git: 45027c0066d0 - main - biology/py-python-libsbml: Update 5.19.0 → 5.20.1
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Date: Mon, 26 Jun 2023 15:53:09 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=45027c0066d01a3ddaefcf99a72d9f84970fff21
commit 45027c0066d01a3ddaefcf99a72d9f84970fff21
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2023-06-26 15:19:57 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2023-06-26 15:53:03 +0000
biology/py-python-libsbml: Update 5.19.0 → 5.20.1
Reported by: portscout
---
biology/py-python-libsbml/Makefile | 5 +-
biology/py-python-libsbml/distinfo | 6 +-
.../files/patch-libsbml__source_src_sbml_SBase.cpp | 2592 ++++++++++++++++++++
3 files changed, 2598 insertions(+), 5 deletions(-)
diff --git a/biology/py-python-libsbml/Makefile b/biology/py-python-libsbml/Makefile
index 5d26e65f429f..d0b1be3400fb 100644
--- a/biology/py-python-libsbml/Makefile
+++ b/biology/py-python-libsbml/Makefile
@@ -1,7 +1,8 @@
PORTNAME= python-libsbml
-DISTVERSION= 5.19.0
+DISTVERSION= 5.20.1
CATEGORIES= biology python
-MASTER_SITES= PYPI
+#MASTER_SITES= PYPI # no tarballs on PYPI
+MASTER_SITES= https://github.com/sbmlteam/python-libsbml/releases/download/v${DISTVERSION}/
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/py-python-libsbml/distinfo b/biology/py-python-libsbml/distinfo
index 6f7129d3cedb..dc3cf221dc71 100644
--- a/biology/py-python-libsbml/distinfo
+++ b/biology/py-python-libsbml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1629231482
-SHA256 (python-libsbml-5.19.0.tar.gz) = 87596017aa76c1284e83247593fe999ab7ba9a84e7488bcf0434b01277858f86
-SIZE (python-libsbml-5.19.0.tar.gz) = 36842483
+TIMESTAMP = 1687747738
+SHA256 (python-libsbml-5.20.1.tar.gz) = 5a10f0a494ba03ffda5190430f80a15516357d2d17698b928a01cbd2e231bf45
+SIZE (python-libsbml-5.20.1.tar.gz) = 48808000
diff --git a/biology/py-python-libsbml/files/patch-libsbml__source_src_sbml_SBase.cpp b/biology/py-python-libsbml/files/patch-libsbml__source_src_sbml_SBase.cpp
new file mode 100644
index 000000000000..8efff8c5aebe
--- /dev/null
+++ b/biology/py-python-libsbml/files/patch-libsbml__source_src_sbml_SBase.cpp
@@ -0,0 +1,2592 @@
+--- libsbml_source/src/sbml/SBase.cpp.orig 2023-06-26 04:05:56 UTC
++++ libsbml_source/src/sbml/SBase.cpp
+@@ -93,7 +93,7 @@ struct DeletePluginEntity
+ struct ClonePluginEntity
+ {
+ SBasePlugin* operator() (const SBasePlugin* sb) {
+- if (!sb) return NULL;
++ if (!sb) return 0;
+ return sb->clone();
+ }
+ };
+@@ -103,7 +103,7 @@ struct ClonePluginEntity
+ SBase*
+ SBase::getElementBySId(const std::string& id)
+ {
+- if (id.empty()) return NULL;
++ if (id.empty()) return 0;
+ return getElementFromPluginsBySId(id);
+ }
+
+@@ -118,7 +118,7 @@ SBase::getElementBySId(const std::string& id) const
+ SBase*
+ SBase::getElementByMetaId(const std::string& metaid)
+ {
+- if (metaid.empty()) return NULL;
++ if (metaid.empty()) return 0;
+ return getElementFromPluginsByMetaId(metaid);
+ }
+
+@@ -188,9 +188,9 @@ SBase::getElementFromPluginsBySId(const std::string& i
+ for (size_t i=0; i < mPlugins.size(); i++)
+ {
+ SBase* subObj = mPlugins[i]->getElementBySId(id);
+- if (subObj != NULL) return subObj;
++ if (subObj != 0) return subObj;
+ }
+- return NULL;
++ return 0;
+ }
+ /** @endcond */
+
+@@ -202,9 +202,9 @@ SBase::getElementFromPluginsByMetaId(const std::string
+ for (size_t i=0; i < mPlugins.size(); i++)
+ {
+ SBase* subObj = mPlugins[i]->getElementByMetaId(metaid);
+- if (subObj != NULL) return subObj;
++ if (subObj != 0) return subObj;
+ }
+- return NULL;
++ return 0;
+ }
+ /** @endcond */
+
+@@ -276,7 +276,7 @@ SBase::transformIdentifiers(IdentifierTransformer* idT
+ }
+
+ // call transformer
+- if (idTransformer != NULL)
++ if (idTransformer != 0)
+ {
+ ret = idTransformer->transform(this);
+ if (ret != LIBSBML_OPERATION_SUCCESS)
+@@ -296,7 +296,7 @@ SBase::getAllElementsFromPlugins(ElementFilter *filter
+ for (size_t i=0; i < mPlugins.size(); i++)
+ {
+ List* sublist = mPlugins[i]->getAllElements(filter);
+- if (sublist != NULL)
++ if (sublist != 0)
+ {
+ if (sublist->getSize() > 0)
+ ret->transferFrom(sublist);
+@@ -316,17 +316,17 @@ SBase::SBase (unsigned int level, unsigned int version
+ mId ( "" )
+ , mName ( "" )
+ , mMetaId ( "" )
+- , mNotes ( NULL )
+- , mAnnotation( NULL )
+- , mSBML ( NULL )
+- , mSBMLNamespaces (NULL)
+- , mUserData(NULL)
++ , mNotes ( 0 )
++ , mAnnotation( 0 )
++ , mSBML ( 0 )
++ , mSBMLNamespaces (0)
++ , mUserData(0)
+ , mSBOTerm ( -1 )
+ , mLine ( 0 )
+ , mColumn ( 0 )
+- , mParentSBMLObject (NULL)
+- , mCVTerms ( NULL )
+- , mHistory ( NULL )
++ , mParentSBMLObject (0)
++ , mCVTerms ( 0 )
++ , mHistory ( 0 )
+ , mHasBeenDeleted (false)
+ , mEmptyString ("")
+ , mURI("")
+@@ -362,17 +362,17 @@ SBase::SBase (const SBMLNamespaces *sbmlns) :
+ mId ( "" )
+ , mName ( "" )
+ , mMetaId ( "" )
+- , mNotes ( NULL )
+- , mAnnotation( NULL )
+- , mSBML ( NULL )
+- , mSBMLNamespaces (NULL)
+- , mUserData(NULL)
++ , mNotes ( 0 )
++ , mAnnotation( 0 )
++ , mSBML ( 0 )
++ , mSBMLNamespaces (0)
++ , mUserData(0)
+ , mSBOTerm ( -1 )
+ , mLine ( 0 )
+ , mColumn ( 0 )
+- , mParentSBMLObject (NULL)
+- , mCVTerms ( NULL )
+- , mHistory ( NULL )
++ , mParentSBMLObject (0)
++ , mCVTerms ( 0 )
++ , mHistory ( 0 )
+ , mHasBeenDeleted (false)
+ , mEmptyString ("")
+ , mURI("")
+@@ -416,17 +416,17 @@ SBase::SBase(const SBase& orig)
+ : mId (orig.mId)
+ , mName (orig.mName)
+ , mMetaId (orig.mMetaId)
+- , mNotes (NULL)
+- , mAnnotation (NULL)
+- , mSBML (NULL)
+- , mSBMLNamespaces(NULL)
++ , mNotes (0)
++ , mAnnotation (0)
++ , mSBML (0)
++ , mSBMLNamespaces(0)
+ , mUserData(orig.mUserData)
+ , mSBOTerm(orig.mSBOTerm)
+ , mLine(orig.mLine)
+ , mColumn(orig.mColumn)
+- , mParentSBMLObject(NULL)
+- , mCVTerms(NULL)
+- , mHistory(NULL)
++ , mParentSBMLObject(0)
++ , mCVTerms(0)
++ , mHistory(0)
+ , mHasBeenDeleted(false)
+ , mEmptyString()
+ , mPlugins(orig.mPlugins.size())
+@@ -439,17 +439,17 @@ SBase::SBase(const SBase& orig)
+ , mElementsOfUnknownPkg (orig.mElementsOfUnknownPkg)
+ , mElementsOfUnknownDisabledPkg (orig.mElementsOfUnknownDisabledPkg)
+ {
+- if(orig.mNotes != NULL)
++ if(orig.mNotes != 0)
+ this->mNotes = new XMLNode(*const_cast<SBase&>(orig).getNotes());
+
+- if(orig.mAnnotation != NULL)
++ if(orig.mAnnotation != 0)
+ this->mAnnotation = new XMLNode(*const_cast<SBase&>(orig).mAnnotation);
+
+- if(orig.getSBMLNamespaces() != NULL)
++ if(orig.getSBMLNamespaces() != 0)
+ this->mSBMLNamespaces =
+ new SBMLNamespaces(*const_cast<SBase&>(orig).getSBMLNamespaces());
+
+- if(orig.mCVTerms != NULL)
++ if(orig.mCVTerms != 0)
+ {
+ this->mCVTerms = new List();
+ unsigned int iMax = orig.mCVTerms->getSize();
+@@ -460,7 +460,7 @@ SBase::SBase(const SBase& orig)
+ }
+ }
+
+- if (orig.mHistory != NULL)
++ if (orig.mHistory != 0)
+ {
+ this->mHistory = orig.mHistory->clone();
+ }
+@@ -481,10 +481,10 @@ SBase::SBase(const SBase& orig)
+ */
+ SBase::~SBase ()
+ {
+- if (mNotes != NULL) delete mNotes;
+- if (mAnnotation != NULL) delete mAnnotation;
+- if (mSBMLNamespaces != NULL) delete mSBMLNamespaces;
+- if (mCVTerms != NULL)
++ if (mNotes != 0) delete mNotes;
++ if (mAnnotation != 0) delete mAnnotation;
++ if (mSBMLNamespaces != 0) delete mSBMLNamespaces;
++ if (mCVTerms != 0)
+ {
+ unsigned int size = mCVTerms->getSize();
+ while (size > 0)
+@@ -494,7 +494,7 @@ SBase::~SBase ()
+ }
+ delete mCVTerms;
+ }
+- if (mHistory != NULL) delete mHistory;
++ if (mHistory != 0) delete mHistory;
+ mHasBeenDeleted = true;
+
+ for_each( mPlugins.begin(), mPlugins.end(), DeletePluginEntity() );
+@@ -514,17 +514,17 @@ SBase& SBase::operator=(const SBase& rhs)
+
+ delete this->mNotes;
+
+- if(rhs.mNotes != NULL)
++ if(rhs.mNotes != 0)
+ this->mNotes = new XMLNode(*const_cast<SBase&>(rhs).getNotes());
+ else
+- this->mNotes = NULL;
++ this->mNotes = 0;
+
+ delete this->mAnnotation;
+
+- if(rhs.mAnnotation != NULL)
++ if(rhs.mAnnotation != 0)
+ this->mAnnotation = new XMLNode(*const_cast<SBase&>(rhs).mAnnotation);
+ else
+- this->mAnnotation = NULL;
++ this->mAnnotation = 0;
+
+ this->mSBML = rhs.mSBML;
+ this->mSBOTerm = rhs.mSBOTerm;
+@@ -539,21 +539,21 @@ SBase& SBase::operator=(const SBase& rhs)
+
+ delete this->mSBMLNamespaces;
+
+- if(rhs.mSBMLNamespaces != NULL)
++ if(rhs.mSBMLNamespaces != 0)
+ this->mSBMLNamespaces =
+ new SBMLNamespaces(*const_cast<SBase&>(rhs).mSBMLNamespaces);
+ else
+- this->mSBMLNamespaces = NULL;
++ this->mSBMLNamespaces = 0;
+
+
+- if(this->mCVTerms != NULL)
++ if(this->mCVTerms != 0)
+ {
+ unsigned int size = this->mCVTerms->getSize();
+ while (size--) delete static_cast<CVTerm*>( this->mCVTerms->remove(0) );
+ delete this->mCVTerms;
+ }
+
+- if(rhs.mCVTerms != NULL)
++ if(rhs.mCVTerms != 0)
+ {
+ this->mCVTerms = new List();
+ unsigned int iMax = rhs.mCVTerms->getSize();
+@@ -565,17 +565,17 @@ SBase& SBase::operator=(const SBase& rhs)
+ }
+ else
+ {
+- this->mCVTerms = NULL;
++ this->mCVTerms = 0;
+ }
+
+ delete this->mHistory;
+- if (rhs.mHistory != NULL)
++ if (rhs.mHistory != 0)
+ {
+ this->mHistory = rhs.mHistory->clone();
+ }
+ else
+ {
+- this->mHistory = NULL;
++ this->mHistory = 0;
+ }
+
+ this->mHasBeenDeleted = rhs.mHasBeenDeleted;
+@@ -630,7 +630,7 @@ SBase::loadPlugins(SBMLNamespaces *sbmlns)
+ const std::string &prefix = xmlns->getPrefix(i);
+ const SBasePluginCreatorBase* sbPluginCreator = sbmlext->getSBasePluginCreator(extPoint);
+
+- if (sbPluginCreator == NULL)
++ if (sbPluginCreator == 0)
+ {
+ sbPluginCreator = sbmlext->getSBasePluginCreator(genericPoint);
+ }
+@@ -824,12 +824,12 @@ SBase::getURI() const
+ const string &package = getPackageName();
+ const SBMLDocument* doc = getSBMLDocument();
+
+- if (doc == NULL)
++ if (doc == 0)
+ return getElementNamespace();
+
+ SBMLNamespaces* sbmlns = doc->getSBMLNamespaces();
+
+- if (sbmlns == NULL)
++ if (sbmlns == 0)
+ return getElementNamespace();
+
+ if (package == "" || package == "core")
+@@ -879,11 +879,11 @@ int
+ SBase::setUserData(void *userData)
+ {
+ this->mUserData = userData;
+- if (userData == NULL && mUserData == NULL)
++ if (userData == 0 && mUserData == 0)
+ {
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+- else if (mUserData != NULL)
++ else if (mUserData != 0)
+ {
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+@@ -896,7 +896,7 @@ SBase::setUserData(void *userData)
+ bool
+ SBase::isSetUserData() const
+ {
+- if (mUserData != NULL)
++ if (mUserData != 0)
+ {
+ return true;
+ }
+@@ -909,8 +909,8 @@ SBase::isSetUserData() const
+ int
+ SBase::unsetUserData()
+ {
+- this->mUserData = NULL;
+- if (mUserData == NULL)
++ this->mUserData = 0;
++ if (mUserData == 0)
+ {
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+@@ -926,11 +926,11 @@ SBase::unsetUserData()
+ XMLNamespaces*
+ SBase::getNamespaces() const
+ {
+- if (mSBML != NULL)
++ if (mSBML != 0)
+ return mSBML->getSBMLNamespaces()->getNamespaces();
+- if (mSBMLNamespaces != NULL)
++ if (mSBMLNamespaces != 0)
+ return mSBMLNamespaces->getNamespaces();
+- return NULL;
++ return 0;
+ }
+
+
+@@ -942,9 +942,9 @@ SBase::getSBMLDocument () const
+ {
+ // if the doc object has been deleted the pointer is
+ // still valid but points to nothing
+- if (mSBML != NULL && mSBML->getHasBeenDeleted())
++ if (mSBML != 0 && mSBML->getHasBeenDeleted())
+ {
+- return NULL;
++ return 0;
+ }
+
+ return mSBML;
+@@ -958,9 +958,9 @@ SBase::getSBMLDocument ()
+ {
+ // if the doc object has been deleted the pointer is
+ // still valid but points to nothing
+- if (mSBML != NULL && mSBML->getHasBeenDeleted())
++ if (mSBML != 0 && mSBML->getHasBeenDeleted())
+ {
+- return NULL;
++ return 0;
+ }
+ return mSBML;
+ }
+@@ -969,9 +969,9 @@ SBase::getParentSBMLObject ()
+ {
+ // if the parent object has been deleted the pointer is
+ // still valid but points to nothing
+- if (mParentSBMLObject != NULL && mParentSBMLObject->getHasBeenDeleted())
++ if (mParentSBMLObject != 0 && mParentSBMLObject->getHasBeenDeleted())
+ {
+- return NULL;
++ return 0;
+ }
+
+ return mParentSBMLObject;
+@@ -982,9 +982,9 @@ SBase::getParentSBMLObject () const
+ {
+ // if the parent object has been deleted the pointer is
+ // still valid but points to nothing
+- if (mParentSBMLObject != NULL && mParentSBMLObject->getHasBeenDeleted())
++ if (mParentSBMLObject != 0 && mParentSBMLObject->getHasBeenDeleted())
+ {
+- return NULL;
++ return 0;
+ }
+
+ return mParentSBMLObject;
+@@ -1068,26 +1068,26 @@ SBase::getModelHistory()
+ Date*
+ SBase::getCreatedDate() const
+ {
+- return (mHistory != NULL) ? mHistory->getCreatedDate() : NULL;
++ return (mHistory != 0) ? mHistory->getCreatedDate() : 0;
+ }
+
+ Date*
+ SBase::getCreatedDate()
+ {
+- return (mHistory != NULL) ? mHistory->getCreatedDate() : NULL;
++ return (mHistory != 0) ? mHistory->getCreatedDate() : 0;
+ }
+
+
+ Date*
+ SBase::getModifiedDate(unsigned int n)
+ {
+- return (mHistory != NULL) ? mHistory->getModifiedDate(n) : NULL;
++ return (mHistory != 0) ? mHistory->getModifiedDate(n) : 0;
+ }
+
+ unsigned int
+ SBase::getNumModifiedDates()
+ {
+- return (mHistory != NULL) ? mHistory->getNumModifiedDates() : NULL;
++ return (mHistory != 0) ? mHistory->getNumModifiedDates() : 0;
+ }
+
+
+@@ -1142,7 +1142,7 @@ SBase::isSetIdAttribute () const
+ bool
+ SBase::isSetNotes () const
+ {
+- return (mNotes != NULL);
++ return (mNotes != 0);
+ }
+
+
+@@ -1154,7 +1154,7 @@ bool
+ SBase::isSetAnnotation () const
+ {
+ const_cast <SBase *> (this)->syncAnnotation();
+- return (mAnnotation != NULL);
++ return (mAnnotation != 0);
+ }
+
+
+@@ -1172,14 +1172,14 @@ SBase::isSetSBOTerm () const
+ bool
+ SBase::isSetModelHistory() const
+ {
+- return (mHistory != NULL);
++ return (mHistory != 0);
+ }
+
+
+ bool
+ SBase::isSetCreatedDate() const
+ {
+- return (mHistory == NULL) ? false : mHistory->isSetCreatedDate();
++ return (mHistory == 0) ? false : mHistory->isSetCreatedDate();
+ }
+
+
+@@ -1187,7 +1187,7 @@ SBase::isSetCreatedDate() const
+ bool
+ SBase::isSetModifiedDate() const
+ {
+- return (mHistory == NULL) ? false : mHistory->isSetModifiedDate();
++ return (mHistory == 0) ? false : mHistory->isSetModifiedDate();
+ }
+
+
+@@ -1304,10 +1304,10 @@ SBase::setAnnotation (const XMLNode* annotation)
+ //
+ //
+
+- if (annotation == NULL)
++ if (annotation == 0)
+ {
+ delete mAnnotation;
+- mAnnotation = NULL;
++ mAnnotation = 0;
+ }
+
+
+@@ -1321,7 +1321,7 @@ SBase::setAnnotation (const XMLNode* annotation)
+ || RDFAnnotationParser::hasHistoryRDFAnnotation(annotation) == true)
+ && isSetMetaId() == false)
+ {
+- mAnnotation = NULL;
++ mAnnotation = 0;
+ return LIBSBML_MISSING_METAID;
+ }
+ else
+@@ -1363,24 +1363,24 @@ SBase::setAnnotation (const XMLNode* annotation)
+ // delete existing mCVTerms
+ //
+ // existing CVTerms (if any) needs to be deleted at any rate, otherwise
+- // unsetAnnotation() ( setAnnotation(NULL) ) doesn't work as expected.
++ // unsetAnnotation() ( setAnnotation(0) ) doesn't work as expected.
+ // (These functions must clear all elements in an annotation.)
+ //
+
+ /* in L3 might be a model history */
+- if (mHistory != NULL)
++ if (mHistory != 0)
+ {
+ delete mHistory;
+- mHistory = NULL;
++ mHistory = 0;
+ }
+
+- if (mCVTerms != NULL)
++ if (mCVTerms != 0)
+ {
+ // delete existing mCVTerms (if any)
+ unsigned int size = mCVTerms->getSize();
+ while (size--) delete static_cast<CVTerm*>( mCVTerms->remove(0) );
+ delete mCVTerms;
+- mCVTerms = NULL;
++ mCVTerms = 0;
+ }
+
+ unsigned int level = getLevel();
+@@ -1392,7 +1392,7 @@ SBase::setAnnotation (const XMLNode* annotation)
+ validNestedTerms = false;
+ }
+
+- if(mAnnotation != NULL
++ if(mAnnotation != 0
+ && RDFAnnotationParser::hasCVTermRDFAnnotation(mAnnotation))
+ {
+ // parse mAnnotation (if any) and set mCVTerms
+@@ -1416,7 +1416,7 @@ SBase::setAnnotation (const XMLNode* annotation)
+ mCVTermsChanged = true;
+ }
+
+- if(getLevel() > 2 && mAnnotation != NULL
++ if(getLevel() > 2 && mAnnotation != 0
+ && RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
+ {
+ // parse mAnnotation (if any) and set mHistory
+@@ -1457,7 +1457,7 @@ SBase::setAnnotation (const std::string& annotation)
+ XMLNode* annt_xmln;
+
+ // you might not have a document !!
+- if (getSBMLDocument() != NULL)
++ if (getSBMLDocument() != 0)
+ {
+ const XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
+ annt_xmln = XMLNode::convertStringToXMLNode(annotation,xmlns);
+@@ -1467,7 +1467,7 @@ SBase::setAnnotation (const std::string& annotation)
+ annt_xmln = XMLNode::convertStringToXMLNode(annotation);
+ }
+
+- if(annt_xmln != NULL)
++ if(annt_xmln != 0)
+ {
+ success = setAnnotation(annt_xmln);
+ delete annt_xmln;
+@@ -1498,13 +1498,13 @@ SBase::appendAnnotation (const XMLNode* annotation)
+ // see bug reported via libsbml-team
+ // https://www.pivotaltracker.com/story/show/166576120
+
+- if (getNumCVTerms() > 0 && mAnnotation == NULL)
++ if (getNumCVTerms() > 0 && mAnnotation == 0)
+ {
+ syncAnnotation();
+ }
+
+
+- if(annotation == NULL)
++ if(annotation == 0)
+ return LIBSBML_OPERATION_SUCCESS;
+
+ // the annotation is an rdf annotation but the object has no metaid
+@@ -1516,7 +1516,7 @@ SBase::appendAnnotation (const XMLNode* annotation)
+ return LIBSBML_MISSING_METAID;
+ }
+
+- XMLNode* new_annotation = NULL;
++ XMLNode* new_annotation = 0;
+ const string& name = annotation->getName();
+
+ // check for annotation tags and add if necessary
+@@ -1532,7 +1532,7 @@ SBase::appendAnnotation (const XMLNode* annotation)
+ }
+
+
+- if (mAnnotation != NULL)
++ if (mAnnotation != 0)
+ {
+ // if mAnnotation is just <annotation/> need to tell
+ // it to no longer be an end
+@@ -1607,14 +1607,14 @@ SBase::appendAnnotation (const std::string& annotation
+ // see bug reported via libsbml-team
+ // https://www.pivotaltracker.com/story/show/166576120
+
+- if (getNumCVTerms() > 0 && mAnnotation == NULL)
++ if (getNumCVTerms() > 0 && mAnnotation == 0)
+ {
+ syncAnnotation();
+ }
+
+ int success = LIBSBML_OPERATION_FAILED;
+ XMLNode* annt_xmln;
+- if (getSBMLDocument() != NULL)
++ if (getSBMLDocument() != 0)
+ {
+ const XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
+ annt_xmln = XMLNode::convertStringToXMLNode(annotation,xmlns);
+@@ -1624,7 +1624,7 @@ SBase::appendAnnotation (const std::string& annotation
+ annt_xmln = XMLNode::convertStringToXMLNode(annotation);
+ }
+
+- if(annt_xmln != NULL)
++ if(annt_xmln != 0)
+ {
+ success = appendAnnotation(annt_xmln);
+ delete annt_xmln;
+@@ -1640,7 +1640,7 @@ SBase::removeTopLevelAnnotationElement(const std::stri
+ {
+
+ int success = LIBSBML_OPERATION_FAILED;
+- if (mAnnotation == NULL)
++ if (mAnnotation == 0)
+ {
+ success = LIBSBML_OPERATION_SUCCESS;
+ return success;
+@@ -1694,11 +1694,11 @@ SBase::removeTopLevelAnnotationElement(const std::stri
+ if (removeEmpty && mAnnotation->getNumChildren() == 0)
+ {
+ delete mAnnotation;
+- mAnnotation = NULL;
++ mAnnotation = 0;
+ }
+
+ // check success
+- if (mAnnotation == NULL || mAnnotation->getIndex(elementName) < 0)
++ if (mAnnotation == 0 || mAnnotation->getIndex(elementName) < 0)
+ {
+ success = LIBSBML_OPERATION_SUCCESS;
+ }
+@@ -1712,7 +1712,7 @@ int
+ SBase::replaceTopLevelAnnotationElement(const XMLNode* annotation)
+ {
+ int success = LIBSBML_OPERATION_FAILED;
+- XMLNode * replacement = NULL;
++ XMLNode * replacement = 0;
+ if (annotation->getName() == "annotation")
+ {
+ if (annotation->getNumChildren() != 1)
+@@ -1747,7 +1747,7 @@ SBase::replaceTopLevelAnnotationElement(const std::str
+ {
+ int success = LIBSBML_OPERATION_FAILED;
+ XMLNode* annt_xmln;
+- if (getSBMLDocument() != NULL)
++ if (getSBMLDocument() != 0)
+ {
+ const XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
+ annt_xmln = XMLNode::convertStringToXMLNode(annotation,xmlns);
+@@ -1757,7 +1757,7 @@ SBase::replaceTopLevelAnnotationElement(const std::str
+ annt_xmln = XMLNode::convertStringToXMLNode(annotation);
+ }
+
+- if(annt_xmln != NULL)
++ if(annt_xmln != 0)
+ {
+ success = replaceTopLevelAnnotationElement(annt_xmln);
+ }
+@@ -1778,10 +1778,10 @@ SBase::setNotes(const XMLNode* notes)
+ {
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+- else if (notes == NULL)
++ else if (notes == 0)
+ {
+ delete mNotes;
+- mNotes = NULL;
++ mNotes = 0;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+
+@@ -1831,7 +1831,7 @@ SBase::setNotes(const XMLNode* notes)
+ && !SyntaxChecker::hasExpectedXHTMLSyntax(mNotes, getSBMLNamespaces()))
+ {
+ delete mNotes;
+- mNotes = NULL;
++ mNotes = 0;
+ return LIBSBML_INVALID_OBJECT;
+ }
+
+@@ -1855,7 +1855,7 @@ SBase::setNotes(const std::string& notes, bool addXHTM
+ XMLNode* notes_xmln;
+
+ // you might not have a document !!
+- if (getSBMLDocument() != NULL)
++ if (getSBMLDocument() != 0)
+ {
+ const XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
+ notes_xmln = XMLNode::convertStringToXMLNode(notes,xmlns);
+@@ -1865,7 +1865,7 @@ SBase::setNotes(const std::string& notes, bool addXHTM
+ notes_xmln = XMLNode::convertStringToXMLNode(notes);
+ }
+
+- if(notes_xmln != NULL)
++ if(notes_xmln != 0)
+ {
+ if (addXHTMLMarkup == true)
+ {
+@@ -1923,7 +1923,7 @@ int
+ SBase::appendNotes(const XMLNode* notes)
+ {
+ int success = LIBSBML_OPERATION_FAILED;
+- if(notes == NULL)
++ if(notes == 0)
+ {
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+@@ -2079,7 +2079,7 @@ SBase::appendNotes(const XMLNode* notes)
+ }
+
+
+- if ( mNotes != NULL )
++ if ( mNotes != 0 )
+ {
+ //------------------------------------------------------------
+ //
+@@ -2272,7 +2272,7 @@ SBase::appendNotes(const std::string& notes)
+
+ XMLNode* notes_xmln;
+ // you might not have a document !!
+- if (getSBMLDocument() != NULL)
++ if (getSBMLDocument() != 0)
+ {
+ const XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
+ notes_xmln = XMLNode::convertStringToXMLNode(notes,xmlns);
+@@ -2282,7 +2282,7 @@ SBase::appendNotes(const std::string& notes)
+ notes_xmln = XMLNode::convertStringToXMLNode(notes);
+ }
+
+- if(notes_xmln != NULL)
++ if(notes_xmln != 0)
+ {
+ success = appendNotes(notes_xmln);
+ delete notes_xmln;
+@@ -2297,7 +2297,7 @@ SBase::setModelHistory(ModelHistory * history)
+ // if there is no parent then the required attributes are not
+ // correctly identified
+ bool dummyParent = false;
+- if (history != NULL && history->getParentSBMLObject() == NULL)
++ if (history != 0 && history->getParentSBMLObject() == 0)
+ {
+ history->setParentSBMLObject(this);
+ dummyParent = true;
+@@ -2324,17 +2324,17 @@ SBase::setModelHistory(ModelHistory * history)
+ {
+ status = LIBSBML_OPERATION_SUCCESS;
+ }
+- else if (history == NULL)
++ else if (history == 0)
+ {
+ delete mHistory;
+- mHistory = NULL;
++ mHistory = 0;
+ mHistoryChanged = true;
+ status = LIBSBML_OPERATION_SUCCESS;
+ }
+ else if (!(history->hasRequiredAttributes()))
+ {
+ delete mHistory;
+- mHistory = NULL;
++ mHistory = 0;
+ status = LIBSBML_INVALID_OBJECT;
+ }
+ else
+@@ -2355,7 +2355,7 @@ SBase::setModelHistory(ModelHistory * history)
+ int
+ SBase::setCreatedDate(Date* date)
+ {
+- if (mHistory != NULL)
++ if (mHistory != 0)
+ {
+ return mHistory->setCreatedDate(date);
+ }
+@@ -2372,7 +2372,7 @@ SBase::setCreatedDate(Date* date)
+ int
+ SBase::addModifiedDate(Date* date)
+ {
+- if (mHistory != NULL)
++ if (mHistory != 0)
+ {
+ return mHistory->addModifiedDate(date);
+ }
+@@ -2459,7 +2459,7 @@ SBase::getAncestorOfType(int type, const std::string&
+ SBase *child;
+ SBase *parent = getParentSBMLObject();
+
+- while ( parent != NULL &&
++ while ( parent != 0 &&
+ !( parent->getPackageName() == "core" &&
+ parent->getTypeCode() == SBML_DOCUMENT )
+ )
+@@ -2474,7 +2474,7 @@ SBase::getAncestorOfType(int type, const std::string&
+ }
+
+ // if we get here we havent found an ancestor of this type
+- return NULL;
++ return 0;
+
+ }
+
+@@ -2488,7 +2488,7 @@ SBase::getAncestorOfType(int type, const std::string p
+ const SBase *child;
+ const SBase *parent = getParentSBMLObject();
+
+- while ( parent != NULL &&
++ while ( parent != 0 &&
+ !( parent->getPackageName() == "core" &&
+ parent->getTypeCode() == SBML_DOCUMENT )
+ )
+@@ -2503,7 +2503,7 @@ SBase::getAncestorOfType(int type, const std::string p
+ }
+
+ // if we get here we havent found an ancestor of this type
+- return NULL;
++ return 0;
+
+ }
+
+@@ -2549,9 +2549,9 @@ SBase::setSBOTerm (const std::string &sboid)
+ int
+ SBase::setNamespaces(XMLNamespaces* xmlns)
+ {
+- if (xmlns == NULL)
++ if (xmlns == 0)
+ {
+- mSBMLNamespaces->setNamespaces(NULL);
++ mSBMLNamespaces->setNamespaces(0);
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+ else
+@@ -2672,7 +2672,7 @@ int
+ SBase::unsetNotes ()
+ {
+ delete mNotes;
+- mNotes = NULL;
++ mNotes = 0;
+ return LIBSBML_OPERATION_SUCCESS;
+ }
+
+@@ -2683,7 +2683,7 @@ SBase::unsetNotes ()
+ int
+ SBase::unsetAnnotation ()
+ {
+- const XMLNode* empty = NULL;
++ const XMLNode* empty = 0;
+ return setAnnotation(empty);
+ }
+
+@@ -2752,7 +2752,7 @@ int SBase::addTermToExistingBag(CVTerm *term, Qualifie
+ unsigned int added = 0;
+ unsigned int length = mCVTerms->getSize();
+
+- CVTerm* nthTerm = NULL;
++ CVTerm* nthTerm = 0;
+
+ if (length == 0) return (int)added;
+
+@@ -2764,7 +2764,7 @@ int SBase::addTermToExistingBag(CVTerm *term, Qualifie
+ {
+ nthTerm = static_cast <CVTerm *>(mCVTerms->get((unsigned int)n));
+
+- if (nthTerm != NULL && biol == nthTerm->getBiologicalQualifierType())
++ if (nthTerm != 0 && biol == nthTerm->getBiologicalQualifierType())
+ {
+ for (int r = 0; r < term->getResources()->getLength(); r++)
+ {
+@@ -2783,7 +2783,7 @@ int SBase::addTermToExistingBag(CVTerm *term, Qualifie
+ {
+ nthTerm = static_cast <CVTerm *>(mCVTerms->get(n));
+
+- if (nthTerm != NULL && model == nthTerm->getModelQualifierType())
++ if (nthTerm != 0 && model == nthTerm->getModelQualifierType())
+ {
+ for (int r = 0; r < term->getResources()->getLength(); r++)
+ {
+@@ -2811,7 +2811,7 @@ SBase::addCVTerm(CVTerm * term, bool newBag)
+ return LIBSBML_MISSING_METAID;
+ }
+
+- if (term == NULL)
++ if (term == 0)
+ {
+ return LIBSBML_OPERATION_FAILED;
+ }
+@@ -2825,7 +2825,7 @@ SBase::addCVTerm(CVTerm * term, bool newBag)
+ */
+ CVTerm * copyTerm = term->clone();
+
+- if (mCVTerms == NULL)
++ if (mCVTerms == 0)
+ {
+ mCVTerms = new List();
+ mCVTerms->add((void *) term->clone());
+@@ -2890,7 +2890,7 @@ SBase::getCVTerms() const
+ unsigned int
+ SBase::getNumCVTerms() const
+ {
+- if (mCVTerms != NULL)
++ if (mCVTerms != 0)
+ {
+ return mCVTerms->getSize();
+ }
+@@ -2912,7 +2912,7 @@ SBase::getNumCVTerms() const
+ CVTerm*
+ SBase::getCVTerm(unsigned int n)
+ {
+- return (mCVTerms) ? static_cast <CVTerm*> (mCVTerms->get(n)) : NULL;
++ return (mCVTerms) ? static_cast <CVTerm*> (mCVTerms->get(n)) : 0;
+ }
+
+
+@@ -2923,16 +2923,16 @@ SBase::getCVTerm(unsigned int n)
+ int
+ SBase::unsetCVTerms()
+ {
+- if (mCVTerms != NULL)
++ if (mCVTerms != 0)
+ {
+ unsigned int size = mCVTerms->getSize();
+ while (size--) delete static_cast<CVTerm*>( mCVTerms->remove(0) );
+ delete mCVTerms;
+ mCVTermsChanged = true;
+ }
+- mCVTerms = NULL;
++ mCVTerms = 0;
+
+- if (mCVTerms != NULL)
++ if (mCVTerms != 0)
*** 1656 LINES SKIPPED ***