[med-svn] [libsbml] 03/14: Merge tag 'upstream/5.13.0+dfsg'
Andreas Tille
tille at debian.org
Thu Dec 15 10:49:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libsbml.
commit 27d47f60e4c9943487a474ef83eb0e80c6af1d3c
Merge: 78971d8 e54fc91
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 14 10:36:22 2016 +0100
Merge tag 'upstream/5.13.0+dfsg'
Upstream version 5.13.0+dfsg
CMakeLists.txt | 14 +-
LICENSE.html | 2 +-
LICENSE.txt | 2 +-
Makefile.in | 2 +-
NEWS.txt | 146 +
README.txt | 2 +-
VERSION.txt | 2 +-
VERSION_PACKAGES.ac | 11 +-
arrays-package.cmake | 2 +-
cmake_uninstall.cmake.in | 244 +-
common.cmake | 2 +-
comp-package.cmake | 2 +-
config/bzip2.m4 | 2 +-
config/chk_swig_version.sh.in | 2 +-
config/csharp.m4 | 2 +-
config/doxygen.m4 | 2 +-
config/expat.m4 | 2 +-
config/java.m4 | 2 +-
config/libcheck.m4 | 4 +-
config/machine.m4 | 2 +-
config/makefile-common-actions.mk | 2 +-
config/makefile-common-vars.mk.in | 3 +-
config/matlab.m4 | 2 +-
config/octave.m4 | 2 +-
config/perl.m4 | 2 +-
config/platform.m4 | 2 +-
config/printJavaDataModel.java | 2 +-
config/python.m4 | 2 +-
config/ruby.m4 | 20 +-
config/runldpath.m4 | 2 +-
config/swig.m4 | 2 +-
config/xercesc.m4 | 2 +-
config/zlib.m4 | 2 +-
configure | 512 +-
configure.ac | 31 +-
distrib-package.cmake | 2 +-
docs/CMakeLists.txt | 2 +-
docs/Makefile.in | 2 +-
docs/src/Makefile.in | 14 +-
docs/src/common-text/astnode-types.html | 2 +-
.../common-text/libsbml-group-groups-intro.html.in | 30 +
docs/src/common-text/libsbml-installation.html.in | 8 +
docs/src/common-text/libsbml-issues.html | 29 +-
docs/src/common-text/pkg-marker-groups.html | 1 +
docs/src/common-text/pkg-marker-groups.txt | 1 +
docs/src/css/libsbml-base-stylesheet.css | 5 +
docs/src/css/libsbml-doxygen-stylesheet.css | 2 +-
docs/src/css/libsbml-python-stylesheet.css | 10 +-
docs/src/doxygen-config-c.txt.cmake | 4 +
docs/src/doxygen-config-c.txt.in | 4 +
docs/src/doxygen-config-common.txt | 4 +
docs/src/doxygen-config-common.txt.cmake | 4 +
docs/src/doxygen-config-cpp.txt.cmake | 3 +-
docs/src/doxygen-config-cpp.txt.in | 3 +-
docs/src/doxygen-config-csharp.txt.cmake | 8 +-
docs/src/doxygen-config-csharp.txt.in | 4 +-
docs/src/doxygen-config-python.txt.cmake | 7 +-
docs/src/doxygen-config-python.txt.in | 3 +-
docs/src/doxygen-layout-c.xml | 1 +
docs/src/doxygen-layout-cpp.xml | 1 +
docs/src/doxygen-layout-csharp.xml | 1 +
docs/src/doxygen-layout-python.xml | 1 +
docs/src/filters/doc-filter-c.py | 2 +-
docs/src/filters/doc-filter-csharp.py | 2 +-
docs/src/filters/doc-filter-python.py | 6 +-
.../java-substitutions/GroupsPkgNamespaces.java | 106 +
.../java-substitutions/libsbmlConstants.java.in | 394 +-
docs/src/libsbml-coding.txt | 7 +-
docs/src/libsbml-csharp-example-files.txt | 7 +
docs/src/libsbml-example-files.txt | 19 +
docs/src/libsbml-groups.txt | 6 +
docs/src/libsbml-installation-guide.txt | 1 +
docs/src/libsbml-java-example-files.html | 18 +
docs/src/libsbml-python-example-files.txt | 12 +
.../python-substitutions/GroupsPkgNamespaces.py | 72 +
docs/src/python-substitutions/libsbml.py | 417 ++
docs/src/utilities/compare-classes.py | 2 +-
docs/src/utilities/compare-constants.py | 2 +-
docs/src/utilities/generate-class-name-list.py | 2 +-
docs/src/utilities/generate-converters-list.py | 2 +-
.../utilities/generate-cplusplus-class-names.py | 2 +-
docs/src/utilities/generate-extensions-summary.py | 4 +-
docs/src/utilities/generate-pkg-stylesheet.py | 47 +-
dyn-package.cmake | 2 +-
examples/CMakeLists.txt | 2 +-
examples/c++/CMakeLists.txt | 2 +-
examples/c++/Makefile.in | 2 +-
examples/c++/addCVTerms.cpp | 2 +-
examples/c++/addCustomValidator.cpp | 2 +-
examples/c++/addModelHistory.cpp | 2 +-
examples/c++/addingEvidenceCodes_1.cpp | 2 +-
examples/c++/addingEvidenceCodes_2.cpp | 2 +-
examples/c++/appendAnnotation.cpp | 2 +-
examples/c++/arrays/CMakeLists.txt | 2 +-
examples/c++/callExternalValidator.cpp | 2 +-
examples/c++/comp/CMakeLists.txt | 2 +-
examples/c++/comp/Makefile.in | 2 +-
examples/c++/comp/SBMLHttpResolverExample.cpp | 2 +-
examples/c++/comp/flattenModel.cpp | 2 +-
examples/c++/comp/flattenModelAdvanced.cpp | 2 +-
examples/c++/comp/spec_example1.cpp | 2 +-
examples/c++/comp/spec_example2.cpp | 2 +-
examples/c++/comp/spec_example3.cpp | 2 +-
examples/c++/comp/spec_example4.cpp | 2 +-
examples/c++/convertReactions.cpp | 214 +-
examples/c++/convertSBML.cpp | 2 +-
examples/c++/convertToL1V1.cpp | 244 +-
examples/c++/createExampleSBML.cpp | 2 +-
examples/c++/dyn/CMakeLists.txt | 2 +-
examples/c++/dyn/dyn_example1.cpp | 2 +-
examples/c++/dyn/dyn_example2.cpp | 2 +-
examples/c++/echoSBML.cpp | 2 +-
examples/c++/fbc/CMakeLists.txt | 2 +-
examples/c++/fbc/Makefile.in | 2 +-
examples/c++/fbc/convertCobraToFbc.cpp | 2 +-
examples/c++/fbc/convertFbcToCobra.cpp | 2 +-
examples/c++/fbc/convertFbcV1ToV2.cpp | 2 +-
examples/c++/fbc/convertFbcV2ToV1.cpp | 2 +-
examples/c++/fbc/fbc_example1.cpp | 2 +-
examples/c++/getAllElementsWithNotes.cpp | 2 +-
examples/c++/groups/CMakeLists.txt | 4 +-
examples/c++/groups/example1.cpp | 121 -
examples/c++/groups/example2.cpp | 321 -
examples/c++/groups/groups_example1.cpp | 122 +
examples/c++/groups/groups_example2.cpp | 323 +
examples/c++/inferUnits.cpp | 2 +-
examples/c++/inlineFunctionDefintions.cpp | 2 +-
examples/c++/layout/CMakeLists.txt | 2 +-
examples/c++/layout/Makefile.in | 2 +-
examples/c++/layout/addLayout.cpp | 2 +-
examples/c++/layout/convertLayout.cpp | 2 +-
examples/c++/multi/multi_example1.cpp | 4 -
examples/c++/multi/multi_example3.cpp | 20 +-
examples/c++/printAnnotation.cpp | 2 +-
examples/c++/printMath.cpp | 2 +-
examples/c++/printNotes.cpp | 2 +-
examples/c++/printRegisteredPackages.cpp | 2 +-
examples/c++/printSBML.cpp | 2 +-
examples/c++/printSupported.cpp | 2 +-
examples/c++/printUnits.cpp | 2 +-
examples/c++/promoteParameters.cpp | 2 +-
examples/c++/qual/CMakeLists.txt | 2 +-
examples/c++/qual/Makefile.in | 2 +-
examples/c++/qual/qual_example1.cpp | 2 +-
examples/c++/readSBML.cpp | 2 +-
examples/c++/renameSId.cpp | 2 +-
examples/c++/rngvalidator.cpp | 2 +-
examples/c++/setIdFromNames.cpp | 2 +-
examples/c++/setNamesFromIds.cpp | 2 +-
examples/c++/stripPackage.cpp | 2 +-
examples/c++/translateL3Math.cpp | 2 +-
examples/c++/translateMath.cpp | 2 +-
examples/c++/unsetAnnotation.cpp | 2 +-
examples/c++/unsetNotes.cpp | 2 +-
examples/c++/util.c | 2 +-
examples/c++/util.h | 2 +-
examples/c++/validateSBML.cpp | 2 +-
examples/c/CMakeLists.txt | 2 +-
examples/c/FormulaGraphvizFormatter.h | 2 +-
examples/c/Makefile.in | 2 +-
examples/c/addCVTerms.c | 2 +-
examples/c/addModelHistory.c | 2 +-
examples/c/addingEvidenceCodes_1.c | 2 +-
examples/c/addingEvidenceCodes_2.c | 2 +-
examples/c/appendAnnotation.c | 2 +-
examples/c/comp/CMakeLists.txt | 2 +-
examples/c/comp/Makefile.in | 2 +-
examples/c/comp/flattenModel.c | 2 +-
examples/c/comp/spec_example1.c | 2 +-
examples/c/convertSBML.c | 2 +-
examples/c/createExampleSBML.c | 2 +-
examples/c/drawMath.c | 2 +-
examples/c/echoSBML.c | 2 +-
examples/c/printAnnotation.c | 2 +-
examples/c/printMath.c | 2 +-
examples/c/printNotes.c | 2 +-
examples/c/printRegisteredPackages.c | 2 +-
examples/c/printSBML.c | 2 +-
examples/c/printSupported.c | 2 +-
examples/c/printUnits.c | 2 +-
examples/c/promoteParameters.c | 2 +-
examples/c/readSBML.c | 2 +-
examples/c/stripPackage.c | 2 +-
examples/c/translateL3Math.c | 2 +-
examples/c/translateMath.c | 2 +-
examples/c/unsetAnnotation.c | 2 +-
examples/c/unsetNotes.c | 2 +-
examples/c/util.c | 2 +-
examples/c/util.h | 2 +-
examples/c/validateSBML.c | 2 +-
examples/comp-package.cmake | 2 +-
examples/csharp/CMakeLists.txt | 2 +-
examples/csharp/GetAllElementsWithNotes.cs | 2 +-
examples/csharp/Makefile.in | 2 +-
examples/csharp/SetIdFromNames.cs | 2 +-
examples/csharp/addCVTerms.cs | 2 +-
examples/csharp/addCustomValidator.cs | 2 +-
examples/csharp/addModelHistory.cs | 2 +-
examples/csharp/addingEvidenceCodes_1.cs | 2 +-
examples/csharp/addingEvidenceCodes_2.cs | 2 +-
examples/csharp/appendAnnotation.cs | 2 +-
examples/csharp/callExternalValidator.cs | 2 +-
examples/csharp/comp/CMakeLists.txt | 2 +-
examples/csharp/comp/CompExample1.cs | 2 +-
examples/csharp/comp/CustomResolver.cs | 147 +
examples/csharp/comp/FlattenModel.cs | 2 +-
examples/csharp/comp/SpecExample1.cs | 2 +-
examples/csharp/comp/SpecExample2.cs | 2 +-
examples/csharp/comp/SpecExample3.cs | 2 +-
examples/csharp/comp/SpecExample4.cs | 2 +-
examples/csharp/convertSBML.cs | 2 +-
examples/csharp/createExampleSBML.cs | 2 +-
examples/csharp/echoSBML.cs | 2 +-
examples/csharp/evaluateCustomMath.cs | 190 +-
examples/csharp/fbc/CMakeLists.txt | 2 +-
examples/csharp/fbc/convertCobraToFbc.cs | 2 +-
examples/csharp/fbc/convertFbcToCobra.cs | 2 +-
examples/csharp/fbc/fbc_example1.cs | 2 +-
examples/csharp/groups/CMakeLists.txt | 52 +-
.../groups/{example1.cs => groups_example1.cs} | 0
examples/csharp/inlineInitialAssignments.cs | 160 +-
examples/csharp/layout/CMakeLists.txt | 2 +-
examples/csharp/printAnnotation.cs | 2 +-
examples/csharp/printMath.cs | 2 +-
examples/csharp/printNotes.cs | 2 +-
examples/csharp/printRegisteredPackages.cs | 2 +-
examples/csharp/printSBML.cs | 2 +-
examples/csharp/printUnits.cs | 2 +-
examples/csharp/printsupported.cs | 2 +-
examples/csharp/promoteParameters.cs | 2 +-
examples/csharp/qual/CMakeLists.txt | 2 +-
examples/csharp/qual/qual_example1.cs | 2 +-
examples/csharp/readSBML.cs | 2 +-
examples/csharp/replaceOneFD.cs | 226 +-
examples/csharp/stripPackage.cs | 2 +-
examples/csharp/translateMath.cs | 2 +-
examples/csharp/unsetAnnotation.cs | 2 +-
examples/csharp/unsetNotes.cs | 2 +-
examples/csharp/validateSBML.cs | 2 +-
examples/dyn-package.cmake | 2 +-
examples/fbc-package.cmake | 2 +-
examples/java/CMakeLists.txt | 2 +-
examples/java/Makefile.in | 2 +-
examples/java/addCVTerms.java | 2 +-
examples/java/addCustomValidator.java | 2 +-
examples/java/addModelHistory.java | 2 +-
examples/java/addingEvidenceCodes_1.java | 2 +-
examples/java/addingEvidenceCodes_2.java | 2 +-
examples/java/appendAnnotation.java | 2 +-
examples/java/callExternalValidator.java | 2 +-
examples/java/comp/CMakeLists.txt | 3 +-
examples/java/comp/customResolver.java | 220 +
examples/java/comp/flattenModel.java | 2 +-
examples/java/convertSBML.java | 2 +-
examples/java/createExampleSBML.java | 2 +-
examples/java/echoSBML.java | 2 +-
examples/java/evaluateCustomMath.java | 272 +-
examples/java/evaluateMath.java | 2 +-
examples/java/fbc/CMakeLists.txt | 2 +-
examples/java/fbc/convertCobraToFbc.java | 2 +-
examples/java/fbc/convertFbcToCobra.java | 2 +-
examples/java/fbc/fbc_example1.java | 2 +-
examples/java/getAllElementsWithNotes.java | 2 +-
examples/java/groups/CMakeLists.txt | 80 +-
examples/java/groups/example1.java | 124 -
examples/java/groups/groups_example1.java | 124 +
examples/java/inlineInitialAssignments.java | 244 +-
examples/java/layout/CMakeLists.txt | 2 +-
examples/java/layout/SimpleLayoutConverter.java | 354 +-
examples/java/printAnnotation.java | 2 +-
examples/java/printMath.java | 2 +-
examples/java/printNotes.java | 2 +-
examples/java/printRegisteredPackages.java | 2 +-
examples/java/printSBML.java | 2 +-
examples/java/printUnits.java | 2 +-
examples/java/printsupported.java | 2 +-
examples/java/promoteParameters.java | 2 +-
examples/java/qual/CMakeLists.txt | 2 +-
examples/java/qual/qual_example1.java | 2 +-
examples/java/readSBML.java | 2 +-
examples/java/replaceOneFD.java | 306 +-
examples/java/setIdFromNames.java | 2 +-
examples/java/spatial/CMakeLists.txt | 2 +-
examples/java/spatial/spatial_example1.java | 2 +-
examples/java/stripPackage.java | 2 +-
examples/java/translateMath.java | 2 +-
examples/java/unsetAnnotation.java | 2 +-
examples/java/unsetNotes.java | 2 +-
examples/java/validateSBML.java | 2 +-
examples/javascript/addCVTerms.js | 2 +-
examples/javascript/addModelHistory.js | 2 +-
examples/javascript/addingEvidenceCodes_1.js | 2 +-
examples/javascript/addingEvidenceCodes_2.js | 2 +-
examples/javascript/appendAnnotation.js | 2 +-
examples/javascript/callExternalValidator.js | 2 +-
examples/javascript/convertSBML.js | 2 +-
examples/javascript/createExampleSBML.js | 2 +-
examples/javascript/echoSBML.js | 2 +-
examples/javascript/printAnnotation.js | 2 +-
examples/javascript/printMath.js | 2 +-
examples/javascript/printNotes.js | 2 +-
examples/javascript/printRegisteredPackages.js | 2 +-
examples/javascript/printSBML.js | 2 +-
examples/javascript/printUnits.js | 2 +-
examples/javascript/printsupported.js | 2 +-
examples/javascript/promoteParameters.js | 2 +-
examples/javascript/readSBML.js | 2 +-
examples/javascript/stripPackage.js | 2 +-
examples/javascript/translateMath.js | 2 +-
examples/javascript/unsetAnnotation.js | 2 +-
examples/javascript/unsetNotes.js | 2 +-
examples/javascript/validateSBML.js | 2 +-
examples/layout-package.cmake | 2 +-
examples/perl/addCVTerms.pl | 2 +-
examples/perl/addCustomValidator.pl | 2 +-
examples/perl/addModelHistory.pl | 2 +-
examples/perl/addingEvidenceCodes_1.pl | 2 +-
examples/perl/addingEvidenceCodes_2.pl | 2 +-
examples/perl/appendAnnotation.pl | 2 +-
examples/perl/callExternalValidator.pl | 2 +-
examples/perl/comp/flattenModel.pl | 2 +-
examples/perl/createExampleSBML.pl | 2 +-
examples/perl/echoSBML.pl | 2 +-
examples/perl/fbc/convertCobraToFbc.pl | 2 +-
examples/perl/fbc/convertFbcToCobra.pl | 2 +-
examples/perl/fbc/example1.pl | 2 +-
.../groups/{example1.pl => groups_example1.pl} | 0
examples/perl/printAnnotation.pl | 2 +-
examples/perl/printNotes.pl | 2 +-
examples/perl/printRegisteredPackages.pl | 2 +-
examples/perl/printUnits.pl | 2 +-
examples/perl/printsupported.pl | 2 +-
examples/perl/promoteParameters.pl | 2 +-
examples/perl/stripPackage.pl | 2 +-
examples/perl/unsetAnnotation.pl | 2 +-
examples/perl/unsetNotes.pl | 2 +-
examples/python/addCVTerms.py | 2 +-
examples/python/addCustomValidator.py | 2 +-
examples/python/addModelHistory.py | 2 +-
examples/python/addingEvidenceCodes_1.py | 2 +-
examples/python/addingEvidenceCodes_2.py | 2 +-
examples/python/appendAnnotation.py | 2 +-
examples/python/callExternalValidator.py | 2 +-
examples/python/comp/flattenModel.py | 2 +-
examples/python/convertSBML.py | 2 +-
examples/python/createExampleSBML.py | 2 +-
examples/python/createSimpleModel.py | 2 +-
examples/python/dyn/dyn_example1.py | 2 +-
examples/python/dyn/dyn_example2.py | 2 +-
examples/python/echoSBML.py | 2 +-
examples/python/evaluateCustomMath.py | 162 +-
examples/python/fbc/convertCobraToFbc.py | 2 +-
examples/python/fbc/convertFbcToCobra.py | 2 +-
examples/python/fbc/fbc_example1.py | 2 +-
examples/python/getAllElementsWithNotes.py | 2 +-
examples/python/groups/example1.py | 115 -
examples/python/groups/groups_example1.py | 115 +
examples/python/inlineInitialAssignments.py | 140 +-
examples/python/layout/convertLayout.py | 2 +-
examples/python/printAnnotation.py | 2 +-
examples/python/printMath.py | 2 +-
examples/python/printNotes.py | 2 +-
examples/python/printRegisteredPackages.py | 2 +-
examples/python/printSBML.py | 2 +-
examples/python/printUnits.py | 2 +-
examples/python/printsupported.py | 2 +-
examples/python/promoteParameters.py | 2 +-
examples/python/qual/qual_example1.py | 2 +-
examples/python/readSBML.py | 2 +-
examples/python/replaceOneFD.py | 182 +-
examples/python/setIdFromNames.py | 2 +-
examples/python/stripPackage.py | 2 +-
examples/python/translateMath.py | 2 +-
examples/python/unsetAnnotation.py | 2 +-
examples/python/unsetNotes.py | 2 +-
examples/python/validateSBML.py | 2 +-
examples/qual-package.cmake | 2 +-
examples/r/addCVTerms.R | 2 +-
examples/r/addModelHistory.R | 2 +-
examples/r/addingEvidenceCodes_1.R | 2 +-
examples/r/addingEvidenceCodes_2.R | 2 +-
examples/r/appendAnnotation.R | 2 +-
examples/r/comp/flattenModel.R | 2 +-
examples/r/convertSBML.R | 2 +-
examples/r/createExampleSBML.R | 2 +-
examples/r/echoSBML.R | 2 +-
examples/r/evaluateMath.R | 2 +-
examples/r/fbc/convertCobraToFbc.R | 2 +-
examples/r/fbc/convertFbcToCobra.R | 2 +-
examples/r/printAnnotation.R | 2 +-
examples/r/printMath.R | 2 +-
examples/r/printNotes.R | 2 +-
examples/r/printRegisteredPackages.R | 2 +-
examples/r/printSBML.R | 2 +-
examples/r/printSupported.R | 2 +-
examples/r/printUnits.R | 2 +-
examples/r/promoteParameters.R | 2 +-
examples/r/readSBML.R | 2 +-
examples/r/stripPackage.R | 2 +-
examples/r/translateMath.R | 2 +-
examples/r/unsetAnnotation.R | 2 +-
examples/r/unsetNotes.R | 2 +-
examples/r/validateSBML.R | 2 +-
examples/ruby/addCVTerms.rb | 2 +-
examples/ruby/addCustomValidator.rb | 2 +-
examples/ruby/addModelHistory.rb | 2 +-
examples/ruby/addingEvidenceCodes_1.rb | 2 +-
examples/ruby/addingEvidenceCodes_2.rb | 2 +-
examples/ruby/appendAnnotation.rb | 2 +-
examples/ruby/callExternalValidator.rb | 2 +-
examples/ruby/comp/flattenModel.rb | 2 +-
examples/ruby/convertSBML.rb | 2 +-
examples/ruby/createExampleSBML.rb | 2 +-
examples/ruby/echoSBML.rb | 2 +-
examples/ruby/fbc/convertCobraToFbc.rb | 2 +-
examples/ruby/fbc/convertFbcToCobra.rb | 2 +-
examples/ruby/fbc/example1.rb | 2 +-
.../groups/{example1.rb => groups_example1.rb} | 0
examples/ruby/printAnnotation.rb | 2 +-
examples/ruby/printMath.rb | 2 +-
examples/ruby/printNotes.rb | 2 +-
examples/ruby/printRegisteredPackages.rb | 2 +-
examples/ruby/printSBML.rb | 2 +-
examples/ruby/printUnits.rb | 2 +-
examples/ruby/printsupported.rb | 2 +-
examples/ruby/promoteParameters.rb | 2 +-
examples/ruby/readSBML.rb | 2 +-
examples/ruby/stripPackage.rb | 2 +-
examples/ruby/translateMath.rb | 2 +-
examples/ruby/unsetAnnotation.rb | 2 +-
examples/ruby/unsetNotes.rb | 2 +-
examples/ruby/validateSBML.rb | 2 +-
examples/sample-models/fbc/fbc_example1.xml | 240 +-
.../from-spec/level-3/algebraicrules.xml | 214 +-
.../from-spec/level-3/assignmentrules.xml | 204 +-
.../from-spec/level-3/boundarycondition.xml | 148 +-
examples/sample-models/from-spec/level-3/delay.xml | 148 +-
.../from-spec/level-3/dimerization.xml | 178 +-
.../from-spec/level-3/enzymekinetics.xml | 182 +-
.../sample-models/from-spec/level-3/events.xml | 210 +-
.../from-spec/level-3/fullydeterminedevent.xml | 162 +-
.../from-spec/level-3/functiondef.xml | 142 +-
.../sample-models/from-spec/level-3/multicomp.xml | 240 +-
.../from-spec/level-3/overdetermined.xml | 106 +-
.../from-spec/level-3/twodimensional.xml | 530 +-
fbc-package.cmake | 12 +-
groups-package.cmake | 90 +-
layout-package.cmake | 2 +-
libsbml.spec.in | 2 +-
multi-package.cmake | 2 +-
qual-package.cmake | 2 +-
render-package.cmake | 2 +-
req-package.cmake | 2 +-
spatial-package.cmake | 2 +-
src/CMakeLists.txt | 2 +-
src/Makefile.in | 2 +-
src/bindings/CMakeLists.txt | 2 +-
src/bindings/Makefile.in | 2 +-
src/bindings/csharp/CMakeLists.txt | 2 +-
src/bindings/csharp/Compiler.cs | 2 +-
src/bindings/csharp/Makefile.in | 34 +-
src/bindings/csharp/TestRW.cs | 2 +-
src/bindings/csharp/TestRunner.cs | 2 +-
src/bindings/csharp/compile-native-files.cmake | 2 +-
src/bindings/csharp/csdoc.i | 730 +-
src/bindings/csharp/csharp-files-win/ASTBase.cs | 2 +-
.../csharp/csharp-files-win/ASTBasePlugin.cs | 2 +-
src/bindings/csharp/csharp-files-win/ASTNode.cs | 6 +-
.../csharp/csharp-files-win/ASTNodeList.cs | 2 +-
.../csharp/csharp-files-win/AlgebraicRule.cs | 2 +-
.../csharp/csharp-files-win/AssignmentRule.cs | 2 +-
src/bindings/csharp/csharp-files-win/CVTerm.cs | 68 +-
src/bindings/csharp/csharp-files-win/CVTermList.cs | 2 +-
.../csharp/csharp-files-win/Compartment.cs | 8 +-
.../csharp/csharp-files-win/CompartmentType.cs | 8 +-
src/bindings/csharp/csharp-files-win/Constraint.cs | 8 +-
.../csharp/csharp-files-win/ConversionOption.cs | 2 +-
.../csharp-files-win/ConversionProperties.cs | 2 +-
src/bindings/csharp/csharp-files-win/Date.cs | 2 +-
src/bindings/csharp/csharp-files-win/DateList.cs | 2 +-
src/bindings/csharp/csharp-files-win/Delay.cs | 8 +-
.../csharp/csharp-files-win/ElementFilter.cs | 2 +-
src/bindings/csharp/csharp-files-win/Event.cs | 8 +-
.../csharp/csharp-files-win/EventAssignment.cs | 8 +-
.../csharp/csharp-files-win/FunctionDefinition.cs | 8 +-
.../csharp-files-win/ISBMLExtensionNamespaces.cs | 2 +-
src/bindings/csharp/csharp-files-win/IdList.cs | 2 +-
.../csharp-files-win/IdentifierTransformer.cs | 2 +-
.../csharp/csharp-files-win/InitialAssignment.cs | 8 +-
src/bindings/csharp/csharp-files-win/KineticLaw.cs | 8 +-
.../csharp/csharp-files-win/L3ParserSettings.cs | 4 +-
src/bindings/csharp/csharp-files-win/ListOf.cs | 13 +-
.../csharp-files-win/ListOfCompartmentTypes.cs | 7 +-
.../csharp/csharp-files-win/ListOfCompartments.cs | 7 +-
.../csharp/csharp-files-win/ListOfConstraints.cs | 7 +-
.../csharp-files-win/ListOfEventAssignments.cs | 7 +-
.../csharp/csharp-files-win/ListOfEvents.cs | 7 +-
.../csharp-files-win/ListOfFunctionDefinitions.cs | 7 +-
.../csharp-files-win/ListOfInitialAssignments.cs | 7 +-
.../csharp-files-win/ListOfLocalParameters.cs | 7 +-
.../csharp/csharp-files-win/ListOfParameters.cs | 7 +-
.../csharp/csharp-files-win/ListOfReactions.cs | 35 +-
.../csharp/csharp-files-win/ListOfRules.cs | 7 +-
.../csharp/csharp-files-win/ListOfSpecies.cs | 7 +-
.../csharp-files-win/ListOfSpeciesReferences.cs | 7 +-
.../csharp/csharp-files-win/ListOfSpeciesTypes.cs | 7 +-
.../csharp-files-win/ListOfUnitDefinitions.cs | 7 +-
.../csharp/csharp-files-win/ListOfUnits.cs | 7 +-
.../csharp/csharp-files-win/LocalParameter.cs | 8 +-
src/bindings/csharp/csharp-files-win/MathML.cs | 2 +-
src/bindings/csharp/csharp-files-win/Model.cs | 43 +-
.../csharp/csharp-files-win/ModelCreator.cs | 2 +-
.../csharp/csharp-files-win/ModelCreatorList.cs | 2 +-
.../csharp/csharp-files-win/ModelHistory.cs | 2 +-
.../csharp-files-win/ModifierSpeciesReference.cs | 8 +-
src/bindings/csharp/csharp-files-win/OFStream.cs | 2 +-
src/bindings/csharp/csharp-files-win/OStream.cs | 2 +-
.../csharp/csharp-files-win/OStringStream.cs | 2 +-
src/bindings/csharp/csharp-files-win/Parameter.cs | 8 +-
src/bindings/csharp/csharp-files-win/Priority.cs | 8 +-
.../csharp/csharp-files-win/RDFAnnotationParser.cs | 2 +-
src/bindings/csharp/csharp-files-win/RateRule.cs | 2 +-
src/bindings/csharp/csharp-files-win/Reaction.cs | 15 +-
src/bindings/csharp/csharp-files-win/Rule.cs | 8 +-
.../csharp-files-win/SBMLConstructorException.cs | 2 +-
.../csharp/csharp-files-win/SBMLConverter.cs | 2 +-
.../csharp-files-win/SBMLConverterRegistry.cs | 2 +-
.../csharp/csharp-files-win/SBMLDocument.cs | 68 +-
.../csharp/csharp-files-win/SBMLDocumentPlugin.cs | 2 +-
src/bindings/csharp/csharp-files-win/SBMLError.cs | 2 +-
.../csharp/csharp-files-win/SBMLErrorLog.cs | 2 +-
.../csharp/csharp-files-win/SBMLExtension.cs | 4 +-
.../csharp-files-win/SBMLExtensionException.cs | 2 +-
.../csharp-files-win/SBMLExtensionRegistry.cs | 2 +-
.../csharp-files-win/SBMLExternalValidator.cs | 2 +-
.../SBMLFunctionDefinitionConverter.cs | 2 +-
.../csharp/csharp-files-win/SBMLIdConverter.cs | 2 +-
.../csharp-files-win/SBMLInferUnitsConverter.cs | 2 +-
.../SBMLInitialAssignmentConverter.cs | 2 +-
.../SBMLLevel1Version1Converter.cs | 6 +-
.../csharp-files-win/SBMLLevelVersionConverter.cs | 2 +-
.../SBMLLocalParameterConverter.cs | 2 +-
.../csharp/csharp-files-win/SBMLNamespaces.cs | 2 +-
.../csharp/csharp-files-win/SBMLNamespacesList.cs | 2 +-
.../csharp-files-win/SBMLReactionConverter.cs | 2 +-
src/bindings/csharp/csharp-files-win/SBMLReader.cs | 2 +-
.../csharp/csharp-files-win/SBMLRuleConverter.cs | 2 +-
.../csharp-files-win/SBMLStripPackageConverter.cs | 2 +-
.../csharp/csharp-files-win/SBMLTransforms.cs | 2 +-
.../csharp/csharp-files-win/SBMLUnitsConverter.cs | 2 +-
.../csharp/csharp-files-win/SBMLValidator.cs | 2 +-
src/bindings/csharp/csharp-files-win/SBMLWriter.cs | 2 +-
src/bindings/csharp/csharp-files-win/SBO.cs | 6 +-
src/bindings/csharp/csharp-files-win/SBase.cs | 16 +-
.../csharp/csharp-files-win/SBaseExtensionPoint.cs | 2 +-
src/bindings/csharp/csharp-files-win/SBaseList.cs | 2 +-
.../csharp/csharp-files-win/SBasePlugin.cs | 3 +-
.../csharp-files-win/SWIGTYPE_p_ASTFunction.cs | 2 +-
.../SWIGTYPE_p_ExpectedAttributes.cs | 2 +-
.../SWIGTYPE_p_FormulaUnitsData.cs | 2 +-
.../csharp/csharp-files-win/SWIGTYPE_p_List.cs | 2 +-
.../csharp-files-win/SWIGTYPE_p_StringBuffer_t.cs | 2 +-
.../csharp-files-win/SWIGTYPE_p_std__ostream.cs | 2 +-
.../SWIGTYPE_p_std__vectorT_XMLError_p_t.cs | 2 +-
.../SWIGTYPE_p_std__vectorT_std__string_t.cs | 2 +-
.../csharp-files-win/SimpleSpeciesReference.cs | 2 +-
src/bindings/csharp/csharp-files-win/Species.cs | 8 +-
.../csharp/csharp-files-win/SpeciesReference.cs | 2 +-
.../csharp/csharp-files-win/SpeciesType.cs | 8 +-
.../csharp/csharp-files-win/StoichiometryMath.cs | 8 +-
.../csharp/csharp-files-win/SyntaxChecker.cs | 2 +-
src/bindings/csharp/csharp-files-win/Trigger.cs | 8 +-
src/bindings/csharp/csharp-files-win/Unit.cs | 8 +-
.../csharp/csharp-files-win/UnitDefinition.cs | 8 +-
.../csharp/csharp-files-win/XMLAttributes.cs | 2 +-
.../csharp-files-win/XMLConstructorException.cs | 2 +-
src/bindings/csharp/csharp-files-win/XMLError.cs | 2 +-
.../csharp/csharp-files-win/XMLErrorLog.cs | 2 +-
.../csharp/csharp-files-win/XMLInputStream.cs | 2 +-
.../csharp/csharp-files-win/XMLNamespaces.cs | 2 +-
src/bindings/csharp/csharp-files-win/XMLNode.cs | 2 +-
.../csharp/csharp-files-win/XMLOutputStream.cs | 114 +-
.../csharp-files-win/XMLOwningOutputFileStream.cs | 2 +-
.../XMLOwningOutputStringStream.cs | 2 +-
src/bindings/csharp/csharp-files-win/XMLToken.cs | 2 +-
src/bindings/csharp/csharp-files-win/XMLTriple.cs | 2 +-
src/bindings/csharp/csharp-files-win/libsbml.cs | 123 +-
.../csharp/csharp-files-win/libsbmlPINVOKE.cs | 83 +-
src/bindings/csharp/csharp-files/ASTBase.cs | 2 +-
src/bindings/csharp/csharp-files/ASTBasePlugin.cs | 2 +-
src/bindings/csharp/csharp-files/ASTNode.cs | 6 +-
src/bindings/csharp/csharp-files/ASTNodeList.cs | 2 +-
src/bindings/csharp/csharp-files/AlgebraicRule.cs | 2 +-
src/bindings/csharp/csharp-files/AssignmentRule.cs | 2 +-
src/bindings/csharp/csharp-files/CVTerm.cs | 68 +-
src/bindings/csharp/csharp-files/CVTermList.cs | 2 +-
src/bindings/csharp/csharp-files/Compartment.cs | 8 +-
.../csharp/csharp-files/CompartmentType.cs | 8 +-
src/bindings/csharp/csharp-files/Constraint.cs | 8 +-
.../csharp/csharp-files/ConversionOption.cs | 2 +-
.../csharp/csharp-files/ConversionProperties.cs | 2 +-
src/bindings/csharp/csharp-files/Date.cs | 2 +-
src/bindings/csharp/csharp-files/DateList.cs | 2 +-
src/bindings/csharp/csharp-files/Delay.cs | 8 +-
src/bindings/csharp/csharp-files/ElementFilter.cs | 2 +-
src/bindings/csharp/csharp-files/Event.cs | 8 +-
.../csharp/csharp-files/EventAssignment.cs | 8 +-
.../csharp/csharp-files/FunctionDefinition.cs | 8 +-
.../csharp-files/ISBMLExtensionNamespaces.cs | 2 +-
src/bindings/csharp/csharp-files/IdList.cs | 2 +-
.../csharp/csharp-files/IdentifierTransformer.cs | 2 +-
.../csharp/csharp-files/InitialAssignment.cs | 8 +-
src/bindings/csharp/csharp-files/KineticLaw.cs | 8 +-
.../csharp/csharp-files/L3ParserSettings.cs | 4 +-
src/bindings/csharp/csharp-files/ListOf.cs | 13 +-
.../csharp/csharp-files/ListOfCompartmentTypes.cs | 7 +-
.../csharp/csharp-files/ListOfCompartments.cs | 7 +-
.../csharp/csharp-files/ListOfConstraints.cs | 7 +-
.../csharp/csharp-files/ListOfEventAssignments.cs | 7 +-
src/bindings/csharp/csharp-files/ListOfEvents.cs | 7 +-
.../csharp-files/ListOfFunctionDefinitions.cs | 7 +-
.../csharp-files/ListOfInitialAssignments.cs | 7 +-
.../csharp/csharp-files/ListOfLocalParameters.cs | 7 +-
.../csharp/csharp-files/ListOfParameters.cs | 7 +-
.../csharp/csharp-files/ListOfReactions.cs | 35 +-
src/bindings/csharp/csharp-files/ListOfRules.cs | 7 +-
src/bindings/csharp/csharp-files/ListOfSpecies.cs | 7 +-
.../csharp/csharp-files/ListOfSpeciesReferences.cs | 7 +-
.../csharp/csharp-files/ListOfSpeciesTypes.cs | 7 +-
.../csharp/csharp-files/ListOfUnitDefinitions.cs | 7 +-
src/bindings/csharp/csharp-files/ListOfUnits.cs | 7 +-
src/bindings/csharp/csharp-files/LocalParameter.cs | 8 +-
src/bindings/csharp/csharp-files/MathML.cs | 2 +-
src/bindings/csharp/csharp-files/Model.cs | 43 +-
src/bindings/csharp/csharp-files/ModelCreator.cs | 2 +-
.../csharp/csharp-files/ModelCreatorList.cs | 2 +-
src/bindings/csharp/csharp-files/ModelHistory.cs | 2 +-
.../csharp-files/ModifierSpeciesReference.cs | 8 +-
src/bindings/csharp/csharp-files/OFStream.cs | 2 +-
src/bindings/csharp/csharp-files/OStream.cs | 2 +-
src/bindings/csharp/csharp-files/OStringStream.cs | 2 +-
src/bindings/csharp/csharp-files/Parameter.cs | 8 +-
src/bindings/csharp/csharp-files/Priority.cs | 8 +-
.../csharp/csharp-files/RDFAnnotationParser.cs | 2 +-
src/bindings/csharp/csharp-files/RateRule.cs | 2 +-
src/bindings/csharp/csharp-files/Reaction.cs | 15 +-
src/bindings/csharp/csharp-files/Rule.cs | 8 +-
.../csharp-files/SBMLConstructorException.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLConverter.cs | 2 +-
.../csharp/csharp-files/SBMLConverterRegistry.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLDocument.cs | 68 +-
.../csharp/csharp-files/SBMLDocumentPlugin.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLError.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLErrorLog.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLExtension.cs | 4 +-
.../csharp/csharp-files/SBMLExtensionException.cs | 2 +-
.../csharp/csharp-files/SBMLExtensionRegistry.cs | 2 +-
.../csharp/csharp-files/SBMLExternalValidator.cs | 2 +-
.../SBMLFunctionDefinitionConverter.cs | 2 +-
.../csharp/csharp-files/SBMLIdConverter.cs | 2 +-
.../csharp/csharp-files/SBMLInferUnitsConverter.cs | 2 +-
.../csharp-files/SBMLInitialAssignmentConverter.cs | 2 +-
.../csharp-files/SBMLLevel1Version1Converter.cs | 6 +-
.../csharp-files/SBMLLevelVersionConverter.cs | 2 +-
.../csharp-files/SBMLLocalParameterConverter.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLNamespaces.cs | 2 +-
.../csharp/csharp-files/SBMLNamespacesList.cs | 2 +-
.../csharp/csharp-files/SBMLReactionConverter.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLReader.cs | 2 +-
.../csharp/csharp-files/SBMLRuleConverter.cs | 2 +-
.../csharp-files/SBMLStripPackageConverter.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLTransforms.cs | 2 +-
.../csharp/csharp-files/SBMLUnitsConverter.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLValidator.cs | 2 +-
src/bindings/csharp/csharp-files/SBMLWriter.cs | 2 +-
src/bindings/csharp/csharp-files/SBO.cs | 6 +-
src/bindings/csharp/csharp-files/SBase.cs | 16 +-
.../csharp/csharp-files/SBaseExtensionPoint.cs | 2 +-
src/bindings/csharp/csharp-files/SBaseList.cs | 2 +-
src/bindings/csharp/csharp-files/SBasePlugin.cs | 3 +-
.../csharp/csharp-files/SWIGTYPE_p_ASTFunction.cs | 2 +-
.../csharp-files/SWIGTYPE_p_ExpectedAttributes.cs | 2 +-
.../csharp-files/SWIGTYPE_p_FormulaUnitsData.cs | 2 +-
.../csharp/csharp-files/SWIGTYPE_p_List.cs | 2 +-
.../csharp-files/SWIGTYPE_p_StringBuffer_t.cs | 2 +-
.../csharp/csharp-files/SWIGTYPE_p_std__ostream.cs | 2 +-
.../SWIGTYPE_p_std__vectorT_XMLError_p_t.cs | 2 +-
.../SWIGTYPE_p_std__vectorT_std__string_t.cs | 2 +-
.../csharp/csharp-files/SimpleSpeciesReference.cs | 2 +-
src/bindings/csharp/csharp-files/Species.cs | 8 +-
.../csharp/csharp-files/SpeciesReference.cs | 2 +-
src/bindings/csharp/csharp-files/SpeciesType.cs | 8 +-
.../csharp/csharp-files/StoichiometryMath.cs | 8 +-
src/bindings/csharp/csharp-files/SyntaxChecker.cs | 2 +-
src/bindings/csharp/csharp-files/Trigger.cs | 8 +-
src/bindings/csharp/csharp-files/Unit.cs | 8 +-
src/bindings/csharp/csharp-files/UnitDefinition.cs | 8 +-
src/bindings/csharp/csharp-files/XMLAttributes.cs | 2 +-
.../csharp/csharp-files/XMLConstructorException.cs | 2 +-
src/bindings/csharp/csharp-files/XMLError.cs | 2 +-
src/bindings/csharp/csharp-files/XMLErrorLog.cs | 2 +-
src/bindings/csharp/csharp-files/XMLInputStream.cs | 2 +-
src/bindings/csharp/csharp-files/XMLNamespaces.cs | 2 +-
src/bindings/csharp/csharp-files/XMLNode.cs | 2 +-
.../csharp/csharp-files/XMLOutputStream.cs | 117 +-
.../csharp-files/XMLOwningOutputFileStream.cs | 2 +-
.../csharp-files/XMLOwningOutputStringStream.cs | 2 +-
src/bindings/csharp/csharp-files/XMLToken.cs | 2 +-
src/bindings/csharp/csharp-files/XMLTriple.cs | 2 +-
src/bindings/csharp/csharp-files/libsbml.cs | 123 +-
src/bindings/csharp/csharp-files/libsbmlPINVOKE.cs | 79 +-
src/bindings/csharp/libsbml.i | 2 +-
src/bindings/csharp/libsbml_wrap-win.cpp | 298 +-
src/bindings/csharp/libsbml_wrap.cpp | 248 +-
src/bindings/csharp/libsbml_wrap.h | 2 +-
.../csharp/local-downcast-converters-comp.i | 20 +-
.../csharp/local-downcast-converters-fbc.i | 26 +-
.../csharp/local-downcast-converters-layout.i | 20 +-
.../csharp/local-downcast-converters-qual.i | 18 +-
src/bindings/csharp/local-downcast-converters.i.in | 28 +-
src/bindings/csharp/local-packages-comp.i | 2 +-
src/bindings/csharp/local-packages-dyn.i | 2 +-
src/bindings/csharp/local-packages-fbc.i | 8 +-
src/bindings/csharp/local-packages-groups.i | 65 +-
src/bindings/csharp/local-packages-layout.i | 2 +-
src/bindings/csharp/local-packages-multi.i | 17 +-
src/bindings/csharp/local-packages-qual.i | 2 +-
src/bindings/csharp/local-packages-req.i | 2 +-
src/bindings/csharp/local-packages-spatial.i | 2 +-
src/bindings/csharp/local-packages.i.in | 3 +
src/bindings/csharp/local.cpp | 2 +-
src/bindings/csharp/local.i | 21 +-
src/bindings/csharp/swig-binding.cmake.in | 182 +-
src/bindings/java/AutoTestRunner.java | 2 +-
src/bindings/java/CMakeLists.txt | 2 +-
src/bindings/java/Makefile.in | 33 +-
src/bindings/java/compile-native-files.cmake | 2 +-
.../java/java-files/org/sbml/libsbml/ASTBase.java | 2 +-
.../java-files/org/sbml/libsbml/ASTBasePlugin.java | 2 +-
.../java/java-files/org/sbml/libsbml/ASTNode.java | 10 +-
.../java-files/org/sbml/libsbml/ASTNodeList.java | 6 +-
.../java-files/org/sbml/libsbml/AlgebraicRule.java | 2 +-
.../org/sbml/libsbml/AssignmentRule.java | 2 +-
.../java/java-files/org/sbml/libsbml/CVTerm.java | 68 +-
.../java-files/org/sbml/libsbml/CVTermList.java | 6 +-
.../java-files/org/sbml/libsbml/Compartment.java | 8 +-
.../org/sbml/libsbml/CompartmentType.java | 8 +-
.../java-files/org/sbml/libsbml/Constraint.java | 8 +-
.../org/sbml/libsbml/ConversionOption.java | 2 +-
.../org/sbml/libsbml/ConversionProperties.java | 22 +-
.../java/java-files/org/sbml/libsbml/Date.java | 2 +-
.../java/java-files/org/sbml/libsbml/DateList.java | 6 +-
.../java/java-files/org/sbml/libsbml/Delay.java | 8 +-
.../java-files/org/sbml/libsbml/ElementFilter.java | 2 +-
.../java/java-files/org/sbml/libsbml/Event.java | 8 +-
.../org/sbml/libsbml/EventAssignment.java | 8 +-
.../org/sbml/libsbml/FunctionDefinition.java | 8 +-
.../org/sbml/libsbml/ISBMLExtensionNamespaces.java | 2 +-
.../java/java-files/org/sbml/libsbml/IdList.java | 2 +-
.../org/sbml/libsbml/IdentifierTransformer.java | 2 +-
.../org/sbml/libsbml/InitialAssignment.java | 8 +-
.../java-files/org/sbml/libsbml/KineticLaw.java | 8 +-
.../org/sbml/libsbml/L3ParserSettings.java | 4 +-
.../java/java-files/org/sbml/libsbml/ListOf.java | 16 +-
.../org/sbml/libsbml/ListOfCompartmentTypes.java | 10 +-
.../org/sbml/libsbml/ListOfCompartments.java | 10 +-
.../org/sbml/libsbml/ListOfConstraints.java | 10 +-
.../org/sbml/libsbml/ListOfEventAssignments.java | 10 +-
.../java-files/org/sbml/libsbml/ListOfEvents.java | 10 +-
.../sbml/libsbml/ListOfFunctionDefinitions.java | 10 +-
.../org/sbml/libsbml/ListOfInitialAssignments.java | 10 +-
.../org/sbml/libsbml/ListOfLocalParameters.java | 10 +-
.../org/sbml/libsbml/ListOfParameters.java | 10 +-
.../org/sbml/libsbml/ListOfReactions.java | 30 +-
.../java-files/org/sbml/libsbml/ListOfRules.java | 10 +-
.../java-files/org/sbml/libsbml/ListOfSpecies.java | 10 +-
.../org/sbml/libsbml/ListOfSpeciesReferences.java | 10 +-
.../org/sbml/libsbml/ListOfSpeciesTypes.java | 10 +-
.../org/sbml/libsbml/ListOfUnitDefinitions.java | 10 +-
.../java-files/org/sbml/libsbml/ListOfUnits.java | 10 +-
.../org/sbml/libsbml/LocalParameter.java | 8 +-
.../java/java-files/org/sbml/libsbml/MathML.java | 2 +-
.../java/java-files/org/sbml/libsbml/Model.java | 37 +-
.../java-files/org/sbml/libsbml/ModelCreator.java | 2 +-
.../org/sbml/libsbml/ModelCreatorList.java | 6 +-
.../java-files/org/sbml/libsbml/ModelHistory.java | 2 +-
.../org/sbml/libsbml/ModifierSpeciesReference.java | 8 +-
.../java/java-files/org/sbml/libsbml/OFStream.java | 2 +-
.../java/java-files/org/sbml/libsbml/OStream.java | 2 +-
.../java-files/org/sbml/libsbml/OStringStream.java | 2 +-
.../java-files/org/sbml/libsbml/Parameter.java | 8 +-
.../java/java-files/org/sbml/libsbml/Priority.java | 8 +-
.../org/sbml/libsbml/RDFAnnotationParser.java | 2 +-
.../java/java-files/org/sbml/libsbml/RateRule.java | 2 +-
.../java/java-files/org/sbml/libsbml/Reaction.java | 13 +-
.../java/java-files/org/sbml/libsbml/Rule.java | 10 +-
.../org/sbml/libsbml/SBMLConstructorException.java | 2 +-
.../java-files/org/sbml/libsbml/SBMLConverter.java | 22 +-
.../org/sbml/libsbml/SBMLConverterRegistry.java | 2 +-
.../java-files/org/sbml/libsbml/SBMLDocument.java | 80 +-
.../org/sbml/libsbml/SBMLDocumentPlugin.java | 2 +-
.../java-files/org/sbml/libsbml/SBMLError.java | 4 +-
.../java-files/org/sbml/libsbml/SBMLErrorLog.java | 2 +-
.../java-files/org/sbml/libsbml/SBMLExtension.java | 2 +-
.../org/sbml/libsbml/SBMLExtensionException.java | 2 +-
.../org/sbml/libsbml/SBMLExtensionRegistry.java | 2 +-
.../org/sbml/libsbml/SBMLExternalValidator.java | 2 +-
.../libsbml/SBMLFunctionDefinitionConverter.java | 22 +-
.../org/sbml/libsbml/SBMLIdConverter.java | 22 +-
.../org/sbml/libsbml/SBMLInferUnitsConverter.java | 22 +-
.../libsbml/SBMLInitialAssignmentConverter.java | 22 +-
.../sbml/libsbml/SBMLLevel1Version1Converter.java | 22 +-
.../sbml/libsbml/SBMLLevelVersionConverter.java | 22 +-
.../sbml/libsbml/SBMLLocalParameterConverter.java | 22 +-
.../org/sbml/libsbml/SBMLNamespaces.java | 2 +-
.../org/sbml/libsbml/SBMLNamespacesList.java | 6 +-
.../org/sbml/libsbml/SBMLReactionConverter.java | 22 +-
.../java-files/org/sbml/libsbml/SBMLReader.java | 2 +-
.../org/sbml/libsbml/SBMLRuleConverter.java | 22 +-
.../sbml/libsbml/SBMLStripPackageConverter.java | 22 +-
.../org/sbml/libsbml/SBMLTransforms.java | 2 +-
.../org/sbml/libsbml/SBMLUnitsConverter.java | 22 +-
.../java-files/org/sbml/libsbml/SBMLValidator.java | 2 +-
.../java-files/org/sbml/libsbml/SBMLWriter.java | 2 +-
.../java/java-files/org/sbml/libsbml/SBO.java | 8 +-
.../java/java-files/org/sbml/libsbml/SBase.java | 16 +-
.../org/sbml/libsbml/SBaseExtensionPoint.java | 2 +-
.../java-files/org/sbml/libsbml/SBaseList.java | 6 +-
.../java-files/org/sbml/libsbml/SBasePlugin.java | 3 +-
.../org/sbml/libsbml/SWIGTYPE_p_ASTFunction.java | 2 +-
.../libsbml/SWIGTYPE_p_ExpectedAttributes.java | 2 +-
.../sbml/libsbml/SWIGTYPE_p_FormulaUnitsData.java | 2 +-
.../org/sbml/libsbml/SWIGTYPE_p_List.java | 2 +-
.../sbml/libsbml/SWIGTYPE_p_StringBuffer_t.java | 2 +-
.../org/sbml/libsbml/SWIGTYPE_p_std__ostream.java | 2 +-
.../SWIGTYPE_p_std__vectorT_XMLError_p_t.java | 2 +-
.../SWIGTYPE_p_std__vectorT_std__string_t.java | 2 +-
.../org/sbml/libsbml/SimpleSpeciesReference.java | 2 +-
.../java/java-files/org/sbml/libsbml/Species.java | 8 +-
.../org/sbml/libsbml/SpeciesReference.java | 2 +-
.../java-files/org/sbml/libsbml/SpeciesType.java | 8 +-
.../org/sbml/libsbml/StoichiometryMath.java | 8 +-
.../java-files/org/sbml/libsbml/SyntaxChecker.java | 2 +-
.../java/java-files/org/sbml/libsbml/Trigger.java | 8 +-
.../java/java-files/org/sbml/libsbml/Unit.java | 8 +-
.../org/sbml/libsbml/UnitDefinition.java | 8 +-
.../java-files/org/sbml/libsbml/XMLAttributes.java | 2 +-
.../org/sbml/libsbml/XMLConstructorException.java | 2 +-
.../java/java-files/org/sbml/libsbml/XMLError.java | 2 +-
.../java-files/org/sbml/libsbml/XMLErrorLog.java | 2 +-
.../org/sbml/libsbml/XMLInputStream.java | 2 +-
.../java-files/org/sbml/libsbml/XMLNamespaces.java | 2 +-
.../java/java-files/org/sbml/libsbml/XMLNode.java | 2 +-
.../org/sbml/libsbml/XMLOutputStream.java | 110 +-
.../sbml/libsbml/XMLOwningOutputFileStream.java | 2 +-
.../sbml/libsbml/XMLOwningOutputStringStream.java | 2 +-
.../java/java-files/org/sbml/libsbml/XMLToken.java | 2 +-
.../java-files/org/sbml/libsbml/XMLTriple.java | 2 +-
.../java/java-files/org/sbml/libsbml/libsbml.java | 94 +-
.../org/sbml/libsbml/libsbmlConstants.java | 9 +-
.../java-files/org/sbml/libsbml/libsbmlJNI.java | 31 +-
src/bindings/java/javadoc.i | 999 ++-
src/bindings/java/libsbml.i | 2 +-
src/bindings/java/libsbml_wrap.cpp | 328 +-
src/bindings/java/libsbml_wrap.h | 2 +-
src/bindings/java/local-downcast-converters-comp.i | 20 +-
src/bindings/java/local-downcast-converters-fbc.i | 26 +-
.../java/local-downcast-converters-layout.i | 20 +-
src/bindings/java/local-downcast-converters-qual.i | 18 +-
src/bindings/java/local-downcast-converters.i.in | 28 +-
src/bindings/java/local-packages-dyn.i | 2 +-
src/bindings/java/local-packages-fbc.i | 8 +-
src/bindings/java/local-packages-groups.i | 77 +-
src/bindings/java/local-packages-multi.i | 41 +-
src/bindings/java/local-packages-req.i | 2 +-
src/bindings/java/local-packages-spatial.i | 2 +-
src/bindings/java/local-packages.i.in | 3 +
src/bindings/java/local.cpp | 2 +-
src/bindings/java/local.i | 10 +-
src/bindings/java/swig-binding.cmake.in | 204 +-
src/bindings/javascript/CMakeLists.txt | 2 +-
src/bindings/javascript/compile-native-files.cmake | 2 +-
src/bindings/javascript/libsbml.i | 2 +-
.../javascript/local-downcast-converters.cpp.in | 34 +-
.../javascript/local-downcast-packages-groups.cpp | 46 +-
.../javascript/local-downcast-packages-multi.cpp | 7 -
.../javascript/local-downcast-plugins-multi.cpp | 4 +
src/bindings/javascript/local-fbc.i | 68 +-
src/bindings/javascript/local-groups.i | 9 +-
src/bindings/javascript/local-multi.i | 2 -
src/bindings/javascript/local-packages.i.in | 3 +
src/bindings/javascript/local.cpp | 2 +-
src/bindings/javascript/local.i | 20 +-
src/bindings/matlab/CMakeLists.txt | 2 +-
src/bindings/matlab/CheckAndConvert.m | 2 +-
src/bindings/matlab/Contents.m | 2 +-
src/bindings/matlab/ConvertFormulaToMathML.m | 2 +-
src/bindings/matlab/Makefile.in | 2 +-
src/bindings/matlab/OutputSBML.cpp | 385 +-
src/bindings/matlab/OutputSBML.m | 2 +-
src/bindings/matlab/TranslateSBML.cpp | 665 +-
src/bindings/matlab/TranslateSBML.m | 2 +-
src/bindings/matlab/buildSBML.m | 2 +-
src/bindings/matlab/installSBML.m | 2 +-
src/bindings/matlab/isFbcEnabled.m | 2 +-
src/bindings/matlab/isSBML_Model.m | 369 +-
src/bindings/matlab/test/Makefile.in | 2 +-
src/bindings/matlab/test/compareFiles.m | 2 +-
src/bindings/matlab/test/test-data/fbcV2.xml | 119 +
src/bindings/matlab/test/test-data/test-greek.xml | 82 +
src/bindings/matlab/test/testBinding.m | 1 +
src/bindings/matlab/test/testOutput.m | 6 +-
src/bindings/matlab/test/testReadFromFile16.m | 2 +-
src/bindings/octave/CMakeLists.txt | 2 +-
src/bindings/octave/Makefile.in | 2 +-
src/bindings/octave/buildLibSBMLOctave.m | 2 +-
src/bindings/octave/test/Makefile.in | 2 +-
src/bindings/perl/CMakeLists.txt | 2 +-
src/bindings/perl/LibSBML.pm | 385 +-
src/bindings/perl/LibSBML.pod | 368 +-
src/bindings/perl/LibSBML_wrap.cxx | 4741 ++++++++-----
src/bindings/perl/Makefile.PL.in | 5 +
src/bindings/perl/local-downcast-converters.cpp.in | 34 +-
.../perl/local-downcast-packages-groups.cpp | 46 +-
.../perl/local-downcast-packages-multi.cpp | 7 -
src/bindings/perl/local-downcast-plugins-multi.cpp | 4 +
src/bindings/perl/local-groups.i | 10 +-
src/bindings/perl/local-multi.i | 2 -
src/bindings/perl/local-packages.i.in | 3 +
src/bindings/perl/local.i | 2 +-
src/bindings/php/CMakeLists.txt | 2 +-
src/bindings/php/libsbml.i | 2 +-
src/bindings/php/local-downcast-converters.cpp.in | 34 +-
.../php/local-downcast-packages-groups.cpp | 46 +-
src/bindings/php/local-downcast-packages-multi.cpp | 7 -
src/bindings/php/local-downcast-plugins-multi.cpp | 4 +
src/bindings/php/local-fbc.i | 68 +-
src/bindings/php/local-groups.i | 7 +-
src/bindings/php/local-multi.i | 2 -
src/bindings/php/local-packages.i.in | 3 +
src/bindings/php/local.cpp | 2 +-
src/bindings/php/local.i | 21 +-
src/bindings/python/CMakeLists.txt | 53 +-
src/bindings/python/Makefile.in | 34 +-
src/bindings/python/add_version.cmake | 43 +
src/bindings/python/doc-converter/rewrite_pydoc.py | 16 +-
src/bindings/python/libsbml-doxygen.py | 6595 ++++++++---------
src/bindings/python/libsbml.i | 2 +-
src/bindings/python/libsbml.py | 7469 +++++++++-----------
src/bindings/python/libsbml_wrap.cpp | 2668 +++++--
src/bindings/python/libsbml_wrap.h | 10 +-
src/bindings/python/local-contrib.i | 2 +-
src/bindings/python/local-doc-extras.i | 2 +-
.../python/local-downcast-converters.cpp.in | 34 +-
.../python/local-downcast-packages-groups.cpp | 40 +-
.../python/local-downcast-packages-multi.cpp | 7 -
.../python/local-downcast-plugins-multi.cpp | 4 +
src/bindings/python/local-groups.i | 7 +-
src/bindings/python/local-multi.i | 2 -
src/bindings/python/local-packages.i.in | 3 +
src/bindings/python/local.cpp | 2 +-
src/bindings/python/local.i | 102 +-
src/bindings/python/pydoc-doxygen.i | 859 +--
src/bindings/python/pydoc-normal.i | 1404 +---
src/bindings/python/setup.cfg | 2 +-
src/bindings/python/setup.py.in | 8 +-
src/bindings/python/test.py | 2 +-
src/bindings/r/CMakeLists.txt | 2 +-
src/bindings/r/configure | 2 +-
src/bindings/r/configure.in | 2 +-
src/bindings/r/create-r-package.cmake | 2 +-
src/bindings/r/create_package.cmake | 9 +-
src/bindings/r/libsbml.i | 4 +-
src/bindings/r/local-downcast-converters.cpp.in | 34 +-
src/bindings/r/local-downcast-packages-groups.cpp | 46 +-
src/bindings/r/local-downcast-packages-multi.cpp | 7 -
src/bindings/r/local-downcast-plugins-multi.cpp | 4 +
src/bindings/r/local-groups.i | 7 +-
src/bindings/r/local-multi.i | 2 -
src/bindings/r/local-packages.i.in | 3 +
src/bindings/r/local.cpp | 2 +-
src/bindings/r/local.i | 30 +-
src/bindings/r/swig-binding.cmake | 146 +-
src/bindings/ruby/CMakeLists.txt | 2 +-
src/bindings/ruby/Makefile.in | 31 +-
src/bindings/ruby/libsbml.i | 2 +-
src/bindings/ruby/libsbml_wrap.cpp | 1122 ++-
src/bindings/ruby/libsbml_wrap.h | 2 +-
src/bindings/ruby/local-downcast-converters.cpp.in | 34 +-
.../ruby/local-downcast-packages-groups.cpp | 47 +-
.../ruby/local-downcast-packages-multi.cpp | 7 -
src/bindings/ruby/local-downcast-plugins-multi.cpp | 4 +
src/bindings/ruby/local-groups.i | 7 +-
src/bindings/ruby/local-multi.i | 2 -
src/bindings/ruby/local-packages.i.in | 3 +
src/bindings/ruby/local.cpp | 2 +-
src/bindings/ruby/local.i | 19 +-
src/bindings/swig/ListWrapper.h | 2 +-
src/bindings/swig/OStream.cpp | 2 +-
src/bindings/swig/OStream.h | 2 +-
src/bindings/swig/arrays-package.h | 2 +-
src/bindings/swig/arrays-package.i | 2 +-
src/bindings/swig/comp-package.h | 2 +-
src/bindings/swig/comp-package.i | 3 +-
src/bindings/swig/fbc-package.h | 2 +-
src/bindings/swig/fbc-package.i | 2 +-
src/bindings/swig/groups-package.h | 88 +-
src/bindings/swig/groups-package.i | 11 +-
src/bindings/swig/libsbml-packages.h.in | 3 +
src/bindings/swig/libsbml-packages.i.in | 3 +
src/bindings/swig/libsbml.h | 2 +-
src/bindings/swig/libsbml.i | 2 +-
src/bindings/swig/libsbmlutils.py | 2 +-
src/bindings/swig/multi-package.h | 2 +-
src/bindings/swig/multi-package.i | 3 +-
src/bindings/swig/qual-package.h | 2 +-
src/bindings/swig/qual-package.i | 2 +-
src/bindings/swig/render-package.h | 2 +-
src/bindings/swig/render-package.i | 2 +-
src/bindings/swig/swigdoc.py | 42 +-
src/comp-package.cmake | 2 +-
src/dyn-package.cmake | 2 +-
src/fbc-package.cmake | 2 +-
src/groups-package.cmake | 179 +-
src/layout-package.cmake | 2 +-
src/multi-package.cmake | 2 +-
src/qual-package.cmake | 2 +-
src/req-package.cmake | 2 +-
src/sbml/AlgebraicRule.cpp | 2 +-
src/sbml/AlgebraicRule.h | 2 +-
src/sbml/AssignmentRule.cpp | 2 +-
src/sbml/AssignmentRule.h | 2 +-
src/sbml/CMakeLists.txt | 2 +-
src/sbml/Compartment.cpp | 2 +-
src/sbml/Compartment.h | 2 +-
src/sbml/CompartmentType.cpp | 2 +-
src/sbml/CompartmentType.h | 2 +-
src/sbml/Constraint.cpp | 2 +-
src/sbml/Constraint.h | 2 +-
src/sbml/Delay.cpp | 2 +-
src/sbml/Delay.h | 2 +-
src/sbml/Event.cpp | 2 +-
src/sbml/Event.h | 2 +-
src/sbml/EventAssignment.cpp | 2 +-
src/sbml/EventAssignment.h | 2 +-
src/sbml/ExpectedAttributes.cpp | 2 +-
src/sbml/ExpectedAttributes.h | 2 +-
src/sbml/FunctionDefinition.cpp | 2 +-
src/sbml/FunctionDefinition.h | 2 +-
src/sbml/InitialAssignment.cpp | 2 +-
src/sbml/InitialAssignment.h | 2 +-
src/sbml/KineticLaw.cpp | 2 +-
src/sbml/KineticLaw.h | 2 +-
src/sbml/ListOf.cpp | 2 +-
src/sbml/ListOf.h | 2 +-
src/sbml/LocalParameter.cpp | 2 +-
src/sbml/LocalParameter.h | 2 +-
src/sbml/Makefile.in | 2 +-
src/sbml/Model.cpp | 2 +-
src/sbml/Model.h | 2 +-
src/sbml/ModifierSpeciesReference.cpp | 2 +-
src/sbml/ModifierSpeciesReference.h | 2 +-
src/sbml/Parameter.cpp | 2 +-
src/sbml/Parameter.h | 2 +-
src/sbml/Priority.cpp | 2 +-
src/sbml/Priority.h | 2 +-
src/sbml/RateRule.cpp | 2 +-
src/sbml/RateRule.h | 2 +-
src/sbml/Reaction.cpp | 2 +-
src/sbml/Reaction.h | 2 +-
src/sbml/Rule.cpp | 7 +-
src/sbml/Rule.h | 2 +-
src/sbml/SBMLConstructorException.cpp | 2 +-
src/sbml/SBMLConstructorException.h | 2 +-
src/sbml/SBMLConvert.cpp | 2 +-
src/sbml/SBMLDocument.cpp | 177 +-
src/sbml/SBMLDocument.h | 10 +-
src/sbml/SBMLError.cpp | 2 +-
src/sbml/SBMLError.h | 2 +-
src/sbml/SBMLErrorLog.cpp | 2 +-
src/sbml/SBMLErrorLog.h | 2 +-
src/sbml/SBMLErrorTable.h | 34 +-
src/sbml/SBMLNamespaces.cpp | 2 +-
src/sbml/SBMLNamespaces.h | 2 +-
src/sbml/SBMLReader.cpp | 2 +-
src/sbml/SBMLReader.h | 2 +-
src/sbml/SBMLTransforms.cpp | 2 +-
src/sbml/SBMLTransforms.h | 2 +-
src/sbml/SBMLTypeCodes.cpp | 2 +-
src/sbml/SBMLTypeCodes.h | 2 +-
src/sbml/SBMLTypes.h | 2 +-
src/sbml/SBMLVisitor.cpp | 2 +-
src/sbml/SBMLVisitor.h | 2 +-
src/sbml/SBMLWriter.cpp | 2 +-
src/sbml/SBMLWriter.h | 2 +-
src/sbml/SBO.cpp | 34 +-
src/sbml/SBO.h | 10 +-
src/sbml/SBase.cpp | 18 +-
src/sbml/SBase.h | 6 +-
src/sbml/SimpleSpeciesReference.cpp | 2 +-
src/sbml/SimpleSpeciesReference.h | 2 +-
src/sbml/Species.cpp | 2 +-
src/sbml/Species.h | 2 +-
src/sbml/SpeciesReference.cpp | 2 +-
src/sbml/SpeciesReference.h | 2 +-
src/sbml/SpeciesType.cpp | 2 +-
src/sbml/SpeciesType.h | 2 +-
src/sbml/StoichiometryMath.cpp | 2 +-
src/sbml/StoichiometryMath.h | 2 +-
src/sbml/SyntaxChecker.cpp | 2 +-
src/sbml/SyntaxChecker.h | 2 +-
src/sbml/Trigger.cpp | 2 +-
src/sbml/Trigger.h | 2 +-
src/sbml/Unit.cpp | 4 +-
src/sbml/Unit.h | 2 +-
src/sbml/UnitDefinition.cpp | 2 +-
src/sbml/UnitDefinition.h | 2 +-
src/sbml/UnitKind.c | 2 +-
src/sbml/UnitKind.h | 2 +-
src/sbml/annotation/CVTerm.cpp | 2 +-
src/sbml/annotation/CVTerm.h | 356 +-
src/sbml/annotation/Date.cpp | 2 +-
src/sbml/annotation/Date.h | 2 +-
src/sbml/annotation/Makefile.in | 2 +-
src/sbml/annotation/ModelCreator.cpp | 2 +-
src/sbml/annotation/ModelCreator.h | 2 +-
src/sbml/annotation/ModelHistory.cpp | 2 +-
src/sbml/annotation/ModelHistory.h | 2 +-
src/sbml/annotation/RDFAnnotation.h | 2 +-
src/sbml/annotation/RDFAnnotationParser.cpp | 2 +-
src/sbml/annotation/RDFAnnotationParser.h | 2 +-
src/sbml/annotation/test/CMakeLists.txt | 2 +-
src/sbml/annotation/test/Makefile.in | 2 +-
src/sbml/annotation/test/TestCVTerms.c | 2 +-
src/sbml/annotation/test/TestCVTerms_newSetters.c | 2 +-
src/sbml/annotation/test/TestCopyAndClone.cpp | 2 +-
src/sbml/annotation/test/TestDate_newSetters.c | 2 +-
src/sbml/annotation/test/TestL3ModelHistory.cpp | 2 +-
.../annotation/test/TestModelCreator_newSetters.c | 2 +-
src/sbml/annotation/test/TestModelHistory.c | 2 +-
.../annotation/test/TestModelHistory_newSetters.c | 2 +-
src/sbml/annotation/test/TestRDFAnnotation.cpp | 2 +-
src/sbml/annotation/test/TestRDFAnnotation2.cpp | 2 +-
src/sbml/annotation/test/TestRDFAnnotationC.c | 2 +-
.../annotation/test/TestRDFAnnotationMetaid.cpp | 2 +-
.../test/TestRDFAnnotationNestedCVTerms.cpp | 2 +-
src/sbml/annotation/test/TestRunner.c | 2 +-
src/sbml/annotation/test/TestSyncAnnotation.cpp | 2 +-
src/sbml/annotation/test/TestValidation.cpp | 2 +-
src/sbml/common/Makefile.in | 2 +-
src/sbml/common/common-documentation.h | 198 +-
src/sbml/common/common.h | 2 +-
src/sbml/common/extern.h | 2 +-
src/sbml/common/libsbml-config-common.h | 2 +-
src/sbml/common/libsbml-config-common.h.cmake | 2 +-
src/sbml/common/libsbml-config-common.h.in | 2 +-
src/sbml/common/libsbml-config.h | 2 +-
src/sbml/common/libsbml-namespace.h | 2 +-
src/sbml/common/libsbml-namespace.h.cmake | 136 +-
src/sbml/common/libsbml-namespace.h.in | 2 +-
src/sbml/common/libsbml-package.h | 6 +-
src/sbml/common/libsbml-package.h.cmake | 108 +-
src/sbml/common/libsbml-package.h.in | 2 +-
src/sbml/common/libsbml-version.cpp | 2 +-
src/sbml/common/libsbml-version.h | 8 +-
src/sbml/common/libsbml-version.h.cmake | 2 +-
src/sbml/common/libsbml-version.h.in | 2 +-
src/sbml/common/operationReturnValues.cpp | 8 +-
src/sbml/common/operationReturnValues.h | 7 +-
src/sbml/common/sbmlfwd.h | 2 +-
src/sbml/compress/CompressCommon.cpp | 2 +-
src/sbml/compress/CompressCommon.h | 2 +-
src/sbml/compress/InputDecompressor.cpp | 2 +-
src/sbml/compress/InputDecompressor.h | 2 +-
src/sbml/compress/Makefile.in | 2 +-
src/sbml/compress/OutputCompressor.cpp | 2 +-
src/sbml/compress/OutputCompressor.h | 2 +-
src/sbml/compress/bzfstream.cpp | 2 +-
src/sbml/compress/bzfstream.h | 2 +-
src/sbml/compress/zipfstream.cpp | 2 +-
src/sbml/compress/zipfstream.h | 2 +-
src/sbml/conversion/ConversionOption.cpp | 2 +-
src/sbml/conversion/ConversionOption.h | 2 +-
src/sbml/conversion/ConversionProperties.cpp | 2 +-
src/sbml/conversion/ConversionProperties.h | 2 +-
src/sbml/conversion/Makefile.in | 2 +-
src/sbml/conversion/RegisterConverters.cpp | 2 +-
src/sbml/conversion/SBMLConverter.cpp | 2 +-
src/sbml/conversion/SBMLConverter.h | 2 +-
src/sbml/conversion/SBMLConverterRegister.h | 2 +-
src/sbml/conversion/SBMLConverterRegistry.cpp | 2 +-
src/sbml/conversion/SBMLConverterRegistry.h | 2 +-
.../conversion/SBMLFunctionDefinitionConverter.cpp | 2 +-
.../conversion/SBMLFunctionDefinitionConverter.h | 2 +-
src/sbml/conversion/SBMLIdConverter.cpp | 2 +-
src/sbml/conversion/SBMLIdConverter.h | 2 +-
src/sbml/conversion/SBMLInferUnitsConverter.cpp | 2 +-
src/sbml/conversion/SBMLInferUnitsConverter.h | 2 +-
.../conversion/SBMLInitialAssignmentConverter.cpp | 2 +-
.../conversion/SBMLInitialAssignmentConverter.h | 2 +-
.../conversion/SBMLLevel1Version1Converter.cpp | 2 +-
src/sbml/conversion/SBMLLevel1Version1Converter.h | 470 +-
src/sbml/conversion/SBMLLevelVersionConverter.cpp | 24 +-
src/sbml/conversion/SBMLLevelVersionConverter.h | 2 +-
.../conversion/SBMLLocalParameterConverter.cpp | 2 +-
src/sbml/conversion/SBMLLocalParameterConverter.h | 2 +-
src/sbml/conversion/SBMLReactionConverter.cpp | 2 +-
src/sbml/conversion/SBMLReactionConverter.h | 2 +-
src/sbml/conversion/SBMLRuleConverter.cpp | 2 +-
src/sbml/conversion/SBMLRuleConverter.h | 2 +-
src/sbml/conversion/SBMLStripPackageConverter.cpp | 2 +-
src/sbml/conversion/SBMLStripPackageConverter.h | 2 +-
src/sbml/conversion/SBMLUnitsConverter.cpp | 2 +-
src/sbml/conversion/SBMLUnitsConverter.h | 2 +-
src/sbml/conversion/test/CMakeLists.txt | 2 +-
src/sbml/conversion/test/TestConversionOption.cpp | 2 +-
.../conversion/test/TestConversionProperties.cpp | 2 +-
.../conversion/test/TestInferUnitsConverter.cpp | 2 +-
.../conversion/test/TestLevelVersionConverter.cpp | 2 +-
src/sbml/conversion/test/TestRunner.c | 2 +-
.../conversion/test/TestSBMLConverterRegistry.cpp | 2 +-
src/sbml/conversion/test/TestSBMLRuleConverter.cpp | 2 +-
.../conversion/test/TestStripPackageConverter.cpp | 2 +-
src/sbml/conversion/test/TestUnitsConverter.cpp | 2 +-
src/sbml/conversion/test/TestUnitsConverter2.cpp | 2 +-
src/sbml/conversion/test/TestUnitsConverterL2.cpp | 2 +-
src/sbml/extension/ASTBasePlugin.cpp | 2 +-
src/sbml/extension/ASTBasePlugin.h | 2 +-
src/sbml/extension/ISBMLExtensionNamespaces.cpp | 2 +-
src/sbml/extension/ISBMLExtensionNamespaces.h | 2 +-
src/sbml/extension/Makefile.in | 2 +-
src/sbml/extension/SBMLDocumentPlugin.cpp | 2 +-
src/sbml/extension/SBMLDocumentPlugin.h | 2 +-
.../extension/SBMLDocumentPluginNotRequired.cpp | 2 +-
src/sbml/extension/SBMLDocumentPluginNotRequired.h | 2 +-
src/sbml/extension/SBMLExtension.cpp | 2 +-
src/sbml/extension/SBMLExtension.h | 2 +-
src/sbml/extension/SBMLExtensionException.cpp | 2 +-
src/sbml/extension/SBMLExtensionException.h | 2 +-
src/sbml/extension/SBMLExtensionNamespaces.cpp | 2 +-
src/sbml/extension/SBMLExtensionNamespaces.h | 2 +-
src/sbml/extension/SBMLExtensionRegister.h | 2 +-
src/sbml/extension/SBMLExtensionRegistry.cpp | 2 +-
src/sbml/extension/SBMLExtensionRegistry.h | 2 +-
src/sbml/extension/SBaseExtensionPoint.cpp | 2 +-
src/sbml/extension/SBaseExtensionPoint.h | 2 +-
src/sbml/extension/SBasePlugin.cpp | 2 +-
src/sbml/extension/SBasePlugin.h | 5 +-
src/sbml/extension/SBasePluginCreator.h | 2 +-
src/sbml/extension/SBasePluginCreatorBase.cpp | 2 +-
src/sbml/extension/SBasePluginCreatorBase.h | 2 +-
src/sbml/extension/test/CMakeLists.txt | 2 +-
src/sbml/extension/test/Makefile.in | 2 +-
src/sbml/extension/test/TestPackage.cpp | 2 +-
src/sbml/extension/test/TestPackage.h | 2 +-
src/sbml/extension/test/TestRunner.c | 2 +-
src/sbml/extension/test/TestSBMLDocumentPlugin.cpp | 2 +-
src/sbml/extension/test/TestSBMLExtension.cpp | 2 +-
.../extension/test/TestSBMLExtensionNamespaces.cpp | 2 +-
.../extension/test/TestSBMLExtensionRegistry.cpp | 2 +-
.../extension/test/TestSBaseExtensionPoint.cpp | 2 +-
src/sbml/extension/test/TestSBasePlugin.cpp | 2 +-
src/sbml/extension/test/TestSBasePluginCreator.cpp | 2 +-
.../extension/test/TestSBasePluginCreatorBase.cpp | 2 +-
src/sbml/extension/test/TestUnknownPackage.cpp | 2 +-
src/sbml/math-legacy/ASTNode.cpp | 18 +-
src/sbml/math-legacy/ASTNode.h | 2 +-
src/sbml/math-legacy/FormulaFormatter.c | 2 +-
src/sbml/math-legacy/FormulaFormatter.h | 2 +-
src/sbml/math-legacy/FormulaParser.c | 2 +-
src/sbml/math-legacy/FormulaParser.h | 2 +-
src/sbml/math-legacy/FormulaTokenizer.c | 13 +-
src/sbml/math-legacy/FormulaTokenizer.h | 2 +-
src/sbml/math-legacy/L3FormulaFormatter.c | 133 +-
src/sbml/math-legacy/L3FormulaFormatter.h | 2 +-
src/sbml/math-legacy/L3Parser.cpp | 478 +-
src/sbml/math-legacy/L3Parser.h | 12 +-
src/sbml/math-legacy/L3ParserSettings.cpp | 2 +-
src/sbml/math-legacy/L3ParserSettings.h | 2 +-
src/sbml/math-legacy/Makefile.in | 2 +-
src/sbml/math-legacy/MathML.cpp | 58 +-
src/sbml/math-legacy/MathML.h | 2 +-
src/sbml/math-legacy/test/CMakeLists.txt | 2 +-
src/sbml/math-legacy/test/Makefile.in | 2 +-
src/sbml/math-legacy/test/TestASTNode.c | 33 +-
src/sbml/math-legacy/test/TestChildFunctions.cpp | 2 +-
src/sbml/math-legacy/test/TestFormulaFormatter.c | 2 +-
src/sbml/math-legacy/test/TestFormulaParser.c | 2 +-
src/sbml/math-legacy/test/TestFormulaTokenizer.c | 2 +-
src/sbml/math-legacy/test/TestGetValue.cpp | 2 +-
src/sbml/math-legacy/test/TestL3FormulaFormatter.c | 66 +-
src/sbml/math-legacy/test/TestL3FormulaParser.cpp | 2 +-
src/sbml/math-legacy/test/TestL3FormulaParserC.c | 2 +-
src/sbml/math-legacy/test/TestReadFromFile1.cpp | 2 +-
src/sbml/math-legacy/test/TestReadFromFile2.cpp | 2 +-
src/sbml/math-legacy/test/TestReadMathML.cpp | 2 +-
src/sbml/math-legacy/test/TestRunner.c | 2 +-
src/sbml/math-legacy/test/TestValidASTNode.cpp | 2 +-
src/sbml/math-legacy/test/TestWriteMathML.cpp | 2 +-
.../math-legacy/test/TestWriteMathMLFromAST.cpp | 2 +-
src/sbml/math/ASTBase.cpp | 4 +-
src/sbml/math/ASTBase.h | 2 +-
src/sbml/math/ASTBinaryFunctionNode.cpp | 2 +-
src/sbml/math/ASTBinaryFunctionNode.h | 2 +-
src/sbml/math/ASTCSymbol.cpp | 2 +-
src/sbml/math/ASTCSymbol.h | 2 +-
src/sbml/math/ASTCSymbolAvogadroNode.cpp | 2 +-
src/sbml/math/ASTCSymbolAvogadroNode.h | 2 +-
src/sbml/math/ASTCSymbolDelayNode.cpp | 2 +-
src/sbml/math/ASTCSymbolDelayNode.h | 2 +-
src/sbml/math/ASTCSymbolTimeNode.cpp | 2 +-
src/sbml/math/ASTCSymbolTimeNode.h | 2 +-
src/sbml/math/ASTCiFunctionNode.cpp | 2 +-
src/sbml/math/ASTCiFunctionNode.h | 2 +-
src/sbml/math/ASTCiNumberNode.cpp | 2 +-
src/sbml/math/ASTCiNumberNode.h | 2 +-
src/sbml/math/ASTCnBase.cpp | 2 +-
src/sbml/math/ASTCnBase.h | 2 +-
src/sbml/math/ASTCnExponentialNode.cpp | 2 +-
src/sbml/math/ASTCnExponentialNode.h | 2 +-
src/sbml/math/ASTCnIntegerNode.cpp | 2 +-
src/sbml/math/ASTCnIntegerNode.h | 2 +-
src/sbml/math/ASTCnRationalNode.cpp | 2 +-
src/sbml/math/ASTCnRationalNode.h | 2 +-
src/sbml/math/ASTCnRealNode.cpp | 2 +-
src/sbml/math/ASTCnRealNode.h | 2 +-
src/sbml/math/ASTConstantNumberNode.cpp | 2 +-
src/sbml/math/ASTConstantNumberNode.h | 2 +-
src/sbml/math/ASTFunction.cpp | 19 +-
src/sbml/math/ASTFunction.h | 2 +-
src/sbml/math/ASTFunctionBase.cpp | 2 +-
src/sbml/math/ASTFunctionBase.h | 2 +-
src/sbml/math/ASTLambdaFunctionNode.cpp | 2 +-
src/sbml/math/ASTLambdaFunctionNode.h | 2 +-
src/sbml/math/ASTNaryFunctionNode.cpp | 2 +-
src/sbml/math/ASTNaryFunctionNode.h | 2 +-
src/sbml/math/ASTNode.cpp | 33 +-
src/sbml/math/ASTNode.h | 8 +-
src/sbml/math/ASTNumber.cpp | 12 +-
src/sbml/math/ASTNumber.h | 2 +-
src/sbml/math/ASTPiecewiseFunctionNode.cpp | 2 +-
src/sbml/math/ASTPiecewiseFunctionNode.h | 2 +-
src/sbml/math/ASTQualifierNode.cpp | 2 +-
src/sbml/math/ASTQualifierNode.h | 2 +-
src/sbml/math/ASTSemanticsNode.cpp | 2 +-
src/sbml/math/ASTSemanticsNode.h | 2 +-
src/sbml/math/ASTTypes.cpp | 2 +-
src/sbml/math/ASTTypes.h | 2 +-
src/sbml/math/ASTUnaryFunctionNode.cpp | 2 +-
src/sbml/math/ASTUnaryFunctionNode.h | 2 +-
src/sbml/math/FormulaFormatter.c | 2 +-
src/sbml/math/FormulaFormatter.h | 2 +-
src/sbml/math/FormulaParser.c | 2 +-
src/sbml/math/FormulaParser.h | 2 +-
src/sbml/math/FormulaTokenizer.c | 10 +-
src/sbml/math/FormulaTokenizer.h | 2 +-
src/sbml/math/L3FormulaFormatter.c | 158 +-
src/sbml/math/L3FormulaFormatter.h | 2 +-
src/sbml/math/L3Parser.h | 2 +-
src/sbml/math/L3ParserSettings.cpp | 2 +-
src/sbml/math/L3ParserSettings.h | 2 +-
src/sbml/math/Makefile.in | 2 +-
src/sbml/math/MathML.cpp | 2 +-
src/sbml/math/MathML.h | 2 +-
src/sbml/math/test/CMakeLists.txt | 2 +-
src/sbml/math/test/Makefile.in | 2 +-
src/sbml/math/test/TestASTNode.c | 29 +-
src/sbml/math/test/TestChildFunctions.cpp | 2 +-
src/sbml/math/test/TestFormulaFormatter.c | 2 +-
src/sbml/math/test/TestFormulaParser.c | 2 +-
src/sbml/math/test/TestFormulaTokenizer.c | 2 +-
src/sbml/math/test/TestGetValue.cpp | 2 +-
src/sbml/math/test/TestL3FormulaFormatter.c | 52 +-
src/sbml/math/test/TestL3FormulaParser.cpp | 2 +-
src/sbml/math/test/TestL3FormulaParserC.c | 2 +-
src/sbml/math/test/TestNewASTNode.cpp | 2 +-
src/sbml/math/test/TestNewReadMathML.cpp | 29 +-
src/sbml/math/test/TestNewWriteMathMLFromAST.cpp | 2 +-
src/sbml/math/test/TestReadFromFile1.cpp | 2 +-
src/sbml/math/test/TestReadFromFile2.cpp | 2 +-
src/sbml/math/test/TestReadMathML.cpp | 2 +-
src/sbml/math/test/TestRunner.c | 2 +-
src/sbml/math/test/TestValidASTNode.cpp | 2 +-
src/sbml/math/test/TestWriteMathML.cpp | 2 +-
src/sbml/math/test/TestWriteMathMLFromAST.cpp | 2 +-
src/sbml/packages/Makefile.in | 2 +-
.../packages/arrays/common/ArraysExtensionTypes.h | 2 +-
src/sbml/packages/arrays/common/arraysfwd.h | 2 +-
.../packages/arrays/extension/ArraysASTPlugin.cpp | 2 +-
.../packages/arrays/extension/ArraysASTPlugin.h | 2 +-
.../packages/arrays/extension/ArraysExtension.cpp | 2 +-
.../packages/arrays/extension/ArraysExtension.h | 2 +-
.../arrays/extension/ArraysSBMLDocumentPlugin.cpp | 2 +-
.../arrays/extension/ArraysSBMLDocumentPlugin.h | 2 +-
.../arrays/extension/ArraysSBasePlugin.cpp | 2 +-
.../packages/arrays/extension/ArraysSBasePlugin.h | 2 +-
.../arrays/math/ASTArraysVectorFunctionNode.cpp | 2 +-
.../arrays/math/ASTArraysVectorFunctionNode.h | 2 +-
src/sbml/packages/arrays/math/test/CMakeLists.txt | 2 +-
.../arrays/math/test/TestArrayInfixParsing.cpp | 2 +-
.../arrays/math/test/TestArrayInfixWriting.cpp | 2 +-
.../packages/arrays/math/test/TestNewASTNode.cpp | 2 +-
.../arrays/math/test/TestNewReadMathML.cpp | 2 +-
.../arrays/math/test/TestNewWriteMathMLFromAST.cpp | 2 +-
src/sbml/packages/arrays/math/test/TestRunner.c | 5 +-
.../arrays/math/test/TestWriteMathMLFromInfix.cpp | 2 +-
src/sbml/packages/arrays/sbml/Dimension.cpp | 2 +-
src/sbml/packages/arrays/sbml/Dimension.h | 2 +-
src/sbml/packages/arrays/sbml/Index.cpp | 2 +-
src/sbml/packages/arrays/sbml/Index.h | 2 +-
.../validator/ArraysConsistencyValidator.cpp | 2 +-
.../arrays/validator/ArraysConsistencyValidator.h | 2 +-
.../ArraysIdentifierConsistencyValidator.cpp | 2 +-
.../ArraysIdentifierConsistencyValidator.h | 2 +-
.../packages/arrays/validator/ArraysSBMLError.h | 2 +-
.../arrays/validator/ArraysSBMLErrorTable.h | 2 +-
.../packages/arrays/validator/ArraysValidator.cpp | 2 +-
.../packages/arrays/validator/ArraysValidator.h | 2 +-
.../constraints/ArraysConsistencyConstraints.cpp | 2 +-
.../ArraysIdentifierConsistencyConstraints.cpp | 2 +-
src/sbml/packages/comp/Makefile.in | 2 +-
src/sbml/packages/comp/common/CompExtensionTypes.h | 2 +-
src/sbml/packages/comp/common/Makefile.in | 2 +-
src/sbml/packages/comp/common/compfwd.h | 2 +-
src/sbml/packages/comp/extension/CompExtension.cpp | 2 +-
src/sbml/packages/comp/extension/CompExtension.h | 2 +-
.../packages/comp/extension/CompModelPlugin.cpp | 9 +-
src/sbml/packages/comp/extension/CompModelPlugin.h | 15 +-
.../comp/extension/CompSBMLDocumentPlugin.cpp | 2 +-
.../comp/extension/CompSBMLDocumentPlugin.h | 19 +-
.../packages/comp/extension/CompSBasePlugin.cpp | 2 +-
src/sbml/packages/comp/extension/CompSBasePlugin.h | 9 +-
src/sbml/packages/comp/extension/Makefile.in | 2 +-
.../packages/comp/extension/test/CMakeLists.txt | 2 +-
src/sbml/packages/comp/extension/test/Makefile.in | 2 +-
.../comp/extension/test/TestCheckConsistency.cpp | 2 +-
.../comp/extension/test/TestExtensionObjects.cpp | 2 +-
.../comp/extension/test/TestMultipleNamespaces.cpp | 2 +-
src/sbml/packages/comp/extension/test/TestRunner.c | 2 +-
src/sbml/packages/comp/sbml/CompBase.cpp | 2 +-
src/sbml/packages/comp/sbml/CompBase.h | 9 +-
src/sbml/packages/comp/sbml/Deletion.cpp | 2 +-
src/sbml/packages/comp/sbml/Deletion.h | 7 +-
.../packages/comp/sbml/ExternalModelDefinition.cpp | 2 +-
.../packages/comp/sbml/ExternalModelDefinition.h | 5 +-
src/sbml/packages/comp/sbml/ListOfDeletions.cpp | 2 +-
src/sbml/packages/comp/sbml/ListOfDeletions.h | 2 +-
.../comp/sbml/ListOfExternalModelDefinitions.cpp | 2 +-
.../comp/sbml/ListOfExternalModelDefinitions.h | 2 +-
.../packages/comp/sbml/ListOfModelDefinitions.cpp | 2 +-
.../packages/comp/sbml/ListOfModelDefinitions.h | 2 +-
src/sbml/packages/comp/sbml/ListOfPorts.cpp | 2 +-
src/sbml/packages/comp/sbml/ListOfPorts.h | 2 +-
.../packages/comp/sbml/ListOfReplacedElements.cpp | 2 +-
.../packages/comp/sbml/ListOfReplacedElements.h | 2 +-
src/sbml/packages/comp/sbml/ListOfSubmodels.cpp | 2 +-
src/sbml/packages/comp/sbml/ListOfSubmodels.h | 2 +-
src/sbml/packages/comp/sbml/Makefile.in | 2 +-
src/sbml/packages/comp/sbml/ModelDefinition.cpp | 2 +-
src/sbml/packages/comp/sbml/ModelDefinition.h | 5 +-
src/sbml/packages/comp/sbml/Port.cpp | 2 +-
src/sbml/packages/comp/sbml/Port.h | 19 +-
src/sbml/packages/comp/sbml/ReplacedBy.cpp | 2 +-
src/sbml/packages/comp/sbml/ReplacedBy.h | 5 +-
src/sbml/packages/comp/sbml/ReplacedElement.cpp | 2 +-
src/sbml/packages/comp/sbml/ReplacedElement.h | 17 +-
src/sbml/packages/comp/sbml/Replacing.cpp | 2 +-
src/sbml/packages/comp/sbml/Replacing.h | 9 +-
src/sbml/packages/comp/sbml/SBaseRef.cpp | 2 +-
src/sbml/packages/comp/sbml/SBaseRef.h | 39 +-
src/sbml/packages/comp/sbml/Submodel.cpp | 2 +-
src/sbml/packages/comp/sbml/Submodel.h | 13 +-
src/sbml/packages/comp/sbml/test/CMakeLists.txt | 2 +-
src/sbml/packages/comp/sbml/test/Makefile.in | 2 +-
src/sbml/packages/comp/sbml/test/TestDeletion.c | 2 +-
.../comp/sbml/test/TestExternalModelDefinition.c | 2 +-
.../packages/comp/sbml/test/TestModelDefinition.c | 2 +-
src/sbml/packages/comp/sbml/test/TestPort.c | 2 +-
.../packages/comp/sbml/test/TestReadWriteSBase.cpp | 2 +-
src/sbml/packages/comp/sbml/test/TestReplacedBy.c | 2 +-
.../packages/comp/sbml/test/TestReplacedElement.c | 2 +-
src/sbml/packages/comp/sbml/test/TestRunner.c | 2 +-
.../packages/comp/sbml/test/TestSBaseObjects.cpp | 2 +-
src/sbml/packages/comp/sbml/test/TestSBaseRef.c | 2 +-
src/sbml/packages/comp/sbml/test/TestSubmodel.c | 2 +-
.../packages/comp/util/CompFlatteningConverter.cpp | 2 +-
.../packages/comp/util/CompFlatteningConverter.h | 2 +-
src/sbml/packages/comp/util/SBMLFileResolver.cpp | 2 +-
src/sbml/packages/comp/util/SBMLFileResolver.h | 2 +-
src/sbml/packages/comp/util/SBMLResolver.cpp | 2 +-
src/sbml/packages/comp/util/SBMLResolver.h | 2 +-
.../packages/comp/util/SBMLResolverRegistry.cpp | 22 +-
src/sbml/packages/comp/util/SBMLResolverRegistry.h | 7 +-
src/sbml/packages/comp/util/SBMLUri.cpp | 2 +-
src/sbml/packages/comp/util/SBMLUri.h | 2 +-
src/sbml/packages/comp/util/test/CMakeLists.txt | 2 +-
.../comp/util/test/TestCompFlatteningConverter.cpp | 5 +-
.../TestCompFlatteningConverterStripPackage.cpp | 2 +-
.../util/test/TestCompFlatteningErrorMessages.cpp | 43 +-
.../comp/util/test/TestCompFlatteningNewFlags.cpp | 2 +-
.../test/TestCompFlatteningUnknownPackageRefs.cpp | 2 +-
.../comp/util/test/TestExternalModelResolving.cpp | 2 +-
src/sbml/packages/comp/util/test/TestRunner.c | 2 +-
.../packages/comp/util/test/TestURIResolvers.cpp | 2 +-
.../comp/util/test/test-data/pnr_submodel.xml | 17 +
.../comp/util/test/test-data/port_and_replace.xml | 24 +
.../comp/validator/CompConsistencyValidator.cpp | 2 +-
.../comp/validator/CompConsistencyValidator.h | 2 +-
.../CompIdentifierConsistencyValidator.cpp | 2 +-
.../validator/CompIdentifierConsistencyValidator.h | 2 +-
src/sbml/packages/comp/validator/CompSBMLError.h | 2 +-
.../packages/comp/validator/CompSBMLErrorTable.h | 2 +-
.../validator/CompUnitConsistencyValidator.cpp | 2 +-
.../comp/validator/CompUnitConsistencyValidator.h | 2 +-
src/sbml/packages/comp/validator/CompValidator.cpp | 2 +-
src/sbml/packages/comp/validator/CompValidator.h | 2 +-
src/sbml/packages/comp/validator/Makefile.in | 2 +-
.../validator/constraints/ClassReplacements.cpp | 2 +-
.../comp/validator/constraints/ClassReplacements.h | 2 +-
.../constraints/CompConsistencyConstraints.cpp | 5 +-
.../CompConsistencyConstraintsDeclared.cxx | 2 +-
.../comp/validator/constraints/CompIdBase.cpp | 2 +-
.../comp/validator/constraints/CompIdBase.h | 2 +-
.../CompIdentifierConsistencyConstraints.cpp | 2 +-
...ompIdentifierConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/CompUnitConsistencyConstraints.cpp | 2 +-
.../CompUnitConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/ExtModelReferenceCycles.cpp | 2 +-
.../constraints/ExtModelReferenceCycles.h | 2 +-
.../comp/validator/constraints/Makefile.in | 2 +-
.../constraints/PackageIdReplacementCheck.cpp | 2 +-
.../constraints/PackageIdReplacementCheck.h | 2 +-
.../constraints/SubmodelReferenceCycles.cpp | 2 +-
.../constraints/SubmodelReferenceCycles.h | 2 +-
.../validator/constraints/UniqueCompIdBase.cpp | 2 +-
.../comp/validator/constraints/UniqueCompIdBase.h | 2 +-
.../validator/constraints/UniqueComponentIds.cpp | 2 +-
.../validator/constraints/UniqueComponentIds.h | 2 +-
.../comp/validator/constraints/UniqueModelIds.cpp | 2 +-
.../comp/validator/constraints/UniqueModelIds.h | 2 +-
.../comp/validator/constraints/UniquePortIds.cpp | 2 +-
.../comp/validator/constraints/UniquePortIds.h | 2 +-
.../validator/constraints/UniquePortReferences.cpp | 2 +-
.../validator/constraints/UniquePortReferences.h | 2 +-
.../constraints/UniqueReplacedReferences.cpp | 2 +-
.../constraints/UniqueReplacedReferences.h | 2 +-
.../validator/constraints/UnitReplacementCheck.cpp | 2 +-
.../validator/constraints/UnitReplacementCheck.h | 2 +-
.../packages/comp/validator/test/CMakeLists.txt | 2 +-
src/sbml/packages/comp/validator/test/Makefile.in | 2 +-
.../test/TestCompConsistencyValidator.cpp | 2 +-
src/sbml/packages/comp/validator/test/TestFile.cpp | 2 +-
src/sbml/packages/comp/validator/test/TestFile.h | 2 +-
.../packages/comp/validator/test/TestValidator.cpp | 2 +-
.../packages/comp/validator/test/TestValidator.h | 2 +-
.../distrib/common/DistribExtensionTypes.h | 2 +-
src/sbml/packages/distrib/common/distribfwd.h | 2 +-
.../distrib/extension/DistribExtension.cpp | 2 +-
.../packages/distrib/extension/DistribExtension.h | 2 +-
.../extension/DistribFunctionDefinitionPlugin.cpp | 2 +-
.../extension/DistribFunctionDefinitionPlugin.h | 2 +-
.../extension/DistribSBMLDocumentPlugin.cpp | 2 +-
.../distrib/extension/DistribSBMLDocumentPlugin.h | 2 +-
.../distrib/extension/DistribSBasePlugin.cpp | 2 +-
.../distrib/extension/DistribSBasePlugin.h | 2 +-
src/sbml/packages/distrib/sbml/DistribInput.cpp | 2 +-
src/sbml/packages/distrib/sbml/DistribInput.h | 2 +-
.../packages/distrib/sbml/DrawFromDistribution.cpp | 2 +-
.../packages/distrib/sbml/DrawFromDistribution.h | 2 +-
src/sbml/packages/distrib/sbml/Uncertainty.cpp | 2 +-
src/sbml/packages/distrib/sbml/Uncertainty.h | 2 +-
.../validator/DistribConsistencyValidator.cpp | 2 +-
.../validator/DistribConsistencyValidator.h | 2 +-
.../DistribIdentifierConsistencyValidator.cpp | 2 +-
.../DistribIdentifierConsistencyValidator.h | 2 +-
.../packages/distrib/validator/DistribSBMLError.h | 2 +-
.../distrib/validator/DistribSBMLErrorTable.h | 2 +-
.../distrib/validator/DistribValidator.cpp | 2 +-
.../packages/distrib/validator/DistribValidator.h | 2 +-
.../constraints/DistribConsistencyConstraints.cpp | 2 +-
.../DistribIdentifierConsistencyConstraints.cpp | 2 +-
src/sbml/packages/dyn-register.cxx | 2 +-
src/sbml/packages/dyn-register.h | 2 +-
src/sbml/packages/dyn/common/DynExtensionTypes.h | 2 +-
src/sbml/packages/dyn/common/dynfwd.h | 2 +-
.../dyn/extension/DynCompartmentPlugin.cpp | 2 +-
.../packages/dyn/extension/DynCompartmentPlugin.h | 2 +-
src/sbml/packages/dyn/extension/DynEventPlugin.cpp | 2 +-
src/sbml/packages/dyn/extension/DynEventPlugin.h | 2 +-
src/sbml/packages/dyn/extension/DynExtension.cpp | 2 +-
src/sbml/packages/dyn/extension/DynExtension.h | 2 +-
.../dyn/extension/DynSBMLDocumentPlugin.cpp | 2 +-
.../packages/dyn/extension/DynSBMLDocumentPlugin.h | 2 +-
src/sbml/packages/dyn/extension/DynSBasePlugin.cpp | 2 +-
src/sbml/packages/dyn/extension/DynSBasePlugin.h | 2 +-
.../packages/dyn/extension/test/CMakeLists.txt | 2 +-
src/sbml/packages/dyn/extension/test/TestRunner.c | 4 +
src/sbml/packages/dyn/sbml/DynElement.cpp | 2 +-
src/sbml/packages/dyn/sbml/DynElement.h | 2 +-
src/sbml/packages/dyn/sbml/SpatialComponent.cpp | 2 +-
src/sbml/packages/dyn/sbml/SpatialComponent.h | 2 +-
.../dyn/validator/DynConsistencyValidator.cpp | 2 +-
.../dyn/validator/DynConsistencyValidator.h | 2 +-
.../DynIdentifierConsistencyValidator.cpp | 2 +-
.../validator/DynIdentifierConsistencyValidator.h | 2 +-
src/sbml/packages/dyn/validator/DynSBMLError.h | 2 +-
.../packages/dyn/validator/DynSBMLErrorTable.h | 2 +-
src/sbml/packages/dyn/validator/DynValidator.cpp | 2 +-
src/sbml/packages/dyn/validator/DynValidator.h | 2 +-
.../constraints/DynConsistencyConstraints.cpp | 2 +-
.../DynIdentifierConsistencyConstraints.cpp | 2 +-
src/sbml/packages/fbc-register.cxx | 2 +-
src/sbml/packages/fbc-register.h | 8 +-
src/sbml/packages/fbc/Makefile.in | 2 +-
src/sbml/packages/fbc/common/FbcExtensionTypes.h | 2 +-
src/sbml/packages/fbc/common/fbcfwd.h | 8 +-
src/sbml/packages/fbc/extension/FbcExtension.cpp | 2 +-
src/sbml/packages/fbc/extension/FbcExtension.h | 2 +-
src/sbml/packages/fbc/extension/FbcModelPlugin.cpp | 61 +-
src/sbml/packages/fbc/extension/FbcModelPlugin.h | 196 +-
.../packages/fbc/extension/FbcReactionPlugin.cpp | 150 +-
.../packages/fbc/extension/FbcReactionPlugin.h | 1014 +--
.../fbc/extension/FbcSBMLDocumentPlugin.cpp | 8 +-
.../packages/fbc/extension/FbcSBMLDocumentPlugin.h | 23 +-
.../packages/fbc/extension/FbcSpeciesPlugin.cpp | 18 +-
src/sbml/packages/fbc/extension/FbcSpeciesPlugin.h | 53 +-
src/sbml/packages/fbc/extension/Makefile.in | 2 +-
.../packages/fbc/extension/test/CMakeLists.txt | 2 +-
src/sbml/packages/fbc/extension/test/Makefile.in | 13 +-
.../fbc/extension/test/TestFbcAssociation.cpp | 603 ++
.../fbc/extension/test/TestReadFbcExtension.cpp | 41 +
src/sbml/packages/fbc/extension/test/TestRunner.c | 2 +
.../fbc/extension/test/test-data/cobra-l2.xml | 18 +-
src/sbml/packages/fbc/sbml/Association.cpp | 2 +-
src/sbml/packages/fbc/sbml/Association.h | 22 +-
src/sbml/packages/fbc/sbml/FbcAnd.cpp | 12 +-
src/sbml/packages/fbc/sbml/FbcAnd.h | 1267 ++--
src/sbml/packages/fbc/sbml/FbcAssociation.cpp | 32 +-
src/sbml/packages/fbc/sbml/FbcAssociation.h | 1448 ++--
src/sbml/packages/fbc/sbml/FbcOr.cpp | 12 +-
src/sbml/packages/fbc/sbml/FbcOr.h | 1259 ++--
src/sbml/packages/fbc/sbml/FluxBound.cpp | 15 +-
src/sbml/packages/fbc/sbml/FluxBound.h | 73 +-
src/sbml/packages/fbc/sbml/FluxObjective.cpp | 8 +-
src/sbml/packages/fbc/sbml/FluxObjective.h | 10 +-
src/sbml/packages/fbc/sbml/GeneAssociation.cpp | 2 +-
src/sbml/packages/fbc/sbml/GeneAssociation.h | 32 +-
src/sbml/packages/fbc/sbml/GeneProduct.cpp | 8 +-
src/sbml/packages/fbc/sbml/GeneProduct.h | 2224 +++---
.../packages/fbc/sbml/GeneProductAssociation.cpp | 12 +-
.../packages/fbc/sbml/GeneProductAssociation.h | 1653 ++---
src/sbml/packages/fbc/sbml/GeneProductRef.cpp | 23 +-
src/sbml/packages/fbc/sbml/GeneProductRef.h | 1520 ++--
src/sbml/packages/fbc/sbml/Makefile.in | 2 +-
src/sbml/packages/fbc/sbml/Objective.cpp | 12 +-
src/sbml/packages/fbc/sbml/Objective.h | 32 +-
src/sbml/packages/fbc/util/CobraToFbcConverter.cpp | 12 +-
src/sbml/packages/fbc/util/CobraToFbcConverter.h | 4 +-
src/sbml/packages/fbc/util/FbcToCobraConverter.cpp | 2 +-
src/sbml/packages/fbc/util/FbcToCobraConverter.h | 4 +-
src/sbml/packages/fbc/util/FbcV1ToV2Converter.cpp | 2 +-
src/sbml/packages/fbc/util/FbcV1ToV2Converter.h | 360 +-
src/sbml/packages/fbc/util/FbcV2ToV1Converter.cpp | 2 +-
src/sbml/packages/fbc/util/FbcV2ToV1Converter.h | 340 +-
.../fbc/validator/FbcConsistencyValidator.cpp | 2 +-
.../fbc/validator/FbcConsistencyValidator.h | 2 +-
.../FbcIdentifierConsistencyValidator.cpp | 2 +-
.../validator/FbcIdentifierConsistencyValidator.h | 2 +-
src/sbml/packages/fbc/validator/FbcSBMLError.h | 2 +-
.../packages/fbc/validator/FbcSBMLErrorTable.h | 12 +-
src/sbml/packages/fbc/validator/FbcValidator.cpp | 2 +-
src/sbml/packages/fbc/validator/FbcValidator.h | 6 +-
src/sbml/packages/fbc/validator/Makefile.in | 2 +-
.../constraints/FbcConsistencyConstraints.cpp | 2 +-
.../FbcConsistencyConstraintsDeclared.cxx | 2 +-
.../FbcIdentifierConsistencyConstraints.cpp | 2 +-
...FbcIdentifierConsistencyConstraintsDeclared.cxx | 2 +-
.../validator/constraints/FluxBoundsConsistent.cpp | 2 +-
.../validator/constraints/FluxBoundsConsistent.h | 2 +-
.../packages/fbc/validator/constraints/Makefile.in | 2 +-
.../constraints/UniqueGeneProductLabels.cpp | 2 +-
.../constraints/UniqueGeneProductLabels.h | 258 +-
.../validator/constraints/UniqueModelWideIds.cpp | 2 +-
.../fbc/validator/constraints/UniqueModelWideIds.h | 2 +-
.../packages/fbc/validator/test/CMakeLists.txt | 2 +-
src/sbml/packages/fbc/validator/test/Makefile.in | 2 +-
.../validator/test/TestFbcConsistencyValidator.cpp | 2 +-
src/sbml/packages/fbc/validator/test/TestFile.cpp | 2 +-
src/sbml/packages/fbc/validator/test/TestFile.h | 2 +-
.../packages/fbc/validator/test/TestValidator.cpp | 2 +-
.../packages/fbc/validator/test/TestValidator.h | 2 +-
.../fbc/validator/test/test-data/Makefile.in | 2 +-
src/sbml/packages/groups-register.cxx | 42 +-
src/sbml/packages/groups-register.h | 36 +-
.../packages/groups/common/GroupsExtensionTypes.h | 60 +-
src/sbml/packages/groups/common/groupsfwd.h | 73 +-
.../packages/groups/extension/GroupsExtension.cpp | 440 +-
.../packages/groups/extension/GroupsExtension.h | 401 +-
.../groups/extension/GroupsModelPlugin.cpp | 616 +-
.../packages/groups/extension/GroupsModelPlugin.h | 529 +-
.../groups/extension/GroupsSBMLDocumentPlugin.cpp | 258 +-
.../groups/extension/GroupsSBMLDocumentPlugin.h | 110 +-
.../groups/extension/test/TestGroupsExtension.cpp | 4 -
.../extension/test/TestGroupsModelPlugin.cpp | 342 +
.../extension/test/TestReadGroupsExtension.cpp | 69 -
.../packages/groups/extension/test/TestRunner.c | 2 +
.../extension/test/test-data/groups-nested1.xml | 31 +
.../extension/test/test-data/groups-nested2.xml | 31 +
.../test/test-data/groups_speciestype_example.xml | 30 -
src/sbml/packages/groups/sbml/Group.cpp | 1301 ++--
src/sbml/packages/groups/sbml/Group.h | 1469 ++--
src/sbml/packages/groups/sbml/ListOfGroups.cpp | 420 ++
src/sbml/packages/groups/sbml/ListOfGroups.h | 494 ++
src/sbml/packages/groups/sbml/ListOfMembers.cpp | 808 +++
src/sbml/packages/groups/sbml/ListOfMembers.h | 763 ++
src/sbml/packages/groups/sbml/Member.cpp | 732 +-
src/sbml/packages/groups/sbml/Member.h | 987 +--
src/sbml/packages/groups/sbml/MemberConstraint.cpp | 1382 ----
src/sbml/packages/groups/sbml/MemberConstraint.h | 969 ---
.../validator/GroupsConsistencyValidator.cpp | 56 +-
.../groups/validator/GroupsConsistencyValidator.h | 75 +-
.../GroupsIdentifierConsistencyValidator.cpp | 56 +-
.../GroupsIdentifierConsistencyValidator.h | 75 +-
.../packages/groups/validator/GroupsSBMLError.h | 88 +-
.../groups/validator/GroupsSBMLErrorTable.h | 442 +-
.../packages/groups/validator/GroupsValidator.cpp | 311 +-
.../packages/groups/validator/GroupsValidator.h | 115 +-
.../constraints/GroupCircularReferences.cpp | 455 ++
.../constraints/GroupCircularReferences.h | 112 +
.../constraints/GroupsConsistencyConstraints.cpp | 144 +-
.../GroupsConsistencyConstraintsDeclared.cxx | 45 +
.../GroupsIdentifierConsistencyConstraints.cpp | 49 +-
...upsIdentifierConsistencyConstraintsDeclared.cxx | 40 +
.../constraints/GroupsUniqueModelWideIds.cpp | 274 +
.../constraints/GroupsUniqueModelWideIds.h | 186 +
.../constraints/LOMembersConsistentReferences.cpp | 221 +
.../constraints/LOMembersConsistentReferences.h | 95 +
.../packages/groups/validator/test/CMakeLists.txt | 60 +
.../packages/groups/validator/test/TestFile.cpp | 199 +
src/sbml/packages/groups/validator/test/TestFile.h | 113 +
.../test/TestGroupsConsistencyValidator.cpp | 164 +
.../groups/validator/test/TestValidator.cpp | 229 +
.../packages/groups/validator/test/TestValidator.h | 81 +
.../general-constraints/4010101-pass-00-01.xml | 16 +
.../general-constraints/4020101-fail-01-01.xml | 16 +
.../general-constraints/4020101-pass-00-01.xml | 16 +
.../general-constraints/4020102-fail-01-01.xml | 16 +
.../general-constraints/4020102-pass-00-01.xml | 16 +
.../general-constraints/4020103-fail-01-01.xml | 16 +
.../general-constraints/4020103-pass-00-01.xml | 16 +
.../general-constraints/4020201-fail-01-01.xml | 23 +
.../general-constraints/4020201-pass-00-01.xml | 16 +
.../general-constraints/4020202-pass-00-01.xml | 16 +
.../general-constraints/4020203-pass-00-01.xml | 16 +
.../general-constraints/4020203-pass-00-02.xml | 17 +
.../general-constraints/4020203-pass-00-03.xml | 17 +
.../general-constraints/4020204-fail-01-01.xml | 16 +
.../general-constraints/4020204-pass-00-01.xml | 16 +
.../general-constraints/4020204-pass-00-02.xml | 16 +
.../general-constraints/4020204-pass-00-03.xml | 16 +
.../general-constraints/4020301-fail-01-01.xml | 16 +
.../general-constraints/4020301-pass-00-01.xml | 16 +
.../general-constraints/4020301-pass-00-02.xml | 16 +
.../general-constraints/4020301-pass-00-03.xml | 16 +
.../general-constraints/4020302-pass-00-01.xml | 16 +
.../general-constraints/4020302-pass-00-02.xml | 17 +
.../general-constraints/4020302-pass-00-03.xml | 17 +
.../general-constraints/4020303-fail-01-01.xml | 16 +
.../general-constraints/4020303-fail-01-02.xml | 16 +
.../general-constraints/4020303-pass-00-01.xml | 16 +
.../general-constraints/4020303-pass-00-02.xml | 16 +
.../general-constraints/4020303-pass-00-03.xml | 16 +
.../general-constraints/4020304-fail-01-01.xml | 19 +
.../general-constraints/4020304-pass-00-01.xml | 16 +
.../general-constraints/4020305-fail-01-01.xml | 16 +
.../general-constraints/4020305-pass-00-01.xml | 16 +
.../general-constraints/4020306-pass-00-01.xml | 16 +
.../general-constraints/4020307-pass-00-01.xml | 16 +
.../general-constraints/4020308-pass-00-01.xml | 16 +
.../general-constraints/4020308-pass-00-02.xml | 17 +
.../general-constraints/4020308-pass-00-03.xml | 17 +
.../general-constraints/4020309-fail-01-01.xml | 16 +
.../general-constraints/4020309-pass-00-01.xml | 16 +
.../general-constraints/4020309-pass-00-02.xml | 16 +
.../general-constraints/4020309-pass-00-03.xml | 16 +
.../general-constraints/4020310-fail-01-01.xml | 16 +
.../general-constraints/4020310-pass-00-01.xml | 16 +
.../general-constraints/4020310-pass-00-02.xml | 16 +
.../general-constraints/4020310-pass-00-03.xml | 16 +
.../general-constraints/4020311-pass-00-01.xml | 16 +
.../general-constraints/4020312-fail-01-01.xml | 20 +
.../general-constraints/4020312-fail-01-02.xml | 20 +
.../general-constraints/4020312-fail-01-03.xml | 20 +
.../general-constraints/4020312-fail-01-04.xml | 20 +
.../general-constraints/4020312-fail-01-05.xml | 26 +
.../general-constraints/4020312-pass-00-01.xml | 15 +
.../general-constraints/4020312-pass-00-02.xml | 20 +
.../general-constraints/4020312-pass-00-03.xml | 20 +
.../general-constraints/4020312-pass-00-04.xml | 20 +
.../general-constraints/4020312-pass-00-05.xml | 20 +
.../general-constraints/4020312-pass-00-06.xml | 20 +
.../general-constraints/4020313-fail-01-01.xml | 18 +
.../general-constraints/4020313-fail-01-02.xml | 18 +
.../general-constraints/4020313-fail-01-03.xml | 18 +
.../general-constraints/4020313-fail-01-04.xml | 18 +
.../general-constraints/4020313-fail-01-05.xml | 18 +
.../general-constraints/4020313-fail-01-06.xml | 18 +
.../general-constraints/4020313-fail-01-07.xml | 24 +
.../general-constraints/4020313-fail-01-08.xml | 24 +
.../general-constraints/4020313-fail-01-09.xml | 24 +
.../general-constraints/4020313-fail-01-10.xml | 24 +
.../general-constraints/4020313-fail-01-11.xml | 24 +
.../general-constraints/4020401-fail-01-01.xml | 16 +
.../general-constraints/4020401-pass-00-01.xml | 16 +
.../general-constraints/4020401-pass-00-02.xml | 16 +
.../general-constraints/4020401-pass-00-03.xml | 16 +
.../general-constraints/4020402-pass-00-01.xml | 16 +
.../general-constraints/4020402-pass-00-02.xml | 18 +
.../general-constraints/4020402-pass-00-03.xml | 18 +
.../general-constraints/4020403-fail-01-01.xml | 16 +
.../general-constraints/4020403-fail-01-02.xml | 16 +
.../general-constraints/4020403-fail-01-03.xml | 16 +
.../general-constraints/4020403-pass-00-01.xml | 16 +
.../general-constraints/4020403-pass-00-02.xml | 16 +
.../general-constraints/4020403-pass-00-03.xml | 16 +
.../general-constraints/4020403-pass-00-04.xml | 16 +
.../general-constraints/4020403-pass-00-05.xml | 16 +
.../general-constraints/4020404-pass-00-01.xml | 16 +
.../general-constraints/4020405-fail-01-01.xml | 16 +
.../general-constraints/4020405-pass-00-01.xml | 16 +
.../general-constraints/4020405-pass-00-02.xml | 21 +
.../general-constraints/4020405-pass-00-03.xml | 21 +
.../general-constraints/4020406-fail-01-01.xml | 16 +
.../general-constraints/4020406-pass-00-01.xml | 16 +
.../general-constraints/4020406-pass-00-02.xml | 21 +
.../general-constraints/4020406-pass-00-03.xml | 21 +
.../4020407-fail-01-01-4020405.xml | 16 +
.../4020408-fail-01-01-4020406.xml | 16 +
.../identifier-constraints/4010301-fail-01-01.xml | 16 +
.../identifier-constraints/4010301-fail-01-02.xml | 16 +
.../identifier-constraints/4010301-fail-01-03.xml | 16 +
.../identifier-constraints/4010301-fail-01-04.xml | 16 +
.../identifier-constraints/4010301-fail-01-05.xml | 19 +
.../identifier-constraints/4010301-fail-01-06.xml | 19 +
.../identifier-constraints/4010301-fail-02-01.xml | 19 +
.../identifier-constraints/4010301-pass-00-01.xml | 16 +
.../identifier-constraints/4010302-fail-01-01.xml | 16 +
.../identifier-constraints/4010302-fail-01-02.xml | 16 +
.../identifier-constraints/4010302-fail-01-03.xml | 16 +
src/sbml/packages/layout/Makefile.in | 2 +-
.../packages/layout/common/LayoutExtensionTypes.h | 2 +-
src/sbml/packages/layout/common/layoutfwd.h | 2 +-
.../packages/layout/extension/LayoutExtension.cpp | 2 +-
.../packages/layout/extension/LayoutExtension.h | 2 +-
.../layout/extension/LayoutModelPlugin.cpp | 2 +-
.../packages/layout/extension/LayoutModelPlugin.h | 2 +-
.../layout/extension/LayoutSBMLDocumentPlugin.cpp | 8 +-
.../layout/extension/LayoutSBMLDocumentPlugin.h | 12 +-
.../extension/LayoutSpeciesReferencePlugin.cpp | 2 +-
.../extension/LayoutSpeciesReferencePlugin.h | 2 +-
src/sbml/packages/layout/extension/Makefile.in | 2 +-
src/sbml/packages/layout/sbml/BoundingBox.cpp | 2 +-
src/sbml/packages/layout/sbml/BoundingBox.h | 2 +-
src/sbml/packages/layout/sbml/CompartmentGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/CompartmentGlyph.h | 2 +-
src/sbml/packages/layout/sbml/CubicBezier.cpp | 2 +-
src/sbml/packages/layout/sbml/CubicBezier.h | 2 +-
src/sbml/packages/layout/sbml/Curve.cpp | 2 +-
src/sbml/packages/layout/sbml/Curve.h | 2 +-
src/sbml/packages/layout/sbml/Dimensions.cpp | 2 +-
src/sbml/packages/layout/sbml/Dimensions.h | 2 +-
src/sbml/packages/layout/sbml/GeneralGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/GeneralGlyph.h | 2 +-
src/sbml/packages/layout/sbml/GraphicalObject.cpp | 2 +-
src/sbml/packages/layout/sbml/GraphicalObject.h | 2 +-
src/sbml/packages/layout/sbml/Layout.cpp | 4 +-
src/sbml/packages/layout/sbml/Layout.h | 2 +-
src/sbml/packages/layout/sbml/LineSegment.cpp | 2 +-
src/sbml/packages/layout/sbml/LineSegment.h | 2 +-
src/sbml/packages/layout/sbml/Makefile.in | 2 +-
src/sbml/packages/layout/sbml/Point.cpp | 2 +-
src/sbml/packages/layout/sbml/Point.h | 2 +-
src/sbml/packages/layout/sbml/ReactionGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/ReactionGlyph.h | 2 +-
src/sbml/packages/layout/sbml/ReferenceGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/ReferenceGlyph.h | 2 +-
src/sbml/packages/layout/sbml/SpeciesGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/SpeciesGlyph.h | 2 +-
.../packages/layout/sbml/SpeciesReferenceGlyph.cpp | 2 +-
.../packages/layout/sbml/SpeciesReferenceGlyph.h | 2 +-
.../packages/layout/sbml/SpeciesReferenceRole.h | 2 +-
src/sbml/packages/layout/sbml/TextGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/TextGlyph.h | 2 +-
src/sbml/packages/layout/sbml/test/CMakeLists.txt | 2 +-
src/sbml/packages/layout/sbml/test/Makefile.in | 2 +-
.../packages/layout/sbml/test/TestBoundingBox.cpp | 2 +-
.../layout/sbml/test/TestCompartmentGlyph.cpp | 2 +-
.../packages/layout/sbml/test/TestCubicBezier.cpp | 2 +-
src/sbml/packages/layout/sbml/test/TestCurve.cpp | 2 +-
.../packages/layout/sbml/test/TestDimensions.cpp | 2 +-
.../packages/layout/sbml/test/TestGeneralGlyph.cpp | 2 +-
.../layout/sbml/test/TestGraphicalObject.cpp | 2 +-
src/sbml/packages/layout/sbml/test/TestLayout.cpp | 2 +-
.../layout/sbml/test/TestLayoutCreation.cpp | 2 +-
.../layout/sbml/test/TestLayoutFormatter.cpp | 2 +-
.../layout/sbml/test/TestLayoutWriting.cpp | 2 +-
.../packages/layout/sbml/test/TestLineSegment.cpp | 2 +-
src/sbml/packages/layout/sbml/test/TestPoint.cpp | 2 +-
.../layout/sbml/test/TestReactionGlyph.cpp | 2 +-
.../layout/sbml/test/TestReferenceGlyph.cpp | 2 +-
src/sbml/packages/layout/sbml/test/TestRunner.c | 2 +-
.../packages/layout/sbml/test/TestSBMLHandler.cpp | 2 +-
.../packages/layout/sbml/test/TestSpeciesGlyph.cpp | 2 +-
.../layout/sbml/test/TestSpeciesReferenceGlyph.cpp | 2 +-
.../packages/layout/sbml/test/TestTextGlyph.cpp | 2 +-
src/sbml/packages/layout/util/LayoutAnnotation.cpp | 2 +-
src/sbml/packages/layout/util/LayoutAnnotation.h | 2 +-
src/sbml/packages/layout/util/LayoutUtilities.cpp | 2 +-
src/sbml/packages/layout/util/LayoutUtilities.h | 2 +-
src/sbml/packages/layout/util/Makefile.in | 2 +-
.../validator/LayoutConsistencyValidator.cpp | 8 +-
.../layout/validator/LayoutConsistencyValidator.h | 8 +-
.../LayoutIdentifierConsistencyValidator.cpp | 8 +-
.../LayoutIdentifierConsistencyValidator.h | 8 +-
.../packages/layout/validator/LayoutSBMLError.h | 8 +-
.../layout/validator/LayoutSBMLErrorTable.h | 8 +-
.../packages/layout/validator/LayoutValidator.cpp | 8 +-
.../packages/layout/validator/LayoutValidator.h | 8 +-
src/sbml/packages/layout/validator/Makefile.in | 2 +-
.../constraints/LayoutConsistencyConstraints.cpp | 8 +-
.../LayoutConsistencyConstraintsDeclared.cxx | 2 +-
.../LayoutIdentifierConsistencyConstraints.cpp | 8 +-
...outIdentifierConsistencyConstraintsDeclared.cxx | 2 +-
.../layout/validator/constraints/Makefile.in | 4 +-
.../validator/constraints/UniqueIdsLayout.cpp | 2 +-
.../layout/validator/constraints/UniqueIdsLayout.h | 2 +-
.../packages/layout/validator/test/CMakeLists.txt | 2 +-
.../packages/layout/validator/test/Makefile.in | 2 +-
.../packages/layout/validator/test/TestFile.cpp | 2 +-
src/sbml/packages/layout/validator/test/TestFile.h | 2 +-
.../test/TestLayoutConsistencyValidator.cpp | 2 +-
.../layout/validator/test/TestValidator.cpp | 2 +-
.../packages/layout/validator/test/TestValidator.h | 2 +-
.../layout/validator/test/test-data/Makefile.in | 2 +-
src/sbml/packages/multi-register.cxx | 2 +-
src/sbml/packages/multi-register.h | 2 +-
.../packages/multi/common/MultiExtensionTypes.h | 5 +-
src/sbml/packages/multi/common/multifwd.h | 3 +-
.../packages/multi/extension/MultiASTPlugin.cpp | 5 +-
src/sbml/packages/multi/extension/MultiASTPlugin.h | 3 +-
src/sbml/packages/multi/extension/MultiExtension.h | 1 -
.../multi/extension/MultiListOfReactionsPlugin.cpp | 46 +-
.../multi/extension/MultiListOfReactionsPlugin.h | 3 +
.../multi/extension/MultiSpeciesPlugin.cpp | 116 +-
.../packages/multi/extension/MultiSpeciesPlugin.h | 83 +-
.../packages/multi/extension/test/CMakeLists.txt | 2 +-
.../multi/extension/test/TestCheckConsistency.cpp | 2 +-
.../packages/multi/extension/test/TestMultiAST.cpp | 1 +
.../multi/extension/test/TestMultiExtension.cpp | 54 +-
.../test/test-data/multi_ci_extension.xml | 52 +-
.../extension/test/test-data/simmune_Ecad.xml | 501 ++
.../packages/multi/sbml/BindingSiteSpeciesType.cpp | 2 +-
.../packages/multi/sbml/BindingSiteSpeciesType.h | 2 +-
.../sbml/DenotedSpeciesTypeComponentIndex.cpp | 758 --
.../multi/sbml/DenotedSpeciesTypeComponentIndex.h | 616 --
.../packages/multi/sbml/IntraSpeciesReaction.cpp | 2 +-
.../packages/multi/sbml/IntraSpeciesReaction.h | 2 +-
src/sbml/packages/multi/sbml/MultiSpeciesType.cpp | 2 +-
.../packages/multi/sbml/OutwardBindingSite.cpp | 2 +-
.../multi/sbml/PossibleSpeciesFeatureValue.cpp | 2 +-
src/sbml/packages/multi/sbml/SpeciesFeature.cpp | 351 +-
src/sbml/packages/multi/sbml/SpeciesFeature.h | 290 +-
.../packages/multi/sbml/SpeciesFeatureChange.cpp | 4 +-
.../packages/multi/sbml/SpeciesFeatureType.cpp | 4 +-
.../packages/multi/sbml/SpeciesFeatureValue.cpp | 2 +-
.../multi/sbml/SpeciesTypeComponentIndex.cpp | 386 +-
.../multi/sbml/SpeciesTypeComponentIndex.h | 261 -
.../sbml/SpeciesTypeComponentMapInProduct.cpp | 6 +-
.../packages/multi/sbml/SpeciesTypeInstance.cpp | 144 +-
src/sbml/packages/multi/sbml/SpeciesTypeInstance.h | 68 -
.../multi/sbml/SubListOfSpeciesFeatures.cpp | 681 ++
.../packages/multi/sbml/SubListOfSpeciesFeatures.h | 492 ++
src/sbml/packages/multi/sbml/test/CMakeLists.txt | 2 +-
src/sbml/packages/multi/sbml/test/Makefile.in | 2 +-
src/sbml/packages/multi/sbml/test/TestRunner.c | 2 +-
src/sbml/packages/multi/validator/MultiSBMLError.h | 40 +-
.../packages/multi/validator/MultiSBMLErrorTable.h | 656 +-
.../packages/multi/validator/MultiValidator.cpp | 250 +-
.../constraints/MultiConsistencyConstraints.cpp | 242 +-
.../MultiConsistencyConstraintsDeclared.cxx | 17 +-
.../multi/validator/constraints/MultiIdBase.cpp | 8 +-
.../multi/validator/constraints/MultiIdBase.h | 3 +-
.../MultiIdentifierConsistencyConstraints.cpp | 6 +-
...ltiIdentifierConsistencyConstraintsDeclared.cxx | 4 +-
.../MultiMathCiCheckRepresentationType.cpp | 4 +-
.../MultiMathCiCheckRepresentationType.h | 2 +-
.../MultiMathCiCheckSpeciesReference.cpp | 6 +-
.../constraints/MultiMathCiCheckSpeciesReference.h | 2 +-
...queCompartmentReferenceIdsWithinCompartment.cpp | 4 +-
...niqueCompartmentReferenceIdsWithinCompartment.h | 2 +-
...eInSpeciesTypeBondIdsWithinMultiSpeciesType.cpp | 4 +-
...queInSpeciesTypeBondIdsWithinMultiSpeciesType.h | 2 +-
.../constraints/UniqueMultiComponentIds.cpp | 22 +-
.../constraints/UniqueMultiComponentIds.h | 2 +-
.../validator/constraints/UniqueMultiIdBase.cpp | 2 +-
.../validator/constraints/UniqueMultiIdBase.h | 2 +-
...ciesFeatureValueIdsWithinSpeciesFeatureType.cpp | 98 -
...peciesFeatureValueIdsWithinSpeciesFeatureType.h | 68 -
...geIdsWithinSpeciesTypeComponentMapInProduct.cpp | 4 +-
...angeIdsWithinSpeciesTypeComponentMapInProduct.h | 2 +-
.../UniqueSpeciesFeatureIdsWithinSpecies.cpp | 4 +-
.../UniqueSpeciesFeatureIdsWithinSpecies.h | 2 +-
...SpeciesFeatureTypeIdsWithinMultiSpeciesType.cpp | 4 +-
...ueSpeciesFeatureTypeIdsWithinMultiSpeciesType.h | 2 +-
...TypeComponentIndexIdsWithinMultiSpeciesType.cpp | 4 +-
...esTypeComponentIndexIdsWithinMultiSpeciesType.h | 2 +-
...peciesTypeInstanceIdsWithinMultiSpeciesType.cpp | 4 +-
...eSpeciesTypeInstanceIdsWithinMultiSpeciesType.h | 2 +-
...queSubListOfSpeciesFeaturesIdsWithinSpecies.cpp | 91 +
...niqueSubListOfSpeciesFeaturesIdsWithinSpecies.h | 68 +
.../packages/multi/validator/test/CMakeLists.txt | 2 +-
.../packages/multi/validator/test/TestFile.cpp | 2 +-
src/sbml/packages/multi/validator/test/TestFile.h | 2 +-
.../test/TestMultiConsistencyValidator.cpp | 17 +-
.../multi/validator/test/TestValidator.cpp | 2 +-
.../packages/multi/validator/test/TestValidator.h | 2 +-
.../general-constraints/7020501-fail-01-01.xml | 2 +-
.../general-constraints/7020805-fail-01-01.xml | 2 +-
.../general-constraints/7020805-pass-00-01.xml | 2 +-
.../general-constraints/7020806-fail-01-01.xml | 2 +-
.../general-constraints/7020806-pass-00-01.xml | 2 +-
.../general-constraints/7020904-fail-01-01.xml | 4 +-
.../general-constraints/7020904-pass-00-01.xml | 4 +-
.../general-constraints/7020905-fail-01-01.xml | 34 -
.../general-constraints/7020905-pass-00-01.xml | 35 -
.../general-constraints/7020906-fail-01-01.xml | 32 -
.../general-constraints/7020906-pass-00-01.xml | 32 -
.../general-constraints/7020907-fail-01-01.xml | 18 +-
.../general-constraints/7021004-fail-01-01.xml | 35 -
.../general-constraints/7021104-fail-01-01.xml | 18 +-
.../general-constraints/7021104-pass-00-01.xml | 18 +-
.../general-constraints/7021105-fail-01-01.xml | 18 +-
.../general-constraints/7021106-fail-01-01.xml | 18 +-
.../general-constraints/7021305-fail-01-01.xml | 23 +
.../general-constraints/7021305-pass-00-01.xml | 2 +-
.../general-constraints/7021904-fail-01-01.xml | 4 +-
.../general-constraints/7021904-pass-00-01.xml | 4 +-
.../general-constraints/7021905-fail-01-01.xml | 4 +-
.../general-constraints/7021906-fail-01-01.xml | 4 +-
.../general-constraints/7022004-fail-01-01.xml | 4 +-
.../general-constraints/7022004-pass-00-01.xml | 4 +-
.../general-constraints/7022005-fail-01-01.xml | 4 +-
.../general-constraints/7022102-fail-01-01.xml | 33 +
.../general-constraints/7022102-fail-01-02.xml | 51 +
.../general-constraints/7022102-pass-00-01.xml | 33 +
.../general-constraints/7022103-fail-01-01.xml | 33 +
.../general-constraints/7022103-pass-00-01.xml | 33 +
src/sbml/packages/qual/Makefile.in | 2 +-
src/sbml/packages/qual/common/Makefile.in | 2 +-
src/sbml/packages/qual/common/QualExtensionTypes.h | 2 +-
src/sbml/packages/qual/common/qualfwd.h | 2 +-
src/sbml/packages/qual/extension/Makefile.in | 2 +-
src/sbml/packages/qual/extension/QualExtension.cpp | 2 +-
src/sbml/packages/qual/extension/QualExtension.h | 2 +-
.../packages/qual/extension/QualModelPlugin.cpp | 15 +-
src/sbml/packages/qual/extension/QualModelPlugin.h | 14 +-
.../qual/extension/QualSBMLDocumentPlugin.cpp | 2 +-
.../qual/extension/QualSBMLDocumentPlugin.h | 10 +-
.../packages/qual/extension/test/CMakeLists.txt | 2 +-
src/sbml/packages/qual/extension/test/Makefile.in | 2 +-
.../qual/extension/test/TestGetAllElements.cpp | 2 +-
.../qual/extension/test/TestQualExtension.cpp | 2 +-
.../qual/extension/test/TestReadQualExtension.cpp | 2 +-
src/sbml/packages/qual/extension/test/TestRunner.c | 2 +-
.../qual/extension/test/TestWriteQualExtension.cpp | 2 +-
src/sbml/packages/qual/sbml/DefaultTerm.cpp | 8 +-
src/sbml/packages/qual/sbml/DefaultTerm.h | 8 +-
src/sbml/packages/qual/sbml/FunctionTerm.cpp | 8 +-
src/sbml/packages/qual/sbml/FunctionTerm.h | 8 +-
src/sbml/packages/qual/sbml/Input.cpp | 8 +-
src/sbml/packages/qual/sbml/Input.h | 8 +-
src/sbml/packages/qual/sbml/Makefile.in | 2 +-
src/sbml/packages/qual/sbml/Output.cpp | 8 +-
src/sbml/packages/qual/sbml/Output.h | 8 +-
src/sbml/packages/qual/sbml/QualitativeSpecies.cpp | 8 +-
src/sbml/packages/qual/sbml/QualitativeSpecies.h | 8 +-
src/sbml/packages/qual/sbml/Transition.cpp | 23 +-
src/sbml/packages/qual/sbml/Transition.h | 23 +-
src/sbml/packages/qual/sbml/test/CMakeLists.txt | 2 +-
src/sbml/packages/qual/sbml/test/Makefile.in | 2 +-
.../packages/qual/sbml/test/TestCopyAndClone.cpp | 2 +-
.../packages/qual/sbml/test/TestDefaultTerm.cpp | 2 +-
.../packages/qual/sbml/test/TestFunctionTerm.cpp | 2 +-
src/sbml/packages/qual/sbml/test/TestInput.cpp | 2 +-
.../qual/sbml/test/TestListOfFunctionTerms.cpp | 2 +-
src/sbml/packages/qual/sbml/test/TestOutput.cpp | 2 +-
.../qual/sbml/test/TestQualitativeSpecies.cpp | 2 +-
src/sbml/packages/qual/sbml/test/TestRunner.c | 2 +-
.../packages/qual/sbml/test/TestTransition.cpp | 2 +-
src/sbml/packages/qual/validator/Makefile.in | 2 +-
.../qual/validator/QualConsistencyValidator.cpp | 2 +-
.../qual/validator/QualConsistencyValidator.h | 2 +-
.../QualIdentifierConsistencyValidator.cpp | 2 +-
.../validator/QualIdentifierConsistencyValidator.h | 2 +-
.../validator/QualMathConsistencyValidator.cpp | 2 +-
.../qual/validator/QualMathConsistencyValidator.h | 2 +-
src/sbml/packages/qual/validator/QualSBMLError.h | 2 +-
.../packages/qual/validator/QualSBMLErrorTable.h | 2 +-
src/sbml/packages/qual/validator/QualValidator.cpp | 2 +-
src/sbml/packages/qual/validator/QualValidator.h | 8 +-
.../qual/validator/constraints/Makefile.in | 2 +-
.../qual/validator/constraints/QSAssignedOnce.cpp | 2 +-
.../qual/validator/constraints/QSAssignedOnce.h | 2 +-
.../validator/constraints/QualCSymbolMathCheck.cpp | 2 +-
.../validator/constraints/QualCSymbolMathCheck.h | 2 +-
.../constraints/QualConsistencyConstraints.cpp | 2 +-
.../QualConsistencyConstraintsDeclared.cxx | 2 +-
.../QualIdentifierConsistencyConstraints.cpp | 2 +-
...ualIdentifierConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/QualMathConsistencyConstraints.cpp | 2 +-
.../QualMathConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/QualUniqueModelWideIds.cpp | 2 +-
.../validator/constraints/QualUniqueModelWideIds.h | 2 +-
.../constraints/ResultBecomesNegative.cpp | 4 +-
.../validator/constraints/ResultBecomesNegative.h | 2 +-
.../validator/constraints/ResultExceedsMaximum.cpp | 4 +-
.../validator/constraints/ResultExceedsMaximum.h | 2 +-
.../packages/qual/validator/test/CMakeLists.txt | 2 +-
src/sbml/packages/qual/validator/test/Makefile.in | 2 +-
src/sbml/packages/qual/validator/test/TestFile.cpp | 2 +-
src/sbml/packages/qual/validator/test/TestFile.h | 2 +-
.../test/TestQualConsistencyValidator.cpp | 2 +-
.../packages/qual/validator/test/TestValidator.cpp | 2 +-
.../packages/qual/validator/test/TestValidator.h | 2 +-
.../qual/validator/test/test-data/Makefile.in | 2 +-
.../packages/render/common/RenderExtensionTypes.h | 2 +-
.../packages/render/extension/RenderExtension.cpp | 2 +-
.../packages/render/extension/RenderExtension.h | 2 +-
.../extension/RenderGraphicalObjectPlugin.cpp | 2 +-
.../render/extension/RenderGraphicalObjectPlugin.h | 2 +-
.../render/extension/RenderLayoutPlugin.cpp | 2 +-
.../packages/render/extension/RenderLayoutPlugin.h | 2 +-
.../render/extension/RenderListOfLayoutsPlugin.cpp | 2 +-
.../render/extension/RenderListOfLayoutsPlugin.h | 2 +-
.../render/extension/RenderSBMLDocumentPlugin.cpp | 2 +-
.../render/extension/RenderSBMLDocumentPlugin.h | 2 +-
src/sbml/packages/render/sbml/ColorDefinition.cpp | 2 +-
src/sbml/packages/render/sbml/ColorDefinition.h | 2 +-
src/sbml/packages/render/sbml/Ellipse.cpp | 2 +-
src/sbml/packages/render/sbml/Ellipse.h | 2 +-
.../render/sbml/GlobalRenderInformation.cpp | 2 +-
.../packages/render/sbml/GlobalRenderInformation.h | 2 +-
src/sbml/packages/render/sbml/GlobalStyle.cpp | 2 +-
src/sbml/packages/render/sbml/GlobalStyle.h | 2 +-
src/sbml/packages/render/sbml/GradientBase.cpp | 2 +-
src/sbml/packages/render/sbml/GradientBase.h | 2 +-
src/sbml/packages/render/sbml/GradientStop.cpp | 2 +-
src/sbml/packages/render/sbml/GradientStop.h | 2 +-
.../packages/render/sbml/GraphicalPrimitive1D.cpp | 2 +-
.../packages/render/sbml/GraphicalPrimitive1D.h | 2 +-
.../packages/render/sbml/GraphicalPrimitive2D.cpp | 2 +-
.../packages/render/sbml/GraphicalPrimitive2D.h | 2 +-
src/sbml/packages/render/sbml/Image.cpp | 2 +-
src/sbml/packages/render/sbml/Image.h | 2 +-
src/sbml/packages/render/sbml/LineEnding.cpp | 2 +-
src/sbml/packages/render/sbml/LineEnding.h | 2 +-
src/sbml/packages/render/sbml/LinearGradient.cpp | 2 +-
src/sbml/packages/render/sbml/LinearGradient.h | 2 +-
.../packages/render/sbml/ListOfCurveElements.cpp | 2 +-
.../packages/render/sbml/ListOfCurveElements.h | 2 +-
.../render/sbml/LocalRenderInformation.cpp | 2 +-
.../packages/render/sbml/LocalRenderInformation.h | 2 +-
src/sbml/packages/render/sbml/LocalStyle.cpp | 2 +-
src/sbml/packages/render/sbml/LocalStyle.h | 2 +-
src/sbml/packages/render/sbml/Polygon.cpp | 2 +-
src/sbml/packages/render/sbml/Polygon.h | 2 +-
src/sbml/packages/render/sbml/RadialGradient.cpp | 2 +-
src/sbml/packages/render/sbml/RadialGradient.h | 2 +-
src/sbml/packages/render/sbml/Rectangle.cpp | 2 +-
src/sbml/packages/render/sbml/Rectangle.h | 2 +-
src/sbml/packages/render/sbml/RelAbsVector.cpp | 2 +-
src/sbml/packages/render/sbml/RelAbsVector.h | 2 +-
.../packages/render/sbml/RenderCubicBezier.cpp | 2 +-
src/sbml/packages/render/sbml/RenderCubicBezier.h | 2 +-
src/sbml/packages/render/sbml/RenderCurve.cpp | 2 +-
src/sbml/packages/render/sbml/RenderCurve.h | 2 +-
src/sbml/packages/render/sbml/RenderGroup.cpp | 2 +-
src/sbml/packages/render/sbml/RenderGroup.h | 2 +-
.../packages/render/sbml/RenderInformationBase.cpp | 2 +-
.../packages/render/sbml/RenderInformationBase.h | 2 +-
src/sbml/packages/render/sbml/RenderPoint.cpp | 2 +-
src/sbml/packages/render/sbml/RenderPoint.h | 2 +-
src/sbml/packages/render/sbml/Style.cpp | 2 +-
src/sbml/packages/render/sbml/Style.h | 2 +-
src/sbml/packages/render/sbml/Text.cpp | 2 +-
src/sbml/packages/render/sbml/Text.h | 2 +-
src/sbml/packages/render/sbml/Transformation.cpp | 2 +-
src/sbml/packages/render/sbml/Transformation.h | 2 +-
src/sbml/packages/render/sbml/Transformation2D.cpp | 2 +-
src/sbml/packages/render/sbml/Transformation2D.h | 2 +-
.../render/sbml/test/TestRenderWriting.cpp | 2 -
.../packages/render/util/RenderLayoutConverter.cpp | 2 +-
.../packages/render/util/RenderLayoutConverter.h | 2 +-
src/sbml/packages/render/util/RenderUtilities.cpp | 2 +-
src/sbml/packages/render/util/RenderUtilities.h | 2 +-
src/sbml/packages/req-register.cxx | 2 +-
src/sbml/packages/req-register.h | 2 +-
src/sbml/packages/req/common/ReqExtensionTypes.h | 2 +-
src/sbml/packages/req/common/reqfwd.h | 2 +-
src/sbml/packages/req/extension/ReqExtension.cpp | 2 +-
src/sbml/packages/req/extension/ReqExtension.h | 2 +-
.../req/extension/ReqSBMLDocumentPlugin.cpp | 2 +-
.../packages/req/extension/ReqSBMLDocumentPlugin.h | 2 +-
src/sbml/packages/req/extension/ReqSBasePlugin.cpp | 2 +-
src/sbml/packages/req/extension/ReqSBasePlugin.h | 2 +-
.../packages/req/extension/test/CMakeLists.txt | 2 +-
src/sbml/packages/req/sbml/ChangedMath.cpp | 2 +-
src/sbml/packages/req/sbml/ChangedMath.h | 2 +-
.../req/validator/ReqConsistencyValidator.cpp | 2 +-
.../req/validator/ReqConsistencyValidator.h | 2 +-
.../ReqIdentifierConsistencyValidator.cpp | 2 +-
.../validator/ReqIdentifierConsistencyValidator.h | 2 +-
src/sbml/packages/req/validator/ReqSBMLError.h | 2 +-
.../packages/req/validator/ReqSBMLErrorTable.h | 2 +-
src/sbml/packages/req/validator/ReqValidator.cpp | 2 +-
src/sbml/packages/req/validator/ReqValidator.h | 2 +-
.../constraints/ReqConsistencyConstraints.cpp | 2 +-
.../ReqIdentifierConsistencyConstraints.cpp | 2 +-
src/sbml/packages/spatial-register.cxx | 2 +-
src/sbml/packages/spatial-register.h | 2 +-
.../spatial/common/SpatialExtensionTypes.h | 2 +-
src/sbml/packages/spatial/common/spatialfwd.h | 2 +-
.../spatial/extension/SpatialCompartmentPlugin.cpp | 2 +-
.../spatial/extension/SpatialCompartmentPlugin.h | 2 +-
.../spatial/extension/SpatialExtension.cpp | 2 +-
.../packages/spatial/extension/SpatialExtension.h | 2 +-
.../spatial/extension/SpatialModelPlugin.cpp | 2 +-
.../spatial/extension/SpatialModelPlugin.h | 2 +-
.../spatial/extension/SpatialParameterPlugin.cpp | 2 +-
.../spatial/extension/SpatialParameterPlugin.h | 2 +-
.../spatial/extension/SpatialReactionPlugin.cpp | 2 +-
.../spatial/extension/SpatialReactionPlugin.h | 2 +-
.../extension/SpatialSBMLDocumentPlugin.cpp | 2 +-
.../spatial/extension/SpatialSBMLDocumentPlugin.h | 2 +-
.../spatial/extension/SpatialSpeciesPlugin.cpp | 2 +-
.../spatial/extension/SpatialSpeciesPlugin.h | 2 +-
.../extension/test/TestReadSpatialExtension.cpp | 4 +-
.../packages/spatial/extension/test/TestRunner.c | 5 +
src/sbml/packages/spatial/sbml/AdjacentDomains.cpp | 2 +-
src/sbml/packages/spatial/sbml/AdjacentDomains.h | 2 +-
.../packages/spatial/sbml/AdvectionCoefficient.cpp | 2 +-
.../packages/spatial/sbml/AdvectionCoefficient.h | 2 +-
.../packages/spatial/sbml/AnalyticGeometry.cpp | 2 +-
src/sbml/packages/spatial/sbml/AnalyticGeometry.h | 2 +-
src/sbml/packages/spatial/sbml/AnalyticVolume.cpp | 2 +-
src/sbml/packages/spatial/sbml/AnalyticVolume.h | 2 +-
src/sbml/packages/spatial/sbml/Boundary.cpp | 2 +-
src/sbml/packages/spatial/sbml/Boundary.h | 2 +-
.../packages/spatial/sbml/BoundaryCondition.cpp | 2 +-
src/sbml/packages/spatial/sbml/BoundaryCondition.h | 2 +-
.../spatial/sbml/CSGHomogeneousTransformation.cpp | 2 +-
.../spatial/sbml/CSGHomogeneousTransformation.h | 2 +-
src/sbml/packages/spatial/sbml/CSGNode.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGNode.h | 2 +-
src/sbml/packages/spatial/sbml/CSGObject.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGObject.h | 2 +-
src/sbml/packages/spatial/sbml/CSGPrimitive.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGPrimitive.h | 2 +-
.../packages/spatial/sbml/CSGPseudoPrimitive.cpp | 2 +-
.../packages/spatial/sbml/CSGPseudoPrimitive.h | 2 +-
src/sbml/packages/spatial/sbml/CSGRotation.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGRotation.h | 2 +-
src/sbml/packages/spatial/sbml/CSGScale.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGScale.h | 2 +-
src/sbml/packages/spatial/sbml/CSGSetOperator.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGSetOperator.h | 2 +-
.../packages/spatial/sbml/CSGTransformation.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGTransformation.h | 2 +-
src/sbml/packages/spatial/sbml/CSGTranslation.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGTranslation.h | 2 +-
src/sbml/packages/spatial/sbml/CSGeometry.cpp | 2 +-
src/sbml/packages/spatial/sbml/CSGeometry.h | 2 +-
.../packages/spatial/sbml/CompartmentMapping.cpp | 2 +-
.../packages/spatial/sbml/CompartmentMapping.h | 2 +-
.../packages/spatial/sbml/CoordinateComponent.cpp | 2 +-
.../packages/spatial/sbml/CoordinateComponent.h | 2 +-
.../packages/spatial/sbml/CoordinateReference.cpp | 2 +-
.../packages/spatial/sbml/CoordinateReference.h | 2 +-
.../packages/spatial/sbml/DiffusionCoefficient.cpp | 2 +-
.../packages/spatial/sbml/DiffusionCoefficient.h | 2 +-
src/sbml/packages/spatial/sbml/Domain.cpp | 2 +-
src/sbml/packages/spatial/sbml/Domain.h | 2 +-
src/sbml/packages/spatial/sbml/DomainType.cpp | 2 +-
src/sbml/packages/spatial/sbml/DomainType.h | 2 +-
src/sbml/packages/spatial/sbml/Geometry.cpp | 2 +-
src/sbml/packages/spatial/sbml/Geometry.h | 2 +-
.../packages/spatial/sbml/GeometryDefinition.cpp | 2 +-
.../packages/spatial/sbml/GeometryDefinition.h | 2 +-
src/sbml/packages/spatial/sbml/InteriorPoint.cpp | 2 +-
src/sbml/packages/spatial/sbml/InteriorPoint.h | 2 +-
src/sbml/packages/spatial/sbml/MixedGeometry.cpp | 2 +-
src/sbml/packages/spatial/sbml/MixedGeometry.h | 2 +-
src/sbml/packages/spatial/sbml/OrdinalMapping.cpp | 2 +-
src/sbml/packages/spatial/sbml/OrdinalMapping.h | 2 +-
.../packages/spatial/sbml/ParametricGeometry.cpp | 2 +-
.../packages/spatial/sbml/ParametricGeometry.h | 2 +-
.../packages/spatial/sbml/ParametricObject.cpp | 4 +-
src/sbml/packages/spatial/sbml/ParametricObject.h | 2 +-
src/sbml/packages/spatial/sbml/SampledField.cpp | 2 +-
src/sbml/packages/spatial/sbml/SampledField.h | 2 +-
.../packages/spatial/sbml/SampledFieldGeometry.cpp | 2 +-
.../packages/spatial/sbml/SampledFieldGeometry.h | 2 +-
src/sbml/packages/spatial/sbml/SampledVolume.cpp | 2 +-
src/sbml/packages/spatial/sbml/SampledVolume.h | 2 +-
src/sbml/packages/spatial/sbml/SpatialPoints.cpp | 2 +-
src/sbml/packages/spatial/sbml/SpatialPoints.h | 2 +-
.../spatial/sbml/SpatialSymbolReference.cpp | 2 +-
.../packages/spatial/sbml/SpatialSymbolReference.h | 2 +-
.../spatial/sbml/TransformationComponents.cpp | 2 +-
.../spatial/sbml/TransformationComponents.h | 2 +-
src/sbml/packages/spatial/sbml/test/CMakeLists.txt | 2 +-
.../spatial/sbml/test/TestCopyAndClone.cpp | 2 +-
.../packages/spatial/sbml/test/TestImageData.cpp | 2 +-
.../spatial/sbml/test/TestParametricObject.cpp | 2 +-
src/sbml/packages/spatial/sbml/test/TestRunner.c | 6 +-
.../sbml/test/TestTransformationComponents.cpp | 2 +-
.../validator/SpatialConsistencyValidator.cpp | 2 +-
.../validator/SpatialConsistencyValidator.h | 2 +-
.../SpatialIdentifierConsistencyValidator.cpp | 2 +-
.../SpatialIdentifierConsistencyValidator.h | 2 +-
.../packages/spatial/validator/SpatialSBMLError.h | 2 +-
.../spatial/validator/SpatialSBMLErrorTable.h | 2 +-
.../spatial/validator/SpatialValidator.cpp | 2 +-
.../packages/spatial/validator/SpatialValidator.h | 2 +-
.../constraints/SpatialConsistencyConstraints.cpp | 2 +-
.../SpatialIdentifierConsistencyConstraints.cpp | 2 +-
src/sbml/test/CMakeLists.txt | 2 +-
src/sbml/test/Makefile.in | 5 +-
src/sbml/test/TestAlgebraicRule.c | 2 +-
src/sbml/test/TestAncestor.cpp | 2 +-
src/sbml/test/TestAssignmentRule.c | 2 +-
src/sbml/test/TestCompartment.c | 2 +-
src/sbml/test/TestCompartmentType.c | 2 +-
src/sbml/test/TestCompartmentType_newSetters.c | 2 +-
src/sbml/test/TestCompartmentVolumeRule.c | 2 +-
src/sbml/test/TestCompartment_newSetters.c | 2 +-
src/sbml/test/TestConsistencyChecks.cpp | 2 +-
src/sbml/test/TestConstraint.c | 2 +-
src/sbml/test/TestConstraint_newSetters.c | 2 +-
src/sbml/test/TestCopyAndClone.cpp | 2 +-
src/sbml/test/TestDelay.c | 2 +-
src/sbml/test/TestEvent.c | 2 +-
src/sbml/test/TestEventAssignment.c | 2 +-
src/sbml/test/TestEventAssignment_newSetters.c | 2 +-
src/sbml/test/TestEvent_newSetters.c | 2 +-
src/sbml/test/TestFunctionDefinition.c | 2 +-
src/sbml/test/TestFunctionDefinition_newSetters.c | 2 +-
src/sbml/test/TestGetMultipleObjects.cpp | 2 +-
src/sbml/test/TestInitialAssignment.c | 2 +-
src/sbml/test/TestInitialAssignment_newSetters.c | 2 +-
src/sbml/test/TestInternalConsistencyChecks.cpp | 2 +-
src/sbml/test/TestKineticLaw.c | 2 +-
src/sbml/test/TestKineticLaw_newSetters.c | 2 +-
src/sbml/test/TestL3Compartment.c | 2 +-
src/sbml/test/TestL3Event.c | 2 +-
src/sbml/test/TestL3KineticLaw.c | 2 +-
src/sbml/test/TestL3LocalParameter.c | 2 +-
src/sbml/test/TestL3Model.c | 2 +-
src/sbml/test/TestL3Parameter.c | 2 +-
src/sbml/test/TestL3Reaction.c | 2 +-
src/sbml/test/TestL3Species.c | 2 +-
src/sbml/test/TestL3SpeciesReference.c | 2 +-
src/sbml/test/TestL3Trigger.c | 2 +-
src/sbml/test/TestL3Unit.c | 2 +-
src/sbml/test/TestLevelCompatibility.cpp | 271 +
src/sbml/test/TestListOf.c | 2 +-
src/sbml/test/TestModel.c | 2 +-
src/sbml/test/TestModel_newSetters.c | 2 +-
src/sbml/test/TestModifierSpeciesReference.c | 2 +-
src/sbml/test/TestParameter.c | 2 +-
src/sbml/test/TestParameterRule.c | 2 +-
src/sbml/test/TestParameter_newSetters.c | 2 +-
src/sbml/test/TestPriority.c | 2 +-
src/sbml/test/TestRateRule.c | 2 +-
src/sbml/test/TestReaction.c | 2 +-
src/sbml/test/TestReaction_newSetters.c | 2 +-
src/sbml/test/TestReadFromFile1.c | 2 +-
src/sbml/test/TestReadFromFile2.c | 2 +-
src/sbml/test/TestReadFromFile3.c | 2 +-
src/sbml/test/TestReadFromFile4.c | 2 +-
src/sbml/test/TestReadFromFile5.cpp | 2 +-
src/sbml/test/TestReadFromFile6.cpp | 2 +-
src/sbml/test/TestReadFromFile7.cpp | 2 +-
src/sbml/test/TestReadFromFile8.cpp | 2 +-
src/sbml/test/TestReadFromFile9.cpp | 2 +-
src/sbml/test/TestReadFromFileL2V5.cpp | 2 +-
src/sbml/test/TestReadSBML.cpp | 2 +-
src/sbml/test/TestRemoveFromParent.cpp | 2 +-
src/sbml/test/TestRenameIDs.cpp | 2 +-
src/sbml/test/TestRequiredAttributes.cpp | 2 +-
src/sbml/test/TestRequiredElements.cpp | 2 +-
src/sbml/test/TestRule.c | 2 +-
src/sbml/test/TestRule_newSetters.c | 2 +-
src/sbml/test/TestRunner.c | 6 +-
src/sbml/test/TestSBMLConstructorException.cpp | 2 +-
src/sbml/test/TestSBMLConvert.c | 2 +-
src/sbml/test/TestSBMLConvertStrict.c | 2 +-
src/sbml/test/TestSBMLDocument.c | 2 +-
src/sbml/test/TestSBMLError.cpp | 2 +-
src/sbml/test/TestSBMLNamespaces.cpp | 2 +-
src/sbml/test/TestSBMLParentObject.cpp | 2 +-
src/sbml/test/TestSBMLTransforms.cpp | 2 +-
src/sbml/test/TestSBMLValidators.cpp | 2 +-
src/sbml/test/TestSBase.cpp | 2 +-
src/sbml/test/TestSBase_newSetters.cpp | 2 +-
src/sbml/test/TestSpecies.c | 2 +-
src/sbml/test/TestSpeciesConcentrationRule.c | 2 +-
src/sbml/test/TestSpeciesReference.c | 2 +-
src/sbml/test/TestSpeciesReference_newSetters.c | 2 +-
src/sbml/test/TestSpeciesType.c | 2 +-
src/sbml/test/TestSpeciesType_newSetters.c | 2 +-
src/sbml/test/TestSpecies_newSetters.c | 2 +-
src/sbml/test/TestStoichiometryMath.c | 2 +-
src/sbml/test/TestSyntaxChecker.c | 2 +-
src/sbml/test/TestTrigger.c | 2 +-
src/sbml/test/TestUnit.c | 2 +-
src/sbml/test/TestUnitDefinition.c | 2 +-
src/sbml/test/TestUnitDefinition_newSetters.c | 2 +-
src/sbml/test/TestUnitKind.c | 2 +-
src/sbml/test/TestUnit_newSetters.c | 2 +-
src/sbml/test/TestWriteL3SBML.cpp | 2 +-
src/sbml/test/TestWriteSBML.cpp | 2 +-
.../test/test-data/inconsistent-l2v1-units-2.xml | 20 +
.../test/test-data/inconsistent-l2v1-units.xml | 20 +
src/sbml/units/FormulaUnitsData.cpp | 2 +-
src/sbml/units/FormulaUnitsData.h | 2 +-
src/sbml/units/Makefile.in | 2 +-
src/sbml/units/UnitFormulaFormatter.cpp | 2 +-
src/sbml/units/UnitFormulaFormatter.h | 2 +-
src/sbml/units/UnitKindList.cpp | 2 +-
src/sbml/units/UnitKindList.h | 2 +-
src/sbml/units/test/CMakeLists.txt | 2 +-
src/sbml/units/test/Makefile.in | 2 +-
.../units/test/TestCalculatedUnitDefinitions.cpp | 2 +-
src/sbml/units/test/TestDerivedUnitDefinitions.cpp | 2 +-
src/sbml/units/test/TestFormulaUnitsData.cpp | 2 +-
src/sbml/units/test/TestRunner.c | 2 +-
src/sbml/units/test/TestUnitFormulaFormatter.cpp | 2 +-
src/sbml/units/test/TestUnitFormulaFormatter1.cpp | 2 +-
src/sbml/units/test/TestUnitFormulaFormatter2.cpp | 2 +-
src/sbml/units/test/TestUnitFormulaFormatter3.cpp | 2 +-
src/sbml/units/test/TestUtilsUnit.cpp | 2 +-
src/sbml/units/test/TestUtilsUnitDefinition.cpp | 2 +-
src/sbml/util/ElementFilter.cpp | 2 +-
src/sbml/util/ElementFilter.h | 2 +-
src/sbml/util/IdFilter.cpp | 2 +-
src/sbml/util/IdFilter.h | 2 +-
src/sbml/util/IdList.cpp | 2 +-
src/sbml/util/IdList.h | 2 +-
src/sbml/util/IdentifierTransformer.cpp | 2 +-
src/sbml/util/IdentifierTransformer.h | 2 +-
src/sbml/util/List.cpp | 2 +-
src/sbml/util/List.h | 2 +-
src/sbml/util/Makefile.in | 2 +-
src/sbml/util/MetaIdFilter.cpp | 2 +-
src/sbml/util/MetaIdFilter.h | 2 +-
src/sbml/util/PrefixTransformer.cpp | 2 +-
src/sbml/util/PrefixTransformer.h | 2 +-
src/sbml/util/Stack.c | 2 +-
src/sbml/util/Stack.h | 2 +-
src/sbml/util/StringBuffer.c | 2 +-
src/sbml/util/StringBuffer.h | 2 +-
src/sbml/util/memory.c | 2 +-
src/sbml/util/memory.h | 2 +-
src/sbml/util/test/CMakeLists.txt | 2 +-
src/sbml/util/test/Makefile.in | 2 +-
src/sbml/util/test/TestList.c | 2 +-
src/sbml/util/test/TestMemory.c | 2 +-
src/sbml/util/test/TestRunner.c | 2 +-
src/sbml/util/test/TestStack.c | 2 +-
src/sbml/util/test/TestStringBuffer.c | 2 +-
src/sbml/util/test/TestUtil.c | 2 +-
src/sbml/util/util.cpp | 2 +-
src/sbml/util/util.h | 2 +-
src/sbml/validator/ConsistencyValidator.cpp | 2 +-
src/sbml/validator/ConsistencyValidator.h | 2 +-
src/sbml/validator/ConstraintMacros.h | 2 +-
.../validator/IdentifierConsistencyValidator.cpp | 2 +-
.../validator/IdentifierConsistencyValidator.h | 2 +-
.../validator/InternalConsistencyValidator.cpp | 2 +-
src/sbml/validator/InternalConsistencyValidator.h | 2 +-
src/sbml/validator/L1CompatibilityValidator.cpp | 2 +-
src/sbml/validator/L1CompatibilityValidator.h | 2 +-
src/sbml/validator/L2v1CompatibilityValidator.cpp | 2 +-
src/sbml/validator/L2v1CompatibilityValidator.h | 2 +-
src/sbml/validator/L2v2CompatibilityValidator.cpp | 2 +-
src/sbml/validator/L2v2CompatibilityValidator.h | 2 +-
src/sbml/validator/L2v3CompatibilityValidator.cpp | 2 +-
src/sbml/validator/L2v3CompatibilityValidator.h | 2 +-
src/sbml/validator/L2v4CompatibilityValidator.cpp | 2 +-
src/sbml/validator/L2v4CompatibilityValidator.h | 2 +-
src/sbml/validator/L3v1CompatibilityValidator.cpp | 2 +-
src/sbml/validator/L3v1CompatibilityValidator.h | 2 +-
src/sbml/validator/Makefile.in | 2 +-
src/sbml/validator/MathMLConsistencyValidator.cpp | 2 +-
src/sbml/validator/MathMLConsistencyValidator.h | 2 +-
src/sbml/validator/ModelingPracticeValidator.cpp | 2 +-
src/sbml/validator/ModelingPracticeValidator.h | 2 +-
src/sbml/validator/OverdeterminedValidator.cpp | 2 +-
src/sbml/validator/OverdeterminedValidator.h | 2 +-
src/sbml/validator/SBMLExternalValidator.cpp | 2 +-
src/sbml/validator/SBMLExternalValidator.h | 2 +-
src/sbml/validator/SBMLInternalValidator.cpp | 2 +-
src/sbml/validator/SBMLInternalValidator.h | 2 +-
src/sbml/validator/SBMLValidator.cpp | 2 +-
src/sbml/validator/SBMLValidator.h | 2 +-
src/sbml/validator/SBOConsistencyValidator.cpp | 2 +-
src/sbml/validator/SBOConsistencyValidator.h | 2 +-
.../validator/StrictUnitConsistencyValidator.cpp | 2 +-
.../validator/StrictUnitConsistencyValidator.h | 132 +-
src/sbml/validator/UnitConsistencyValidator.cpp | 2 +-
src/sbml/validator/UnitConsistencyValidator.h | 2 +-
src/sbml/validator/VConstraint.cpp | 2 +-
src/sbml/validator/VConstraint.h | 2 +-
src/sbml/validator/Validator.cpp | 2 +-
src/sbml/validator/Validator.h | 2 +-
.../validator/constraints/ArgumentsUnitsCheck.cpp | 2 +-
.../validator/constraints/ArgumentsUnitsCheck.h | 2 +-
.../constraints/ArgumentsUnitsCheckWarnings.cpp | 2 +-
.../constraints/ArgumentsUnitsCheckWarnings.h | 2 +-
.../validator/constraints/AssignmentCycles.cpp | 2 +-
src/sbml/validator/constraints/AssignmentCycles.h | 2 +-
.../constraints/AssignmentRuleOrdering.cpp | 2 +-
.../validator/constraints/AssignmentRuleOrdering.h | 2 +-
.../validator/constraints/CiElementMathCheck.cpp | 2 +-
.../validator/constraints/CiElementMathCheck.h | 2 +-
.../validator/constraints/CiElementNot0DComp.cpp | 2 +-
.../validator/constraints/CiElementNot0DComp.h | 234 +-
.../constraints/CompartmentOutsideCycles.cpp | 2 +-
.../constraints/CompartmentOutsideCycles.h | 2 +-
.../constraints/ConsistencyConstraints.cpp | 2 +-
.../constraints/ConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/DuplicateTopLevelAnnotation.cpp | 2 +-
.../constraints/DuplicateTopLevelAnnotation.h | 2 +-
.../constraints/EqualityArgsMathCheck.cpp | 2 +-
.../validator/constraints/EqualityArgsMathCheck.h | 2 +-
.../validator/constraints/ExponentUnitsCheck.cpp | 2 +-
.../validator/constraints/ExponentUnitsCheck.h | 2 +-
.../constraints/FunctionApplyMathCheck.cpp | 2 +-
.../validator/constraints/FunctionApplyMathCheck.h | 2 +-
.../constraints/FunctionDefinitionRecursion.cpp | 2 +-
.../constraints/FunctionDefinitionRecursion.h | 226 +-
.../constraints/FunctionDefinitionVars.cpp | 2 +-
.../validator/constraints/FunctionDefinitionVars.h | 2 +-
.../constraints/FunctionNoArgsMathCheck.cpp | 2 +-
.../constraints/FunctionNoArgsMathCheck.h | 2 +-
.../constraints/FunctionReferredToExists.cpp | 2 +-
.../constraints/FunctionReferredToExists.h | 2 +-
src/sbml/validator/constraints/IdBase.cpp | 2 +-
src/sbml/validator/constraints/IdBase.h | 2 +-
.../IdentifierConsistencyConstraints.cpp | 2 +-
.../IdentifierConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/InternalConsistencyConstraints.cpp | 2 +-
.../InternalConsistencyConstraintsDeclared.cxx | 2 +-
.../validator/constraints/KineticLawUnitsCheck.cpp | 2 +-
.../validator/constraints/KineticLawUnitsCheck.h | 2 +-
src/sbml/validator/constraints/KineticLawVars.cpp | 2 +-
src/sbml/validator/constraints/KineticLawVars.h | 2 +-
.../constraints/L1CompatibilityConstraints.cpp | 2 +-
.../L1CompatibilityConstraintsDeclared.cxx | 2 +-
.../constraints/L2v1CompatibilityConstraints.cpp | 2 +-
.../L2v1CompatibilityConstraintsDeclared.cxx | 2 +-
.../constraints/L2v2CompatibilityConstraints.cpp | 2 +-
.../L2v2CompatibilityConstraintsDeclared.cxx | 2 +-
.../constraints/L2v3CompatibilityConstraints.cpp | 2 +-
.../L2v3CompatibilityConstraintsDeclared.cxx | 2 +-
.../constraints/L2v4CompatibilityConstraints.cpp | 2 +-
.../L2v4CompatibilityConstraintsDeclared.cxx | 2 +-
.../constraints/L3v1CompatibilityConstraints.cpp | 2 +-
.../L3v1CompatibilityConstraintsDeclared.cxx | 2 +-
src/sbml/validator/constraints/LambdaMathCheck.cpp | 2 +-
src/sbml/validator/constraints/LambdaMathCheck.h | 2 +-
.../constraints/LocalParameterMathCheck.cpp | 2 +-
.../constraints/LocalParameterMathCheck.h | 2 +-
.../constraints/LocalParameterShadowsIdInModel.cpp | 2 +-
.../constraints/LocalParameterShadowsIdInModel.h | 2 +-
.../validator/constraints/LogicalArgsMathCheck.cpp | 2 +-
.../validator/constraints/LogicalArgsMathCheck.h | 2 +-
src/sbml/validator/constraints/Makefile.in | 2 +-
src/sbml/validator/constraints/MathMLBase.cpp | 14 +-
src/sbml/validator/constraints/MathMLBase.h | 2 +-
.../constraints/MathMLConsistencyConstraints.cpp | 2 +-
.../MathMLConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/ModelingPracticeConstraints.cpp | 2 +-
.../ModelingPracticeConstraintsDeclared.cxx | 2 +-
.../validator/constraints/NumberArgsMathCheck.cpp | 8 +-
.../validator/constraints/NumberArgsMathCheck.h | 2 +-
.../validator/constraints/NumericArgsMathCheck.cpp | 2 +-
.../validator/constraints/NumericArgsMathCheck.h | 2 +-
.../constraints/NumericReturnMathCheck.cpp | 2 +-
.../validator/constraints/NumericReturnMathCheck.h | 2 +-
.../validator/constraints/OverDeterminedCheck.cpp | 2 +-
.../validator/constraints/OverDeterminedCheck.h | 2 +-
.../constraints/OverdeterminedConstraints.cpp | 2 +-
.../OverdeterminedConstraintsDeclared.cxx | 2 +-
.../constraints/PieceBooleanMathCheck.cpp | 27 +-
.../validator/constraints/PieceBooleanMathCheck.h | 2 +-
.../constraints/PiecewiseValueMathCheck.cpp | 2 +-
.../constraints/PiecewiseValueMathCheck.h | 2 +-
src/sbml/validator/constraints/PowerUnitsCheck.cpp | 8 +-
src/sbml/validator/constraints/PowerUnitsCheck.h | 2 +-
.../constraints/SBOConsistencyConstraints.cpp | 2 +-
.../SBOConsistencyConstraintsDeclared.cxx | 2 +-
.../constraints/SpeciesReactionOrRule.cpp | 2 +-
.../validator/constraints/SpeciesReactionOrRule.h | 2 +-
.../constraints/StoichiometryMathVars.cpp | 2 +-
.../validator/constraints/StoichiometryMathVars.h | 2 +-
.../StrictUnitConsistencyConstraints.cpp | 38 +-
.../StrictUnitConsistencyConstraintsDeclared.cxx | 2 +-
src/sbml/validator/constraints/UniqueIdBase.cpp | 2 +-
src/sbml/validator/constraints/UniqueIdBase.h | 2 +-
.../constraints/UniqueIdsForUnitDefinitions.cpp | 2 +-
.../constraints/UniqueIdsForUnitDefinitions.h | 2 +-
.../constraints/UniqueIdsInKineticLaw.cpp | 2 +-
.../validator/constraints/UniqueIdsInKineticLaw.h | 2 +-
.../validator/constraints/UniqueIdsInModel.cpp | 2 +-
src/sbml/validator/constraints/UniqueIdsInModel.h | 2 +-
src/sbml/validator/constraints/UniqueMetaId.cpp | 2 +-
src/sbml/validator/constraints/UniqueMetaId.h | 2 +-
.../UniqueSpeciesTypesInCompartment.cpp | 2 +-
.../constraints/UniqueSpeciesTypesInCompartment.h | 2 +-
.../UniqueSymbolsInInitialAssignments.cpp | 2 +-
.../UniqueSymbolsInInitialAssignments.h | 2 +-
.../constraints/UniqueVarsInEventAssignments.cpp | 2 +-
.../constraints/UniqueVarsInEventAssignments.h | 2 +-
.../constraints/UniqueVarsInEventsAndRules.cpp | 2 +-
.../constraints/UniqueVarsInEventsAndRules.h | 2 +-
.../UniqueVarsInInitialAssignmentsAndRules.cpp | 2 +-
.../UniqueVarsInInitialAssignmentsAndRules.h | 2 +-
.../validator/constraints/UniqueVarsInRules.cpp | 2 +-
src/sbml/validator/constraints/UniqueVarsInRules.h | 2 +-
.../constraints/UnitConsistencyConstraints.cpp | 4 +-
.../UnitConsistencyConstraintsDeclared.cxx | 2 +-
src/sbml/validator/constraints/UnitsBase.cpp | 2 +-
src/sbml/validator/constraints/UnitsBase.h | 2 +-
.../validator/constraints/ValidCnUnitsValue.cpp | 2 +-
src/sbml/validator/constraints/ValidCnUnitsValue.h | 2 +-
src/sbml/validator/test/CMakeLists.txt | 2 +-
src/sbml/validator/test/Makefile.in | 2 +-
.../validator/test/TestConsistencyValidator.cpp | 2 +-
src/sbml/validator/test/TestFile.cpp | 2 +-
src/sbml/validator/test/TestFile.h | 2 +-
src/sbml/validator/test/TestValidator.cpp | 28 +-
src/sbml/validator/test/TestValidator.h | 2 +-
src/sbml/validator/test/test-data/Makefile.in | 2 +-
.../libsbml-constraints/99505-pass-00-02.xml | 46 +
.../libsbml-constraints/99505-pass-00-03.xml | 38 +
.../libsbml-constraints/99505-pass-00-04.xml | 30 +
.../libsbml-constraints/99505-pass-00-05.xml | 30 +
.../libsbml-constraints/99505-pass-00-06.xml | 30 +
.../20502-fail-01-13.xml | 2 +-
.../20910-fail-01-02.xml | 44 +
.../Makefile.in | 2 +-
.../10218-fail-01-11-10213.xml | 34 +
.../sbml-mathml-constraints/10218-fail-01-12.xml | 36 +
.../sbml-mathml-constraints/10218-fail-01-13.xml | 36 +
.../sbml-mathml-constraints/10218-fail-02-10.xml | 37 +
.../{10501-fail-01-40.xml => 10501-pass-00-60.xml} | 0
.../sbml-unit-constraints/10513-pass-00-21.xml | 110 +
.../sbml-unit-constraints/10541-pass-00-54.xml | 87 +
src/sbml/xml/ExpatAttributes.cpp | 2 +-
src/sbml/xml/ExpatAttributes.h | 2 +-
src/sbml/xml/ExpatHandler.cpp | 8 +-
src/sbml/xml/ExpatHandler.h | 2 +-
src/sbml/xml/ExpatParser.cpp | 2 +-
src/sbml/xml/ExpatParser.h | 2 +-
src/sbml/xml/LibXMLAttributes.cpp | 2 +-
src/sbml/xml/LibXMLAttributes.h | 2 +-
src/sbml/xml/LibXMLHandler.cpp | 2 +-
src/sbml/xml/LibXMLHandler.h | 2 +-
src/sbml/xml/LibXMLNamespaces.cpp | 2 +-
src/sbml/xml/LibXMLNamespaces.h | 2 +-
src/sbml/xml/LibXMLParser.cpp | 2 +-
src/sbml/xml/LibXMLParser.h | 2 +-
src/sbml/xml/LibXMLTranscode.cpp | 2 +-
src/sbml/xml/LibXMLTranscode.h | 2 +-
src/sbml/xml/Makefile.in | 2 +-
src/sbml/xml/XMLAttributes.cpp | 4 +-
src/sbml/xml/XMLAttributes.h | 2 +-
src/sbml/xml/XMLBuffer.cpp | 2 +-
src/sbml/xml/XMLBuffer.h | 2 +-
src/sbml/xml/XMLConstructorException.cpp | 2 +-
src/sbml/xml/XMLConstructorException.h | 2 +-
src/sbml/xml/XMLError.cpp | 2 +-
src/sbml/xml/XMLError.h | 2 +-
src/sbml/xml/XMLErrorLog.cpp | 2 +-
src/sbml/xml/XMLErrorLog.h | 2 +-
src/sbml/xml/XMLExtern.h | 2 +-
src/sbml/xml/XMLFileBuffer.cpp | 2 +-
src/sbml/xml/XMLFileBuffer.h | 2 +-
src/sbml/xml/XMLHandler.cpp | 2 +-
src/sbml/xml/XMLHandler.h | 2 +-
src/sbml/xml/XMLInputStream.cpp | 4 +-
src/sbml/xml/XMLInputStream.h | 2 +-
src/sbml/xml/XMLLogOverride.cpp | 2 +-
src/sbml/xml/XMLLogOverride.h | 2 +-
src/sbml/xml/XMLMemoryBuffer.cpp | 2 +-
src/sbml/xml/XMLMemoryBuffer.h | 2 +-
src/sbml/xml/XMLNamespaces.cpp | 2 +-
src/sbml/xml/XMLNamespaces.h | 2 +-
src/sbml/xml/XMLNode.cpp | 2 +-
src/sbml/xml/XMLNode.h | 2 +-
src/sbml/xml/XMLOutputStream.cpp | 119 +-
src/sbml/xml/XMLOutputStream.h | 78 +-
src/sbml/xml/XMLParser.cpp | 2 +-
src/sbml/xml/XMLParser.h | 2 +-
src/sbml/xml/XMLToken.cpp | 2 +-
src/sbml/xml/XMLToken.h | 2 +-
src/sbml/xml/XMLTokenizer.cpp | 5 +-
src/sbml/xml/XMLTokenizer.h | 2 +-
src/sbml/xml/XMLTriple.cpp | 2 +-
src/sbml/xml/XMLTriple.h | 2 +-
src/sbml/xml/XercesAttributes.cpp | 2 +-
src/sbml/xml/XercesAttributes.h | 2 +-
src/sbml/xml/XercesHandler.cpp | 2 +-
src/sbml/xml/XercesHandler.h | 2 +-
src/sbml/xml/XercesNamespaces.cpp | 2 +-
src/sbml/xml/XercesNamespaces.h | 2 +-
src/sbml/xml/XercesParser.cpp | 2 +-
src/sbml/xml/XercesParser.h | 2 +-
src/sbml/xml/XercesTranscode.cpp | 2 +-
src/sbml/xml/XercesTranscode.h | 2 +-
src/sbml/xml/test/CMakeLists.txt | 2 +-
src/sbml/xml/test/Makefile.in | 2 +-
src/sbml/xml/test/TestCopyAndClone.cpp | 2 +-
src/sbml/xml/test/TestRunner.c | 2 +-
src/sbml/xml/test/TestXMLAttributes.cpp | 2 +-
src/sbml/xml/test/TestXMLAttributesC.c | 2 +-
src/sbml/xml/test/TestXMLError.cpp | 2 +-
src/sbml/xml/test/TestXMLErrorC.c | 2 +-
src/sbml/xml/test/TestXMLErrorLog.c | 2 +-
src/sbml/xml/test/TestXMLExceptions.cpp | 2 +-
src/sbml/xml/test/TestXMLInputStream.c | 2 +-
src/sbml/xml/test/TestXMLNamespaces.c | 2 +-
src/sbml/xml/test/TestXMLNode.cpp | 2 +-
src/sbml/xml/test/TestXMLNode_newSetters.c | 2 +-
src/sbml/xml/test/TestXMLOutputStream.c | 2 +-
src/sbml/xml/test/TestXMLToken.c | 2 +-
src/sbml/xml/test/TestXMLToken_newSetters.c | 2 +-
src/sbml/xml/test/TestXMLTriple.c | 2 +-
src/spatial-package.cmake | 2 +-
2751 files changed, 54015 insertions(+), 37985 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libsbml.git
More information about the debian-med-commit
mailing list