def writeProtectedFunctions(output, element, package, elementDict):
listOf = generalFunctions.getListOfClassName(elementDict, element)
generalFunctions.writeInternalStart(output)
output.write('/*\n')
output.write(' * Creates a new {0} in this {1}\n'.format(element, listOf))
output.write(' */\n')
output.write('SBase*\n{0}::createObject(XMLInputStream& stream)\n'.format(listOf))
output.write('{\n' )
output.write(' const std::string& name = stream.peek().getName();\n')
output.write(' SBase* object = NULL;\n\n')
name = strFunctions.lowerFirst(element)
if elementDict.has_key('elementName'):
name = elementDict['elementName']
output.write(' if (name == "{0}")\n'.format(name))
output.write(' {\n')
output.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(package.upper(), package.lower()))
output.write(' object = new {0}({1}ns);\n'.format(element, package.lower()))
output.write(' appendAndOwn(object);\n')
output.write(' delete {0}ns;\n'.format(package.lower()))
output.write(' }\n\n')
# need to create concrete objects
if elementDict.has_key('concrete'):
for elem in generalFunctions.getConcretes(elementDict['root'], elementDict['concrete']):
output.write(' if (name == "{0}")\n'.format(strFunctions.lowerFirst(elem['name'])))
output.write(' {\n')
output.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(package.upper(), package.lower()))
output.write(' object = new {0}({1}ns);\n'.format(elem['element'], package.lower()))
output.write(' appendAndOwn(object);\n')
output.write(' delete {0}ns;\n'.format(package.lower()))
output.write(' }\n\n')
output.write(' return object;\n')
output.write('}\n\n\n')
generalFunctions.writeInternalEnd(output)
generalFunctions.writeInternalStart(output)
output.write('/*\n')
output.write(' * Write the namespace for the {0} package.\n'.format(package))
output.write(' */\n')
output.write('void\n{0}::writeXMLNS(XMLOutputStream& stream) const\n'.format(listOf))
output.write('{\n' )
output.write(' XMLNamespaces xmlns;\n\n')
output.write(' std::string prefix = getPrefix();\n\n')
output.write(' if (prefix.empty())\n')
output.write(' {\n')
output.write(' XMLNamespaces* thisxmlns = getNamespaces();\n')
output.write(' if (thisxmlns && thisxmlns->hasURI({0}'.format(package))
output.write('Extension::getXmlnsL3V1V1()))\n')
output.write(' {\n')
output.write(' xmlns.add({0}Extension::getXmlnsL3V1V1(),prefix);\n'.format(package))
output.write(' }\n')
output.write(' }\n\n')
output.write(' stream << xmlns;\n')
output.write('}\n\n\n')
generalFunctions.writeInternalEnd(output)
def writeMemberFunctions(fileOut, object, plugin):
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(
object, plugin))
fileOut.write(' *\n')
fileOut.write(
' * @return the {0} from object in this {1} object.\n'.format(
object, plugin))
fileOut.write(' */\n')
fileOut.write(' const {0}* get{0} () const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(
object, plugin))
fileOut.write(' *\n')
fileOut.write(
' * @return the {0} from object in this {1} object.\n'.format(
object, plugin))
fileOut.write(' */\n')
fileOut.write(' {0}* get{0} ();\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Predicate returning @c true or @c false depending on ')
fileOut.write('whether the\n \"{0}\" '.format(object))
fileOut.write('element has been set.\n *\n')
fileOut.write(' * @return @c true if the \"{0}\"'.format(object))
fileOut.write(' element has been set,\n')
fileOut.write(' * otherwise @c false is returned.\n')
fileOut.write(' */\n')
fileOut.write(' bool isSet{0}() const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Sets the {0} element in this {1} object.\n'.format(
object, plugin))
fileOut.write(' *\n')
fileOut.write(' * @param {0} the {0}* to be set.\n'.format(
strFunctions.lowerFirst(object), object))
fileOut.write(' *\n')
fileOut.write(
' * @return integer value indicating success/failure of the\n')
fileOut.write(' * function. @if clike The value is drawn from the\n')
fileOut.write(
' * enumeration #OperationReturnValues_t. @endif The possible values\n'
)
fileOut.write(' * returned by this function are:\n')
fileOut.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
fileOut.write(' */\n')
fileOut.write(' int set{0} (const {0}* {1});\n\n\n'.format(
object, strFunctions.lowerFirst(object)))
fileOut.write(' /**\n')
fileOut.write(
' * Creates a new {0} object and adds it to the {1} object.\n'.
format(object, plugin))
fileOut.write(' *\n')
fileOut.write(
' * @return the newly created {0} object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* create{0} ();\n\n\n'.format(object))
def writeGetElementNameHeader(outFile, element, isSedListOf):
if isSedListOf == True:
element = writeListOf(element)
outFile.write('\t/**\n')
outFile.write('\t * Returns the XML element name of this object, which for {0}, is\n'.format(element))
outFile.write('\t * always @c "{0}".\n'.format(strFunctions.lowerFirst(element)))
outFile.write('\t *\n')
outFile.write('\t * @return the name of this element, i.e. @c "{0}".\n'.format(strFunctions.lowerFirst(element)))
outFile.write('\t */\n')
outFile.write('\tvirtual const std::string& getElementName () const;\n\n\n')
def writeCreateObject(fileOut, mem, ifCount, pkg):
name = strFunctions.cap(mem['name'])
if ifCount == 1:
fileOut.write(' if (name == "{0}" ) \n'.format(strFunctions.lowerFirst(name)))
else:
fileOut.write(' else if (name == "{0}" ) \n'.format(strFunctions.lowerFirst(name)))
fileOut.write(' { \n')
fileOut.write(' m{0} = new {0}({1}ns);\n\n'.format(name, pkg.lower()))
fileOut.write(' object = m{0};\n\n'.format(name))
fileOut.write(' } \n')
def writeGetElementNameHeader(outFile, element, isSedListOf):
if isSedListOf == True:
element = writeListOf(element)
outFile.write(' /**\n')
outFile.write(' * Returns the XML element name of this object, which for {0}, is\n'.format(element))
outFile.write(' * always @c "{0}".\n'.format(strFunctions.lowerFirst(element)))
outFile.write(' *\n')
outFile.write(' * @return the name of this element, i.e. @c "{0}".\n'.format(strFunctions.lowerFirst(element)))
outFile.write(' */\n')
outFile.write(' virtual const std::string& getElementName () const;\n\n\n')
def writeCreateObject(fileOut, mem, ifCount, pkg):
name = strFunctions.cap(mem['name'])
if ifCount == 1:
fileOut.write(' if (name == "{0}" ) \n'.format(
strFunctions.lowerFirst(name)))
else:
fileOut.write(' else if (name == "{0}" ) \n'.format(
strFunctions.lowerFirst(name)))
fileOut.write(' { \n')
fileOut.write(' m{0} = new {0}({1}ns);\n\n'.format(name, pkg.lower()))
fileOut.write(' object = m{0};\n\n'.format(name))
fileOut.write(' } \n')
def writePlugins(fileOut, name, plugins):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('if (pkgName == "{0}")\n'.format(name))
fileOut.write('{\n')
for i in range(0, len(plugins)):
plugin = plugins[i]
if (i == 0):
fileOut.write(' if ')
else:
fileOut.write(' else if ')
typecode = 'SBML_{0}'.format(createSBase(plugin['sbase'].upper()))
if plugin.has_key('typecode') and plugin['typecode'] != None:
typecode = plugin['typecode']
fileOut.write('(sb->getTypeCode() == {0})\n'.format(typecode))
fileOut.write(' {\n')
if typecode != 'SBML_LIST_OF':
fileOut.write(' return SWIGTYPE_p_{0}{1}Plugin;\n'.format(
strFunctions.cap(name), plugin['sbase']))
else:
fileOut.write(' std::string name = sb->getElementName();\n')
fileOut.write(' if(name == "{0}")\n'.format(
strFunctions.lowerFirst(plugin['sbase'])))
fileOut.write(' return SWIGTYPE_p_{0}{1}Plugin;\n'.format(
strFunctions.cap(name), plugin['sbase']))
fileOut.write(' }\n')
fileOut.write('}\n')
fileOut.write('\n')
fileOut.write('#endif // USE_{0} \n\n'.format(capName))
def writePlugins(fileOut, name, plugins):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('if (pkgName == "{0}")\n'.format(name))
fileOut.write('{\n')
for i in range (0, len(plugins)):
plugin = plugins[i]
if (i == 0):
fileOut.write(' if ')
else:
fileOut.write(' else if ')
typecode = 'SBML_{0}'.format(createSBase(plugin['sbase'].upper()))
if plugin.has_key('typecode') and plugin['typecode'] != None:
typecode = plugin['typecode']
fileOut.write('(sb->getTypeCode() == {0})\n'.format(typecode))
fileOut.write(' {\n')
if typecode != 'SBML_LIST_OF':
fileOut.write(' return SWIGTYPE_p_{0}{1}Plugin;\n'.format(strFunctions.cap(name), plugin['sbase']))
else:
fileOut.write(' std::string name = sb->getElementName();\n')
fileOut.write(' if(name == "{0}")\n'.format(strFunctions.lowerFirst(plugin['sbase'])))
fileOut.write(' return SWIGTYPE_p_{0}{1}Plugin;\n'.format(strFunctions.cap(name), plugin['sbase']))
fileOut.write(' }\n')
fileOut.write('}\n')
fileOut.write('\n')
fileOut.write('#endif // USE_{0} \n\n'.format(capName))
def writeMemberFunctions(fileOut, object, plugin):
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(object, plugin))
fileOut.write(' *\n')
fileOut.write(' * @return the {0} from object in this {1} object.\n'.format(object, plugin))
fileOut.write(' */\n')
fileOut.write(' const {0}* get{0} () const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(object, plugin))
fileOut.write(' *\n')
fileOut.write(' * @return the {0} from object in this {1} object.\n'.format(object, plugin))
fileOut.write(' */\n')
fileOut.write(' {0}* get{0} ();\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Predicate returning @c true or @c false depending on ')
fileOut.write('whether the\n \"{0}\" '.format(object))
fileOut.write('element has been set.\n *\n')
fileOut.write(' * @return @c true if the \"{0}\"'.format(object))
fileOut.write(' element has been set,\n')
fileOut.write(' * otherwise @c false is returned.\n')
fileOut.write(' */\n')
fileOut.write(' bool isSet{0}() const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Sets the {0} element in this {1} object.\n'.format(object, plugin))
fileOut.write(' *\n')
fileOut.write(' * @param {0} the {0}* to be set.\n'.format(strFunctions.lowerFirst(object), object))
fileOut.write(' *\n')
fileOut.write(' * @return integer value indicating success/failure of the\n')
fileOut.write(' * function. @if clike The value is drawn from the\n')
fileOut.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
fileOut.write(' * returned by this function are:\n')
fileOut.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
fileOut.write(' */\n')
fileOut.write(' int set{0} (const {0}* {1});\n\n\n'.format(object, strFunctions.lowerFirst(object)))
fileOut.write(' /**\n')
fileOut.write(' * Creates a new {0} object and adds it to the {1} object.\n'.format(object, plugin))
fileOut.write(' *\n')
fileOut.write(' * @return the newly created {0} object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* create{0} ();\n\n\n'.format(object))
def writeGetElementNameCPPCode(outFile, element, isSedListOf=False, dict=None):
outFile.write('/*\n')
outFile.write(' * Returns the XML element name of this object\n')
outFile.write(' */\n')
outFile.write('const std::string&\n{0}::getElementName () const\n'.format(element))
outFile.write('{\n')
if dict != None and dict.has_key('elementName'):
if isSedListOf:
outFile.write('\tstatic const string name = "listOf{0}s";\n'.format(strFunctions.cap(dict['elementName'])))
else:
outFile.write('\tstatic const string name = "{0}";\n'.format(dict['elementName']))
else:
outFile.write('\tstatic const string name = "{0}";\n'.format(strFunctions.lowerFirst(element)))
outFile.write('\treturn name;\n')
outFile.write('}\n\n\n')
def writeGetElementNameCPPCode(outFile, element, isSedListOf=False, dict=None):
outFile.write('/*\n')
outFile.write(' * Returns the XML element name of this object\n')
outFile.write(' */\n')
outFile.write(
'const std::string&\n{0}::getElementName () const\n'.format(element))
outFile.write('{\n')
if dict != None and dict.has_key('elementName'):
if isSedListOf:
outFile.write(
'\tstatic const string name = "listOf{0}s";\n'.format(
strFunctions.cap(dict['elementName'])))
else:
outFile.write('\tstatic const string name = "{0}";\n'.format(
dict['elementName']))
else:
outFile.write('\tstatic const string name = "{0}";\n'.format(
strFunctions.lowerFirst(element)))
outFile.write('\treturn name;\n')
outFile.write('}\n\n\n')
def writeLOFunctions(fileOut, object, nameOfClass, pkg):
ob = strFunctions.objAbbrev(object)
fileOut.write('/*\n')
fileOut.write(' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('const ListOf{0}s* \n'.format(object))
fileOut.write('{0}::getListOf{1}s () const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return &this->m{0}s;\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('ListOf{0}s* \n'.format(object))
fileOut.write('{0}::getListOf{1}s ()\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return &this->m{0}s;\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} object that belongs to the given index.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('const {0}*\n'.format(object))
fileOut.write('{0}::get{1}(unsigned int n) const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return static_cast<const {0}*>(m{0}s.get(n));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} object that belongs to the given index.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('{0}*\n'.format(object))
fileOut.write('{0}::get{1}(unsigned int n)\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return static_cast<{0}*>(m{0}s.get(n));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} object based on its identifier.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('const {0}*\n'.format(object))
fileOut.write('{0}::get{1}(const std::string& sid) const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return static_cast<const {0}*>(m{0}s.get(sid));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} object based on its identifier.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('{0}*\n'.format(object))
fileOut.write('{0}::get{1}(const std::string& sid)\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return static_cast<{0}*>(m{0}s.get(sid));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Adds a copy of the given {0} to the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('int\n')
fileOut.write('{2}::add{0} (const {0}* {1})\n'.format(object, strFunctions.lowerFirst(object), nameOfClass))
fileOut.write('{\n')
fileOut.write(' if ({0} == NULL)\n'.format(strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_OPERATION_FAILED;\n')
fileOut.write(' }\n')
fileOut.write(' else if ({0}->hasRequiredElements() == false)\n'.format(strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_INVALID_OBJECT;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getLevel() != {0}->getLevel())\n'.format(strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_LEVEL_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getVersion() != {0}->getVersion())\n'.format(strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getPackageVersion() != {0}->getPackageVersion())\n'.format(strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_PKG_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else\n')
fileOut.write(' {\n')
fileOut.write(' m{0}s.append({1});\n'.format(object, strFunctions.lowerFirst(object)))
fileOut.write(' }\n\n')
fileOut.write(' return LIBSBML_OPERATION_SUCCESS;\n\n')
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Creates a new {0} object and adds it to the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{1}::create{0} ()\n'.format(object, nameOfClass))
fileOut.write('{\n')
fileOut.write(' {0}* {1} = NULL;\n\n'.format(object, ob))
fileOut.write(' try\n')
fileOut.write(' {\n')
fileOut.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(pkg.upper(), pkg.lower()))
fileOut.write(' {0} = new {1}({2}ns);\n'.format(ob, object, pkg.lower()))
fileOut.write(' delete {0}ns;\n'.format(pkg.lower()))
fileOut.write(' }\n')
fileOut.write(' catch(...)\n')
fileOut.write(' {\n')
fileOut.write(' }\n\n')
fileOut.write(' if ({0} != NULL)\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' m{0}s.appendAndOwn({1});\n'.format(object, ob))
fileOut.write(' }\n\n')
fileOut.write(' return {0};\n'.format(ob))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Removes the nth {0} object from this plugin object\n'.format(object))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{1}::remove{0}(unsigned int n)\n'.format(object, nameOfClass))
fileOut.write('{\n')
fileOut.write(' return static_cast<{0}*>(m{0}s.remove(n));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Removes the {0} object with the given id from this plugin object\n'.format(object))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{1}::remove{0}(const std::string& sid)\n'.format(object, nameOfClass))
fileOut.write('{\n')
fileOut.write(' return static_cast<{0}*>(m{0}s.remove(sid));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the number of {0} objects in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('unsigned int \n')
fileOut.write('{1}::getNum{0}s () const\n'.format(object, nameOfClass))
fileOut.write('{\n')
fileOut.write(' return m{0}s.size();\n'.format(object))
fileOut.write('}\n\n\n')
def writeJava(fileOut, name, plugins, classes):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('/**\n')
fileOut.write(
' * Adds DownCastBase(long cPtr, boolean owner) method for the {0} package extension\n'
.format(name))
fileOut.write(' */\n')
fileOut.write('%typemap(javacode) {0}Extension\n'.format(
strFunctions.cap(name)))
fileOut.write('%{\n')
fileOut.write(
' public SBasePlugin DowncastSBasePlugin(long cPtr, boolean owner)\n')
fileOut.write(' {\n')
fileOut.write(' if (cPtr == 0) return null;\n\n')
fileOut.write(' SBasePlugin sbp = new SBasePlugin(cPtr, false);\n')
fileOut.write(' SBase sb = sbp.getParentSBMLObject();\n\n')
fileOut.write(' switch( sb.getTypeCode() )\n')
fileOut.write(' {\n')
listOfPlugins = []
for plugin in plugins:
typecode = 'SBML_{0}'.format(createSBase(plugin['sbase'].upper()))
if plugin.has_key('typecode') and plugin['typecode'] != None:
typecode = plugin['typecode']
if typecode != 'SBML_LIST_OF':
fileOut.write(' case (int) libsbml.{0}:\n'.format(typecode))
fileOut.write(
' return new {0}{1}Plugin(cPtr, owner);\n\n'.format(
strFunctions.cap(name), plugin['sbase']))
else:
listOfPlugins.append(plugin)
if len(listOfPlugins) > 0:
fileOut.write(' case (int) libsbml.SBML_LIST_OF:\n')
fileOut.write(' {\n')
fileOut.write(' String name = sb.getElementName();\n')
for plugin in listOfPlugins:
fileOut.write(' if (name.equals("{0}"))\n'.format(
strFunctions.lowerFirst(plugin['sbase'])))
fileOut.write(
' return new {0}{1}Plugin(cPtr, owner);\n\n'.format(
strFunctions.cap(name), plugin['sbase']))
fileOut.write(' return new SBasePlugin(cPtr, owner);\n')
fileOut.write(' }\n')
fileOut.write(' default:\n')
fileOut.write(' return new SBasePlugin(cPtr, owner);\n')
fileOut.write(' }\n')
fileOut.write(' }\n\n')
fileOut.write(' public SBase DowncastSBase(long cPtr, boolean owner)\n')
fileOut.write(' {\n')
fileOut.write(' if (cPtr == 0) return null;\n\n')
fileOut.write(' SBase sb = new SBase(cPtr, false);\n')
fileOut.write(' switch( sb.getTypeCode() )\n')
fileOut.write(' {\n')
fileOut.write(' case (int) libsbml.SBML_LIST_OF:\n')
fileOut.write(' String name = sb.getElementName();\n')
for i in range(0, len(classes)):
if (classes[i]['hasListOf'] == True):
loName = strFunctions.listOfName(classes[i]['name'])
if classes[i].has_key('lo_elementName'):
loName = classes[i]['lo_elementName']
if (i == 0):
fileOut.write(
' if (name.equals("{0}"))\n'.format(loName))
else:
fileOut.write(
' else if (name.equals("{0}"))\n'.format(loName))
fileOut.write(' {\n')
fileOut.write(' return new {0}(cPtr, owner);\n'.format(
generalFunctions.getListOfClassName(classes[i],
classes[i]['name'])))
fileOut.write(' }\n')
fileOut.write('\n return new ListOf(cPtr, owner);\n\n')
for i in range(0, len(classes)):
if classes[i]['typecode'] != 'HACK':
fileOut.write(' case (int) libsbml.{0}:\n'.format(
classes[i]['typecode']))
fileOut.write(' return new {0}(cPtr, owner);\n\n'.format(
classes[i]['name']))
fileOut.write(' default:\n')
fileOut.write(' return new SBase(cPtr, owner);\n')
fileOut.write(' }\n')
fileOut.write(' }\n\n')
fileOut.write('%}\n\n')
fileOut.write('COVARIANT_RTYPE_CLONE({0}Extension)\n'.format(
strFunctions.cap(name)))
for i in range(0, len(classes)):
if classes[i]['typecode'] != 'HACK':
fileOut.write('COVARIANT_RTYPE_CLONE({0})\n'.format(
classes[i]['name']))
for i in range(0, len(classes)):
if (classes[i]['hasListOf'] == True):
loName = generalFunctions.getListOfClassName(
classes[i], classes[i]['name'])
fileOut.write('COVARIANT_RTYPE_CLONE({0})\n'.format(
strFunctions.cap(loName)))
fileOut.write('\n')
for i in range(0, len(classes)):
if (classes[i]['hasListOf'] == True):
fileOut.write('COVARIANT_RTYPE_LISTOF_GET_REMOVE({0})\n'.format(
classes[i]['name']))
fileOut.write('\n')
fileOut.write('SBMLCONSTRUCTOR_EXCEPTION({0}PkgNamespaces)\n'.format(
strFunctions.cap(name)))
for i in range(0, len(classes)):
if classes[i]['typecode'] != 'HACK':
fileOut.write('SBMLCONSTRUCTOR_EXCEPTION({0})\n'.format(
classes[i]['name']))
for i in range(0, len(classes)):
if (classes[i]['hasListOf'] == True):
loName = generalFunctions.getListOfClassName(
classes[i], classes[i]['name'])
fileOut.write('SBMLCONSTRUCTOR_EXCEPTION({0})\n'.format(
strFunctions.cap(loName)))
fileOut.write('\n')
for i in range(0, len(classes)):
if (classes[i]['abstract'] == True
or isBaseClassForOthers(classes[i], classes)):
fileOut.write('//\n')
fileOut.write(
'// Convert {0} objects into the most specific object possible.\n'
.format(classes[i]['name']))
fileOut.write('//\n')
fileOut.write('%typemap("javaout") {0}*\n'.format(
classes[i]['name']))
fileOut.write('{\n')
fileOut.write(
' return ({0}) libsbml.DowncastSBase($jnicall, $owner);\n'.
format(classes[i]['name']))
fileOut.write('}\n')
fileOut.write('\n')
fileOut.write('\n')
fileOut.write('#endif /* USE_{0} */\n\n'.format(capName))
def writeConstructors(element, package, output, attrs, hasChildren=False, hasMath=False, elementDict=None, childrenOverwrite=False):
baseClass = 'SBase'
if elementDict != None and elementDict.has_key('baseClass'):
baseClass = elementDict['baseClass']
output.write('/*\n')
output.write(' * Creates a new {0}'.format(element))
output.write(' with the given level, version, and package version.\n */\n')
output.write('{0}::{0} (unsigned int level, unsigned int version, unsigned int pkgVersion)\n'.format(element))
output.write(' : {0}(level, version)\n'.format(baseClass))
writeAttributes(attrs, output, 1)
if childrenOverwrite:
output.write(' , mElementName("{0}")\n'.format(strFunctions.lowerFirst(elementDict['name'])))
output.write('{\n')
output.write(' // set an SBMLNamespaces derived object of this package\n')
output.write(' setSBMLNamespacesAndOwn(new {0}PkgNamespaces(level, version, pkgVersion));\n'.format(package))
if hasChildren == True or hasMath == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Creates a new {0}'.format(element))
output.write(' with the given {0}PkgNamespaces object.\n */\n'.format(package))
output.write('{0}::{0} ({1}PkgNamespaces* {2}ns)\n'.format(element, package, package.lower()))
output.write(' : {1}({0}ns)\n'.format(package.lower(), baseClass))
writeAttributes(attrs, output, 2, package.lower())
if childrenOverwrite:
output.write(' , mElementName("{0}")\n'.format(strFunctions.lowerFirst(elementDict['name'])))
output.write('{\n')
output.write(' // set the element namespace of this object\n')
output.write(' setElementNamespace({0}ns->getURI());\n'.format(package.lower()))
if hasChildren == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write('\n // load package extensions bound with this object (if any) \n')
output.write(' loadPlugins({0}ns);\n'.format(package.lower()))
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Copy constructor for {0}.\n */\n'.format(element))
output.write('{0}::{0} (const {0}& orig)\n'.format(element, package, package.lower()))
output.write(' : {0}(orig)\n'.format(baseClass))
output.write('{\n')
writeCopyAttributes(attrs, output, ' ', 'orig')
if childrenOverwrite:
output.write(' mElementName = orig.mElementName;\n')
if hasChildren == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Assignment for {0}.\n */\n'.format(element))
output.write('{0}&\n{0}::operator=(const {0}& rhs)\n'.format(element))
output.write('{\n')
output.write(' if (&rhs != this)\n')
output.write(' {\n')
output.write(' {0}::operator=(rhs);\n'.format(baseClass))
writeCopyAttributes(attrs, output, ' ', 'rhs')
if childrenOverwrite:
output.write(' mElementName = rhs.mElementName;\n')
if hasChildren == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write(' }\n')
output.write(' return *this;\n')
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Clone for {0}.\n */\n'.format(element))
output.write('{0}*\n{0}::clone () const\n'.format(element))
output.write('{\n')
output.write(' return new {0}(*this);\n'.format(element))
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Destructor for {0}.\n */\n'.format(element))
output.write('{0}::~{0} ()\n'.format(element))
output.write('{\n')
if hasMath == True:
output.write(' delete mMath;\n')
output.write(' mMath = NULL;\n')
for i in range (0, len(attrs)):
current = attrs[i];
if current['type'] == 'element' and current['name'] != 'math':
output.write(' delete m{0};\n'.format(strFunctions.cap(current['name'])))
output.write(' m{0} = NULL;\n'.format(strFunctions.cap(current['name'])))
elif current['type'] == 'array':
output.write(' if (m{0} != NULL)\n'.format(strFunctions.cap(current['name'])))
output.write(' delete[] m{0};\n'.format(strFunctions.cap(current['name'])))
output.write(' m{0} = NULL;\n'.format(strFunctions.cap(current['name'])))
output.write('}\n\n\n')
def writeLOFunctions(fileOut, object, nameOfClass, pkg):
ob = strFunctions.objAbbrev(object)
fileOut.write('/*\n')
fileOut.write(
' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('const ListOf{0}s* \n'.format(object))
fileOut.write('{0}::getListOf{1}s () const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return &this->m{0}s;\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('ListOf{0}s* \n'.format(object))
fileOut.write('{0}::getListOf{1}s ()\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return &this->m{0}s;\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Returns the {0} object that belongs to the given index.\n'.format(
object))
fileOut.write(' */\n')
fileOut.write('const {0}*\n'.format(object))
fileOut.write('{0}::get{1}(unsigned int n) const\n'.format(
nameOfClass, object))
fileOut.write('{\n')
fileOut.write(
' return static_cast<const {0}*>(m{0}s.get(n));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Returns the {0} object that belongs to the given index.\n'.format(
object))
fileOut.write(' */\n')
fileOut.write('{0}*\n'.format(object))
fileOut.write('{0}::get{1}(unsigned int n)\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return static_cast<{0}*>(m{0}s.get(n));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Returns the {0} object based on its identifier.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('const {0}*\n'.format(object))
fileOut.write('{0}::get{1}(const std::string& sid) const\n'.format(
nameOfClass, object))
fileOut.write('{\n')
fileOut.write(
' return static_cast<const {0}*>(m{0}s.get(sid));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Returns the {0} object based on its identifier.\n'.format(object))
fileOut.write(' */\n')
fileOut.write('{0}*\n'.format(object))
fileOut.write('{0}::get{1}(const std::string& sid)\n'.format(
nameOfClass, object))
fileOut.write('{\n')
fileOut.write(
' return static_cast<{0}*>(m{0}s.get(sid));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Adds a copy of the given {0} to the ListOf{0}s in this plugin object.\n'
.format(object))
fileOut.write(' */\n')
fileOut.write('int\n')
fileOut.write('{2}::add{0} (const {0}* {1})\n'.format(
object, strFunctions.lowerFirst(object), nameOfClass))
fileOut.write('{\n')
fileOut.write(' if ({0} == NULL)\n'.format(
strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_OPERATION_FAILED;\n')
fileOut.write(' }\n')
fileOut.write(' else if ({0}->hasRequiredElements() == false)\n'.format(
strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_INVALID_OBJECT;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getLevel() != {0}->getLevel())\n'.format(
strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_LEVEL_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getVersion() != {0}->getVersion())\n'.format(
strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(
' else if (getPackageVersion() != {0}->getPackageVersion())\n'.format(
strFunctions.lowerFirst(object)))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_PKG_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else\n')
fileOut.write(' {\n')
fileOut.write(' m{0}s.append({1});\n'.format(
object, strFunctions.lowerFirst(object)))
fileOut.write(' }\n\n')
fileOut.write(' return LIBSBML_OPERATION_SUCCESS;\n\n')
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Creates a new {0} object and adds it to the ListOf{0}s in this plugin object.\n'
.format(object))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{1}::create{0} ()\n'.format(object, nameOfClass))
fileOut.write('{\n')
fileOut.write(' {0}* {1} = NULL;\n\n'.format(object, ob))
fileOut.write(' try\n')
fileOut.write(' {\n')
fileOut.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(
pkg.upper(), pkg.lower()))
fileOut.write(' {0} = new {1}({2}ns);\n'.format(ob, object,
pkg.lower()))
fileOut.write(' delete {0}ns;\n'.format(pkg.lower()))
fileOut.write(' }\n')
fileOut.write(' catch(...)\n')
fileOut.write(' {\n')
fileOut.write(' }\n\n')
fileOut.write(' if ({0} != NULL)\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' m{0}s.appendAndOwn({1});\n'.format(object, ob))
fileOut.write(' }\n\n')
fileOut.write(' return {0};\n'.format(ob))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Removes the nth {0} object from this plugin object\n'.format(
object))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{1}::remove{0}(unsigned int n)\n'.format(
object, nameOfClass))
fileOut.write('{\n')
fileOut.write(
' return static_cast<{0}*>(m{0}s.remove(n));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Removes the {0} object with the given id from this plugin object\n'
.format(object))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{1}::remove{0}(const std::string& sid)\n'.format(
object, nameOfClass))
fileOut.write('{\n')
fileOut.write(
' return static_cast<{0}*>(m{0}s.remove(sid));\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Returns the number of {0} objects in this plugin object.\n'.format(
object))
fileOut.write(' */\n')
fileOut.write('unsigned int \n')
fileOut.write('{1}::getNum{0}s () const\n'.format(object, nameOfClass))
fileOut.write('{\n')
fileOut.write(' return m{0}s.size();\n'.format(object))
fileOut.write('}\n\n\n')
def writeFunctions(fileOut, object, nameOfClass, pkg):
ob = strFunctions.lowerFirst(object)
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(
object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('const {0}* \n'.format(object))
fileOut.write('{0}::get{1} () const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return m{0};\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(
object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{0}::get{1} ()\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return m{0};\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * @return @c true if the \"{0}\"'.format(object))
fileOut.write(' element has been set,\n')
fileOut.write(' */\n')
fileOut.write('bool \n'.format(object))
fileOut.write('{0}::isSet{1} () const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return (m{0} != NULL);\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Sets the {0} element in this {1} object.\n'.format(
object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('int\n'.format(object))
fileOut.write('{0}::set{1}(const {1}* {2})\n'.format(
nameOfClass, object, ob))
fileOut.write('{\n')
fileOut.write(' if ({0} == NULL)\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_OPERATION_FAILED;\n')
fileOut.write(' }\n')
fileOut.write(
' else if ({0}->hasRequiredElements() == false)\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_INVALID_OBJECT;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getLevel() != {0}->getLevel())\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_LEVEL_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getVersion() != {0}->getVersion())\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(
' else if (getPackageVersion() != {0}->getPackageVersion())\n'.format(
ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_PKG_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else\n')
fileOut.write(' {\n')
fileOut.write(' delete m{0};\n'.format(object))
fileOut.write(' m{0} = static_cast<{0}*>({1}->clone());\n'.format(
object, ob))
fileOut.write(' return LIBSBML_OPERATION_SUCCESS;\n')
fileOut.write(' }\n')
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(
' * Creates a new {0} object and adds it to the {1} object.\n'.format(
object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('{0}*\n'.format(object))
fileOut.write('{0}::create{1}()\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' delete m{0};\n'.format(object))
fileOut.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(
pkg.upper(), pkg.lower()))
fileOut.write(' m{0} = new {0}({1}ns);\n\n'.format(object, pkg.lower()))
fileOut.write(
' m{0}->setSBMLDocument(this->getSBMLDocument());\n\n'.format(object))
fileOut.write(' delete {0}ns;\n\n'.format(pkg.lower()))
fileOut.write(' return m{0};\n'.format(object))
fileOut.write('}\n\n\n')
def writeFunctions(fileOut, object, nameOfClass, pkg):
ob = strFunctions.lowerFirst(object)
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('const {0}* \n'.format(object))
fileOut.write('{0}::get{1} () const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return m{0};\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Returns the {0} from this {1} object.\n'.format(object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('{0}* \n'.format(object))
fileOut.write('{0}::get{1} ()\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return m{0};\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * @return @c true if the \"{0}\"'.format(object))
fileOut.write(' element has been set,\n')
fileOut.write(' */\n')
fileOut.write('bool \n'.format(object))
fileOut.write('{0}::isSet{1} () const\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' return (m{0} != NULL);\n'.format(object))
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Sets the {0} element in this {1} object.\n'.format(object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('int\n'.format(object))
fileOut.write('{0}::set{1}(const {1}* {2})\n'.format(nameOfClass, object, ob))
fileOut.write('{\n')
fileOut.write(' if ({0} == NULL)\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_OPERATION_FAILED;\n')
fileOut.write(' }\n')
fileOut.write(' else if ({0}->hasRequiredElements() == false)\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_INVALID_OBJECT;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getLevel() != {0}->getLevel())\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_LEVEL_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getVersion() != {0}->getVersion())\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else if (getPackageVersion() != {0}->getPackageVersion())\n'.format(ob))
fileOut.write(' {\n')
fileOut.write(' return LIBSBML_PKG_VERSION_MISMATCH;\n')
fileOut.write(' }\n')
fileOut.write(' else\n')
fileOut.write(' {\n')
fileOut.write(' delete m{0};\n'.format(object))
fileOut.write(' m{0} = static_cast<{0}*>({1}->clone());\n'.format(object, ob))
fileOut.write(' return LIBSBML_OPERATION_SUCCESS;\n')
fileOut.write(' }\n')
fileOut.write('}\n\n\n')
fileOut.write('/*\n')
fileOut.write(' * Creates a new {0} object and adds it to the {1} object.\n'.format(object, nameOfClass))
fileOut.write(' */\n')
fileOut.write('{0}*\n'.format(object))
fileOut.write('{0}::create{1}()\n'.format(nameOfClass, object))
fileOut.write('{\n')
fileOut.write(' delete m{0};\n'.format(object))
fileOut.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(pkg.upper(), pkg.lower()))
fileOut.write(' m{0} = new {0}({1}ns);\n\n'.format(object, pkg.lower()))
fileOut.write(' m{0}->setSBMLDocument(this->getSBMLDocument());\n\n'.format(object))
fileOut.write(' delete {0}ns;\n\n'.format(pkg.lower()))
fileOut.write(' return m{0};\n'.format(object))
fileOut.write('}\n\n\n')
def writeFunctions(fileOut, object):
fileOut.write(' /**\n')
fileOut.write(
' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return ListOf{0}s object in this plugin object.\n'.format(
object))
fileOut.write(' */\n')
fileOut.write(
' const ListOf{0}s* getListOf{0}s () const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return ListOf{0}s object in this plugin object.\n'.format(
object))
fileOut.write(' */\n')
fileOut.write(' ListOf{0}s* getListOf{0}s ();\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Returns the {0} object that belongs to the given index. If the \n'
.format(object))
fileOut.write(' * index is invalid, NULL is returned.\n')
fileOut.write(' *\n')
fileOut.write(
' * @param n the index number of the {0} to get\n'.format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return the nth {0} in the ListOf{0}s\n'.format(object))
fileOut.write(' */\n')
fileOut.write(
' const {0}* get{0}(unsigned int n) const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Returns the {0} object that belongs to the given index. If the \n'
.format(object))
fileOut.write(' * index is invalid, NULL is returned.\n')
fileOut.write(' *\n')
fileOut.write(
' * @param n the index number of the {0} to get\n'.format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return the nth {0} in the ListOf{0}s\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* get{0}(unsigned int n);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Returns the {0} object based on its identifier.\n'.format(
object))
fileOut.write(' *\n')
fileOut.write(
' * @param sid a string representing the id of the {0} to get\n'.
format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return {0} in the ListOf{0}s with the given id\n'.format(
object))
fileOut.write(' * or NULL if no such {0} exists.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @see get(unsigned int n)\n')
fileOut.write(' * @see size()\n')
fileOut.write(' */\n')
fileOut.write(
' const {0}* get{0}(const std::string& sid) const;\n\n\n'.format(
object))
fileOut.write(' /**\n')
fileOut.write(
' * Returns the {0} object based on its identifier.\n'.format(
object))
fileOut.write(' *\n')
fileOut.write(
' * @param sid a string representing the id of the {0} to get\n'.
format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return {0} in the ListOf{0}s with the given id\n'.format(
object))
fileOut.write(' * or NULL if no such {0} exists.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @see get(unsigned int n)\n')
fileOut.write(' * @see size()\n')
fileOut.write(' */\n')
fileOut.write(
' {0}* get{0}(const std::string& sid);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Adds a copy of the given {0} to the ListOf{0}s in this plugin object.\n'
.format(object))
fileOut.write(' *\n')
fileOut.write(' * @param {0} the {0} to be added.\n'.format(
strFunctions.lowerFirst(object), object))
fileOut.write(' *\n')
fileOut.write(
' * @return integer value indicating success/failure of the\n')
fileOut.write(' * function. @if clike The value is drawn from the\n')
fileOut.write(
' * enumeration #OperationReturnValues_t. @endif The possible values\n'
)
fileOut.write(' * returned by this function are:\n')
fileOut.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
fileOut.write(' */\n')
fileOut.write(' int add{0} (const {0}* {1});\n\n\n'.format(
object, strFunctions.lowerFirst(object)))
fileOut.write(' /**\n')
fileOut.write(
' * Creates a new {0} object and adds it to the ListOf{0}s in this plugin object.\n'
.format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return the newly created {0} object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* create{0} ();\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Removes the nth {0} object from this plugin object\n'.format(
object))
fileOut.write(' * and returns a pointer to it.\n')
fileOut.write(' *\n')
fileOut.write(
' * The caller owns the returned object and is responsible for\n')
fileOut.write(' * deleting it.\n')
fileOut.write(' *\n')
fileOut.write(
' * @param n the index of the {0} to remove\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the {0} object removed \n'.format(object))
fileOut.write(' * or NULL index was out of range.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* remove{0}(unsigned int n);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Removes the {0} object with the given id from this plugin object\n'
.format(object))
fileOut.write(' * and returns a pointer to it.\n')
fileOut.write(' *\n')
fileOut.write(
' * The caller owns the returned object and is responsible for\n')
fileOut.write(' * deleting it.\n')
fileOut.write(' *\n')
fileOut.write(
' * @param sid a string representing the id of the {0} to remove\n'.
format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the {0} object removed \n'.format(object))
fileOut.write(' * or NULL if no such {0} exists.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(
' {0}* remove{0}(const std::string& sid);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(
' * Returns the number of {0} objects in this plugin object.\n'.
format(object))
fileOut.write(' *\n')
fileOut.write(
' * @return the number of {0} objects in this plugin object.\n'.
format(object))
fileOut.write(' */\n')
fileOut.write(' unsigned int getNum{0}s () const;\n\n\n'.format(object))
def writeJava(fileOut, name, plugins, classes):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('/**\n')
fileOut.write(' * Adds DownCastBase(long cPtr, boolean owner) method for the {0} package extension\n'.format(name))
fileOut.write(' */\n')
fileOut.write('%typemap(javacode) {0}Extension\n'.format(strFunctions.cap(name)))
fileOut.write('%{\n')
fileOut.write(' public SBasePlugin DowncastSBasePlugin(long cPtr, boolean owner)\n')
fileOut.write(' {\n')
fileOut.write(' if (cPtr == 0) return null;\n\n')
fileOut.write(' SBasePlugin sbp = new SBasePlugin(cPtr, false);\n')
fileOut.write(' SBase sb = sbp.getParentSBMLObject();\n\n')
fileOut.write(' switch( sb.getTypeCode() )\n')
fileOut.write(' {\n')
listOfPlugins = []
for plugin in plugins:
typecode = 'SBML_{0}'.format(createSBase(plugin['sbase'].upper()))
if plugin.has_key('typecode') and plugin['typecode'] != None:
typecode = plugin['typecode']
if typecode != 'SBML_LIST_OF':
fileOut.write(' case (int) libsbml.{0}:\n'.format(typecode))
fileOut.write(' return new {0}{1}Plugin(cPtr, owner);\n\n'.format(strFunctions.cap(name), plugin['sbase']))
else:
listOfPlugins.append(plugin)
if len(listOfPlugins) > 0:
fileOut.write(' case (int) libsbml.SBML_LIST_OF:\n')
fileOut.write(' {\n')
fileOut.write(' String name = sb.getElementName();\n')
for plugin in listOfPlugins:
fileOut.write(' if (name.equals("{0}"))\n'.format(strFunctions.lowerFirst(plugin['sbase'])))
fileOut.write(' return new {0}{1}Plugin(cPtr, owner);\n\n'.format(strFunctions.cap(name), plugin['sbase']))
fileOut.write(' return new SBasePlugin(cPtr, owner);\n')
fileOut.write(' }\n')
fileOut.write(' default:\n')
fileOut.write(' return new SBasePlugin(cPtr, owner);\n')
fileOut.write(' }\n')
fileOut.write(' }\n\n')
fileOut.write(' public SBase DowncastSBase(long cPtr, boolean owner)\n')
fileOut.write(' {\n')
fileOut.write(' if (cPtr == 0) return null;\n\n')
fileOut.write(' SBase sb = new SBase(cPtr, false);\n')
fileOut.write(' switch( sb.getTypeCode() )\n')
fileOut.write(' {\n')
fileOut.write(' case (int) libsbml.SBML_LIST_OF:\n')
fileOut.write(' String name = sb.getElementName();\n')
for i in range (0, len(classes)):
if (classes[i]['hasListOf'] == True):
loName = strFunctions.listOfName(classes[i]['name'])
if classes[i].has_key('lo_elementName'):
loName = classes[i]['lo_elementName']
if (i==0):
fileOut.write(' if (name.equals("{0}"))\n'.format(loName))
else :
fileOut.write(' else if (name.equals("{0}"))\n'.format(loName))
fileOut.write(' {\n')
fileOut.write(' return new {0}(cPtr, owner);\n'.format(generalFunctions.getListOfClassName (classes[i], classes[i]['name'])))
fileOut.write(' }\n')
fileOut.write('\n return new ListOf(cPtr, owner);\n\n')
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
fileOut.write(' case (int) libsbml.{0}:\n'.format(classes[i]['typecode']))
fileOut.write(' return new {0}(cPtr, owner);\n\n'.format(classes[i]['name']))
fileOut.write(' default:\n')
fileOut.write(' return new SBase(cPtr, owner);\n')
fileOut.write(' }\n')
fileOut.write(' }\n\n')
fileOut.write('%}\n\n')
fileOut.write('COVARIANT_RTYPE_CLONE({0}Extension)\n'.format(strFunctions.cap(name)))
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
fileOut.write('COVARIANT_RTYPE_CLONE({0})\n'.format(classes[i]['name']))
for i in range (0, len(classes)):
if (classes[i]['hasListOf'] == True):
loName = generalFunctions.getListOfClassName (classes[i], classes[i]['name'])
fileOut.write('COVARIANT_RTYPE_CLONE({0})\n'.format(strFunctions.cap(loName)))
fileOut.write('\n')
for i in range (0, len(classes)):
if (classes[i]['hasListOf'] == True):
fileOut.write('COVARIANT_RTYPE_LISTOF_GET_REMOVE({0})\n'.format(classes[i]['name']))
fileOut.write('\n')
fileOut.write('SBMLCONSTRUCTOR_EXCEPTION({0}PkgNamespaces)\n'.format(strFunctions.cap(name)))
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
fileOut.write('SBMLCONSTRUCTOR_EXCEPTION({0})\n'.format(classes[i]['name']))
for i in range (0, len(classes)):
if (classes[i]['hasListOf'] == True):
loName = generalFunctions.getListOfClassName (classes[i], classes[i]['name'])
fileOut.write('SBMLCONSTRUCTOR_EXCEPTION({0})\n'.format(strFunctions.cap(loName)))
fileOut.write('\n')
for i in range (0, len(classes)):
if (classes[i]['abstract'] == True or isBaseClassForOthers(classes[i], classes)):
fileOut.write('//\n')
fileOut.write('// Convert {0} objects into the most specific object possible.\n'.format(classes[i]['name']))
fileOut.write('//\n')
fileOut.write('%typemap("javaout") {0}*\n'.format(classes[i]['name']))
fileOut.write('{\n')
fileOut.write(' return ({0}) libsbml.DowncastSBase($jnicall, $owner);\n'.format(classes[i]['name']))
fileOut.write('}\n')
fileOut.write('\n')
fileOut.write('\n')
fileOut.write('#endif /* USE_{0} */\n\n'.format(capName))
def writeConstructors(element, package, output, attrs, hasChildren=False, hasMath=False, elementDict=None, childrenOverwrite=False):
baseClass = 'SBase'
if elementDict != None and elementDict.has_key('baseClass'):
baseClass = elementDict['baseClass']
output.write('/*\n')
output.write(' * Creates a new {0}'.format(element))
output.write(' with the given level, version, and package version.\n */\n')
output.write('{0}::{0} (unsigned int level, unsigned int version, unsigned int pkgVersion)\n'.format(element))
output.write(' : {0}(level, version)\n'.format(baseClass))
writeAttributes(attrs, output, 1)
if childrenOverwrite:
output.write(' , mElementName("{0}")\n'.format(strFunctions.lowerFirst(elementDict['name'])))
output.write('{\n')
output.write(' // set an SBMLNamespaces derived object of this package\n')
output.write(' setSBMLNamespacesAndOwn(new {0}PkgNamespaces(level, version, pkgVersion));\n'.format(package))
if hasChildren == True or hasMath == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Creates a new {0}'.format(element))
output.write(' with the given {0}PkgNamespaces object.\n */\n'.format(package))
output.write('{0}::{0} ({1}PkgNamespaces* {2}ns)\n'.format(element, package, package.lower()))
output.write(' : {1}({0}ns)\n'.format(package.lower(), baseClass))
writeAttributes(attrs, output, 2, package.lower())
if childrenOverwrite:
output.write(' , mElementName("{0}")\n'.format(strFunctions.lowerFirst(elementDict['name'])))
output.write('{\n')
output.write(' // set the element namespace of this object\n')
output.write(' setElementNamespace({0}ns->getURI());\n'.format(package.lower()))
if hasChildren == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write('\n // load package extensions bound with this object (if any) \n')
output.write(' loadPlugins({0}ns);\n'.format(package.lower()))
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Copy constructor for {0}.\n */\n'.format(element))
output.write('{0}::{0} (const {0}& orig)\n'.format(element, package, package.lower()))
output.write(' : {0}(orig)\n'.format(baseClass))
output.write('{\n')
output.write(' if (&orig == NULL)\n')
output.write(' {\n')
output.write(' throw SBMLConstructorException("Null argument to copy constructor");\n')
output.write(' }\n')
output.write(' else\n')
output.write(' {\n')
writeCopyAttributes(attrs, output, ' ', 'orig')
if childrenOverwrite:
output.write(' mElementName = orig.mElementName;\n')
if hasChildren == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write(' }\n')
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Assignment for {0}.\n */\n'.format(element))
output.write('{0}&\n{0}::operator=(const {0}& rhs)\n'.format(element))
output.write('{\n')
output.write(' if (&rhs == NULL)\n')
output.write(' {\n')
output.write(' throw SBMLConstructorException("Null argument to assignment");\n')
output.write(' }\n')
output.write(' else if (&rhs != this)\n')
output.write(' {\n')
output.write(' {0}::operator=(rhs);\n'.format(baseClass))
writeCopyAttributes(attrs, output, ' ', 'rhs')
if childrenOverwrite:
output.write(' mElementName = rhs.mElementName;\n')
if hasChildren == True:
output.write('\n // connect to child objects\n')
output.write(' connectToChild();\n')
output.write(' }\n')
output.write(' return *this;\n')
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Clone for {0}.\n */\n'.format(element))
output.write('{0}*\n{0}::clone () const\n'.format(element))
output.write('{\n')
output.write(' return new {0}(*this);\n'.format(element))
output.write('}\n\n\n')
output.write('/*\n')
output.write(' * Destructor for {0}.\n */\n'.format(element))
output.write('{0}::~{0} ()\n'.format(element))
output.write('{\n')
if hasMath == True:
output.write(' delete mMath;\n')
output.write(' mMath = NULL;\n')
for i in range (0, len(attrs)):
current = attrs[i];
if current['type'] == 'element' and current['name'] != 'math':
output.write(' delete m{0};\n'.format(strFunctions.cap(current['name'])))
output.write(' m{0} = NULL;\n'.format(strFunctions.cap(current['name'])))
elif current['type'] == 'array':
output.write(' if (m{0} != NULL)\n'.format(strFunctions.cap(current['name'])))
output.write(' delete[] m{0};\n'.format(strFunctions.cap(current['name'])))
output.write(' m{0} = NULL;\n'.format(strFunctions.cap(current['name'])))
output.write('}\n\n\n')
def writeFunctions(fileOut, object):
fileOut.write(' /**\n')
fileOut.write(' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return ListOf{0}s object in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' const ListOf{0}s* getListOf{0}s () const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return ListOf{0}s object in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' ListOf{0}s* getListOf{0}s ();\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} object that belongs to the given index. If the \n'.format(object))
fileOut.write(' * index is invalid, NULL is returned.\n')
fileOut.write(' *\n')
fileOut.write(' * @param n the index number of the {0} to get\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the nth {0} in the ListOf{0}s\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' const {0}* get{0}(unsigned int n) const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} object that belongs to the given index. If the \n'.format(object))
fileOut.write(' * index is invalid, NULL is returned.\n')
fileOut.write(' *\n')
fileOut.write(' * @param n the index number of the {0} to get\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the nth {0} in the ListOf{0}s\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* get{0}(unsigned int n);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} object based on its identifier.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @param sid a string representing the id of the {0} to get\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return {0} in the ListOf{0}s with the given id\n'.format(object))
fileOut.write(' * or NULL if no such {0} exists.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @see get(unsigned int n)\n')
fileOut.write(' * @see size()\n')
fileOut.write(' */\n')
fileOut.write(' const {0}* get{0}(const std::string& sid) const;\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the {0} object based on its identifier.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @param sid a string representing the id of the {0} to get\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return {0} in the ListOf{0}s with the given id\n'.format(object))
fileOut.write(' * or NULL if no such {0} exists.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @see get(unsigned int n)\n')
fileOut.write(' * @see size()\n')
fileOut.write(' */\n')
fileOut.write(' {0}* get{0}(const std::string& sid);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Adds a copy of the given {0} to the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @param {0} the {0} to be added.\n'.format(strFunctions.lowerFirst(object), object))
fileOut.write(' *\n')
fileOut.write(' * @return integer value indicating success/failure of the\n')
fileOut.write(' * function. @if clike The value is drawn from the\n')
fileOut.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
fileOut.write(' * returned by this function are:\n')
fileOut.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
fileOut.write(' */\n')
fileOut.write(' int add{0} (const {0}* {1});\n\n\n'.format(object, strFunctions.lowerFirst(object)))
fileOut.write(' /**\n')
fileOut.write(' * Creates a new {0} object and adds it to the ListOf{0}s in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the newly created {0} object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* create{0} ();\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Removes the nth {0} object from this plugin object\n'.format(object))
fileOut.write(' * and returns a pointer to it.\n')
fileOut.write(' *\n')
fileOut.write(' * The caller owns the returned object and is responsible for\n')
fileOut.write(' * deleting it.\n')
fileOut.write(' *\n')
fileOut.write(' * @param n the index of the {0} to remove\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the {0} object removed \n'.format(object))
fileOut.write(' * or NULL index was out of range.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* remove{0}(unsigned int n);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Removes the {0} object with the given id from this plugin object\n'.format(object))
fileOut.write(' * and returns a pointer to it.\n')
fileOut.write(' *\n')
fileOut.write(' * The caller owns the returned object and is responsible for\n')
fileOut.write(' * deleting it.\n')
fileOut.write(' *\n')
fileOut.write(' * @param sid a string representing the id of the {0} to remove\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the {0} object removed \n'.format(object))
fileOut.write(' * or NULL if no such {0} exists.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' {0}* remove{0}(const std::string& sid);\n\n\n'.format(object))
fileOut.write(' /**\n')
fileOut.write(' * Returns the number of {0} objects in this plugin object.\n'.format(object))
fileOut.write(' *\n')
fileOut.write(' * @return the number of {0} objects in this plugin object.\n'.format(object))
fileOut.write(' */\n')
fileOut.write(' unsigned int getNum{0}s () const;\n\n\n'.format(object))
def writeProtectedFunctions(output, element, package, elementDict):
listOf = generalFunctions.getListOfClassName(elementDict, element)
generalFunctions.writeInternalStart(output)
output.write('/*\n')
output.write(' * Creates a new {0} in this {1}\n'.format(element, listOf))
output.write(' */\n')
output.write(
'SBase*\n{0}::createObject(XMLInputStream& stream)\n'.format(listOf))
output.write('{\n')
output.write(' const std::string& name = stream.peek().getName();\n')
output.write(' SBase* object = NULL;\n\n')
name = strFunctions.lowerFirst(element)
if elementDict.has_key('elementName'):
name = elementDict['elementName']
output.write(' if (name == "{0}")\n'.format(name))
output.write(' {\n')
output.write(' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(
package.upper(), package.lower()))
output.write(' object = new {0}({1}ns);\n'.format(
element, package.lower()))
output.write(' appendAndOwn(object);\n')
output.write(' delete {0}ns;\n'.format(package.lower()))
output.write(' }\n\n')
# need to create concrete objects
if elementDict.has_key('concrete'):
for elem in generalFunctions.getConcretes(elementDict['root'],
elementDict['concrete']):
output.write(' if (name == "{0}")\n'.format(
strFunctions.lowerFirst(elem['name'])))
output.write(' {\n')
output.write(
' {0}_CREATE_NS({1}ns, getSBMLNamespaces());\n'.format(
package.upper(), package.lower()))
output.write(' object = new {0}({1}ns);\n'.format(
elem['element'], package.lower()))
output.write(' appendAndOwn(object);\n')
output.write(' delete {0}ns;\n'.format(package.lower()))
output.write(' }\n\n')
output.write(' return object;\n')
output.write('}\n\n\n')
generalFunctions.writeInternalEnd(output)
generalFunctions.writeInternalStart(output)
output.write('/*\n')
output.write(
' * Write the namespace for the {0} package.\n'.format(package))
output.write(' */\n')
output.write(
'void\n{0}::writeXMLNS(XMLOutputStream& stream) const\n'.format(
listOf))
output.write('{\n')
output.write(' XMLNamespaces xmlns;\n\n')
output.write(' std::string prefix = getPrefix();\n\n')
output.write(' if (prefix.empty())\n')
output.write(' {\n')
output.write(' XMLNamespaces* thisxmlns = getNamespaces();\n')
output.write(' if (thisxmlns && thisxmlns->hasURI({0}'.format(package))
output.write('Extension::getXmlnsL3V1V1()))\n')
output.write(' {\n')
output.write(
' xmlns.add({0}Extension::getXmlnsL3V1V1(),prefix);\n'.format(
package))
output.write(' }\n')
output.write(' }\n\n')
output.write(' stream << xmlns;\n')
output.write('}\n\n\n')
generalFunctions.writeInternalEnd(output)