def writeRequiredMethods(fileOut, attribs):
fileOut.write(
' //---------------------------------------------------------------\n'
)
fileOut.write(' //\n')
fileOut.write(' // overridden virtual functions for read/write/check\n')
fileOut.write(' //\n')
fileOut.write(
' //---------------------------------------------------------------\n\n'
)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(
' * Subclasses must override this method to create, store, and then\n'
)
fileOut.write(
' * return an SBML object corresponding to the next XMLToken in the\n'
)
fileOut.write(
' * XMLInputStream if they have their specific elements.\n')
fileOut.write(' *\n')
fileOut.write(
' * @return the SBML object corresponding to next XMLToken in the\n')
fileOut.write(
' * XMLInputStream or NULL if the token was not recognized.\n')
fileOut.write(' */\n')
fileOut.write(
' virtual SBase* createObject (XMLInputStream& stream);\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(
' * Subclasses must override this method to write out their contained\n'
)
fileOut.write(
' * SBML objects as XML elements if they have their specific elements.\n'
)
fileOut.write(' */\n')
fileOut.write(
' virtual void writeElements (XMLOutputStream& stream) const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
fileOut.write(' /**\n')
fileOut.write(
' * Checks if this plugin object has all the required elements.\n')
fileOut.write(' *\n')
fileOut.write(' * Subclasses must override this method \n')
fileOut.write(' * if they have their specific elements.\n')
fileOut.write(' *\n')
fileOut.write(
' * @return true if this plugin object has all the required elements\n'
)
fileOut.write(' * otherwise false will be returned.\n')
fileOut.write(' */\n')
fileOut.write(' virtual bool hasRequiredElements () const;\n\n\n')
fileOut.write(
' //---------------------------------------------------------------\n\n\n'
)
generalFunctions.writeAddExpectedHeader(fileOut)
generalFunctions.writeReadAttributesHeader(fileOut)
generalFunctions.writeWriteAttributesHeader(fileOut)
def createValidatorHeader(pkg):
inputFile = os.path.dirname(__file__) + '/templateValidHead.txt'
headerName = pkg + 'Validator.h'
header = open(headerName, 'w')
nameOfElement = pkg + 'Validator'
fileHeaders.addFilename(header, headerName, nameOfElement)
fileHeaders.addLicence(header)
header.write('\n#ifndef {0}Validator__H\n'.format(pkg))
header.write('#define {0}Validator__H\n\n\n'.format(pkg))
header.write('#ifdef __cplusplus\n\n\n')
generalFunctions.writeInternalStart(header)
header.write('#include <list>\n')
header.write('#include <string>\n')
generalFunctions.writeInternalEnd(header)
input = open(inputFile, 'r')
for line in input:
if line[0:13] != 'TEMPLATE_STOP':
line = replaceTags(line, pkg)
header.write(line)
else:
break
header.write('#endif /* __cplusplus*/\n')
header.write('#endif /* {0}Validator__H */\n'.format(pkg))
input.close()
header.close()
def writeProtectedFunctions(output, element, package, name, elementDict):
type = elementDict['name']
elName = elementDict['name']
if elementDict.has_key('elementName'):
elName = strFunctions.cap(elementDict['elementName'])
if elementDict.has_key('element'):
type = elementDict['element']
listOf = generalFunctions.writeListOf(elName)
generalFunctions.writeInternalStart(output)
output.write('/*\n')
output.write(' * Creates a new {0} in this {1}\n'.format(element, listOf))
output.write(' */\n')
output.write(
'SedBase*\n{0}::createObject(XMLInputStream& stream)\n'.format(listOf))
output.write('{\n')
output.write('\tconst std::string& name = stream.peek().getName();\n')
output.write('\tSedBase* object = NULL;\n\n')
if elementDict == None or elementDict.has_key('abstract') == False or (
elementDict.has_key('abstract')
and elementDict['abstract'] == False):
output.write('\tif (name == "{0}")\n'.format(name))
output.write('\t{\n')
output.write(
'\t\tobject = new {0}(getSedNamespaces());\n'.format(element))
output.write('\t\tappendAndOwn(object);\n\t}\n\n')
elif elementDict != None and elementDict.has_key('concrete'):
for elem in elementDict['concrete']:
output.write('\tif (name == "{0}")\n'.format(elem['name']))
output.write('\t{\n')
output.write('\t\tobject = new {0}(getSedNamespaces());\n'.format(
elem['element']))
output.write('\t\tappendAndOwn(object);\n\t}\n\n')
output.write('\treturn 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('\tXMLNamespaces xmlns;\n\n')
output.write('\tstd::string prefix = getPrefix();\n\n')
output.write('\tif (prefix.empty())\n')
output.write('\t{\n')
output.write(
'\t\tif (getNamespaces() != NULL && !getNamespaces()->hasURI(SEDML_XMLNS_L1))\n'
)
output.write('\t\t{\n')
output.write('\t\t\txmlns.add(SEDML_XMLNS_L1,prefix);\n')
output.write('\t\t}\n')
output.write('\t}\n\n')
output.write('\tstream << xmlns;\n')
output.write('}\n\n\n')
generalFunctions.writeInternalEnd(output)
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 writeReadAttMethods(fileOut):
fileOut.write('#ifndef SWIG\n\n')
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Reads the attributes of corresponding package in SBMLDocument element\n')
fileOut.write(' */\n')
fileOut.write(' virtual void readAttributes (const XMLAttributes& attributes, \n')
fileOut.write(' const ExpectedAttributes& expectedAttributes);\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
fileOut.write('#endif // SWIG\n\n')
def writeErrorTableStart(fileOut, element, pkg):
fileOut.write('\n\n');
fileOut.write('#ifndef {0}_H__\n'.format(element))
fileOut.write('#define {0}_H__\n'.format(element))
fileOut.write('\n\n');
fileOut.write('#include <sbml/packages/{0}/validator/{1}SBMLError.h>\n\n'.format(pkg.lower(), pkg))
fileOut.write('LIBSBML_CPP_NAMESPACE_BEGIN\n\n')
generalFunctions.writeInternalStart(fileOut)
fileOut.write('static const packageErrorTableEntry {0}ErrorTable[] = \n'.format(pkg.lower()))
fileOut.write('{\n')
def writeProtectedFunctions(output, element, package, name, elementDict):
type = elementDict['name']
elName = elementDict['name']
if elementDict.has_key('elementName'):
elName = strFunctions.cap(elementDict['elementName'])
if elementDict.has_key('element'):
type = elementDict['element']
listOf = generalFunctions.writeListOf(elName)
generalFunctions.writeInternalStart(output)
output.write('/*\n')
output.write(' * Creates a new {0} in this {1}\n'.format(element, listOf))
output.write(' */\n')
output.write('SedBase*\n{0}::createObject(XMLInputStream& stream)\n'.format(listOf))
output.write('{\n' )
output.write(' const std::string& name = stream.peek().getName();\n')
output.write(' SedBase* object = NULL;\n\n')
if elementDict == None or elementDict.has_key('abstract') == False or (elementDict.has_key('abstract') and elementDict['abstract'] == False):
output.write(' if (name == "{0}")\n'.format(name))
output.write(' {\n')
output.write(' object = new {0}(getSedNamespaces());\n'.format(element))
output.write(' appendAndOwn(object);\n }\n\n')
elif elementDict != None and elementDict.has_key('concrete'):
for elem in elementDict['concrete']:
output.write(' if (name == "{0}")\n'.format(elem['name']))
output.write(' {\n')
output.write(' object = new {0}(getSedNamespaces());\n'.format(elem['element']))
output.write(' appendAndOwn(object);\n }\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(' if (getNamespaces() != NULL && !getNamespaces()->hasURI(SEDML_XMLNS_L1) && !getNamespaces()->hasURI(SEDML_XMLNS_L1V2) && !getNamespaces()->hasURI(SEDML_XMLNS_L1V3))\n')
output.write(' {\n')
output.write(' if (getVersion() == 2) xmlns.add(SEDML_XMLNS_L1V2,prefix);\n')
output.write(' else if (getVersion() == 3) xmlns.add(SEDML_XMLNS_L1V3,prefix);\n')
output.write(' else xmlns.add(SEDML_XMLNS_L1V2,prefix);\n')
output.write(' }\n')
output.write(' }\n\n')
output.write(' stream << xmlns;\n')
output.write('}\n\n\n')
generalFunctions.writeInternalEnd(output)
def writeProtectedFunctions(output, element, package, elementDict = None):
listOf = generalFunctions.getListOfClassName(elementDict, elementDict['name'])
generalFunctions.writeInternalStart(output)
output.write(' /**\n')
output.write(' * Creates a new {0} in this {1}\n'.format(element, listOf))
output.write(' */\n')
output.write(' virtual SBase* createObject(XMLInputStream& stream);\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(' virtual void writeXMLNS(XMLOutputStream& stream) const;\n\n\n')
generalFunctions.writeInternalEnd(output)
def createConsistencyFiles(pkg, type): nameOfElement = pkg + type + 'ConsistencyValidator' fileName = nameOfElement + '.h' output = open(fileName, 'w') generalFunctions.writeInternalStart(output) fileHeaders.addFilename(output, fileName, nameOfElement) fileHeaders.addLicence(output) writeConsistencyHeader(output, nameOfElement, pkg, type) fileName1 = nameOfElement + '.cpp' output1 = open(fileName1, 'w') generalFunctions.writeInternalStart(output1) fileHeaders.addFilename(output1, fileName1, nameOfElement) fileHeaders.addLicence(output1) writeConsistencyFile(output1, nameOfElement, pkg, type)
def writeInitFunction(fileOut, pkg):
generalFunctions.writeInternalStart(fileOut)
fileOut.write('\t/**\n')
fileOut.write('\t * Initializes {0} extension by creating an object of this class with \n'.format(pkg.lower()))
fileOut.write('\t * required SedBasePlugin derived objects and registering the object \n')
fileOut.write('\t * to the SEDMLExtensionRegistry class.\n')
fileOut.write('\t *\n')
fileOut.write('\t * (NOTE) This function is automatically invoked when creating the following\n')
fileOut.write('\t * global object in {0}Extension.cpp\n'.format(pkg))
fileOut.write('\t *\n')
fileOut.write('\t * static SEDMLExtensionRegister<{0}Extension> {1}ExtensionRegistry;\n'.format(pkg, pkg.lower()))
fileOut.write('\t *\n')
fileOut.write('\t */\n')
fileOut.write('\tstatic void init();\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
def writeOtherFunctions(fileOut, nameOfClass, pkg):
# indent = strFunctions.getIndent(nameOfClass)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n * ' )
fileOut.write('Returns boolean based on whether flattening of a comp model has been implemented.\n')
fileOut.write(' *\n')
fileOut.write(' * @returns @c true if flattening for composed models has been implemented,\n')
fileOut.write(' * false otherwise.\n')
fileOut.write(' */\n')
fileOut.write(' virtual bool isCompFlatteningImplemented() const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n * ' )
fileOut.write('Check consistency function.\n')
fileOut.write(' */\n')
fileOut.write(' virtual unsigned int checkConsistency();\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
def createConstraintsFile(pkg, type):
nameOfElement = pkg + type + 'ConsistencyConstraints'
fileName = nameOfElement + '.cpp'
output = open(fileName, 'w')
generalFunctions.writeInternalStart(output)
fileHeaders.addFilename(output, fileName, nameOfElement)
fileHeaders.addLicence(output)
output.write('\n#ifndef AddingConstraintsToValidator\n\n')
output.write('#include <sbml/validator/VConstraint.h>\n\n')
output.write('#include <sbml/packages/{0}/validator/{1}SBMLError.h>\n\n'.format(pkg.lower(), pkg))
output.write('#endif /* AddingConstrainstToValidator */\n\n')
output.write('#include <sbml/validator/ConstraintMacros.h>\n\n')
output.write('/** @cond doxygenIgnored */\n\n')
output.write('using namespace std;\n\n')
output.write('/** @endcond */\n\n')
output.write('/** PUT CONSTRAINTS HERE */\n\n')
generalFunctions.writeInternalEnd(output)
def writeClassEnd(fileOut, members, attribs, plugin):
fileOut.write('protected:\n\n')
generalFunctions.writeInternalStart(fileOut)
for i in range (0, len(members)):
mem = members[i]
if mem['isListOf'] == True:
fileOut.write(' ListOf{0}s m{0}s;\n'.format(mem['name']))
else:
fileOut.write(' {0}* m{0};\n'.format(mem['name']))
for i in range (0, len(attribs)):
mem = attribs[i]
writeHeader.writeAtt(mem, fileOut);
fileOut.write('\n')
generalFunctions.writeInternalEnd(fileOut)
if plugin.has_key('addDecls'):
fileOut.write(open(plugin['addDecls'], 'r').read())
fileOut.write('};\n\n\n')
def writeClassEnd(fileOut, members, attribs, plugin):
fileOut.write('protected:\n\n')
generalFunctions.writeInternalStart(fileOut)
for i in range(0, len(members)):
mem = members[i]
if mem['isListOf'] == True:
fileOut.write(' ListOf{0}s m{0}s;\n'.format(mem['name']))
else:
fileOut.write(' {0}* m{0};\n'.format(mem['name']))
for i in range(0, len(attribs)):
mem = attribs[i]
writeHeader.writeAtt(mem, fileOut)
fileOut.write('\n')
generalFunctions.writeInternalEnd(fileOut)
if plugin.has_key('addDecls'):
fileOut.write(open(plugin['addDecls'], 'r').read())
fileOut.write('};\n\n\n')
def writeProtectedFunctions(output, element, package, elementDict=None):
listOf = generalFunctions.getListOfClassName(elementDict,
elementDict['name'])
generalFunctions.writeInternalStart(output)
output.write(' /**\n')
output.write(' * Creates a new {0} in this {1}\n'.format(
element, listOf))
output.write(' */\n')
output.write(
' virtual SBase* createObject(XMLInputStream& stream);\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(
' virtual void writeXMLNS(XMLOutputStream& stream) const;\n\n\n')
generalFunctions.writeInternalEnd(output)
def writeErrorFunction(fileOut, pkg):
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Return the entry in the error table at this index. \n')
fileOut.write(' *\n')
fileOut.write(' * @param index an unsigned intgere representing the index of the error in the {0}SBMLErrorTable\n'.format(pkg))
fileOut.write(' *\n')
fileOut.write(' * @return packageErrorTableEntry object in the {0}SBMLErrorTable corresponding to the index given.\n'.format(pkg))
fileOut.write(' */\n')
fileOut.write(' virtual packageErrorTableEntry getErrorTable(unsigned int index) const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Return the index in the error table with the given errorId. \n')
fileOut.write(' *\n')
fileOut.write(' * @param errorId an unsigned intgere representing the errorId of the error in the {0}SBMLErrorTable\n'.format(pkg))
fileOut.write(' *\n')
fileOut.write(' * @return unsigned integer representing the index in the {0}SBMLErrorTable corresponding to the errorId given.\n'.format(pkg))
fileOut.write(' */\n')
fileOut.write(' virtual unsigned int getErrorTableIndex(unsigned int errorId) const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Return the offset for the errorId range for the {0} L3 package. \n'.format(pkg.lower()))
fileOut.write(' *\n')
fileOut.write(' * @return unsigned intege representing the offset for errors {0}SBMLErrorTable.\n'.format(pkg))
fileOut.write(' */\n')
fileOut.write(' virtual unsigned int getErrorIdOffset() const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
def writeRequiredMethods(fileOut, attribs):
fileOut.write(' //---------------------------------------------------------------\n')
fileOut.write(' //\n')
fileOut.write(' // overridden virtual functions for read/write/check\n')
fileOut.write(' //\n')
fileOut.write(' //---------------------------------------------------------------\n\n')
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Subclasses must override this method to create, store, and then\n')
fileOut.write(' * return an SBML object corresponding to the next XMLToken in the\n')
fileOut.write(' * XMLInputStream if they have their specific elements.\n')
fileOut.write(' *\n')
fileOut.write(' * @return the SBML object corresponding to next XMLToken in the\n')
fileOut.write(' * XMLInputStream or NULL if the token was not recognized.\n')
fileOut.write(' */\n')
fileOut.write(' virtual SBase* createObject (XMLInputStream& stream);\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Subclasses must override this method to write out their contained\n')
fileOut.write(' * SBML objects as XML elements if they have their specific elements.\n')
fileOut.write(' */\n')
fileOut.write(' virtual void writeElements (XMLOutputStream& stream) const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Checks if this plugin object has all the required elements.\n')
fileOut.write(' *\n')
fileOut.write(' * Subclasses must override this method \n')
fileOut.write(' * if they have their specific elements.\n')
fileOut.write(' *\n')
fileOut.write(' * @return true if this plugin object has all the required elements\n')
fileOut.write(' * otherwise false will be returned.\n')
fileOut.write(' */\n')
fileOut.write(' virtual bool hasRequiredElements () const;\n\n\n')
fileOut.write(' //---------------------------------------------------------------\n\n\n')
generalFunctions.writeAddExpectedHeader(fileOut)
generalFunctions.writeReadAttributesHeader(fileOut)
generalFunctions.writeWriteAttributesHeader(fileOut)
def writeErrorTable(fileOut, element, pkg, offset, classes):
fileOut.write('\n\n');
fileOut.write('#ifndef {0}_H__\n'.format(element))
fileOut.write('#define {0}_H__\n'.format(element))
fileOut.write('\n\n');
fileOut.write('#include <sbml/packages/{0}/validator/{1}SBMLError.h>\n\n'.format(pkg.lower(), pkg))
fileOut.write('LIBSBML_CPP_NAMESPACE_BEGIN\n\n')
generalFunctions.writeInternalStart(fileOut)
fileOut.write('static const packageErrorTableEntry {0}ErrorTable[] = \n'.format(pkg.lower()))
fileOut.write('{\n')
fileOut.write(' //{0}\n'.format(offset+10100));
fileOut.write(' {')
fileOut.write(' {0}UnknownError,\n'.format(pkg));
fileOut.write(' "Unknown error from {0}",\n'.format(pkg.lower()))
fileOut.write(' LIBSBML_CAT_GENERAL_CONSISTENCY,\n')
fileOut.write(' LIBSBML_SEV_ERROR,\n')
fileOut.write(' "Unknown error from {0}",\n'.format(pkg.lower()))
fileOut.write(' { " "\n')
fileOut.write(' }\n')
fileOut.write(' }\n\n')
fileOut.write('};\n\n')
fileOut.write('\nLIBSBML_CPP_NAMESPACE_END\n\n')
generalFunctions.writeInternalEnd(fileOut)
fileOut.write('#endif /* {0}_h__ */\n\n'.format(element))
def writeInitFunction(fileOut, pkg):
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(
' * Initializes {0} extension by creating an object of this class with \n'
.format(pkg.lower()))
fileOut.write(
' * required SBasePlugin derived objects and registering the object \n'
)
fileOut.write(' * to the SBMLExtensionRegistry class.\n')
fileOut.write(' *\n')
fileOut.write(
' * (NOTE) This function is automatically invoked when creating the following\n'
)
fileOut.write(
' * global object in {0}Extension.cpp\n'.format(pkg))
fileOut.write(' *\n')
fileOut.write(
' * static SBMLExtensionRegister<{0}Extension> {1}ExtensionRegistry;\n'
.format(pkg, pkg.lower()))
fileOut.write(' *\n')
fileOut.write(' */\n')
fileOut.write(' static void init();\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
def writeErrorFunction(fileOut, pkg, nameOfClass, offset):
generalFunctions.writeInternalStart(fileOut)
fileOut.write('/*\n')
fileOut.write(' * Return error table entry. \n')
fileOut.write(' */\n')
fileOut.write('packageErrorTableEntry\n')
fileOut.write(
'{0}::getErrorTable(unsigned int index) const\n'.format(nameOfClass))
fileOut.write('{\n')
fileOut.write(' return {0}ErrorTable[index];\n'.format(pkg.lower()))
fileOut.write('}\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write('/*\n')
fileOut.write(' * Return error table index for this id. \n')
fileOut.write(' */\n')
fileOut.write('unsigned int\n')
fileOut.write(
'{0}::getErrorTableIndex(unsigned int errorId) const\n'.format(
nameOfClass))
fileOut.write('{\n')
fileOut.write(
' unsigned int tableSize = sizeof({0}ErrorTable)/sizeof({0}ErrorTable[0]);\n'
.format(pkg.lower()))
fileOut.write(' unsigned int index = 0;\n\n')
fileOut.write(' for(unsigned int i = 0; i < tableSize; i++)\n')
fileOut.write(' {\n')
fileOut.write(' if (errorId == {0}ErrorTable[i].code)\n'.format(
pkg.lower()))
fileOut.write(' {\n')
fileOut.write(' index = i;\n')
fileOut.write(' break;\n')
fileOut.write(' }\n\n')
fileOut.write(' }\n\n')
fileOut.write(' return index;\n')
fileOut.write('}\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write('/*\n')
fileOut.write(' * Return error offset. \n')
fileOut.write(' */\n')
fileOut.write('unsigned int\n')
fileOut.write('{0}::getErrorIdOffset() const\n'.format(nameOfClass))
fileOut.write('{\n')
fileOut.write(' return {0};\n'.format(offset))
fileOut.write('}\n\n')
generalFunctions.writeInternalEnd(fileOut)
def writeErrorFunction(fileOut, pkg):
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(' * Return the entry in the error table at this index. \n')
fileOut.write(' *\n')
fileOut.write(
' * @param index an unsigned intgere representing the index of the error in the {0}SBMLErrorTable\n'
.format(pkg))
fileOut.write(' *\n')
fileOut.write(
' * @return packageErrorTableEntry object in the {0}SBMLErrorTable corresponding to the index given.\n'
.format(pkg))
fileOut.write(' */\n')
fileOut.write(
' virtual packageErrorTableEntry getErrorTable(unsigned int index) const;\n\n\n'
)
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(
' * Return the index in the error table with the given errorId. \n')
fileOut.write(' *\n')
fileOut.write(
' * @param errorId an unsigned intgere representing the errorId of the error in the {0}SBMLErrorTable\n'
.format(pkg))
fileOut.write(' *\n')
fileOut.write(
' * @return unsigned integer representing the index in the {0}SBMLErrorTable corresponding to the errorId given.\n'
.format(pkg))
fileOut.write(' */\n')
fileOut.write(
' virtual unsigned int getErrorTableIndex(unsigned int errorId) const;\n\n\n'
)
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' /**\n')
fileOut.write(
' * Return the offset for the errorId range for the {0} L3 package. \n'
.format(pkg.lower()))
fileOut.write(' *\n')
fileOut.write(
' * @return unsigned intege representing the offset for errors {0}SBMLErrorTable.\n'
.format(pkg))
fileOut.write(' */\n')
fileOut.write(' virtual unsigned int getErrorIdOffset() const;\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
def writeClassDefn(fileOut, nameOfClass, pkg, members, attribs, plugin):
fileOut.write('class LIBSBML_EXTERN {0} : public SBasePlugin\n'.format(nameOfClass))
fileOut.write('{\npublic:\n\n')
writeConstructors(fileOut, nameOfClass, pkg)
writeRequiredMethods(fileOut, attribs)
writeGetFunctions(fileOut, pkg, members, nameOfClass, attribs)
generalFunctions.writeSetDocHeader(fileOut)
# TO DO - these properly
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' virtual void connectToParent (SBase* sbase);\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' virtual void enablePackageInternal(const std::string& pkgURI,\n')
fileOut.write(' const std::string& pkgPrefix, bool flag);\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' virtual bool accept (SBMLVisitor& v) const;\n\n')
generalFunctions.writeInternalEnd(fileOut)
writeClassEnd(fileOut, members, attribs, plugin)
def writeErrorFunction(fileOut, pkg, nameOfClass, offset):
generalFunctions.writeInternalStart(fileOut)
fileOut.write('/*\n')
fileOut.write(' * Return error table entry. \n')
fileOut.write(' */\n')
fileOut.write('packageErrorTableEntry\n')
fileOut.write('{0}::getErrorTable(unsigned int index) const\n'.format(nameOfClass))
fileOut.write('{\n')
fileOut.write(' return {0}ErrorTable[index];\n'.format(pkg.lower()))
fileOut.write('}\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write('/*\n')
fileOut.write(' * Return error table index for this id. \n')
fileOut.write(' */\n')
fileOut.write('unsigned int\n')
fileOut.write('{0}::getErrorTableIndex(unsigned int errorId) const\n'.format(nameOfClass))
fileOut.write('{\n')
fileOut.write(' unsigned int tableSize = sizeof({0}ErrorTable)/sizeof({0}ErrorTable[0]);\n'.format(pkg.lower()))
fileOut.write(' unsigned int index = 0;\n\n')
fileOut.write(' for(unsigned int i = 0; i < tableSize; i++)\n')
fileOut.write(' {\n')
fileOut.write(' if (errorId == {0}ErrorTable[i].code)\n'.format(pkg.lower()))
fileOut.write(' {\n')
fileOut.write(' index = i;\n')
fileOut.write(' break;\n')
fileOut.write(' }\n\n')
fileOut.write(' }\n\n')
fileOut.write(' return index;\n')
fileOut.write('}\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write('/*\n')
fileOut.write(' * Return error offset. \n')
fileOut.write(' */\n')
fileOut.write('unsigned int\n')
fileOut.write('{0}::getErrorIdOffset() const\n'.format(nameOfClass))
fileOut.write('{\n')
fileOut.write(' return {0};\n'.format(offset))
fileOut.write('}\n\n')
generalFunctions.writeInternalEnd(fileOut)
def writeClassDefn(fileOut, nameOfClass, pkg, members, attribs, plugin):
fileOut.write(
'class LIBSBML_EXTERN {0} : public SBasePlugin\n'.format(nameOfClass))
fileOut.write('{\npublic:\n\n')
writeConstructors(fileOut, nameOfClass, pkg)
writeRequiredMethods(fileOut, attribs)
writeGetFunctions(fileOut, pkg, members, nameOfClass, attribs)
generalFunctions.writeSetDocHeader(fileOut)
# TO DO - these properly
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' virtual void connectToParent (SBase* sbase);\n\n\n')
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(
' virtual void enablePackageInternal(const std::string& pkgURI,\n')
fileOut.write(
' const std::string& pkgPrefix, bool flag);\n\n\n'
)
generalFunctions.writeInternalEnd(fileOut)
generalFunctions.writeInternalStart(fileOut)
fileOut.write(' virtual bool accept (SBMLVisitor& v) const;\n\n')
generalFunctions.writeInternalEnd(fileOut)
writeClassEnd(fileOut, members, attribs, plugin)
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 writeClassEnd(fileOut):
fileOut.write('protected:\n\n')
generalFunctions.writeInternalStart(fileOut)
generalFunctions.writeInternalEnd(fileOut)
fileOut.write('};\n\n\n')
def createValidatorFile(pkg, classes):
inputFile = os.path.dirname(__file__) + '/templateValidCPP.txt'
fileName = pkg + 'Validator.cpp'
output = open(fileName, 'w')
nameOfElement = pkg + 'Validator'
fileHeaders.addFilename(output, fileName, nameOfElement)
fileHeaders.addLicence(output)
output.write('#include <sbml/validator/VConstraint.h>\n\n')
output.write('#include <sbml/packages/{0}/common/{1}ExtensionTypes.h>\n'.format(pkg.lower(), pkg))
output.write('#include <sbml/packages/{0}/validator/{1}Validator.h>\n\n'.format(pkg.lower(), pkg))
generalFunctions.writeInternalStart(output)
output.write('using namespace std;\n\n')
generalFunctions.writeInternalEnd(output)
output.write('LIBSBML_CPP_NAMESPACE_BEGIN\n\n')
input = open(inputFile, 'r')
for line in input:
if line[0:13] != 'TEMPLATE_STOP':
line = replaceTags(line, pkg)
output.write(line)
else:
break
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
output.write(' ConstraintSet<{0}> m{0};\n'.format(classes[i]['name']))
for line in input:
if line[0:13] != 'TEMPLATE_STOP':
line = replaceTags(line, pkg)
output.write(line)
else:
break
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
output.write(' if (dynamic_cast< TConstraint<{0}>* >(c) != NULL)\n'.format(classes[i]['name']))
output.write(' {\n')
output.write(' m{0}.add( static_cast< TConstraint<{0}>* >(c) );\n'.format(classes[i]['name']))
output.write(' return;\n }\n\n')
for line in input:
if line[0:13] != 'TEMPLATE_STOP':
line = replaceTags(line, pkg)
output.write(line)
else:
break
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
output.write(' bool visit (const {0} &x)\n'.format(classes[i]['name']))
output.write(' {\n')
output.write(' v.m{0}Constraints->m{1}.applyTo(m, x);\n'.format(pkg, classes[i]['name']))
output.write(' return !v.m{0}Constraints->m{1}.empty();\n'.format(pkg, classes[i]['name']))
output.write(' }\n\n')
output.write(' virtual bool visit(const SBase &x)\n')
output.write(' {\n')
output.write(' if (x.getPackageName() != "{0}")\n'.format(pkg.lower()))
output.write(' {\n return SBMLVisitor::visit(x);\n }\n\n')
output.write(' int code = x.getTypeCode();\n\n')
output.write(' const ListOf* list = dynamic_cast<const ListOf*>(&x);\n\n')
output.write(' if (list != NULL)\n')
output.write(' {\n')
output.write(' return SBMLVisitor::visit(x);\n')
output.write(' }\n')
output.write(' else\n')
output.write(' {\n')
order = 0
for i in range (0, len(classes)):
if classes[i]['typecode'] != 'HACK':
if order == 0:
output.write(' if (code == {0})\n'.format(classes[i]['typecode']))
order = order + 1
else:
output.write(' else if (code == {0})\n'.format(classes[i]['typecode']))
output.write(' {\n')
output.write(' return visit((const {0}&)x);\n'.format(classes[i]['name']))
output.write(' }\n')
for line in input:
if line[0:13] != 'TEMPLATE_STOP':
line = replaceTags(line, pkg)
output.write(line)
else:
break
input.close()
output.close()
