object (via XMLError::getSeverity()) and then comparing it to the
* value @link XMLErrorSeverity_t#LIBSBML_SEV_WARNING LIBSBML_SEV_WARNING@endlink from the
* @if clike enumeration #XMLErrorSeverity_t. @else set of predefined
- * severity codes.@endif
+ * severity codes.@endif@~
*
* @return @c true if this error is a warning, @c false otherwise.
*
@@ -893,7 +893,7 @@
* object (via XMLError::getSeverity()) and then comparing it to the
* value @link XMLErrorSeverity_t#LIBSBML_SEV_ERROR LIBSBML_SEV_ERROR@endlink from the
* @if clike enumeration #XMLErrorSeverity_t. @else set of predefined
- * severity codes.@endif
+ * severity codes.@endif@~
*
* @return @c true if this error is an error, @c false otherwise.
*
@@ -911,7 +911,7 @@
* This is equivalent to obtaining the severity code from an XMLError
* object (via XMLError::getSeverity()) and then comparing it to the
* value @link XMLErrorSeverity_t#LIBSBML_SEV_FATAL LIBSBML_SEV_FATAL@endlink from the
- * @if clike enumeration #XMLErrorSeverity_t. @else set of predefined severity codes.@endif
+ * @if clike enumeration #XMLErrorSeverity_t. @else set of predefined severity codes.@endif@~
*
* @return @c true if this error is a fatal error, @c false otherwise.
*
@@ -929,7 +929,7 @@
* This is equivalent to obtaining the category identifier from an
* XMLError object (via XMLError::getCategory()) and then comparing it to
* the value @link XMLErrorCategory_t#LIBSBML_CAT_INTERNAL LIBSBML_CAT_INTERNAL@endlink from the
- * @if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif
+ * @if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif@~
*
* @return @c true or @c false
*
@@ -946,7 +946,7 @@
* This is equivalent to obtaining the category identifier from an
* XMLError object (via XMLError::getCategory()) and then comparing it to
* the value @link XMLErrorCategory_t#LIBSBML_CAT_SYSTEM LIBSBML_CAT_SYSTEM@endlink from the
- * @if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif
+ * @if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif@~
*
* @return @c true or @c false
*
@@ -964,7 +964,7 @@
* This is equivalent to obtaining the category identifier from an
* XMLError object (via XMLError::getCategory()) and then comparing it to
* the value @link XMLErrorCategory_t#LIBSBML_CAT_XML LIBSBML_CAT_XML@endlink from the
- * @if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif
+ * @if clike enumeration #XMLErrorCategory_t. @else set of predefined category codes.@endif@~
*
* @return @c true or @c false
*
@@ -982,7 +982,7 @@
* This is equivalent to obtaining the error identifier from an
* XMLError object (via XMLError::getErrorId()) and then comparing it to
* the value XMLUnknownError or UnknownError from the
- * @if clike enumeration #XMLErrorCode_t. @else set of predefined error codes.@endif
+ * @if clike enumeration #XMLErrorCode_t. @else set of predefined error codes.@endif@~
*
* @return @c true or @c false
*/
@@ -1026,7 +1026,7 @@
* @param code the error code whose message is sought; it must be a
* predefined value from @if clike <a class="el" href="#XMLErrorCode_t">
* XMLErrorCode_t</a>. @else <a class="el" href="#XMLErrorCode_t">the set
- * of predefined error identifiers</a>.@endif
+ * of predefined error identifiers</a>.@endif@~
*/
static const std::string getStandardMessage (const int code);
Modified: branches/L3Parser/src/sbml/xml/XMLErrorLog.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLErrorLog.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLErrorLog.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -40,7 +40,7 @@
* mismatched tags or other problems).
*
* A typical approach for using this error log is to first use
- * @if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif
+ * @if java XMLErrorLog::getNumErrors()@else getNumErrors()@endif@~
* to inquire how many XMLError object instances it contains, and then to
* iterate over the list of objects one at a time using
* getError(unsigned int n) const. Indexing in the list begins at 0.
@@ -160,7 +160,7 @@
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
- * @li @link OperationReturnValues_t#@link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
int setParser (const XMLParser* p);
@@ -200,7 +200,7 @@
* @param stream the ostream or ostringstream object indicating where
* the output should be printed.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
void printErrors (std::ostream& stream = std::cerr) const;
Modified: branches/L3Parser/src/sbml/xml/XMLExtern.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLExtern.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLExtern.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -49,7 +49,8 @@
# define LIBLAX_EXTERN
# endif
-
+#undef BEGIN_C_DECLS
+#undef END_C_DECLS
#if defined(__cplusplus)
# define BEGIN_C_DECLS extern "C" {
# define END_C_DECLS }
Modified: branches/L3Parser/src/sbml/xml/XMLHandler.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLHandler.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLHandler.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -28,7 +28,7 @@
* @class XMLHandler
* @brief Class providing a unified interface to different XML parsers.
*
- * @if notclike @internal @endif
+ * @if notclike @internal @endif@~
*/
#ifndef XMLHandler_h
Modified: branches/L3Parser/src/sbml/xml/XMLInputStream.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLInputStream.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLInputStream.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -27,7 +27,7 @@
*
* @class XMLInputStream
*
- * @if notclike @internal @endif
+ * @if notclike @internal @endif@~
*/
#ifndef XMLInputStream_h
@@ -72,7 +72,7 @@
*
* @p errorLog the XMLErrorLog object to use.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLInputStream ( const char* content
, bool isFile = true
@@ -160,10 +160,10 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
- * @li @link OperationReturnValues_t#@link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
int setErrorLog (XMLErrorLog* log);
Modified: branches/L3Parser/src/sbml/xml/XMLNamespaces.cpp
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLNamespaces.cpp 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLNamespaces.cpp 2012-08-22 16:29:46 UTC (rev 16253)
@@ -519,7 +519,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -542,7 +542,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -563,7 +563,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INDEX_EXCEEDS_SIZE
@@ -585,7 +585,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
Modified: branches/L3Parser/src/sbml/xml/XMLNamespaces.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLNamespaces.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLNamespaces.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -93,7 +93,7 @@
*
* @param orig the XMLNamespaces object to copy
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
XMLNamespaces(const XMLNamespaces& orig);
@@ -105,7 +105,7 @@
* @param rhs The XMLNamespaces object whose values are used as the basis
* of the assignment.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
XMLNamespaces& operator=(const XMLNamespaces& rhs);
@@ -148,7 +148,7 @@
* @li @link OperationReturnValues_t#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT @endlink
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
int add (const std::string& uri, const std::string& prefix = "");
@@ -321,7 +321,7 @@
* prefix, or an empty string if no such prefix-and-URI pair exists
* in this XMLNamespaces object
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*
* @see getURI()
*/
Modified: branches/L3Parser/src/sbml/xml/XMLNode.cpp
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLNode.cpp 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLNode.cpp 2012-08-22 16:29:46 UTC (rev 16253)
@@ -501,9 +501,25 @@
if (children > 0)
{
- for (unsigned int c = 0; c < children; ++c) stream << getChild(c);
+ bool haveTextNode = false;
+ for (unsigned int c = 0; c < children; ++c)
+ {
+ const XMLNode& current = getChild(c);
+ stream << current;
+ haveTextNode |= current.isText();
+ }
+
if (!mTriple.isEmpty())
+ {
+ // edge case ... we have an element with a couple of elements, and
+ // one is a text node (ugly!) in this case we can get a hanging
+ // indent ... so we downindent ...
+ if (children > 1 && haveTextNode)
+ {
+ stream.downIndent();
+ }
stream.endElement( mTriple );
+ }
}
else if ( isStart() && !isEnd() )
{
@@ -784,7 +800,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -848,7 +864,7 @@
* @param n an integer the index of the resource to be deleted
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_OBJECT
@@ -887,7 +903,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1118,7 +1134,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1146,7 +1162,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1178,7 +1194,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1215,7 +1231,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1240,7 +1256,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1267,7 +1283,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1294,7 +1310,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1320,7 +1336,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1344,7 +1360,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1744,7 +1760,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1773,7 +1789,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1798,7 +1814,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1823,7 +1839,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1848,7 +1864,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2252,7 +2268,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2274,7 +2290,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2296,7 +2312,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
Modified: branches/L3Parser/src/sbml/xml/XMLNode.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLNode.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLNode.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -134,7 +134,7 @@
else:
# None is not a dummy node.
@endverbatim
- * @endif
+ * @endif@~
*/
#ifndef XMLNode_h
@@ -185,7 +185,7 @@
* @param line an unsigned int, the line number (default = 0).
* @param column an unsigned int, the column number (default = 0).
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLNode ( const XMLTriple& triple
, const XMLAttributes& attributes
@@ -202,7 +202,7 @@
* @param line an unsigned int, the line number (default = 0).
* @param column an unsigned int, the column number (default = 0).
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLNode ( const XMLTriple& triple
, const XMLAttributes& attributes
@@ -217,7 +217,7 @@
* @param line an unsigned int, the line number (default = 0).
* @param column an unsigned int, the column number (default = 0).
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLNode ( const XMLTriple& triple
, const unsigned int line = 0
@@ -231,7 +231,7 @@
* @param line an unsigned int, the line number (default = 0).
* @param column an unsigned int, the column number (default = 0).
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLNode ( const std::string& chars
, const unsigned int line = 0
@@ -263,7 +263,7 @@
*
* @param orig the XMLNode instance to copy.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p orig is @c NULL.
*/
XMLNode(const XMLNode& orig);
@@ -275,7 +275,7 @@
* @param rhs The XMLNode object whose values are used as the basis
* of the assignment.
*
- * @throws @if python ValueError @else XMLConstructorException @endif
+ * @throws @if python ValueError @else XMLConstructorException @endif@~
* Thrown if the argument @p rhs is @c NULL.
*/
XMLNode& operator=(const XMLNode& rhs);
@@ -495,7 +495,7 @@
* @return a XMLNode which is converted from string @p xmlstr. If the
* conversion failed, this method returns @c NULL.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
static XMLNode* convertStringToXMLNode(const std::string& xmlstr,
const XMLNamespaces* xmlns = NULL);
Modified: branches/L3Parser/src/sbml/xml/XMLOutputStream.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLOutputStream.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLOutputStream.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -27,7 +27,7 @@
*
* @class XMLOutputStream
*
- * @if notclike @internal @endif
+ * @if notclike @internal @endif@~
*/
#ifndef XMLOutputStream_h
@@ -58,7 +58,7 @@
/**
* Creates a new XMLOutputStream that wraps stream.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLOutputStream ( std::ostream& stream
, const std::string& encoding = "UTF-8"
@@ -318,7 +318,7 @@
/**
* Outputs indentation whitespace.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
void writeIndent (bool isEnd = false);
@@ -408,7 +408,7 @@
/**
* Creates a new XMLOutputStream that wraps stream.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLOutputStringStream ( std::ostringstream& stream
, const std::string& encoding = "UTF-8"
@@ -431,7 +431,7 @@
/**
* Creates a new XMLOutputStream that wraps stream.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLOutputFileStream ( std::ofstream& stream
, const std::string& encoding = "UTF-8"
Modified: branches/L3Parser/src/sbml/xml/XMLParser.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLParser.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLParser.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -30,7 +30,7 @@
* @class XMLParser
* @brief Class providing a unified interface to different XML parsers.
*
- * @if notclike @internal @endif
+ * @if notclike @internal @endif@~
*/
#ifndef XMLParser_h
@@ -64,7 +64,7 @@
* If the XML compatibility layer has been linked against only a single
* XML library, the library parameter is ignored.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
static XMLParser* create ( XMLHandler& handler
, const std::string library = "" );
@@ -85,7 +85,7 @@
*
* @return true if the parse was successful, false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
virtual bool parse (const char* content, bool isFile = true) = 0;
@@ -106,7 +106,7 @@
* @return true if the first step of the progressive parse was
* successful, false otherwise.
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
virtual bool parseFirst (const char* content, bool isFile = true) = 0;
@@ -153,7 +153,7 @@
* function. The possible values
* returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS @endlink
- * @li @link OperationReturnValues_t#@link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink @endlink
+ * @li @link OperationReturnValues_t#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED @endlink
*/
int setErrorLog (XMLErrorLog* log);
Modified: branches/L3Parser/src/sbml/xml/XMLToken.cpp
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLToken.cpp 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLToken.cpp 2012-08-22 16:29:46 UTC (rev 16253)
@@ -342,7 +342,7 @@
* @note if local name with the same namespace URI already exists in the
* attribute set, its value and prefix will be replaced.
*
- * @docnote The native C++ implementation of this method defines a
+ * The native C++ implementation of this method defines a
* default argument value. In the documentation generated for different
* libSBML language bindings, you may or may not see corresponding
* arguments in the method declarations. For example, in Java, a default
@@ -487,7 +487,7 @@
* @return the index of an attribute with the given local name and namespace URI,
* or -1 if not present.
*
- * @docnote The native C++ implementation of this method defines a
+ * The native C++ implementation of this method defines a
* default argument value. In the documentation generated for different
* libSBML language bindings, you may or may not see corresponding
* arguments in the method declarations. For example, in Java, a default
@@ -645,7 +645,7 @@
* returned.
* Use hasAttr(name, uri) to test for attribute existence.
*
- * @docnote The native C++ implementation of this method defines a
+ * The native C++ implementation of this method defines a
* default argument value. In the documentation generated for different
* libSBML language bindings, you may or may not see corresponding
* arguments in the method declarations. For example, in Java, a default
@@ -711,17 +711,7 @@
* @return @c true if an attribute with the given local name and namespace
* URI exists in the attribute set in this XMLToken, @c false otherwise.
*
- * @docnote The native C++ implementation of this method defines a
- * default argument value. In the documentation generated for different
- * libSBML language bindings, you may or may not see corresponding
- * arguments in the method declarations. For example, in Java, a default
- * argument is handled by declaring two separate methods, with one of
- * them having the argument and the other one lacking the argument.
- * However, the libSBML documentation will be @em identical for both
- * methods. Consequently, if you are reading this and do not see an
- * argument even though one is described, please look for descriptions of
- * other variants of this method near where this one appears in the
- * documentation.
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
bool
XMLToken::hasAttr (const std::string name, const std::string uri) const
@@ -1420,7 +1410,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -1514,7 +1504,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1541,7 +1531,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1573,7 +1563,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1610,7 +1600,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1634,7 +1624,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1661,7 +1651,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1688,7 +1678,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1714,7 +1704,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -1738,7 +1728,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2133,7 +2123,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2163,7 +2153,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2188,7 +2178,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2213,7 +2203,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2238,7 +2228,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2481,7 +2471,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_INVALID_XML_OPERATION
@@ -2659,7 +2649,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2681,7 +2671,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
@@ -2703,7 +2693,7 @@
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
- * enumeration #OperationReturnValues_t. @endif The possible values
+ * enumeration #OperationReturnValues_t. @endif@~ The possible values
* returned by this function are:
* @li LIBSBML_OPERATION_SUCCESS
* @li LIBSBML_OPERATION_FAILED
Modified: branches/L3Parser/src/sbml/xml/XMLToken.h
===================================================================
--- branches/L3Parser/src/sbml/xml/XMLToken.h 2012-08-22 15:59:26 UTC (rev 16252)
+++ branches/L3Parser/src/sbml/xml/XMLToken.h 2012-08-22 16:29:46 UTC (rev 16253)
@@ -77,7 +77,7 @@
* @param line an unsigned int, the line number (default = 0).
* @param column an unsigned int, the column number (default = 0).
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLToken ( const XMLTriple& triple
, const XMLAttributes& attributes
@@ -94,7 +94,7 @@
* @param line an unsigned int, the line number (default = 0).
* @param column an unsigned int, the column number (default = 0).
*
- * @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
+ * @if notcpp @htmlinclude warn-default-args-in-docs.html @endif@~
*/
XMLToken ( const XMLTriple& triple
, const XMLAttributes& attributes
@@ -109,7 +109,7 @@
...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-22 15:59:42
|
Revision: 16252
http://sbml.svn.sourceforge.net/sbml/?rev=16252&view=rev
Author: sarahkeating
Date: 2012-08-22 15:59:26 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/L3Parser/Makefile.in
branches/L3Parser/configure
branches/L3Parser/layout-package.cmake
branches/L3Parser/src/CMakeLists.txt
branches/L3Parser/src/bindings/CMakeLists.txt
branches/L3Parser/src/bindings/Makefile.in
branches/L3Parser/src/bindings/csharp/CMakeLists.txt
branches/L3Parser/src/bindings/csharp/Makefile.in
branches/L3Parser/src/bindings/csharp/Properties/AssemblyInfo.cs
branches/L3Parser/src/bindings/csharp/Properties/AssemblyInfo.cs.in
branches/L3Parser/src/bindings/csharp/Properties/AssemblyInfoTR.cs
branches/L3Parser/src/bindings/csharp/TestRW.cs
branches/L3Parser/src/bindings/csharp/TestRunner.cs
branches/L3Parser/src/bindings/csharp/local-packages-layout.i
branches/L3Parser/src/bindings/csharp/test/annotation/TestCVTerms_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestDate_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestModelCreator_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestModelHistory_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestRDFAnnotation.cs
branches/L3Parser/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestCompartmentType_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestCompartment_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestEvent_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestL3KineticLaw.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestL3Species.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestModel.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestModel_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestParameter_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReaction_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReadFromFile6.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReadFromFile7.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestReadFromFile8.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestRequiredAttributes.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestRequiredElements.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSBMLConvertStrict.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSpeciesReference_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSpeciesType_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSpecies_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestUnitDefinition_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestUnit_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/xml/TestXMLNode_newSetters.cs
branches/L3Parser/src/bindings/csharp/test/xml/TestXMLToken.cs
branches/L3Parser/src/bindings/csharp/test/xml/TestXMLToken_newSetters.cs
branches/L3Parser/src/bindings/java/CMakeLists.txt
branches/L3Parser/src/bindings/java/Makefile.in
branches/L3Parser/src/bindings/java/local-packages-layout.i
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestRDFAnnotation.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartmentType_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestCompartment_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestEvent_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestInternalConsistencyChecks.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3KineticLaw.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3LocalParameter.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestL3Trigger.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestModel_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestParameter_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReaction_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile6.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile7.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestReadFromFile8.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestRequiredAttributes.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestRequiredElements.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSBase_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSpeciesReference_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSpeciesType_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSpecies_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestSyntaxChecker.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestUnitDefinition_newSetters.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestUnit_newSetters.java
branches/L3Parser/src/bindings/matlab/ConvertFormulaToMathML.m
branches/L3Parser/src/bindings/matlab/FindMatlab.cmake
branches/L3Parser/src/bindings/matlab/Makefile.in
branches/L3Parser/src/bindings/matlab/OutputSBML.c
branches/L3Parser/src/bindings/matlab/buildSBML.m
branches/L3Parser/src/bindings/matlab/installSBML.m
branches/L3Parser/src/bindings/matlab/isoctave.m
branches/L3Parser/src/bindings/matlab/test/Makefile.in
branches/L3Parser/src/bindings/matlab/test/testIsSBMLModel.m
branches/L3Parser/src/bindings/matlab/test/testReadFlags.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile1.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile10.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile11.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile12.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile13.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile14.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile15.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile2.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile3.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile4.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile5.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile6.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile7.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile8.m
branches/L3Parser/src/bindings/matlab/test/testReadFromFile9.m
branches/L3Parser/src/bindings/octave/.svnignore
branches/L3Parser/src/bindings/octave/Makefile.in
branches/L3Parser/src/bindings/octave/test/Makefile.in
branches/L3Parser/src/bindings/perl/CMakeLists.txt
branches/L3Parser/src/bindings/perl/Makefile.in
branches/L3Parser/src/bindings/perl/local-downcast-packages-layout.cpp
branches/L3Parser/src/bindings/perl/local-layout.i
branches/L3Parser/src/bindings/perl/local-packages.i.in
branches/L3Parser/src/bindings/perl/local.i
branches/L3Parser/src/bindings/perl/t/02__ReadFromFileL3.t
branches/L3Parser/src/bindings/perl/t/03__DowncastSBase.t
branches/L3Parser/src/bindings/perl/t/04__ListOf.t
branches/L3Parser/src/bindings/perl/t/05__AssignmentRule.t
branches/L3Parser/src/bindings/perl/t/05__Compartment.t
branches/L3Parser/src/bindings/perl/t/05__Event.t
branches/L3Parser/src/bindings/perl/t/05__KineticLaw.t
branches/L3Parser/src/bindings/perl/t/05__Model.t
branches/L3Parser/src/bindings/perl/t/05__ModelL3.t
branches/L3Parser/src/bindings/perl/t/05__Parameter.t
branches/L3Parser/src/bindings/perl/t/06__TestReadSBML.t
branches/L3Parser/src/bindings/perl/t/06__TestReadSBMLL3.t
branches/L3Parser/src/bindings/perl/t/06__TestWriteSBML.t
branches/L3Parser/src/bindings/perl/t/06__TestWriteSBMLL3.t
branches/L3Parser/src/bindings/python/.svnignore
branches/L3Parser/src/bindings/python/CMakeLists.txt
branches/L3Parser/src/bindings/python/Makefile.in
branches/L3Parser/src/bindings/python/doc-converter/README.txt
branches/L3Parser/src/bindings/python/doc-converter/argparse.py
branches/L3Parser/src/bindings/python/doc-converter/rewrite_pydoc.py
branches/L3Parser/src/bindings/python/local-downcast-packages-layout.cpp
branches/L3Parser/src/bindings/python/local-layout.i
branches/L3Parser/src/bindings/python/local-packages.i.in
branches/L3Parser/src/bindings/python/local.cpp
branches/L3Parser/src/bindings/python/local.i
branches/L3Parser/src/bindings/python/setup.py.in
branches/L3Parser/src/bindings/python/test/annotation/TestRDFAnnotation.py
branches/L3Parser/src/bindings/python/test/sbml/.svnignore
branches/L3Parser/src/bindings/python/test/sbml/TestCompartmentType_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestCompartment_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestEvent_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestInternalConsistencyChecks.py
branches/L3Parser/src/bindings/python/test/sbml/TestL3KineticLaw.py
branches/L3Parser/src/bindings/python/test/sbml/TestL3LocalParameter.py
branches/L3Parser/src/bindings/python/test/sbml/TestL3Trigger.py
branches/L3Parser/src/bindings/python/test/sbml/TestModel_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestParameter_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestReaction_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestReadFromFile6.py
branches/L3Parser/src/bindings/python/test/sbml/TestReadFromFile7.py
branches/L3Parser/src/bindings/python/test/sbml/TestReadFromFile8.py
branches/L3Parser/src/bindings/python/test/sbml/TestRequiredAttributes.py
branches/L3Parser/src/bindings/python/test/sbml/TestRequiredElements.py
branches/L3Parser/src/bindings/python/test/sbml/TestSBase_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSpeciesReference_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSpeciesType_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSpecies_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestSyntaxChecker.py
branches/L3Parser/src/bindings/python/test/sbml/TestUnitDefinition_newSetters.py
branches/L3Parser/src/bindings/python/test/sbml/TestUnit_newSetters.py
branches/L3Parser/src/bindings/python/test.py
branches/L3Parser/src/bindings/ruby/CMakeLists.txt
branches/L3Parser/src/bindings/ruby/Makefile.in
branches/L3Parser/src/bindings/ruby/local-downcast-packages-layout.cpp
branches/L3Parser/src/bindings/ruby/local-layout.i
branches/L3Parser/src/bindings/ruby/local-packages.i.in
branches/L3Parser/src/bindings/ruby/test/annotation/TestRDFAnnotation.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestAlgebraicRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestAssignmentRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestCompartment.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestCompartmentType.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestCompartmentVolumeRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestConstraint.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestEvent.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestEventAssignment.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestFunctionDefinition.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestInitialAssignment.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestInternalConsistencyChecks.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestKineticLaw.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestL3KineticLaw.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestL3LocalParameter.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestL3Trigger.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestListOf.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestModel.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestModifierSpeciesReference.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestParameter.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestParameterRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRateRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReaction.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile1.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile2.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile3.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile4.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile6.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile7.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestReadFromFile8.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRequiredAttributes.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRequiredElements.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSBMLConvert.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSBMLDocument.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSBase_newSetters.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpecies.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpeciesConcentrationRule.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpeciesReference.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestSpeciesType.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestUnit.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestUnitDefinition.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestUnitKind.rb
branches/L3Parser/src/bindings/swig/OStream.h
branches/L3Parser/src/bindings/swig/layout-package.h
branches/L3Parser/src/bindings/swig/layout-package.i
branches/L3Parser/src/bindings/swig/libsbml.h
branches/L3Parser/src/bindings/swig/libsbml.i
branches/L3Parser/src/bindings/swig/std_set.i
branches/L3Parser/src/bindings/swig/swigdoc.py
branches/L3Parser/src/layout-package.cmake
branches/L3Parser/src/sbml/AlgebraicRule.cpp
branches/L3Parser/src/sbml/Delay.h
branches/L3Parser/src/sbml/FunctionDefinition.cpp
branches/L3Parser/src/sbml/SBase.h
branches/L3Parser/src/sbml/Trigger.cpp
branches/L3Parser/src/sbml/validator/SBMLInternalValidator.h
branches/L3Parser/src/sbml/validator/test/TestFile.cpp
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-27.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-28.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-35.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-36.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-37.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10503-fail-01-01-99507.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10503-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10503-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-26.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-27.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-28.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-23.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-24.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-31.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-32.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10514-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-22.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-23.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-24.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-27.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-28.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-15.xml
Added Paths:
-----------
branches/L3Parser/src/bindings/csharp/test/annotation/TestSyncAnnotation.cs
branches/L3Parser/src/bindings/csharp/test/math/TestL3FormulaParserC.cs
branches/L3Parser/src/bindings/csharp/test/sbml/TestGetMultipleObjects.cs
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/annotation/TestSyncAnnotation.java
branches/L3Parser/src/bindings/java/test/org/sbml/libsbml/test/sbml/TestGetMultipleObjects.java
branches/L3Parser/src/bindings/matlab/mexopts-xcode43.sh
branches/L3Parser/src/bindings/matlab/mexopts-xcode45.sh
branches/L3Parser/src/bindings/python/doc-converter/.svnignore
branches/L3Parser/src/bindings/python/doc-converter/test/cases/.svnignore
branches/L3Parser/src/bindings/python/local-contrib.i
branches/L3Parser/src/bindings/python/test/annotation/TestSyncAnnotation.py
branches/L3Parser/src/bindings/python/test/math/TestL3FormulaParserC.py
branches/L3Parser/src/bindings/python/test/sbml/TestGetMultipleObjects.py
branches/L3Parser/src/bindings/r/
branches/L3Parser/src/bindings/ruby/test/annotation/TestSyncAnnotation.rb
branches/L3Parser/src/bindings/ruby/test/math/TestL3FormulaParserC.rb
branches/L3Parser/src/bindings/ruby/test/sbml/TestGetMultipleObjects.rb
Property Changed:
----------------
branches/L3Parser/src/bindings/octave/
branches/L3Parser/src/bindings/python/
branches/L3Parser/src/bindings/python/doc-converter/
branches/L3Parser/src/bindings/python/doc-converter/test/cases/
branches/L3Parser/src/bindings/python/test/sbml/
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-27.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-28.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-35.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-36.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10501-pass-00-37.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10503-fail-01-01-99507.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10503-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10503-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-26.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-27.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-fail-01-28.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-23.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-24.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-31.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10511-pass-00-32.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-fail-01-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-12.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10512-pass-00-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-fail-01-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10513-pass-00-16.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10514-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-15.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-22.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-23.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-fail-01-24.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-18.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-19.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-20.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-27.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10521-pass-00-28.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-01.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-02.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-03.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-09.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-10.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-fail-01-11.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-05.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-06.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-07.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-14.xml
branches/L3Parser/src/sbml/validator/test/test-data/sbml-unit-constraints/10522-pass-00-15.xml
Modified: branches/L3Parser/Makefile.in
===================================================================
--- branches/L3Parser/Makefile.in 2012-08-22 14:37:05 UTC (rev 16251)
+++ branches/L3Parser/Makefile.in 2012-08-22 15:59:26 UTC (rev 16252)
@@ -5,22 +5,22 @@
## Author(s) : SBML Team <sbm...@ca...>
## Organization: California Institute of Technology
## Created : 2004-05-31
-##
+##
## <!--------------------------------------------------------------------------
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
-## Copyright (C) 2009-2012 jointly by the following organizations:
+## Copyright (C) 2009-2012 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
-##
+##
## Copyright (C) 2006-2008 by the California Institute of Technology,
-## Pasadena, CA, USA
-##
-## Copyright (C) 2002-2005 jointly by the following organizations:
+## Pasadena, CA, USA
+##
+## Copyright (C) 2002-2005 jointly by the following organizations:
## 1. California Institute of Technology, Pasadena, CA, USA
## 2. Japan Science and Technology Agency, Japan
-##
+##
## This library is free software; you can redistribute it and/or modify it
## under the terms of the GNU Lesser General Public License as published by
## the Free Software Foundation. A copy of the license agreement is provided
@@ -40,7 +40,7 @@
include @top_srcdir@/config/makefile-common-vars.mk
# `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
+# `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.
srcdir = @srcdir@
@@ -77,6 +77,7 @@
examples/c/printUnits.c \
examples/c/readSBML.c \
examples/c/translateMath.c \
+ examples/c/translateL3Math.c \
examples/c/util.c \
examples/c/util.h \
examples/c/validateSBML.c \
@@ -102,6 +103,7 @@
examples/c++/printUnits.cpp \
examples/c++/readSBML.cpp \
examples/c++/translateMath.cpp \
+ examples/c++/translateL3Math.cpp \
examples/c++/unsetAnnotation.cpp \
examples/c++/unsetNotes.cpp \
examples/c++/util.c \
@@ -286,7 +288,7 @@
NEWS.txt \
README.txt \
VERSION.txt \
- $(examples)
+ $(examples)
# Variables `subdirs', `headers', `sources', `libraries', `extra_CPPFLAGS',
# `extra_CXXFLAGS', `extra_LDFLAGS', `extra_clean', and `distfiles' are
@@ -349,10 +351,10 @@
configure \
configure.ac \
libsbml.spec.in \
- CMakeLists.txt \
- common.cmake \
- layout-package.cmake \
- $(examples)
+ CMakeLists.txt \
+ common.cmake \
+ layout-package.cmake \
+ $(examples)
# The files listed in `extra_distclean' are items created by configure or
# make, and that are removed by the default rules for `make distclean' in
@@ -361,14 +363,16 @@
extra_distclean = config.status config.cache config.log autom4te.cache \
src/sbml/common/config.h src/sbml/common/stamp-h1 config/lt_link_helper.sh \
config/mkoctfile_wrapper.sh libtool doltlibtool doltcompile \
- config/makefile-common-vars.mk config/chk_swig_version.sh
+ config/makefile-common-vars.mk config/chk_swig_version.sh \
+ examples/c/Makefile examples/c++/Makefile examples/csharp/Makefile \
+ examples/java/Makefile
# It's safer to remove and recreate the copy of the include files (in the
# 'include' directory) after a make clean. Previously we did it in a make
# distclean only, but I've run into situations where the copy didn't get
# updated. This is a bit of a sledgehammer, but it's not too bad.
-extra_clean = include libsbml.pc libsbml.spec
+extra_clean = include libsbml.pc libsbml.spec config/*.class
ifeq "$(HOST_TYPE)" "cygwin"
extra_clean += libsbml.la
@@ -431,7 +435,7 @@
$(MAKE) -$(MAKEFLAGS) -w -C macosx $(MAKECMDGOALS)
else
$(MAKE) -w -C macosx $(MAKECMDGOALS)
-endif
+endif
#
# Create an RPM distribution.
@@ -466,7 +470,7 @@
base-libs = -lsbml -lstdc++ -lm
-COMPRESS_CPFLAGS = ${ZLIB_CPPFLAGS} ${BZ2_CPPFLAGS}
+COMPRESS_CPFLAGS = ${ZLIB_CPPFLAGS} ${BZ2_CPPFLAGS}
COMPRESS_LDFLAGS = ${ZLIB_LDFLAGS} ${BZ2_LDFLAGS}
COMPRESS_LIBS = ${ZLIB_LIBS} ${BZ2_LIBS}
@@ -515,7 +519,7 @@
(such as Linux), you will also need to do one of the following:
1) run 'ldconfig' (see the man page if this is unfamiliar)
2) set the LD_LIBRARY_PATH (or equivalent) environment variable
- to contain the path "$(DESTDIR)$(LIBDIR)" so that programs can
+ to contain the path "$(DESTDIR)$(LIBDIR)" so that programs can
find the libSBML library at run-time.
endef
@@ -523,21 +527,21 @@
The installation of libSBML is finished. To use the library, you
may also need to set your DYLD_LIBRARY_PATH environment to contain
- the path "$(DESTDIR)$(LIBDIR)" so that programs can find the
+ the path "$(DESTDIR)$(LIBDIR)" so that programs can find the
libSBML library at run-time.
endef
define uninstall-warning-msg
Uninstallation complete. WARNING: if you have run libSBML's 'configure'
- utility since the time of the last installation of libSBML on this computer,
+ utility since the time of the last installation of libSBML on this computer,
the uninstallation just performed may not have removed all of the libSBML
files. The 'make uninstall' command only knows about the files installed
by libSBML according to its MOST RECENT CONFIGURATION.
endef
-install: all install-recursive install-warnings install-pc
+install: all install-recursive install-warnings install-pc
# Only in the case of Java can we make the docs without doxygen.
ifdef USE_JAVA
@@ -564,7 +568,7 @@
install-pc: libsbml.pc
$(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
-uninstall: uninstall-recursive uninstall-libsbml-pc
+uninstall: uninstall-recursive uninstall-libsbml-pc
@if test -d "$(DESTDIR)$(LIBDIR)"; then \
if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
echo rmdir "$(DESTDIR)$(LIBDIR)"; \
Modified: branches/L3Parser/configure
===================================================================
--- branches/L3Parser/configure 2012-08-22 14:37:05 UTC (rev 16251)
+++ branches/L3Parser/configure 2012-08-22 15:59:26 UTC (rev 16252)
@@ -1,7 +1,7 @@
#! /bin/sh
-# From configure.ac Revision: 15481 .
+# From configure.ac Revision: 16048 .
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.68 for libSBML 5.4.1.
+# Generated by GNU Autoconf 2.68 for libSBML 5.6.0.
#
# Report bugs to <lib...@ca...>.
#
@@ -715,8 +715,8 @@
# Identity of this package.
PACKAGE_NAME='libSBML'
PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.4.1'
-PACKAGE_STRING='libSBML 5.4.1'
+PACKAGE_VERSION='5.6.0'
+PACKAGE_STRING='libSBML 5.6.0'
PACKAGE_BUGREPORT='lib...@ca...'
PACKAGE_URL='http://sbml.org/Software/libSBML'
@@ -862,8 +862,9 @@
PYTHON_EXT
PYTHON_LIBS
PYTHON_LDFLAGS
+USE_PYTHON
+PYTHON_CONFIG
PYTHON_CPPFLAGS
-USE_PYTHON
PYTHON
HAS_GCC_WNO_LONG_DOUBLE
ACLOCAL
@@ -897,6 +898,7 @@
build_cpu
build
USE_COMPRESSION
+LIBSBML_HAS_PACKAGE_LAYOUT
USE_LAYOUT
LIBSBML_BETA_VERSION
LIBSBML_REVISION_VERSION
@@ -951,6 +953,7 @@
enable_m64
enable_universal_binary
with_python
+with_python_interpreter
with_perl
with_java
with_java_bin_check
@@ -1537,7 +1540,7 @@
# 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 5.4.1 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.6.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1602,7 +1605,7 @@
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of libSBML 5.4.1:";;
+ short | recursive ) echo "Configuration of libSBML 5.6.0:";;
esac
cat <<\_ACEOF
@@ -1630,6 +1633,8 @@
--with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
--without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
--with-python[=PREFIX] generate Python interface library [default=no]
+ --with-python-interpreter[=PATH]
+ set path to Python interpreter [default=autodetect]
--with-perl[=PREFIX] generate Perl interface library [default=no]
--with-java[=PREFIX] generate Java interface library [default=no]
--without-jre-check disable checking for 32 vs. 64-bit JRE
@@ -1742,7 +1747,7 @@
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-libSBML configure 5.4.1
+libSBML configure 5.6.0
generated by GNU Autoconf 2.68
Copyright (C) 2010 Free Software Foundation, Inc.
@@ -2461,7 +2466,7 @@
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by libSBML $as_me 5.4.1, which was
+It was created by libSBML $as_me 5.6.0, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ $0 $@
@@ -2851,7 +2856,7 @@
ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
-LIBSBML_VERSION_NUMERIC=50401
+LIBSBML_VERSION_NUMERIC=50600
@@ -2859,11 +2864,11 @@
-LIBSBML_MINOR_VERSION=4
+LIBSBML_MINOR_VERSION=6
-LIBSBML_REVISION_VERSION=1
+LIBSBML_REVISION_VERSION=0
@@ -2903,8 +2908,13 @@
$as_echo "#define USE_LAYOUT 1" >>confdefs.h
+
+$as_echo "#define LIBSBML_HAS_PACKAGE_LAYOUT 1" >>confdefs.h
+
USE_LAYOUT=1
+ LIBSBML_HAS_PACKAGE_LAYOUT=1
+
fi
@@ -4612,14 +4622,89 @@
fi
+
+# Check whether --with-python-interpreter was given.
+if test "${with_python_interpreter+set}" = set; then :
+ withval=$with_python_interpreter; PYTHON=$withval
+else
+ PYTHON=no
+fi
+
+
if test $with_python != no; then
- if test $with_python != yes;
- then
- with_python=`echo $with_python | sed -e 's,\(.*\)/$,\1,g'`
+ python_dir=""
- # Extract the first word of "python", so it can be a program name with args.
+ if test "$PYTHON" != no ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $PYTHON exists" >&5
+$as_echo_n "checking whether $PYTHON exists... " >&6; }
+ if test -f "$PYTHON" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+ as_fn_error $? "$PYTHON does not exist." "$LINENO" 5
+ fi
+ if test $with_python != yes; then
+ if test -d "$with_python" ; then
+ python_dir="$with_python/bin"
+ else
+ python_dir=`$as_dirname -- "$PYTHON" ||
+$as_expr X"$PYTHON" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$PYTHON" : 'X\(//\)[^/]' \| \
+ X"$PYTHON" : 'X\(//\)$' \| \
+ X"$PYTHON" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$PYTHON" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ fi
+ else
+ python_dir=`$as_dirname -- "$PYTHON" ||
+$as_expr X"$PYTHON" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$PYTHON" : 'X\(//\)[^/]' \| \
+ X"$PYTHON" : 'X\(//\)$' \| \
+ X"$PYTHON" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$PYTHON" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ fi
+ else
+ if test $with_python != yes; then
+ with_python=`echo $with_python | sed -e 's,\(.*\)/$,\1,g'`
+
+ # Extract the first word of "python", so it can be a program name with args.
set dummy python; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
@@ -4660,8 +4745,8 @@
fi
- else
- # Extract the first word of "python", so it can be a program name with args.
+ else
+ # Extract the first word of "python", so it can be a program name with args.
set dummy python; ac_word=$2
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
$as_echo_n "checking for $ac_word... " >&6; }
@@ -4701,11 +4786,35 @@
fi
+ fi
+ python_dir=`$as_dirname -- "$PYTHON" ||
+$as_expr X"$PYTHON" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$PYTHON" : 'X\(//\)[^/]' \| \
+ X"$PYTHON" : 'X\(//\)$' \| \
+ X"$PYTHON" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$PYTHON" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
fi
- if test -z $PYTHON -o "$PYTHON" = "no" -o ! -f $PYTHON;
+ if test -z "$PYTHON" -o "$PYTHON" = "no" -o ! -f "$PYTHON";
then
- as_fn_error $? "*** python missing - please install first or check config.log ***" "$LINENO" 5
+ as_fn_error $? "*** cannot find python -- please install it or check config.log ***" "$LINENO" 5
fi
@@ -4720,78 +4829,250 @@
PYTHON_VERSION=`"$PYTHON" -c "import sys; print(sys.version[:3])"`
- PYTHON_NAME="python${PYTHON_VERSION}"
+ PYTHON_NAME="python$PYTHON_VERSION"
- PYTHON_H="${PYTHON_PREFIX}/include/${PYTHON_NAME}/Python.h"
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python.h" >&5
-$as_echo_n "checking for Python.h... " >&6; }
- if test -z $PYTHON_H || ! test -f $PYTHON_H;
- then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python include path" >&5
+$as_echo_n "checking for Python include path... " >&6; }
+ if test -z "$PYTHON_CPPFLAGS"; then
+ python_path=`$PYTHON -c "import distutils.sysconfig; \
+ print (distutils.sysconfig.get_python_inc ());"`
+ if test -n "${python_path}"; then
+ python_path="-I$python_path"
+ fi
+ PYTHON_CPPFLAGS=$python_path
+ fi
+ case $host in
+ *darwin*)
+ ;;
+ *cygwin* | *mingw*)
+ PYTHON_CPPFLAGS="$PYTHON_CPPFLAGS -DUSE_DL_IMPORT"
+ ;;
+ *)
+ ;;
+ esac
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PYTHON_CPPFLAGS" >&5
+$as_echo "$PYTHON_CPPFLAGS" >&6; }
+
+
+
+ if test -d "$python_dir" ; then
+ # Extract the first word of "${PYTHON_NAME}-config", so it can be a program name with args.
+set dummy ${PYTHON_NAME}-config; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_path_PYTHON_CONFIG+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $PYTHON_CONFIG in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_PYTHON_CONFIG="$PYTHON_CONFIG" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $python_dir
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_PYTHON_CONFIG="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ test -z "$ac_cv_path_PYTHON_CONFIG" && ac_cv_path_PYTHON_CONFIG="no"
+ ;;
+esac
+fi
+PYTHON_CONFIG=$ac_cv_path_PYTHON_CONFIG
+if test -n "$PYTHON_CONFIG"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PYTHON_CONFIG" >&5
+$as_echo "$PYTHON_CONFIG" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
$as_echo "no" >&6; }
- as_fn_error $? "*** $PYTHON_H missing - please install first or check config.log ***" "$LINENO" 5
+fi
+
+
+ else
+ # Extract the first word of "${PYTHON_NAME}-config", so it can be a program name with args.
+set dummy ${PYTHON_NAME}-config; ac_word=$2
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if ${ac_cv_path_PYTHON_CONFIG+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+ case $PYTHON_CONFIG in
+ [\\/]* | ?:[\\/]*)
+ ac_cv_path_PYTHON_CONFIG="$PYTHON_CONFIG" # Let the user override the test with a path.
+ ;;
+ *)
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_path_PYTHON_CONFIG="$as_dir/$ac_word$ac_exec_ext"
+ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+ done
+IFS=$as_save_IFS
+
+ ;;
+esac
+fi
+PYTHON_CONFIG=$ac_cv_path_PYTHON_CONFIG
+if test -n "$PYTHON_CONFIG"; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PYTHON_CONFIG" >&5
+$as_echo "$PYTHON_CONFIG" >&6; }
+else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
fi
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
+ if test -n "$PYTHON_CONFIG" ; then
- case $host in
- *darwin*)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking $PYTHON_CONFIG --ldflags" >&5
+$as_echo_n "checking $PYTHON_CONFIG --ldflags... " >&6; }
+ PYTHON_LDFLAGS=`"$PYTHON_CONFIG" --ldflags`
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
+$as_echo "done" >&6; }
- if test `expr "${PYTHON_PREFIX}" ':' '/Library/Frameworks/.*'` -ne 0; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking $PYTHON_CONFIG --libs" >&5
+$as_echo_n "checking $PYTHON_CONFIG --libs... " >&6; }
+ PYTHON_LIBS=`"$PYTHON_CONFIG" --libs`
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
+$as_echo "done" >&6; }
- PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
- PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -F/Library/Frameworks -framework Python"
- elif test `expr "${PYTHON_PREFIX}" ':' '/System/Library/Frameworks/.*'` -ne 0; then
+ case $host in
+ *darwin*)
- PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
- PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -F/System/Library/Frameworks -framework Python"
+ PYTHON_EXT="so"
- else
- macosx_version=`sw_vers -productVersion | cut -d"." -f1,2`
- if test ${macosx_version} '>' 10.2; then
- PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
- PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -undefined dynamic_lookup"
+ PYTHON_CPPFLAGS=`echo $PYTHON_CPPFLAGS | sed -e 's/-Wstrict-prototypes//'`
- else
- PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
- PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -bundle_loader ${PYTHON}"
- fi
- fi
+ tmp_v=`"$PYTHON" -c "import sys; print(sys.version[:1])"`
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking if we can trust $PYTHON_CONFIG --libs" >&5
+$as_echo_n "checking if we can trust $PYTHON_CONFIG --libs... " >&6; }
+ if test $tmp_v -ge 3; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no, we're not using those values" >&5
+$as_echo "no, we're not using those values" >&6; }
+
+ tmp_e=`"$PYTHON" -c "from distutils import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"`
+ tmp_sl=`"$PYTHON" -c "from distutils import sysconfig; print(sysconfig.get_config_var('SYSLIBS'))"`
+
+ if test $tmp_e -eq 0; then
+ tmp_pl=`"$PYTHON" -c "from distutils import sysconfig; print('-L' + sysconfig.get_config_var('LIBPL'))"`
+ PYTHON_LDFLAGS="$tmp_pl $tmp_sl"
+ else
+ PYTHON_LDFLAGS="$tmp_sl"
+ fi
+
+ tmp_l=`"$PYTHON" -c "from distutils import sysconfig; print(sysconfig.get_config_var('LIBS'))"`
+ PYTHON_LIBS="$tmp_l -lpython$PYTHON_VERSION"
+ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes, it's probably okay" >&5
+$as_echo "yes, it's probably okay" >&6; }
+ fi
+
+
+ if test $with_python != yes; then
+ PYTHON_LDFLAGS="$PYTHON_LDFLAGS -L$with_python/lib"
+ fi
+
+ ;;
+ *cygwin* | *mingw*)
+ PYTHON_EXT="dll"
+ ;;
+ *)
+ PYTHON_EXT="so"
+ ;;
+ esac
+
+ else
+
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: No $PYTHON_CONFIG found -- we'll have to guess at the settings" >&5
+$as_echo "$as_me: WARNING: No $PYTHON_CONFIG found -- we'll have to guess at the settings" >&2;}
+
+
+ case $host in
+ *darwin*)
+
+ if test `expr "${PYTHON_PREFIX}" ':' '/Library/Frameworks/.*'` -ne 0; then
+
+ PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -F/Library/Frameworks -framework Python"
+
+ elif test `expr "${PYTHON_PREFIX}" ':' '/System/Library/Frameworks/.*'` -ne 0; then
+
+ PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -F/System/Library/Frameworks -framework Python"
+
+ else
+ macosx_version=`sw_vers -productVersion | cut -d"." -f1,2`
+ if test ${macosx_version} '>' 10.2; then
+
+ PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -undefined dynamic_lookup"
+
+ else
+
+ PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload -bundle_loader ${PYTHON}"
+
+ fi
+ fi
+
+ PYTHON_EXT="so"
+ ;;
+ *cygwin* | *mingw*)
+ PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib${LIBSUFFIX}/${PYTHON_NAME}/config"
+ PYTHON_LIBS="-l${PYTHON_NAME}"
+ PYTHON_EXT="dll"
+ ;;
+ *)
+ PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib${LIBSUFFIX}/${PYTHON_NAME}/config"
+ PYTHON_LIBS="-l${PYTHON_NAME}"
+ PYTHON_EXT="so"
+ ;;
+ esac
+
+ fi
+
+ case $host in
+ *darwin*)
+
RUN_LDPATH="$RUN_LDPATH:${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-dynload"
-
- # MacOS X note: this MUST remain .so even though we use .dylib for libsbml.
- PYTHON_EXT="so"
- ;;
+ ;;
*cygwin* | *mingw*)
- PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME} -DUSE_DL_IMPORT"
- PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib${LIBSUFFIX}/${PYTHON_NAME}/config"
- PYTHON_LIBS="-l${PYTHON_NAME}"
RUN_LDPATH="$RUN_LDPATH:${PYTHON_PREFIX}/lib${LIBSUFFIX}/${PYTHON_NAME}/config"
- PYTHON_EXT="dll"
- ;;
- *)
- PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
- PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib${LIBSUFFIX}/${PYTHON_NAME}/config"
- PYTHON_LIBS="-l${PYTHON_NAME}"
+ ;;
+ *)
RUN_LDPATH="$RUN_LDPATH:${PYTHON_PREFIX}/lib${LIBSUFFIX}/${PYTHON_NAME}/config"
- PYTHON_EXT="so"
- ;;
+ ;;
esac
-
python_platform=`("$PYTHON" -c "import platform; print(platform.platform())") 2>/dev/null`
case $host in
@@ -5058,7 +5339,6 @@
esac
-
python_dir="src/bindings/python"
if test "$with_swig" = "no" -o -z "$with_swig" ; then
@@ -8536,12 +8816,12 @@
fi
- DOXYGEN_MIN_VERSION=1.6.3
- DOXYGEN_MAX_VERSION=1.6.3
+ DOXYGEN_MIN_VERSION=1.7.0
+ DOXYGEN_MAX_VERSION=1.8.7
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking $DOXYGEN version >= 1.6.3" >&5
-$as_echo_n "checking $DOXYGEN version >= 1.6.3... " >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking $DOXYGEN version >= 1.7.0" >&5
+$as_echo_n "checking $DOXYGEN version >= 1.7.0... " >&6; }
version=`"$DOXYGEN" --version | tr -d '\015'`
@@ -9301,7 +9581,7 @@
;;
*-*-irix6*)
# Find out which ABI we are using.
- echo '#line 9304 "configure"' > conftest.$ac_ext
+ echo '#line 9584 "configure"' > conftest.$ac_ext
if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
(eval $ac_compile) 2>&5
ac_status=$?
@@ -11519,11 +11799,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:11522: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:11802: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:11526: \$? = $ac_status" >&5
+ echo "$as_me:11806: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -11809,11 +12089,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:11812: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:12092: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:11816: \$? = $ac_status" >&5
+ echo "$as_me:12096: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -11913,11 +12193,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:11916: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:12196: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:11920: \$? = $ac_status" >&5
+ echo "$as_me:12200: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -13938,7 +14218,7 @@
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
-#line 13941 "configure"
+#line 14221 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -14038,7 +14318,7 @@
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<EOF
-#line 14041 "configure"
+#line 14321 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -16383,11 +16663,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:16386: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:16666: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:16390: \$? = $ac_status" >&5
+ echo "$as_me:16670: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -16487,11 +16767,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:16490: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:16770: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:16494: \$? = $ac_status" >&5
+ echo "$as_me:16774: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -18070,11 +18350,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:18073: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:18353: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:18077: \$? = $ac_status" >&5
+ echo "$as_me:18357: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -18174,11 +18454,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:18177: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:18457: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:18181: \$? = $ac_status" >&5
+ echo "$as_me:18461: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -20344,11 +20624,11 @@
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:20347: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:20627: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:20351: \$? = $ac_status" >&5
+ echo "$as_me:20631: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recogniz...
[truncated message content] |
|
From: <sar...@us...> - 2012-08-22 14:37:15
|
Revision: 16251
http://sbml.svn.sourceforge.net/sbml/?rev=16251&view=rev
Author: sarahkeating
Date: 2012-08-22 14:37:05 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
create branch to start playing with plugging into astnodes
Added Paths:
-----------
branches/libsbml-ast-plugin/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2012-08-22 14:24:32
|
Revision: 16250
http://sbml.svn.sourceforge.net/sbml/?rev=16250&view=rev
Author: sarahkeating
Date: 2012-08-22 14:24:13 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
merged from current trunk
Modified Paths:
--------------
branches/libsbml-l2v5-l3v2/AUTHORS.txt
branches/libsbml-l2v5-l3v2/CMakeLists.txt
branches/libsbml-l2v5-l3v2/NEWS.txt
branches/libsbml-l2v5-l3v2/README.txt
branches/libsbml-l2v5-l3v2/VERSION.txt
branches/libsbml-l2v5-l3v2/common.cmake
branches/libsbml-l2v5-l3v2/config/python.m4
branches/libsbml-l2v5-l3v2/configure
branches/libsbml-l2v5-l3v2/configure.ac
branches/libsbml-l2v5-l3v2/dev/utilities/comparelinenumbers/LibSBMLLineNumbers.cs
branches/libsbml-l2v5-l3v2/dev/utilities/comparelinenumbers/README.txt
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/CMakeCache_32.txt.in
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/CMakeCache_64.txt.in
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/CMakeLists.txt
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/configure-build.cmake
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/install_libsbml_script_xml_win32.iss.in
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/install_libsbml_script_xml_win64.iss.in
branches/libsbml-l2v5-l3v2/dev/utilities/new_installer/python/CMakeLists.txt
branches/libsbml-l2v5-l3v2/dev/utilities/testconstructors/README.txt
branches/libsbml-l2v5-l3v2/dev/utilities/testconstructors/TestConstructors.cs
branches/libsbml-l2v5-l3v2/docs/FindDoxygen.cmake
branches/libsbml-l2v5-l3v2/docs/src/DoxygenLayout.xml
branches/libsbml-l2v5-l3v2/docs/src/common-text/base-units.html
branches/libsbml-l2v5-l3v2/docs/src/doxygen-base-stylesheet.css
branches/libsbml-l2v5-l3v2/docs/src/doxygen-config-common.txt
branches/libsbml-l2v5-l3v2/docs/src/doxygen-footer.html
branches/libsbml-l2v5-l3v2/docs/src/doxygen-header.html
branches/libsbml-l2v5-l3v2/docs/src/doxygen-navtree.css
branches/libsbml-l2v5-l3v2/docs/src/libsbml-authors.html
branches/libsbml-l2v5-l3v2/docs/src/libsbml-installation.html.in
branches/libsbml-l2v5-l3v2/docs/src/libsbml-issues.html
branches/libsbml-l2v5-l3v2/docs/src/libsbml-java-overview.html
branches/libsbml-l2v5-l3v2/examples/c/CMakeLists.txt
branches/libsbml-l2v5-l3v2/examples/c/addCVTerms.c
branches/libsbml-l2v5-l3v2/examples/c/addModelHistory.c
branches/libsbml-l2v5-l3v2/examples/c/addingEvidenceCodes_1.c
branches/libsbml-l2v5-l3v2/examples/c/addingEvidenceCodes_2.c
branches/libsbml-l2v5-l3v2/examples/c/appendAnnotation.c
branches/libsbml-l2v5-l3v2/examples/c/createExampleSBML.c
branches/libsbml-l2v5-l3v2/examples/c/printAnnotation.c
branches/libsbml-l2v5-l3v2/examples/c/printNotes.c
branches/libsbml-l2v5-l3v2/examples/c/printRegisteredPackages.c
branches/libsbml-l2v5-l3v2/examples/c/printSupported.c
branches/libsbml-l2v5-l3v2/examples/c/printUnits.c
branches/libsbml-l2v5-l3v2/examples/c/translateL3Math.c
branches/libsbml-l2v5-l3v2/examples/c/unsetAnnotation.c
branches/libsbml-l2v5-l3v2/examples/c/unsetNotes.c
branches/libsbml-l2v5-l3v2/examples/c++/CMakeLists.txt
branches/libsbml-l2v5-l3v2/examples/c++/addCustomValidator.cpp
branches/libsbml-l2v5-l3v2/examples/c++/callExternalValidator.cpp
branches/libsbml-l2v5-l3v2/examples/c++/printRegisteredPackages.cpp
branches/libsbml-l2v5-l3v2/examples/c++/printSupported.cpp
branches/libsbml-l2v5-l3v2/examples/csharp/addCVTerms.cs
branches/libsbml-l2v5-l3v2/examples/csharp/addCustomValidator.cs
branches/libsbml-l2v5-l3v2/examples/csharp/addModelHistory.cs
branches/libsbml-l2v5-l3v2/examples/csharp/addingEvidenceCodes_1.cs
branches/libsbml-l2v5-l3v2/examples/csharp/addingEvidenceCodes_2.cs
branches/libsbml-l2v5-l3v2/examples/csharp/appendAnnotation.cs
branches/libsbml-l2v5-l3v2/examples/csharp/callExternalValidator.cs
branches/libsbml-l2v5-l3v2/examples/csharp/convertSBML.cs
branches/libsbml-l2v5-l3v2/examples/csharp/createExampleSBML.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printAnnotation.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printMath.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printNotes.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printRegisteredPackages.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printSBML.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printUnits.cs
branches/libsbml-l2v5-l3v2/examples/csharp/printsupported.cs
branches/libsbml-l2v5-l3v2/examples/csharp/readSBML.cs
branches/libsbml-l2v5-l3v2/examples/csharp/translateMath.cs
branches/libsbml-l2v5-l3v2/examples/csharp/unsetAnnotation.cs
branches/libsbml-l2v5-l3v2/examples/csharp/unsetNotes.cs
branches/libsbml-l2v5-l3v2/examples/java/addCustomValidator.java
branches/libsbml-l2v5-l3v2/examples/java/addingEvidenceCodes_1.java
branches/libsbml-l2v5-l3v2/examples/java/addingEvidenceCodes_2.java
branches/libsbml-l2v5-l3v2/examples/java/callExternalValidator.java
branches/libsbml-l2v5-l3v2/examples/java/createExampleSBML.java
branches/libsbml-l2v5-l3v2/examples/java/printRegisteredPackages.java
branches/libsbml-l2v5-l3v2/examples/java/printsupported.java
branches/libsbml-l2v5-l3v2/examples/layout/CMakeLists.txt
branches/libsbml-l2v5-l3v2/examples/layout/addLayout.cpp
branches/libsbml-l2v5-l3v2/examples/layout/convertLayout.cpp
branches/libsbml-l2v5-l3v2/examples/layout/example1-L3.cpp
branches/libsbml-l2v5-l3v2/examples/layout/example1.cpp
branches/libsbml-l2v5-l3v2/examples/layout/example2-L3.cpp
branches/libsbml-l2v5-l3v2/examples/layout/example2.cpp
branches/libsbml-l2v5-l3v2/examples/layout/example3-L3.cpp
branches/libsbml-l2v5-l3v2/examples/layout/example3.cpp
branches/libsbml-l2v5-l3v2/examples/python/addingEvidenceCodes_1.py
branches/libsbml-l2v5-l3v2/layout-package.cmake
branches/libsbml-l2v5-l3v2/src/CMakeLists.txt
branches/libsbml-l2v5-l3v2/src/bindings/CMakeLists.txt
branches/libsbml-l2v5-l3v2/src/bindings/csharp/CMakeLists.txt
branches/libsbml-l2v5-l3v2/src/bindings/csharp/Properties/AssemblyInfo.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/Properties/AssemblyInfo.cs.in
branches/libsbml-l2v5-l3v2/src/bindings/csharp/Properties/AssemblyInfoTR.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/TestRW.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/TestRunner.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/local-packages-layout.i
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestCVTerms_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestDate_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestModelCreator_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestModelHistory_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestRDFAnnotation.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestRDFAnnotationC.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/annotation/TestSyncAnnotation.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/math/TestL3FormulaParserC.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestCompartmentType_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestCompartment_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestEvent_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestInternalConsistencyChecks.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestL3KineticLaw.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestL3Species.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestModel.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestModel_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestParameter_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestReaction_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestReadFromFile6.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestReadFromFile7.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestReadFromFile8.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestRequiredAttributes.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestRequiredElements.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSBMLConvert.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSBMLConvertStrict.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSBase_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSpeciesReference_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSpeciesType_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSpecies_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestSyntaxChecker.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestUnitDefinition_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/sbml/TestUnit_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/xml/TestXMLNode_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/xml/TestXMLToken.cs
branches/libsbml-l2v5-l3v2/src/bindings/csharp/test/xml/TestXMLToken_newSetters.cs
branches/libsbml-l2v5-l3v2/src/bindings/java/CMakeLists.txt
branches/libsbml-l2v5-l3v2/src/bindings/java/local-packages-layout.i
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From: <sar...@us...> - 2012-08-22 11:39:47
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Revision: 16249
http://sbml.svn.sourceforge.net/sbml/?rev=16249&view=rev
Author: sarahkeating
Date: 2012-08-22 11:39:41 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
latest pdf
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/qual-spec.pdf
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <sar...@us...> - 2012-08-22 11:36:59
|
Revision: 16248
http://sbml.svn.sourceforge.net/sbml/?rev=16248&view=rev
Author: sarahkeating
Date: 2012-08-22 11:36:48 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
making figures the right size to fit
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex
trunk/specifications/sbml-level-3/version-1/qual/spec/main.tex
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual-qualitative-species-future-uml.pdf
trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual-transition-future-uml.pdf
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex 2012-08-22 09:10:58 UTC (rev 16247)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex 2012-08-22 11:36:48 UTC (rev 16248)
@@ -6,14 +6,23 @@
To account for qualitative models where parameters are not (all) instantiated, as well as models for which timing constraints are specified, an extension of the current specification was contemplated. Here, we briefly recapitulate the elements and attributes that have been discarded in the current specification, with the intent to fuel discussions on future extensions.
-\begin{figure}
-\includegraphics{figs/qual_future_directions.pdf}
-\caption The definitions of the classe \listOf{SymbolicValues}, \qual{SymbolicValue} and \qual{TemporisationMath} and additional related attributes for existing classes.}
- \label{qual_future_directions}}
+%\begin{figure}
+%\includegraphics{figs/qual_future_directions.pdf}
+%\caption {The definitions of the classe \listOf{SymbolicValues}, \qual{SymbolicValue} and \qual{TemporisationMath} and additional related attributes for existing classes.}
+% \label{qual_future_directions}
+%\end{figure}
+
\subsection{Symbols}
\subsection*{Definition of \qualt{SymbolicValue}} % (fold)
+
+\begin{figure}[hb]
+ \includegraphics{figs/qual-qualitative-species-future-uml.pdf}
+ \caption{Possible future extensions of the \QualitativeSpecies class.}
+ \label{qual_future_directions}
+\end{figure}
+
The \qual{QualitativeSpecies} element may contain at most one \listOf{SymbolicValues} that contains zero or more \qual{SymbolicValue}s. An empty list is allowed, and useful for e.g. adding annotations.
The \qual{SymbolicValue} element defines a non instantiated parameter. Such symbols may represent the different solutions of piecewise linear differential equations, along with different thresholds.
@@ -35,6 +44,12 @@
\subsection{Temporisation}
+\begin{figure}[hb]
+ \includegraphics{figs/qual-transition-future-uml.pdf}
+ \caption{Possible future extensions of the \Transition class.}
+ \label{qual_future_directions}
+\end{figure}
+
\paragraph{The \attr{temporisationType} attribute:} %% attribute of Transition
The \attr{temporisationType} is an \type{enumeration} the ``temporisation'' of the \qual{Transition}, that is the updating policy associated with the \qual{Transition}. It can be set to \const{timer}, \const{priority}, \const{sustain}, \const{proportion} or \const{rate}.
This attribute is optional.
@@ -42,7 +57,7 @@
\paragraph{The \attr{temporisationValue} attribute and the \sbml{TemporisationMath} element:}
-The attribute \attr{temporisationValue} and the element \sbml{TemporisationMath} allow the specification of the ``temporisation'' of the \qual{Transition} under the corresponding \qual{FunctionTerm}. Both are optional. Depending on the value of the \attrp{temporisationType}, either one or both could be used.
+The attribute \attr{temporisationValue} and the element \sbml{TemporisationMath} allow the specification of the ``temporisation'' of the \qual{Transition} under the corresponding \qual{FunctionTerm}. Both are optional. Depending on the value of the \attr{temporisationType}, either one or both could be used.
The \attr{temporisationValue} is a \type{double}. The element \sbml{TemporisationMath} holds a MathML function returning a \type{double}.
Added: trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual-qualitative-species-future-uml.pdf
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual-qualitative-species-future-uml.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual-transition-future-uml.pdf
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual-transition-future-uml.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/main.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/main.tex 2012-08-22 09:10:58 UTC (rev 16247)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/main.tex 2012-08-22 11:36:48 UTC (rev 16248)
@@ -7,8 +7,8 @@
\packageTitle{Qualitative Models}
\packageVersion{Version 1.0 (Draft)}
-\packageVersionDate{14th Aug 2012}
-\packageGeneralURL{}
+\packageVersionDate{22nd Aug 2012}
+\packageGeneralURL{http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Qualitative_Models_(qual)}
\packageThisVersionURL{}
\author{%
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sar...@us...> - 2012-08-22 09:11:05
|
Revision: 16247
http://sbml.svn.sourceforge.net/sbml/?rev=16247&view=rev
Author: sarahkeating
Date: 2012-08-22 09:10:58 +0000 (Wed, 22 Aug 2012)
Log Message:
-----------
updated with additions from Claudine
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex
trunk/specifications/sbml-level-3/version-1/qual/spec/best-practices.tex
Added Paths:
-----------
trunk/specifications/sbml-level-3/version-1/qual/spec/Figures_examples/qual_future_directions.key
trunk/specifications/sbml-level-3/version-1/qual/spec/Figures_examples/qual_future_directions.pdf
trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual_future_directions.pdf
Added: trunk/specifications/sbml-level-3/version-1/qual/spec/Figures_examples/qual_future_directions.key
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/qual/spec/Figures_examples/qual_future_directions.key
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/specifications/sbml-level-3/version-1/qual/spec/Figures_examples/qual_future_directions.pdf
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/qual/spec/Figures_examples/qual_future_directions.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex 2012-08-21 23:11:56 UTC (rev 16246)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/apx-future-directions.tex 2012-08-22 09:10:58 UTC (rev 16247)
@@ -3,7 +3,46 @@
\section{Future directions}
\label{apdx-future}
+To account for qualitative models where parameters are not (all) instantiated, as well as models for which timing constraints are specified, an extension of the current specification was contemplated. Here, we briefly recapitulate the elements and attributes that have been discarded in the current specification, with the intent to fuel discussions on future extensions.
+
+
+\begin{figure}
+\includegraphics{figs/qual_future_directions.pdf}
+\caption The definitions of the classe \listOf{SymbolicValues}, \qual{SymbolicValue} and \qual{TemporisationMath} and additional related attributes for existing classes.}
+ \label{qual_future_directions}}
+
\subsection{Symbols}
+\subsection*{Definition of \qualt{SymbolicValue}} % (fold)
+The \qual{QualitativeSpecies} element may contain at most one \listOf{SymbolicValues} that contains zero or more \qual{SymbolicValue}s. An empty list is allowed, and useful for e.g. adding annotations.
+The \qual{SymbolicValue} element defines a non instantiated parameter. Such symbols may represent the different solutions of piecewise linear differential equations, along with different thresholds.
+
+\paragraph{The \attr{id} and \attr{name} attributes}
+These attributes are used according to the SBML L3.1 Section 3.3. The attribute \attr{id} is mandatory and \attr{name} is optional.
+
+\paragraph{The \attr{rank} attribute}
+The \attr{rank} is an \type{integer} that defines the position of the symbol in the \listOf{SymbolicValues}. This attribute is optional.
+
+
+\paragraph{The \attr{thresholdLevel} and \attr{thresholdSymbol} attributes:} %% of Input
+The \attr{thresholdLevel} is an \type{integer} and \attr{thresholdSymbol} is a \type{SIdRef}. They are optional and exclusive.
+
+\paragraph{The \attr{resultLevel} and \attr{resultSymbol} attributes:} %% in FunctionTerm
+The result of the term is described by a \attr{resultLevel} or a \attr{resultSymbol}. Both are optional, but one of them must be defined.
+
+
+\const{assignmentSymbol}: The symbol associated to the \attr{qualitativeSpecies} is set to the \attr{resultSymbol} of the selected term.
+
\subsection{Temporisation}
+\paragraph{The \attr{temporisationType} attribute:} %% attribute of Transition
+The \attr{temporisationType} is an \type{enumeration} the ``temporisation'' of the \qual{Transition}, that is the updating policy associated with the \qual{Transition}. It can be set to \const{timer}, \const{priority}, \const{sustain}, \const{proportion} or \const{rate}.
+This attribute is optional.
+
+
+
+\paragraph{The \attr{temporisationValue} attribute and the \sbml{TemporisationMath} element:}
+The attribute \attr{temporisationValue} and the element \sbml{TemporisationMath} allow the specification of the ``temporisation'' of the \qual{Transition} under the corresponding \qual{FunctionTerm}. Both are optional. Depending on the value of the \attrp{temporisationType}, either one or both could be used.
+
+The \attr{temporisationValue} is a \type{double}. The element \sbml{TemporisationMath} holds a MathML function returning a \type{double}.
+
Modified: trunk/specifications/sbml-level-3/version-1/qual/spec/best-practices.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/qual/spec/best-practices.tex 2012-08-21 23:11:56 UTC (rev 16246)
+++ trunk/specifications/sbml-level-3/version-1/qual/spec/best-practices.tex 2012-08-22 09:10:58 UTC (rev 16247)
@@ -25,13 +25,13 @@
\LRG Any qualitativeSpecies which attribute \qual{constant} is set to "false" should appear as the output of a transition (meaning there is a process governing its evolution). Conversely, any qualitativeSpecies that appears as the output of a transition should have its attribute \qual{constant} set to false.
\medskip
-\PN The \qual{transitionEffect} of an \qual{Input} is set to "consumption", unless this input is connected to the transition by a test arc (meaning the transition has no effect on its marking). The \qual{thresholdLevel} indicates the weight of the arc from this place to the transition (when not specified, it is set to $1$). It is used to specify the enabling conditions of the transition (and to indicate the number of tokens consumed by the firing of this transition). The \qual{sign} attribute should not be defined.
+\PN The \qual{transitionEffect} of an \qual{Input} is set to "consumption", unless this input is connected to the transition by a test arc (meaning the transition has no effect on its marking). The \qual{thresholdLevel} indicates the weight of the arc from this place to the transition and is required. It is used to specify the enabling conditions of the transition (and to indicate the number of tokens consumed by the firing of this transition). The \qual{sign} attribute should not be defined.
\medskip
-\LRG The \qual{transitionEffect} of an \qual{Input} is set to "none". The \qual{thresholdLevel} indicates the level for which the species participates to the transition (when not defined, its default value is $1$). The \qual{sign} attribute indicates the type of effect on the output of the transition (the regulated species): "positive" (activation), "negative" (inhibition), "dual" (positive or negative depending e.g. on co-factors) or "unknown".
+\LRG The \qual{transitionEffect} of an \qual{Input} is set to "none". The \qual{thresholdLevel}, when specified, indicates the level for which the species participates to the transition (in this case, any reference to the input \qual{id} attribute in a <ci> element within a functionTerm of the transition refers to the value of this \qual{thresholdLevel}). The \qual{sign} attribute indicates the type of effect on the output of the transition (the regulated species): "positive" (activation), "negative" (inhibition), "dual" (positive or negative depending e.g. on co-factors) or "unknown". It is optional and mainly used for graphical purposes.
\medskip
-\PN The \qual{transitionEffect} of an \qual{Output} is set to "production". The \qual{outputLevel} indicates the weight of the arc from the transition to this place (when not defined, its default value is $1$). It is used to define the number of tokens produced by the firing of this transition.
+\PN The \qual{transitionEffect} of an \qual{Output} is set to "production". The \qual{outputLevel} indicates the weight of the arc from the transition to this place, it should be defined and is interpreted as the number of tokens produced by the firing of this transition.
\medskip
\LRG The \qual{transitionEffect} of an \qual{Output} is set to "assignmentLevel". The \qual{outputLevel} should not be defined, the level assigned to this species being defined by the \qual{resultLevel} of the transition.
Added: trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual_future_directions.pdf
===================================================================
(Binary files differ)
Property changes on: trunk/specifications/sbml-level-3/version-1/qual/spec/figs/qual_future_directions.pdf
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2012-08-21 23:12:02
|
Revision: 16246
http://sbml.svn.sourceforge.net/sbml/?rev=16246&view=rev
Author: mhucka
Date: 2012-08-21 23:11:56 +0000 (Tue, 21 Aug 2012)
Log Message:
-----------
Tagging the 2.1.1 release.
Added Paths:
-----------
tags/test-suite/rel-2.1.1/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2012-08-21 22:45:17
|
Revision: 16245
http://sbml.svn.sourceforge.net/sbml/?rev=16245&view=rev
Author: mhucka
Date: 2012-08-21 22:45:10 +0000 (Tue, 21 Aug 2012)
Log Message:
-----------
Added makefile directives to clean the directories, so that when we generate
archives, we don't accidentally leave in things like old SED-ML files.
Modified Paths:
--------------
trunk/test-suite/Makefile
trunk/test-suite/NEWS.txt
Modified: trunk/test-suite/Makefile
===================================================================
--- trunk/test-suite/Makefile 2012-08-21 22:42:26 UTC (rev 16244)
+++ trunk/test-suite/Makefile 2012-08-21 22:45:10 UTC (rev 16245)
@@ -46,6 +46,9 @@
cases/semantic/%-model.html: cases/semantic/%-model.m
$(call make_html,$@)
+clean-html:
+ rm -f $(cases-html-files)
+
#
# 'make plots'
#
@@ -73,42 +76,47 @@
convert-all-svg-to-jpg:
java -jar src/imported/batik/batik-rasterizer.jar -m image/jpeg -q 0.9 $(cases-svg-files)
+clean-plots:
+ rm -f $(cases-svg-files)
+ rm -f $(cases-jpg-files)
+
#
# 'make sedml'
#
ifeq "`uname`" "Darwin"
define make_sedml_files
+ @echo "Creating SED-ML for $(1)"
env DYLD_LIBRARY_PATH="src/utilities/sedml:$(DYLD_LIBRARY_PATH)" \
mono ./src/utilities/sedml/GenerateSedML.exe -c `dirname $(1)` -a
endef
else
define make_sedml_files
+ @echo "Creating SED-ML for $(1)"
env LD_LIBRARY_PATH="src/utilities/sedml:$(DYLD_LIBRARY_PATH)" \
mono ./src/utilities/sedml/GenerateSedML.exe -c `dirname $(1)` -a
endef
endif
-cases-sbml-files = $(wildcard cases/semantic/*/*-sbml-l[1234]v[0-9].xml)
-cases-sedml-l1v2-files = $(patsubst %-l1v2.xml,%-l1v2-sedml.xml,$(cases-sbml-files))
-cases-sedml-l2v1-files = $(patsubst %-l2v1.xml,%-l2v1-sedml.xml,$(cases-sbml-files))
-cases-sedml-l2v2-files = $(patsubst %-l2v2.xml,%-l2v2-sedml.xml,$(cases-sbml-files))
-cases-sedml-l2v3-files = $(patsubst %-l2v3.xml,%-l2v3-sedml.xml,$(cases-sbml-files))
-cases-sedml-l2v4-files = $(patsubst %-l2v4.xml,%-l2v4-sedml.xml,$(cases-sbml-files))
-cases-sedml-l3v1-files = $(patsubst %-l3v1.xml,%-l3v1-sedml.xml,$(cases-sbml-files))
-all-sedml-files = $(cases-sedml-l1v2-files) \
- $(cases-sedml-l2v1-files) \
- $(cases-sedml-l2v2-files) \
- $(cases-sedml-l2v3-files) \
- $(cases-sedml-l2v4-files) \
- $(cases-sedml-l3v1-files)
+cases-sbml-files = $(wildcard cases/semantic/*/*-sbml-l[1234]v[0-9].xml)
+all-sedml-files := $(patsubst %-l1v2.xml,%-l1v2-sedml.xml,$(cases-sbml-files))
+all-sedml-files := $(patsubst %-l2v1.xml,%-l2v1-sedml.xml,$(all-sedml-files))
+all-sedml-files := $(patsubst %-l2v2.xml,%-l2v2-sedml.xml,$(all-sedml-files))
+all-sedml-files := $(patsubst %-l2v3.xml,%-l2v3-sedml.xml,$(all-sedml-files))
+all-sedml-files := $(patsubst %-l2v4.xml,%-l2v4-sedml.xml,$(all-sedml-files))
+all-sedml-files := $(patsubst %-l3v1.xml,%-l3v1-sedml.xml,$(all-sedml-files))
-sedml: $(all-sedml-files)
-
cases/semantic/%-sedml.xml: cases/semantic/%.xml src/utilities/sedml/GenerateSedML.exe
$(call make_sedml_files,$@)
+sedml: $(all-sedml-files)
+
+# Note: a simple rm -f $(all-sedml-files) doesn't work -- arg list is too long.
+clean-sedml:
+ $(foreach f,$(wildcard cases/semantic/*/*-sedml.xml),$(shell rm -f $f))
+
+
# -----------------------------------------------------------------------------
# Case archive, for the test runner
# -----------------------------------------------------------------------------
@@ -117,10 +125,11 @@
# ".zipexcludes" in this directory contains a list of files to be excluded
# from the zip archive created.
-today = $(shell date +"%F")
-ts-file = .cases-archive-date
-map-file = cases/semantic/.cases-tags-map
-contents = cases/semantic \
+today = $(shell date +"%F")
+cases-dist-name = sbml-test-cases-$(today).zip
+ts-file = .cases-archive-date
+map-file = cases/semantic/.cases-tags-map
+contents = cases/semantic \
$(ts-file) \
$(map-file) \
COPYING.html \
@@ -131,7 +140,7 @@
cases-dist: html plots sedml tags-map
@echo $(today) > $(ts-file)
make $(map-file)
- zip -r sbml-test-cases-$(today).zip $(contents) -x@.zipexcludes
+ zip -r $(cases-dist-name) $(contents) -x@.zipexcludes
@echo "---------------------------------------------------------------"
@echo "Next: upload zip file to SourceForge as updated test cases dist."
@echo "Please don't forget to do 'svn commit' for the time-stamp file."
@@ -142,7 +151,10 @@
@echo "Making tags map file:"
src/utilities/make-tag-map/make-tag-map.sh $(map-file)
+clean-cases-dist:
+ rm -f $(cases-dist-name)
+
# -----------------------------------------------------------------------------
# Standalone Application distribution
# -----------------------------------------------------------------------------
@@ -159,13 +171,19 @@
VERSION.txt \
docs/formatted/standalone-user-manual
dist-jar = src/front-ends/standalone/dist/SBMLTestSuite.jar
+dist-zip = $(dist-dir).zip
standalone-dist:
mkdir -p $(dist-dir)
cp -r $(dist-files) $(dist-dir)
cp $(dist-jar) $(dist-dir)
- zip -r $(dist-dir).zip $(dist-dir)
+ zip -r $(dist-zip) $(dist-dir)
+clean-dist:
+ rm -f $(dist-zip)
+ rm -rf $(dist-dir)
+
+
# -----------------------------------------------------------------------------
# make docs
# -----------------------------------------------------------------------------
@@ -218,13 +236,25 @@
README-HACKING.html: README-HACKING.txt
markdown README-HACKING.txt > README-HACKING.html
+clean-readme:
+ rm -f README-HACKING.html
+
# -----------------------------------------------------------------------------
-# Common special targets
+# Cleaning.
# -----------------------------------------------------------------------------
-.PHONY: docs html plots sedml readme-html
+clean: clean-readme clean-dist clean-cases-dist clean-html clean-plots clean-sedml
+
+# -----------------------------------------------------------------------------
+# Common special targets.
+# -----------------------------------------------------------------------------
+
+.PHONY: docs html plots sedml readme-html clean \
+ clean-readme clean-dist clean-cases-dist clean-html \
+ clean-plots clean-sedml
+
.SUFFIXES: .png .svg .jpg .csv .html .xml .txt
# -----------------------------------------------------------------------------
Modified: trunk/test-suite/NEWS.txt
===================================================================
--- trunk/test-suite/NEWS.txt 2012-08-21 22:42:26 UTC (rev 16244)
+++ trunk/test-suite/NEWS.txt 2012-08-21 22:45:10 UTC (rev 16245)
@@ -1,6 +1,31 @@
The Systems Biology Markup Language (SBML) Test Suite
NEWS -- history of user-visible changes
+=== Version 2.1.1 release (2012-08-21)
+
+General note: it is not clearly stated anywhere, but test case
+directories do not always contain all Level/Version combinations of
+SBML. This happens for cases that contain a feature handled
+differently in one SBML Level compared to another. In other words, in
+the individual cases/semantic/* directories, you may find models that
+are only provided in SBML Level 2 or Level 3 form, and this is normal;
+it does not indicate models are missing.
+
+* Bug fixes:
+
+ - In the version 2.1.0 cases archive distribution file, some case
+ directories contained SED-ML files even though there were no
+ corresponding SBML model. This happened for Level 3 versions of
+ some models and changed between releases 2.0 and 2.1; the Level 3
+ versions of some cases were split out as separate cases in release
+ 2.1, leaving only the Level 1-2 versions in the original test case
+ directory. Unfortunately, when we generated the distribution
+ archive, we didn't properly delete all SED-ML files before
+ regenerating them, and so some old SED-ML files were left from the
+ time before the Level 3 models were split out as new cases. This
+ problem was reported by Ilya Kiselev from DevelopmentOnTheEdge.com.
+
+
=== Version 2.1.0 release (2012-08-06)
* Bug fixes:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2012-08-21 22:42:32
|
Revision: 16244
http://sbml.svn.sourceforge.net/sbml/?rev=16244&view=rev
Author: mhucka
Date: 2012-08-21 22:42:26 +0000 (Tue, 21 Aug 2012)
Log Message:
-----------
Fixed typos that caused the "Wiky"-based HTML generator to fail with a spectacularly obscure error about "window not found".
Modified Paths:
--------------
trunk/test-suite/cases/semantic/00634/00634-model.m
trunk/test-suite/cases/semantic/00635/00635-model.m
trunk/test-suite/cases/semantic/00636/00636-model.m
trunk/test-suite/cases/semantic/00637/00637-model.m
trunk/test-suite/cases/semantic/00638/00638-model.m
trunk/test-suite/cases/semantic/00639/00639-model.m
Modified: trunk/test-suite/cases/semantic/00634/00634-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00634/00634-model.m 2012-08-21 19:41:13 UTC (rev 16243)
+++ trunk/test-suite/cases/semantic/00634/00634-model.m 2012-08-21 22:42:26 UTC (rev 16244)
@@ -19,7 +19,7 @@
The model contains one rule which assigns value to species S3:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Assignment | S3 | $multiply[k1, S2]$ |]
+ | Assignment | S3 | $multiply(k1, S2)$ |]
The assignmentRule applies the functionDefinition defined as:
Modified: trunk/test-suite/cases/semantic/00635/00635-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00635/00635-model.m 2012-08-21 19:41:13 UTC (rev 16243)
+++ trunk/test-suite/cases/semantic/00635/00635-model.m 2012-08-21 22:42:26 UTC (rev 16244)
@@ -19,7 +19,7 @@
The model contains one rule which assigns value to species S3:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Assignment | S3 | $multiply[k1, S2]$ |]
+ | Assignment | S3 | $multiply(k1, S2)$ |]
The assignmentRule applies the functionDefinition defined as:
Modified: trunk/test-suite/cases/semantic/00636/00636-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00636/00636-model.m 2012-08-21 19:41:13 UTC (rev 16243)
+++ trunk/test-suite/cases/semantic/00636/00636-model.m 2012-08-21 22:42:26 UTC (rev 16244)
@@ -19,7 +19,7 @@
The model contains one rule which assigns value to species S3:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Assignment | S3 | $multiply[k1, S2]$ |]
+ | Assignment | S3 | $multiply(k1, S2)$ |]
The assignmentRule applies the functionDefinition defined as:
Modified: trunk/test-suite/cases/semantic/00637/00637-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00637/00637-model.m 2012-08-21 19:41:13 UTC (rev 16243)
+++ trunk/test-suite/cases/semantic/00637/00637-model.m 2012-08-21 22:42:26 UTC (rev 16244)
@@ -19,7 +19,7 @@
The model contains one rule which assigns value to species S3:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Assignment | S3 | $multiply[k1, S2]$ |]
+ | Assignment | S3 | $multiply(k1, S2)$ |]
The assignmentRule applies the functionDefinition defined as:
Modified: trunk/test-suite/cases/semantic/00638/00638-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00638/00638-model.m 2012-08-21 19:41:13 UTC (rev 16243)
+++ trunk/test-suite/cases/semantic/00638/00638-model.m 2012-08-21 22:42:26 UTC (rev 16244)
@@ -19,7 +19,7 @@
The model contains one rule which assigns value to species S3:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Assignment | S3 | $multiply[k1, S2]$ |]
+ | Assignment | S3 | $multiply(k1, S2)$ |]
The assignmentRule applies the functionDefinition defined as:
Modified: trunk/test-suite/cases/semantic/00639/00639-model.m
===================================================================
--- trunk/test-suite/cases/semantic/00639/00639-model.m 2012-08-21 19:41:13 UTC (rev 16243)
+++ trunk/test-suite/cases/semantic/00639/00639-model.m 2012-08-21 22:42:26 UTC (rev 16244)
@@ -19,7 +19,7 @@
The model contains one rule which assigns value to species S3:
[{width:30em,margin-left:5em}| *Type* | *Variable* | *Formula* |
- | Assignment | S3 | $multiply[k1, S2]$ |]
+ | Assignment | S3 | $multiply(k1, S2)$ |]
The assignmentRule applies the functionDefinition defined as:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2012-08-21 19:41:24
|
Revision: 16243
http://sbml.svn.sourceforge.net/sbml/?rev=16243&view=rev
Author: mhucka
Date: 2012-08-21 19:41:13 +0000 (Tue, 21 Aug 2012)
Log Message:
-----------
Restored the MD5 attribute.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex
trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex
trunk/specifications/sbml-level-3/version-1/comp/spec/syntax.tex
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex 2012-08-16 22:02:48 UTC (rev 16242)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex 2012-08-21 19:41:13 UTC (rev 16243)
@@ -447,12 +447,12 @@
SBML Level~3 Package Specification for Hierarchical Model Composition,
Version~1, \sec{externalmodeldefinition-class}.) }
-%\consistencyRule{comp-20306}{The value of the \token{comp:\-md5}
-% attribute on an \ExternalModelDefinition object should match the
-% calculated MD5 checksum of the SBML document referenced by the
-% \token{comp:\-\-source} attribute. (References: SBML Level~3 Package
-% Specification for Hierarchical Model Composition, Version~1,
-% \sec{externalmodeldefinition-class}.) }
+\consistencyRule{comp-20306}{The value of the \token{comp:\-md5}
+ attribute, if present on an \ExternalModelDefinition object, should
+ match the calculated MD5 checksum of the SBML document referenced by
+ the \token{comp:\-\-source} attribute. (References: SBML Level~3
+ Package Specification for Hierarchical Model Composition, Version~1,
+ \sec{externalmodeldefinition-class}.) }
\validRule{comp-20307}{The value of a \token{comp:\-\-source} attribute
on an \ExternalModelDefinition object must always conform to the
@@ -466,11 +466,11 @@
Level~3 Package Specification for Hierarchical Model Composition,
Version~1, \sec{externalmodeldefinition-class}.) }
-%\validRule{comp-20309}{The value of a \token{comp:\-md5} attribute on an
-% \ExternalModelDefinition object must always conform to the syntax of
-% type \primtype{string}. (References: SBML Level~3 Package
-% Specification for Hierarchical Model Composition Package Version~1
-% \sec{externalmodeldefinition-class}.) }
+\validRule{comp-20309}{The value of a \token{comp:\-md5} attribute on an
+ \ExternalModelDefinition object must always conform to the syntax of
+ type \primtype{string}. (References: SBML Level~3 Package
+ Specification for Hierarchical Model Composition Package Version~1
+ \sec{externalmodeldefinition-class}.) }
\validRule{comp-20310}{An \ExternalModelDefinition object must not
reference an \ExternalModelDefinition in a different SBML document
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex 2012-08-16 22:02:48 UTC (rev 16242)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex 2012-08-21 19:41:13 UTC (rev 16243)
@@ -7,9 +7,9 @@
\packageTitle{Hierarchical Model Composition}
\packageVersion{Version 1 (Release Candidate 1)}
-\packageVersionDate{14 August 2012}
+\packageVersionDate{21 August 2012}
\packageGeneralURL{http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/comp}
-\packageThisVersionURL{http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/comp/14_August_2012}
+\packageThisVersionURL{http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/comp/XXXXX}
\author{%
\begin{tabular}{c>{\hspace{20pt}}c}
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/syntax.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/syntax.tex 2012-08-16 22:02:48 UTC (rev 16242)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/syntax.tex 2012-08-21 19:41:13 UTC (rev 16243)
@@ -285,9 +285,7 @@
\ExternalModelDefinition contains two required attributes
(\token{source} and \token{id}) and three optional attributes
-(\token{modelRef}
-%, \token{md5}
-and \token{name}). These attributes are
+(\token{modelRef}, \token{md5} and \token{name}). These attributes are
explained below.
@@ -384,61 +382,59 @@
\end{example}
+\paragraph{The \fixttspace\token{md5} attribute}
-%\paragraph{The \fixttspace\token{md5} attribute}
+The optional \token{md5} attribute takes a \primtype{string} value. If
+set, it must be an MD5 checksum value computed over the document
+referenced by \token{source}. This checksum can serve as a data
+integrity check over the contents of the \token{source}. Applications
+may use this to verify that the contents have not changed since the time
+that the \ExternalModelDefinition reference was constructed. The
+procedure for using the \token{md5} attribute is described in
+\tab{md5-procedures}.
-%The optional \token{md5} attribute takes a \primtype{string} value. If
-%set, it must be an MD5 checksum value computed over the document
-%referenced by \token{source}. This checksum can be used as a data integrity
-%check over the contents of the \token{source}. Applications may use
-%this to verify that the contents have not changed since the time that
-%the \ExternalModelDefinition reference was constructed. The procedure
-%for using the \token{md5} attribute is described in
-%\tab{md5-procedures}.
+\begin{table}[thb]
+ \begin{edtable}{tabular}{p{1in}l@{\hspace{0.75ex}}p{5in}}
+ \toprule
+ \textbf{Case} & \multicolumn{2}{l}{\textbf{Procedure}} \\
+ \midrule
+ Creating and writing & 1.& Compute the MD5 hash for the document located at \token{source}.\\
+ an SBML document & 2.& Store the hash value as the value of the \token{md5} attribute. \\
+ \midrule
+ Reading an SBML & 1.& Read the value of the \token{md5} attribute.\\
+ document & 2.& Read the document at the location indicated by the
+ \token{source} attribute value.\\
+ & 3.& Compute the MD5 hash for the document.\\
+ & 4.& Compare the computed MD5 value to the value in the \token{md5} attribute.
+ If they are identical, assume the document has not changed since the
+ time the \ExternalModelDefinition object was defined; if the values
+ are different, assume that the document indicated by \token{source}
+ has changed. \\
+ \bottomrule
+ \end{edtable}
+ \caption{Procedures for using the \token{md5} attribute on
+ \ExternalModelDefinition.}
+ \label{md5-procedures}
+\end{table}
-%\begin{table}[thb]
-% \begin{edtable}{tabular}{p{1in}l@{\hspace{0.75ex}}p{5in}}
-% \toprule
-% \textbf{Case} & \multicolumn{2}{l}{\textbf{Procedure}} \\
-% \midrule
-% Creating and writing & 1.& Compute the MD5 hash for the document located at \token{source}.\\
-% an SBML document & 2.& Store the hash value as the value of the \token{md5} attribute. \\
-% \midrule
-% Reading an SBML & 1.& Read the value of the \token{md5} attribute.\\
-% document & 2.& Read the document at the location indicated by the
-% \token{source} attribute value.\\
-% & 3.& Compute the MD5 hash for the document.\\
-% & 4.& Compare the computed MD5 value to the value in the \token{md5} attribute.
-% If they are identical, assume the document has not changed since the
-% time the \ExternalModelDefinition object was defined; if the values
-% are different, assume that the document indicated by \token{source}
-% has changed. \\
-% \bottomrule
-% \end{edtable}
-% \caption{Procedures for using the \token{md5} attribute on
-% \ExternalModelDefinition.}
-% \label{md5-procedures}
-%\end{table}
+Software tools encountering a difference in the MD5 checksums should
+warn their users that a discrepancy exists, because a difference in the
+documents may imply a difference in the mathematical interpretation of
+the models.
-%Software tools encountering a difference in the MD5 checksums should
-%warn their users that a discrepancy exists, because a difference in the
-%documents may imply a difference in the mathematical interpretation of
-%the models.
+Note that the MD5 approach is not without limitations. An MD5 hash is
+typically expressed as a 32-digit hexadecimal number. If a difference
+arises in the checksum values, there is no way to determine the cause of
+the difference without an component-by-component comparison of the
+models. (Even a difference in annotations, which cannot affect a
+models' mathematical interpretations, will result in a difference in the
+MD5 checksum values.) On the other hand, it is also not impossible that
+two different documents yield the \emph{same} MD5 hash value (due to
+hash collision), although it is extremely unlikely in practice. In any
+event, the MD5 approach is intended as an optional, simple and fast data
+integrity check, and not a final answer.
-%Note that the MD5 approach is not without limitations. An MD5 hash is
-%typically expressed as a 32-digit hexadecimal number. If a difference
-%arises in the checksum values, there is no way to determine the cause of
-%the difference without an component-by-component comparison of the
-%models. (Even a difference in annotations, which cannot affect a models' mathematical
-%interpretations, will result in a difference in the MD5 checksum
-%values.) On the other hand, it is also not impossible that two
-%different documents yield the \emph{same} MD5 hash value, although it is
-%extremely unlikely in practice. In any event, the MD5 approach is
-%intended as an optional, simple and fast data integrity check, and not a
-%final answer.
-
-% -----------------------------------------------------------------------------
\subsection{The extended \class{Model} class}
\label{model-class}
\label{listofsubmodels-class}
@@ -453,7 +449,6 @@
the \Port class; the class \Submodel is defined in \sec{submodel-class}.
\begin{figure}[hbt]
- \vspace*{1em} % Hack to improve the page break
\begin{overpic}{figs/extended-model-uml}
\put(70.5,36.9){\emph{\sec*{submodel-class}}}
\put(88.25,23.75){\emph{\sec*{sbaseref-class}}}
@@ -685,11 +680,10 @@
object.
Because the model namespace is defined per SBML document, it is possible
-to define and include a new model namespace by creating a new document,
-then importing one or more of those models using the
+to define and include a new model namespace by creating a new document
+and then importing one or more of those models using the
\ExternalModelDefinition class. \sec{namespaces} discusses the
-important topic of identifier scoping in the Hierarchical Model
-Composition package.
+important topic of identifier scoping.
\paragraph{The \fixttspace\token{timeConversionFactor} attribute}
@@ -852,18 +846,19 @@
shown in \fig*{extended-sbase-uml}.
\begin{figure}[hbt]
+ \vspace*{-1ex}
\begin{overpic}{figs/extended-sbase-uml}
\put(88.5,40.25){\emph{\sec*{sbaseref-class}}}
\end{overpic}
- \vspace*{-2ex}
+ \vspace*{-3ex}
\caption{The extension of \SBase and the definition of the
\ListOfReplacedElements and \ReplacedElement classes. The \SBaseRef
class is defined in \sec{sbaseref-class}.}
\label{extended-sbase-uml}
\end{figure}
-Since \SBase in SBML is the abstract base class of all other SBML object
-classes, the extension of \SBase means all SBML objects gain the ability
+\SBase in SBML is the abstract base class of all other SBML object
+classes; consequently, the extension of \SBase means all SBML objects gain the ability
to define how they replace (or are replaced by) components in submodels.
Replacements are a general mechanism that serve multiple purposes. At
their most basic, they allow a model builder to make a statement of the
@@ -1088,11 +1083,10 @@
\subsubsection{The \fixttspace\tokenNC{replacedBy} subcomponent}
-As mentioned above, the extension of \SBase defined in
-\fig{extended-sbase-uml} introduces a new optional subcomponent,
-\token{replacedBy}. Its value, if present on a given \SBase-derived
-object, must be a single object of the \ReplacedBy class, described
-below.
+The extension of \SBase defined in \fig{extended-sbase-uml} introduces a
+new optional subcomponent, \token{replacedBy}. Its value, if present on
+a given \SBase-derived object, must be a single object of the
+\ReplacedBy class, described below.
\subsubsection{The \ReplacedBy class}
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|
|
From: <mh...@us...> - 2012-08-16 22:02:55
|
Revision: 16242
http://sbml.svn.sourceforge.net/sbml/?rev=16242&view=rev
Author: mhucka
Date: 2012-08-16 22:02:48 +0000 (Thu, 16 Aug 2012)
Log Message:
-----------
Switched the order of 5.2 and 5.3, per Chris Myers's recommendation.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/spec/best-practices.tex
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/best-practices.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/best-practices.tex 2012-08-16 18:08:16 UTC (rev 16241)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/best-practices.tex 2012-08-16 22:02:48 UTC (rev 16242)
@@ -87,53 +87,6 @@
component that you wish to reference.
-\subsection{Best practices for deletions and replacements}
-\label{best-practices-deletions}
-\label{best-practices-replacements}
-
-If you replace or delete an element that itself has children, those
-children are considered to be deleted unless replaced. This can have
-repercussions on other aspects of a model; for example, if you replace a
-\KineticLaw object, any annotations that referred to the meta
-identifiers of its local parameters will become invalid. One approach
-to dealing with this, in the case of annotations, is to explicitly
-delete the no-longer-valid annotations or replace them by new ones. It
-is legal to delete explicitly a component that is deleted by
-implication, if you need to refer to it elsewhere---the resulting model
-is exactly the same.
-
-% From Chris:
-
-%In an SBaseRef, an element can potentially be referenced in three ways, by its identifier (SId), port identifier (PortId), or meta identifier (metaId). It is best if an element is referred to in a consistent way. Therefore, when an element can be referred to using a PortId, this should be preferred. The second choice should be to refer to its SId. Only as a last resort should it be referred to by its metaId.
-
-%In the case that it does not have any of these identifiers, there is no way to refer to the element in a deletion or replacement defined in this specification. In this case, a copy must be made of the original model such that it can be modified. (Presumably, the original model was readable in the first place, or else composition would have been impossible anyway.) Copying a model and making one?s own version may have additional benefits, such as the ability to control versions explicitly and references. A second method may be to delete or replace the parent object of the element you wish to replace, assuming that element has an identifier, meta identifier, or port identifier. When this is performed, the errant element will be deleted implicitly, allowing you to create replacements in the containing model without overlapping functionality.
-
-% \subsection{Best practices for deletions and replacements}
-% \label{best-practices-deletions}
-% \label{best-practices-replacements}
-
-% Note that there may be model composition situations in which a model
-% contains elements that do not have an identifier, nor a meta identifier,
-% nor a port identifier. In that case, there is no way to refer to it
-% using the with the \Deletion or \ReplacedElement objects defined in this specification. A viable alternative to use in
-% that case is to copy the original model and modify it, either to perform
-% the desired deletions directly or to add the necessary identifiers so
-% that \Deletion objects can be defined and used in a submodel.
-% (Presumably, the original model was readable in the first place, or else
-% composition would have been impossible anyway.) Copying a model and
-% making one's own version may have additional benefits, such as the
-% ability to control versions explicitly and references. A second method may be to delete or replace the parent object of the element you wish to replace, assuming that element has an identifier, meta identifier, or port identifier. When this is performed, the errant element will be deleted implicitly, allowing you to create replacements in the containing model without overlapping functionality.
-
-% .... However, don't go overboard with this capability: it is legal in
-% this scheme to replace an Event with a Species, but it is probably never
-% wise. We expect that tools written to produce hierarchical SBML will
-% have their own restrictions that make sense in context. This relaxation
-% of the official validation allows freer intercompatibility with other
-% package extensions-it may be that a Species could be validly replaced by
-% a multi-component species, or it may not, but we will rely here on the
-% normal validation rules that package supplies to dictate the results.
-
-
\subsection{Best practices for using ports}
\label{best-practices-ports}
@@ -199,3 +152,51 @@
% elements be listed under all M replacement elements, to make things
% easier on visualization software that may try to display the results.
+
+
+\subsection{Best practices for deletions and replacements}
+\label{best-practices-deletions}
+\label{best-practices-replacements}
+
+If you replace or delete an element that itself has children, those
+children are considered to be deleted unless replaced. This can have
+repercussions on other aspects of a model; for example, if you replace a
+\KineticLaw object, any annotations that referred to the meta
+identifiers of its local parameters will become invalid. One approach
+to dealing with this, in the case of annotations, is to explicitly
+delete the no-longer-valid annotations or replace them by new ones. It
+is legal to delete explicitly a component that is deleted by
+implication, if you need to refer to it elsewhere---the resulting model
+is exactly the same.
+
+% From Chris:
+
+%In an SBaseRef, an element can potentially be referenced in three ways, by its identifier (SId), port identifier (PortId), or meta identifier (metaId). It is best if an element is referred to in a consistent way. Therefore, when an element can be referred to using a PortId, this should be preferred. The second choice should be to refer to its SId. Only as a last resort should it be referred to by its metaId.
+
+%In the case that it does not have any of these identifiers, there is no way to refer to the element in a deletion or replacement defined in this specification. In this case, a copy must be made of the original model such that it can be modified. (Presumably, the original model was readable in the first place, or else composition would have been impossible anyway.) Copying a model and making one?s own version may have additional benefits, such as the ability to control versions explicitly and references. A second method may be to delete or replace the parent object of the element you wish to replace, assuming that element has an identifier, meta identifier, or port identifier. When this is performed, the errant element will be deleted implicitly, allowing you to create replacements in the containing model without overlapping functionality.
+
+% \subsection{Best practices for deletions and replacements}
+% \label{best-practices-deletions}
+% \label{best-practices-replacements}
+
+% Note that there may be model composition situations in which a model
+% contains elements that do not have an identifier, nor a meta identifier,
+% nor a port identifier. In that case, there is no way to refer to it
+% using the with the \Deletion or \ReplacedElement objects defined in this specification. A viable alternative to use in
+% that case is to copy the original model and modify it, either to perform
+% the desired deletions directly or to add the necessary identifiers so
+% that \Deletion objects can be defined and used in a submodel.
+% (Presumably, the original model was readable in the first place, or else
+% composition would have been impossible anyway.) Copying a model and
+% making one's own version may have additional benefits, such as the
+% ability to control versions explicitly and references. A second method may be to delete or replace the parent object of the element you wish to replace, assuming that element has an identifier, meta identifier, or port identifier. When this is performed, the errant element will be deleted implicitly, allowing you to create replacements in the containing model without overlapping functionality.
+
+% .... However, don't go overboard with this capability: it is legal in
+% this scheme to replace an Event with a Species, but it is probably never
+% wise. We expect that tools written to produce hierarchical SBML will
+% have their own restrictions that make sense in context. This relaxation
+% of the official validation allows freer intercompatibility with other
+% package extensions-it may be that a Species could be validly replaced by
+% a multi-component species, or it may not, but we will rely here on the
+% normal validation rules that package supplies to dictate the results.
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mh...@us...> - 2012-08-16 18:08:22
|
Revision: 16241
http://sbml.svn.sourceforge.net/sbml/?rev=16241&view=rev
Author: mhucka
Date: 2012-08-16 18:08:16 +0000 (Thu, 16 Aug 2012)
Log Message:
-----------
Added an explicit \clearpage to move a page break to a better location.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex 2012-08-16 18:07:52 UTC (rev 16240)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/apdx-validation.tex 2012-08-16 18:08:16 UTC (rev 16241)
@@ -293,6 +293,8 @@
Specification for Hierarchical Model Composition, Version~1,
\sec{replacedelement-deletion}.) }
+\clearpage
+
\validRule{comp-10310}{The value of a
\token{comp:\-con\-version\-Factor} attribute on a \ReplacedElement
object must always conform to the syntax of the SBML data type
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|
|
From: <mh...@us...> - 2012-08-16 18:07:58
|
Revision: 16240
http://sbml.svn.sourceforge.net/sbml/?rev=16240&view=rev
Author: mhucka
Date: 2012-08-16 18:07:52 +0000 (Thu, 16 Aug 2012)
Log Message:
-----------
We're going to try to include the best practices section after all.
Modified Paths:
--------------
trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex
Modified: trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex 2012-08-16 18:07:34 UTC (rev 16239)
+++ trunk/specifications/sbml-level-3/version-1/comp/spec/main.tex 2012-08-16 18:07:52 UTC (rev 16240)
@@ -51,7 +51,7 @@
\input{background}
\input{syntax}
\input{examples}
-%\input{best-practices}
+\input{best-practices}
%\input{other}
\setcounter{secnumdepth}{3}
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