git: 820169db0255 - main - biology/py-python-libsbml: update 5.20.1 → 5.20.4
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Tue, 12 Nov 2024 10:18:15 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=820169db025585e057616768133d3b686e4dc4ef
commit 820169db025585e057616768133d3b686e4dc4ef
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-11-12 09:45:25 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-11-12 10:18:13 +0000
biology/py-python-libsbml: update 5.20.1 → 5.20.4
---
biology/py-python-libsbml/Makefile | 2 +-
biology/py-python-libsbml/distinfo | 6 +-
.../files/patch-libsbml__source_src_sbml_SBase.cpp | 2592 --------------------
3 files changed, 4 insertions(+), 2596 deletions(-)
diff --git a/biology/py-python-libsbml/Makefile b/biology/py-python-libsbml/Makefile
index 8d5ef70851be..c42034eb0b90 100644
--- a/biology/py-python-libsbml/Makefile
+++ b/biology/py-python-libsbml/Makefile
@@ -1,5 +1,5 @@
PORTNAME= python-libsbml
-DISTVERSION= 5.20.1
+DISTVERSION= 5.20.4
CATEGORIES= biology python
#MASTER_SITES= PYPI # no tarballs on PYPI
MASTER_SITES= https://github.com/sbmlteam/python-libsbml/releases/download/v${DISTVERSION}/
diff --git a/biology/py-python-libsbml/distinfo b/biology/py-python-libsbml/distinfo
index dc3cf221dc71..26af45c03fd7 100644
--- a/biology/py-python-libsbml/distinfo
+++ b/biology/py-python-libsbml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1687747738
-SHA256 (python-libsbml-5.20.1.tar.gz) = 5a10f0a494ba03ffda5190430f80a15516357d2d17698b928a01cbd2e231bf45
-SIZE (python-libsbml-5.20.1.tar.gz) = 48808000
+TIMESTAMP = 1731400774
+SHA256 (python-libsbml-5.20.4.tar.gz) = c9d57cb81661eec7d9ec3a0efa463999d6cd389418dfdbeea764664f3a44617a
+SIZE (python-libsbml-5.20.4.tar.gz) = 48841959
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
deleted file mode 100644
index 8efff8c5aebe..000000000000
--- a/biology/py-python-libsbml/files/patch-libsbml__source_src_sbml_SBase.cpp
+++ /dev/null
@@ -1,2592 +0,0 @@
---- 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)
- return LIBSBML_OPERATION_FAILED;
- else
- return LIBSBML_OPERATION_SUCCESS;
-@@ -2942,11 +2942,11 @@ SBase::unsetCVTerms()
- int
*** 1651 LINES SKIPPED ***