Date: Mon, 26 Jun 2023 15:53:09 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 45027c0066d0 - main - =?utf-8?Q?biology/py-python-libsbml:=20Update=205.19.0=20=E2=86=92=205.20.1?= Message-ID: <202306261553.35QFr9af063114@gitrepo.freebsd.org>
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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 ***
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