def writeSwigHeader(fileOut, name, plugins, classes):
capName = strFunctions.cap(name)
fileOut.write('#ifdef USE_{0}\n\n'.format(name.upper()))
fileOut.write(
'#include <sbml/packages/{0}/extension/{1}Extension.h>\n'.format(
name, capName))
alreadyIncluded = []
for plugin in plugins:
package = name
if plugin.has_key('package') and plugin['package'] != None:
package = plugin['package']
capPackageName = strFunctions.cap(package)
if package != name and alreadyIncluded.count(package) == 0:
alreadyIncluded.append(package)
fileOut.write(
'#include <sbml/packages/{0}/extension/{1}Extension.h>\n'.
format(package, capPackageName))
fileOut.write(
'#include <sbml/packages/{0}/common/{1}ExtensionTypes.h>\n'.
format(package, capPackageName))
fileOut.write(
'#include <sbml/packages/{0}/extension/{1}{2}Plugin.h>\n'.format(
name, capName, plugin['sbase']))
fileOut.write(
'#include <sbml/packages/{0}/common/{1}ExtensionTypes.h>\n'.format(
name, capName))
for clazz in classes:
if clazz['typecode'] != 'HACK':
fileOut.write('#include <sbml/packages/{0}/sbml/{1}.h>\n'.format(
name, clazz['name']))
fileOut.write('\n')
fileOut.write('#endif // USE_{0} \n\n'.format(name.upper()))
def writeGetFunction(attrib, output, element):
att = generalFunctions.parseAttributeForC(attrib)
attName = att[0]
capAttName = att[1]
attType = att[2]
if att[3] == 'const char *':
attTypeCode = 'char *'
else:
attTypeCode = att[3]
num = att[4]
if attrib['type'] != 'element' and attrib['type'] != 'lo_element':
output.write('LIBSEDML_EXTERN\n')
output.write('{0}\n'.format(attTypeCode))
output.write('{0}_get{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
elif attrib['type'] == 'element':
if attrib['name'] == 'Math' or attrib['name'] == 'math':
output.write('LIBSEDML_EXTERN\n')
output.write('ASTNode_t*\n')
output.write('{0}_getMath'.format(element))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
else:
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t*\n'.format(strFunctions.cap(attrib['element'])))
output.write('{0}_get{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t*\n'.format(strFunctions.cap(attrib['element'])))
output.write('{0}_create{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
def writeCreateObject(outFile, element, sbmltypecode, attribs, isSedListOf, hasChildren=False, hasMath=False,baseClass='SedBase'):
if (isSedListOf == True or hasChildren == False) and baseClass == 'SedBase':
return;
outFile.write('/**\n')
outFile.write(' * return the SEDML object corresponding to next XMLToken.\n')
outFile.write(' */\n')
outFile.write('SedBase*\n{0}::createObject(XMLInputStream& stream)\n'.format(element))
outFile.write('{\n')
if baseClass == 'SedBase':
outFile.write(' SedBase* object = NULL;\n\n')
else:
outFile.write(' SedBase* object = {0}::createObject(stream);\n\n'.format(baseClass))
if hasChildren or hasMath:
outFile.write(' const string& name = stream.peek().getName();\n\n')
for i in range (0, len(attribs)):
current = attribs[i]
if current.has_key('lo_elementName'):
outFile.write(' if (name == "{0}")\n'.format(current['lo_elementName']))
outFile.write(' {\n')
outFile.write(' object = &m{0};\n'.format(strFunctions.capp(current['name'])))
outFile.write(' }\n\n')
elif current['type'] == 'lo_element':
outFile.write(' if (name == "listOf{0}")\n'.format(strFunctions.capp(current['name'])))
outFile.write(' {\n')
outFile.write(' object = &m{0};\n'.format(strFunctions.capp(current['name'])))
outFile.write(' }\n\n')
elif current['type'] == 'element' and (current['name'] !='Math' and current['name'] != 'math'):
outFile.write(' if (name == "{0}")\n'.format(current['name']))
outFile.write(' {\n')
outFile.write(' m{0}= new {1}();\n'.format(strFunctions.cap(current['name']), current['element']))
outFile.write(' object = m{0};\n'.format(strFunctions.cap(current['name'])))
outFile.write(' }\n\n')
outFile.write(' connectToChild();\n\n')
outFile.write(' return object;\n')
outFile.write('}\n\n\n')
def writeWriteElementsCPPCode(outFile, element, attributes, hasChildren=False, hasMath=False, baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('/*\n')
outFile.write(' * write contained elements\n')
outFile.write(' */\n')
outFile.write('void\n{0}::writeElements (XMLOutputStream& stream) const\n'.format(element))
outFile.write('{\n')
outFile.write('\t{0}::writeElements(stream);\n'.format(baseClass))
if hasChildren == True:
for i in range(0, len(attributes)):
if attributes[i]['type'] == 'element' and (attributes[i]['name'] != 'Math' and attributes[i]['name'] != 'math'):
outFile.write('\tif (isSet{0}() == true)\n'.format(strFunctions.cap(attributes[i]['name'])))
outFile.write('\t{\n\t\t')
outFile.write('m{0}->write(stream);'.format(strFunctions.cap(attributes[i]['name'])))
outFile.write('\n\t}\n')
if attributes[i]['type'] == 'lo_element':
outFile.write('\tif (getNum{0}s() > 0)\n'.format(strFunctions.cap(attributes[i]['name'])))
outFile.write('\t{\n\t\t')
outFile.write('m{0}.write(stream);'.format(strFunctions.cap(attributes[i]['name'])))
outFile.write('\n\t}\n')
if hasMath == True:
for i in range(0, len(attributes)):
if attributes[i]['type'] == 'element' and attributes[i]['name'] == 'Math' or attributes[i]['name'] == 'math':
outFile.write('\tif (isSet{0}() == true)\n'.format('Math'))
outFile.write('\t{\n\t\twriteMathML(getMath(), stream, NULL);\n\t}\n')
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def writeCopyAttributes(attrs, output, tabs, name):
for i in range(0, len(attrs)):
attName = strFunctions.cap(attrs[i]['name'])
atttype = attrs[i]['type']
if atttype == 'array':
output.write('{0}m{1} = NULL;\n'.format(tabs, attName, name))
output.write('{0}set{1}({2}.m{1}, {2}.m{1}Length);\n'.format(tabs, attName, name))
elif atttype != 'lo_element' and atttype != 'inline_lo_element':
if atttype != 'element':
output.write('{0}m{1} = {2}.m{1};\n'.format(tabs, attName, name))
else:
output.write('{0}if ({2}.m{1} != NULL)\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
output.write('{0}'.format(tabs))
output.write('{\n')
if attrs[i]['name'] != 'math':
output.write('{0} m{1} = {2}.m{1}->clone();\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
else:
output.write('{0} m{1} = {2}.m{1}->deepCopy();\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
output.write('{0}'.format(tabs))
output.write('}\n')
output.write('{0}else\n'.format(tabs))
output.write('{0}'.format(tabs))
output.write('{\n')
output.write('{0} m{1} = NULL;\n'.format(tabs, strFunctions.cap(attrs[i]['name'])))
output.write('{0}'.format(tabs))
output.write('}\n')
else:
if attName.endswith('x'):
output.write('{0}m{1}es = {2}.m{1}es;\n'.format(tabs, attName, name))
elif attName.endswith('s'):
output.write('{0}m{1} = {2}.m{1};\n'.format(tabs, attName, name))
else:
output.write('{0}m{1}s = {2}.m{1}s;\n'.format(tabs, attName, name))
if atttype == 'double' or atttype == 'int' or atttype == 'uint' or atttype == 'bool':
output.write('{0}mIsSet{1} = {2}.mIsSet{1};\n'.format(tabs, attName, name))
def writeLocal(fileOut, name, classes):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n\n'.format(capName))
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 = strFunctions.listOfName(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(out) {0}*\n'.format(classes[i]['name']))
fileOut.write('{\n')
fileOut.write(' $result = SWIG_NewPointerObj($1, GetDowncastSwigTypeForPackage($1, "{0}"), $owner | %newpointer_flags);\n'.format(name))
fileOut.write('}\n')
fileOut.write('\n')
fileOut.write('\n')
fileOut.write('#endif // USE_{0} \n\n'.format(capName))
def writeCreateObject(outFile, element, sbmltypecode, attribs, isSedListOf, hasChildren=False, hasMath=False,baseClass='SedBase'):
if (isSedListOf == True or hasChildren == False) and baseClass == 'SedBase':
return;
outFile.write('/**\n')
outFile.write(' * return the SEDML object corresponding to next XMLToken.\n')
outFile.write(' */\n')
outFile.write('SedBase*\n{0}::createObject(XMLInputStream& stream)\n'.format(element))
outFile.write('{\n')
if baseClass == 'SedBase':
outFile.write('\tSedBase* object = NULL;\n\n')
else:
outFile.write('\tSedBase* object = {0}::createObject(stream);\n\n'.format(baseClass))
if hasChildren or hasMath:
outFile.write('\tconst string& name = stream.peek().getName();\n\n')
for i in range (0, len(attribs)):
current = attribs[i]
if current.has_key('lo_elementName'):
outFile.write('\tif (name == "{0}")\n'.format(current['lo_elementName']))
outFile.write('\t{\n')
outFile.write('\t\tobject = &m{0};\n'.format(strFunctions.capp(current['name'])))
outFile.write('\t}\n\n')
elif current['type'] == 'lo_element':
outFile.write('\tif (name == "listOf{0}")\n'.format(strFunctions.capp(current['name'])))
outFile.write('\t{\n')
outFile.write('\t\tobject = &m{0};\n'.format(strFunctions.capp(current['name'])))
outFile.write('\t}\n\n')
elif current['type'] == 'element' and (current['name'] !='Math' and current['name'] != 'math'):
outFile.write('\tif (name == "{0}")\n'.format(current['name']))
outFile.write('\t{\n')
outFile.write('\t\tm{0}= new {1}();\n'.format(strFunctions.cap(current['name']), current['element']))
outFile.write('\t\tobject = m{0};\n'.format(strFunctions.cap(current['name'])))
outFile.write('\t}\n\n')
outFile.write('\tconnectToChild();\n\n')
outFile.write('\treturn object;\n')
outFile.write('}\n\n\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 parseAttribute(attrib):
attName = attrib['name']
capAttName = strFunctions.cap(attName)
reqd = attrib['reqd']
if attrib['type'] == 'SId':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'SIdRef':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'UnitSIdRef':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'UnitSId':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'string':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'double':
attType = 'double'
attTypeCode = 'double'
num = True
elif attrib['type'] == 'int':
attType = 'integer'
attTypeCode = 'int'
num = True
elif attrib['type'] == 'uint':
attType = 'unsigned integer'
attTypeCode = 'unsigned int'
num = True
elif attrib['type'] == 'bool':
attType = 'boolean'
attTypeCode = 'bool'
num = False
elif attrib['type'] == 'element':
attType = 'element'
if attrib['name'] == 'math' or attrib['name'] == 'Math':
attTypeCode = 'ASTNode*'
else:
#attTypeCode = 'element-not-done'
if attrib.has_key('element'):
attTypeCode = '{0}*'.format(attrib['element'])
else:
attTypeCode = '{0}*'.format(strFunctions.cap(attrib['name']))
num = False
elif attrib['type'] == 'lo_element':
attType = 'lo_element'
attTypeCode = attrib['element']
num = False
else:
attType = 'FIX ME'
attTypeCode = 'FIX ME'
num = False
return [attName, capAttName, attType, attTypeCode, num, reqd]
def parseAttribute(attrib):
attName = attrib['name']
capAttName = strFunctions.cap(attName)
reqd = attrib['reqd']
if attrib['type'] == 'SId':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'SIdRef':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'UnitSIdRef':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'UnitSId':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'string':
attType = 'string'
attTypeCode = 'std::string&'
num = False
elif attrib['type'] == 'double':
attType = 'double'
attTypeCode = 'double'
num = True
elif attrib['type'] == 'int':
attType = 'integer'
attTypeCode = 'int'
num = True
elif attrib['type'] == 'uint':
attType = 'unsigned integer'
attTypeCode = 'unsigned int'
num = True
elif attrib['type'] == 'bool':
attType = 'boolean'
attTypeCode = 'bool'
num = False
elif attrib['type'] == 'element':
attType = 'element'
if attrib['name'] == 'math' or attrib['name'] == 'Math':
attTypeCode = 'ASTNode*'
else:
#attTypeCode = 'element-not-done'
if attrib.has_key('element'):
attTypeCode = '{0}*'.format(attrib['element'])
else:
attTypeCode = '{0}*'.format(strFunctions.cap(attrib['name']))
num = False
elif attrib['type'] == 'lo_element':
attType = 'lo_element'
attTypeCode = attrib['element']
num = False
else:
attType = 'FIX ME'
attTypeCode = 'FIX ME'
num = False
return [attName, capAttName, attType, attTypeCode, num, reqd]
def writeIncludes(fileOut, pkg, element, members, attribs):
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/common/extern.h>\n')
fileOut.write('\n\n')
fileOut.write('#ifdef __cplusplus\n')
fileOut.write('\n\n')
fileOut.write('#include <sbml/extension/SBasePlugin.h>\n')
for i in range(0, len(members)):
mem = members[i]
fileOut.write('#include <sbml/packages/{0}/sbml/{1}.h>\n'.format(
pkg.lower(), mem['name']))
if len(members) == 0:
fileOut.write(
'#include <sbml/packages/{0}/extension/{1}Extension.h>\n'.format(
pkg.lower(), pkg))
for i in range(0, len(attribs)):
if (attribs[i]['type'] == 'element'
or attribs[i]['type'] == 'lo_element' or attribs[i]['type']
== 'inline_lo_element') and attribs[i]['name'] != 'math':
if (attribs[i]['element'] == None):
fileOut.write(
'#include <sbml/packages/{0}/sbml/{1}.h>\n'.format(
pkg.lower(), strFunctions.cap(attribs[i]['name'])))
else:
fileOut.write(
'#include <sbml/packages/{0}/sbml/{1}.h>\n'.format(
pkg.lower(), strFunctions.cap(attribs[i]['element'])))
fileOut.write('\n\n')
fileOut.write('LIBSBML_CPP_NAMESPACE_BEGIN\n')
fileOut.write('\n\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 writeLocal(fileOut, name, classes):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n\n'.format(capName))
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 = strFunctions.listOfName(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(out) {0}*\n'.format(classes[i]['name']))
fileOut.write('{\n')
fileOut.write(
' $result = SWIG_NewPointerObj($1, GetDowncastSwigTypeForPackage($1, "{0}"), $owner | %newpointer_flags);\n'
.format(name))
fileOut.write('}\n')
fileOut.write('\n')
fileOut.write('\n')
fileOut.write('#endif // USE_{0} \n\n'.format(capName))
def writeCopyAttributes(attrs, output, tabs, name):
for i in range(0, len(attrs)):
attName = strFunctions.cap(attrs[i]['name'])
atttype = attrs[i]['type']
if atttype == 'array':
output.write('{0}m{1} = NULL;\n'.format(tabs, attName, name))
output.write('{0}set{1}({2}.m{1}, {2}.m{1}Length);\n'.format(tabs, attName, name))
elif atttype != 'lo_element' and atttype != 'inline_lo_element':
if atttype != 'element':
output.write('{0}m{1} = {2}.m{1};\n'.format(tabs, attName, name))
else:
output.write('{0}if ({2}.m{1} != NULL)\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
output.write('{0}'.format(tabs))
output.write('{\n')
if attrs[i]['name'] != 'math':
output.write('{0} m{1} = {2}.m{1}->clone();\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
else:
output.write('{0} m{1} = {2}.m{1}->deepCopy();\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
output.write('{0}'.format(tabs))
output.write('}\n')
output.write('{0}else\n'.format(tabs))
output.write('{0}'.format(tabs))
output.write('{\n')
output.write('{0} m{1} = NULL;\n'.format(tabs, strFunctions.cap(attrs[i]['name'])))
output.write('{0}'.format(tabs))
output.write('}\n')
else:
if attName.endswith('x'):
output.write('{0}m{1}es = {2}.m{1}es;\n'.format(tabs, attName, name))
elif attName.endswith('s'):
output.write('{0}m{1} = {2}.m{1};\n'.format(tabs, attName, name))
else:
output.write('{0}m{1}s = {2}.m{1}s;\n'.format(tabs, attName, name))
if atttype == 'double' or atttype == 'int' or atttype == 'uint' or atttype == 'bool':
output.write('{0}mIsSet{1} = {2}.mIsSet{1};\n'.format(tabs, attName, name))
def writeCopyAttributes(attrs, output, tabs, name):
for i in range(0, len(attrs)):
attName = strFunctions.cap(attrs[i]['name'])
atttype = attrs[i]['type']
if atttype == 'element' and attName == 'Math':
output.write('{0}m{1} = {2}.m{1} != NULL ? {2}.m{1}->deepCopy() : NULL;\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
else:
output.write('{0}m{1} = {2}.m{1};\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
if atttype == 'double' or atttype == 'int' or atttype == 'uint' or atttype == 'bool':
output.write('{0}mIsSet{1} = {2}.mIsSet{1};\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
def writeAtt(atttype, name, output, constType, pkg):
if atttype == 'SId' or atttype == 'SIdRef' or atttype == 'UnitSId' or atttype == 'UnitSIdRef' or atttype == 'string':
output.write('\t, m{0} ("")\n'.format(strFunctions.cap(name)))
elif atttype == 'element':
output.write('\t, m{0} (NULL)\n'.format(strFunctions.cap(name)))
elif atttype == 'lo_element':
output.write('\t, m{0} ('.format(strFunctions.cap(name)))
if constType == 0:
output.write(')\n')
elif constType == 1:
output.write('level, version)\n')
elif constType == 2:
output.write('{0}ns)\n'.format(pkg))
elif atttype == 'double':
output.write('\t, m{0} (numeric_limits<double>::quiet_NaN())\n'.format(
strFunctions.cap(name)))
output.write('\t, mIsSet{0} (false)\n'.format(strFunctions.cap(name)))
elif atttype == 'int' or atttype == 'uint':
output.write('\t, m{0} (SEDML_INT_MAX)\n'.format(
strFunctions.cap(name)))
output.write('\t, mIsSet{0} (false)\n'.format(strFunctions.cap(name)))
elif atttype == 'bool':
output.write('\t, m{0} (false)\n'.format(strFunctions.cap(name)))
output.write('\t, mIsSet{0} (false)\n'.format(strFunctions.cap(name)))
else:
output.write('\tFIX ME {0};\n'.format(name))
def writeListOfSubElements(attrib, output, element):
loname = generalFunctions.writeListOf(strFunctions.cap(attrib['name']))
output.write('LIBSEDML_EXTERN\n')
output.write('int\n')
output.write('{0}_add{1}({0}_t * {2}, '.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write('{0}_t * {1});\n\n\n'.format(
attrib['element'], strFunctions.objAbbrev(attrib['element'])))
if attrib.has_key('abstract') == False or (attrib.has_key('abstract') and
attrib['abstract'] == False):
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_create{1}({0}_t * {2}'.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write(');\n\n\n')
elif attrib.has_key('concrete'):
for elem in attrib['concrete']:
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(elem['element']))
output.write('{0}_create{1}({0}_t * {2}'.format(
element, strFunctions.cap(elem['name']),
strFunctions.objAbbrev(element)))
output.write(');\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('SedListOf_t *\n')
output.write('{0}_get{1}({0}_t * {2})'.format(
element, loname, strFunctions.objAbbrev(element)))
output.write(';\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_get{1}({0}_t * {2}, '.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write('unsigned int n);\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_get{1}ById({0}_t * {2}, '.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write('const char * sid);\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('unsigned int\n')
output.write('{0}_getNum{1}s({0}_t * {2}'.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write(');\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_remove{1}({0}_t * {2}, '.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write('unsigned int n);\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_remove{1}ById({0}_t * {2}, '.format(
element, strFunctions.cap(attrib['name']),
strFunctions.objAbbrev(element)))
output.write('const char * sid);\n\n\n')
def writeReadOtherXMLCPPCode(outFile, element, hasMath = True, attribs = None, baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('bool\n{0}::readOtherXML (XMLInputStream& stream)\n'.format(element))
outFile.write('{\n')
outFile.write(' bool read = false;\n')
outFile.write(' const string& name = stream.peek().getName();\n\n')
if hasMath == True:
outFile.write(' if (name == "math")\n {\n')
outFile.write(' const XMLToken elem = stream.peek();\n')
outFile.write(' const std::string prefix = checkMathMLNamespace(elem);\n\n')
#outFile.write(' if (stream.getSedNamespaces() == NULL)\n {\n')
#outFile.write(' stream.setSedNamespaces(new SedNamespaces(getLevel(), getVersion()));\n }\n\n')
outFile.write(' delete mMath;\n')
outFile.write(' mMath = readMathML(stream, prefix);\n')
#outFile.write(' if (mMath != NULL)\n {\n mMath->setParentSEDMLObject(this);\n }\n')
outFile.write(' read = true;\n }\n\n')
elif containsType(attribs, 'XMLNode*'):
node = getByType(attribs, 'XMLNode*')
outFile.write(' if (name == "{0}")\n'.format(node['name']))
outFile.write(' {\n')
outFile.write(' const XMLToken& token = stream.next();\n')
outFile.write(' stream.skipText();\n')
outFile.write(' m{0} = new XMLNode(stream);\n'.format(strFunctions.cap(node['name'])))
outFile.write(' stream.skipPastEnd(token);\n')
outFile.write(' read = true;\n }\n\n')
elif containsType(attribs, 'DimensionDescription*'):
node = getByType(attribs, 'DimensionDescription*')
outFile.write(' if (name == "{0}")\n'.format(node['name']))
outFile.write(' {\n')
outFile.write(' const XMLToken& token = stream.next();\n')
outFile.write(' m{0} = new DimensionDescription();\n'.format(strFunctions.cap(node['name'])))
outFile.write(' m{0}->read(stream);\n'.format(strFunctions.cap(node['name'])))
outFile.write(' stream.skipPastEnd(token);\n')
outFile.write(' read = true;\n }\n\n')
elif containsType(attribs, 'std::vector<double>'):
elem = getByType(attribs, 'std::vector<double>')
outFile.write(' while (stream.peek().getName() == "{0}")\n'.format(elem['name']))
outFile.write(' {\n')
outFile.write(' stream.next(); // consume start\n')
outFile.write(' stringstream text;\n')
outFile.write(' while(stream.isGood() && stream.peek().isText())\n')
outFile.write(' text << stream.next().getCharacters();\n')
outFile.write(' double value; text >> value;\n')
outFile.write(' if (!text.fail())\n')
outFile.write(' m{0}.push_back(value);\n'.format(strFunctions.capp(elem['name'])))
outFile.write(' stream.next(); // consume end\n')
outFile.write(' read = true;\n')
outFile.write(' }\n')
outFile.write(' if ({0}::readOtherXML(stream))\n'.format(baseClass))
outFile.write(' {\n read = true;\n }\n')
outFile.write(' return read;\n')
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def writeCopyAttributes(attrs, output, tabs, name):
for i in range(0, len(attrs)):
attName = strFunctions.cap(attrs[i]['name'])
atttype = attrs[i]['type']
if atttype == 'element' and attName == 'Math':
output.write('{0}m{1} = {2}.m{1} != NULL ? {2}.m{1}->deepCopy() : NULL;\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
elif atttype == 'XMLNode*' or atttype == 'DimensionDescription*':
output.write('{0}m{1} = {2}.m{1} != NULL ? {2}.m{1}->clone() : NULL;\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
else:
output.write('{0}m{1} = {2}.m{1};\n'.format(tabs, strFunctions.capp(attrs[i]['name'], atttype == 'lo_element' or atttype == 'std::vector<double>'), name))
if atttype == 'double' or atttype == 'int' or atttype == 'uint' or atttype == 'bool':
output.write('{0}mIsSet{1} = {2}.mIsSet{1};\n'.format(tabs, strFunctions.cap(attrs[i]['name']), name))
def writeJavaNS(fileOut, name):
capName = name.upper()
fileOut.write('/**\n')
fileOut.write(' * casting to most specific SBMLNamespaces object\n */\n\n')
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('%pragma(java) modulecode =\n')
fileOut.write('%{\n')
fileOut.write(' if (ns.hasURI({0}Extension.getXmlnsL3V1V1()))\n'.format(strFunctions.cap(name)))
fileOut.write(' {\n')
fileOut.write(' return new {0}PkgNamespaces(cPtr, owner);\n'.format(strFunctions.cap(name)))
fileOut.write(' }\n')
fileOut.write('%}\n')
fileOut.write('#endif /* USE_{0} */\n\n'.format(capName))
def writeCopyAttributes(attrs, output, tabs, name):
for i in range(0, len(attrs)):
attName = strFunctions.cap(attrs[i]['name'])
atttype = attrs[i]['type']
if atttype == 'element' and attName == 'Math':
output.write(
'{0}m{1} = {2}.m{1} != NULL ? {2}.m{1}->deepCopy() : NULL;\n'.
format(tabs, strFunctions.cap(attrs[i]['name']), name))
else:
output.write('{0}m{1} = {2}.m{1};\n'.format(
tabs, strFunctions.cap(attrs[i]['name']), name))
if atttype == 'double' or atttype == 'int' or atttype == 'uint' or atttype == 'bool':
output.write('{0}mIsSet{1} = {2}.mIsSet{1};\n'.format(
tabs, strFunctions.cap(attrs[i]['name']), name))
def writeAtt(atttype, name, output, constType, pkg):
if atttype == 'SId' or atttype == 'SIdRef' or atttype == 'UnitSId' or atttype == 'UnitSIdRef' or atttype == 'string':
output.write('\t, m{0} ("")\n'.format(strFunctions.cap(name)))
elif atttype == 'element' or atttype == 'XMLNode*':
output.write('\t, m{0} (NULL)\n'.format(strFunctions.cap(name)))
elif atttype == 'lo_element':
output.write('\t, m{0} ('.format(strFunctions.capp(name)))
if constType == 0:
output.write(')\n')
elif constType == 1:
output.write('level, version)\n')
elif constType == 2:
output.write('{0}ns)\n'.format(pkg))
elif atttype == 'double':
output.write('\t, m{0} (numeric_limits<double>::quiet_NaN())\n'.format(strFunctions.cap(name)))
output.write('\t, mIsSet{0} (false)\n'.format(strFunctions.cap(name)))
elif atttype == 'int' or atttype == 'uint':
output.write('\t, m{0} (SEDML_INT_MAX)\n'.format(strFunctions.cap(name)))
output.write('\t, mIsSet{0} (false)\n'.format(strFunctions.cap(name)))
elif atttype == 'bool':
output.write('\t, m{0} (false)\n'.format(strFunctions.cap(name)))
output.write('\t, mIsSet{0} (false)\n'.format(strFunctions.cap(name)))
elif atttype == 'std::vector<double>':
output.write('\t, m{0} ()\n'.format(strFunctions.capp(name)))
else:
output.write('\tFIX ME {0};\n'.format(name))
def writeJavaNS(fileOut, name):
capName = name.upper()
fileOut.write('/**\n')
fileOut.write(' * casting to most specific SBMLNamespaces object\n */\n\n')
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('%pragma(java) modulecode =\n')
fileOut.write('%{\n')
fileOut.write(' if (ns.hasURI({0}Extension.getXmlnsL3V1V1()))\n'.format(
strFunctions.cap(name)))
fileOut.write(' {\n')
fileOut.write(' return new {0}PkgNamespaces(cPtr, owner);\n'.format(
strFunctions.cap(name)))
fileOut.write(' }\n')
fileOut.write('%}\n')
fileOut.write('#endif /* USE_{0} */\n\n'.format(capName))
def writeListOfSubFunctions(attrib, output, element, elementDict):
loname = generalFunctions.writeListOf(strFunctions.cap(attrib['name']))
output.write(' /**\n')
output.write(' * Returns the \"{0}\"'.format(loname))
output.write(' in this {0} object.\n'.format(element))
output.write(' *\n')
output.write(' * @return the \"{0}\"'.format(loname))
output.write(' attribute of this {0}.\n'.format(element))
output.write(' */\n')
output.write(' const {0}*'.format(loname))
output.write(' getListOf{0}s() const;\n\n\n'.format(strFunctions.cap(attrib['name'])))
writeListOfHeader.writeGetFunctions(output, strFunctions.cap(attrib['name']), attrib['element'], True, element)
output.write(' /**\n')
output.write(' * Adds a copy the given \"{0}\" to this {1}.\n'.format(attrib['element'], element))
output.write(' *\n')
output.write(' * @param {0}; the {1} object to add\n'.format(strFunctions.objAbbrev(attrib['element']), attrib['element']))
output.write(' *\n')
output.write(' * @return integer value indicating success/failure of the\n')
output.write(' * function. @if clike The value is drawn from the\n')
output.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
output.write(' * returned by this function are:\n')
output.write(' * @li LIBSEDML_OPERATION_SUCCESS\n')
output.write(' * @li LIBSEDML_INVALID_ATTRIBUTE_VALUE\n')
output.write(' */\n')
output.write(' int add{0}(const {1}* {2});\n\n\n'.format(strFunctions.cap(attrib['name']), attrib['element'], strFunctions.objAbbrev(attrib['element'])))
output.write(' /**\n')
output.write(' * Get the number of {0} objects in this {1}.\n'.format(attrib['element'], element))
output.write(' *\n')
output.write(' * @return the number of {0} objects in this {1}\n'.format(attrib['element'], element))
output.write(' */\n')
output.write(' unsigned int getNum{0}s() const;\n\n\n'.format(strFunctions.cap(attrib['name'])))
if attrib.has_key('abstract') == False or (attrib.has_key('abstract') and attrib['abstract'] == False):
output.write(' /**\n')
output.write(' * Creates a new {0} object, adds it to this {1}s\n'.format(attrib['element'], element))
output.write(' * {0} and returns the {1} object created.\n'.format(loname, attrib['element']))
output.write(' *\n')
output.write(' * @return a new {0} object instance\n'.format(attrib['element']))
output.write(' *\n')
output.write(' * @see add{0}(const {1}* {2})\n'.format(strFunctions.cap(attrib['name']), attrib['element'], strFunctions.objAbbrev(attrib['element'])))
output.write(' */\n')
output.write(' {0}* create{1}();\n\n\n'.format(attrib['element'], strFunctions.cap(attrib['name'])))
elif attrib.has_key('concrete'):
for elem in attrib['concrete']:
output.write(' /**\n')
output.write(' * Creates a new {0} object, adds it to this {1}s\n'.format(elem['element'], element))
output.write(' * {0} and returns the {1} object created.\n'.format(loname, elem['element']))
output.write(' *\n')
output.write(' * @return a new {0} object instance\n'.format(elem['element']))
output.write(' *\n')
output.write(' * @see add{0}(const {0}* {1})\n'.format(attrib['element'], strFunctions.objAbbrev(attrib['element'])))
output.write(' */\n')
output.write(' {0}* create{1}();\n\n\n'.format(elem['element'], strFunctions.cap(elem['name'])))
writeListOfHeader.writeRemoveFunctions(output, strFunctions.cap(attrib['name']), attrib['element'], True, element)
def writeUnsetFunction(attrib, output, element):
attName = attrib['name']
capAttName = strFunctions.cap(attName)
if attrib['type'] == 'lo_element' or attrib['type'] == 'inline_lo_element':
return
elif attrib['type'] == 'element':
output.write(' /**\n')
output.write(' * Unsets the \"{0}\"'.format(attName))
output.write(' element of this {0}.\n'.format(element))
output.write(' *\n')
output.write(' * @return integer value indicating success/failure of the\n')
output.write(' * function. @if clike The value is drawn from the\n')
output.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
output.write(' * returned by this function are:\n')
output.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
output.write(' * @li LIBSBML_OPERATION_FAILED\n')
output.write(' */\n')
output.write(' virtual int unset{0}();\n\n\n'.format(capAttName))
else:
output.write(' /**\n')
output.write(' * Unsets the value of the \"{0}\"'.format(attName))
output.write(' attribute of this {0}.\n'.format(element))
output.write(' *\n')
output.write(' * @return integer value indicating success/failure of the\n')
output.write(' * function. @if clike The value is drawn from the\n')
output.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
output.write(' * returned by this function are:\n')
output.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
output.write(' * @li LIBSBML_OPERATION_FAILED\n')
output.write(' */\n')
output.write(' virtual int unset{0}();\n\n\n'.format(capAttName))
def writeConnectToParent(outFile,
element,
sbmltypecode,
attribs,
isSedListOf,
hasChildren=False,
hasMath=False,
baseClass='SedBase'):
#print 'isSedListOf={0} hasChildren={1} hasMath={2}'.format(isSedListOf, hasChildren, hasMath)
if isSedListOf or hasChildren == False:
return
outFile.write('/*\n')
outFile.write(
' * Read values from the given XMLAttributes set into their specific fields.\n'
)
outFile.write(' */\n')
outFile.write('void\n{0}::connectToChild ()\n'.format(element))
outFile.write('{\n')
outFile.write('\t{0}::connectToChild();\n\n'.format(baseClass))
for i in range(0, len(attribs)):
current = attribs[i]
if current['type'] == 'lo_element':
outFile.write('\tm{0}.connectToParent(this);\n'.format(
strFunctions.cap(current['name'])))
outFile.write('}\n\n\n')
def writeCommonCPPCode(outFile,
element,
sbmltypecode,
attribs,
isSedListOf,
hasChildren=False,
hasMath=False,
elementDict=None,
baseClass='SedBase'):
type = elementDict['name']
name = elementDict['name']
if elementDict.has_key('elementName'):
name = strFunctions.cap(elementDict['elementName'])
if elementDict.has_key('element'):
type = elementDict['element']
if isSedListOf == True:
element = writeListOf(name)
writeGetElementNameCPPCode(outFile, element, isSedListOf, elementDict)
if hasChildren or baseClass != 'SedBase':
writeCreateObject(outFile, element, sbmltypecode, attribs, isSedListOf,
hasChildren, hasMath, baseClass)
writeConnectToParent(outFile, element, sbmltypecode, attribs,
isSedListOf, hasChildren, hasMath, baseClass)
writeGetTypeCodeCPPCode(outFile, element, sbmltypecode, isSedListOf)
if isSedListOf == False:
writeHasReqdAttribCPPCode(outFile, element, attribs, baseClass)
if hasChildren == True or hasMath == True:
writeHasReqdElementsCPPCode(outFile, element, attribs, baseClass)
def writeUnsetFunction(attrib, output, element):
attName = attrib['name']
capAttName = strFunctions.cap(attName)
if attrib['type'] == 'lo_element' or attrib['type'] == 'inline_lo_element':
return
elif attrib['type'] == 'element':
output.write(' /**\n')
output.write(' * Unsets the \"{0}\"'.format(attName))
output.write(' element of this {0}.\n'.format(element))
output.write(' *\n')
output.write(' * @return integer value indicating success/failure of the\n')
output.write(' * function. @if clike The value is drawn from the\n')
output.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
output.write(' * returned by this function are:\n')
output.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
output.write(' * @li LIBSBML_OPERATION_FAILED\n')
output.write(' */\n')
output.write(' virtual int unset{0}();\n\n\n'.format(capAttName))
else:
output.write(' /**\n')
output.write(' * Unsets the value of the \"{0}\"'.format(attName))
output.write(' attribute of this {0}.\n'.format(element))
output.write(' *\n')
output.write(' * @return integer value indicating success/failure of the\n')
output.write(' * function. @if clike The value is drawn from the\n')
output.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
output.write(' * returned by this function are:\n')
output.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
output.write(' * @li LIBSBML_OPERATION_FAILED\n')
output.write(' */\n')
output.write(' virtual int unset{0}();\n\n\n'.format(capAttName))
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 writeSetDocCPPCode(outFile, element,attribs, baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('/*\n')
outFile.write(' * Sets the parent SedDocument.\n')
outFile.write(' */\n')
outFile.write('void\n{0}::setSedDocument (SedDocument* d)\n'.format(element))
outFile.write('{\n')
outFile.write('\t{0}::setSedDocument(d);\n'.format(baseClass))
for i in range (0, len(attribs)):
if attribs[i]['type'] == 'lo_element' or ( attribs[i]['type'] == 'element' and attribs[i]['name'] != 'math'):
if attribs[i]['reqd'] == True or attribs[i]['type'] == 'lo_element':
outFile.write('\tm{0}.setSedDocument(d);\n'.format(strFunctions.capp(attribs[i]['name'], attribs[i]['type'] == 'lo_element')))
else:
outFile.write('\tif (m{0} != NULL)\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('\t\tm{0}->setSedDocument(d);\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def writeSetDocCPPCode(outFile, element,attribs, baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('/*\n')
outFile.write(' * Sets the parent SedDocument.\n')
outFile.write(' */\n')
outFile.write('void\n{0}::setSedDocument (SedDocument* d)\n'.format(element))
outFile.write('{\n')
outFile.write(' {0}::setSedDocument(d);\n'.format(baseClass))
for i in range (0, len(attribs)):
if attribs[i]['type'] == 'lo_element' or ( attribs[i]['type'] == 'element' and attribs[i]['name'] != 'math'):
if attribs[i]['reqd'] == True or attribs[i]['type'] == 'lo_element':
outFile.write(' m{0}.setSedDocument(d);\n'.format(strFunctions.capp(attribs[i]['name'], attribs[i]['type'] == 'lo_element')))
else:
outFile.write(' if (m{0} != NULL)\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write(' m{0}->setSedDocument(d);\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def createHeader(element, header):
type = element['name']
name = element['name']
if element.has_key('elementName'):
name = strFunctions.cap(element['elementName'])
if element.has_key('element'):
type = element['element']
writeClass(header, name, type, element['package'], element)
def writeExt(fileOut, name):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('if (pkgName == "{0}")\n'.format(name))
fileOut.write('{\n')
fileOut.write(' return SWIGTYPE_p_{0}Extension;\n'.format(strFunctions.cap(name)))
fileOut.write('}\n')
fileOut.write('#endif // USE_{0} \n\n'.format(capName))
def addCMakeFilename(outFile, filename, element):
outFile.write(
'#################################################################################\n'
)
outFile.write('#\n')
outFile.write('# @file: {0}\n'.format(filename))
outFile.write('# @brief: CMake configuration for L3 {0} package\n'.format(
strFunctions.cap(element)))
outFile.write('# @author: Generated by autocreate code\n#\n')
def writeConnectToParent(outFile, element, sbmltypecode, attribs, isSedListOf, hasChildren=False, hasMath=False, baseClass='SedBase'):
#print 'isSedListOf={0} hasChildren={1} hasMath={2}'.format(isSedListOf, hasChildren, hasMath)
if isSedListOf or hasChildren == False:
return;
outFile.write('/*\n')
outFile.write(' * Read values from the given XMLAttributes set into their specific fields.\n')
outFile.write(' */\n')
outFile.write('void\n{0}::connectToChild ()\n'.format(element))
outFile.write('{\n')
outFile.write('\t{0}::connectToChild();\n\n'.format(baseClass))
for i in range (0, len(attribs)):
if attribs[i]['type'] == 'lo_element' or ( attribs[i]['type'] == 'element' and attribs[i]['name'] != 'math'):
if attribs[i]['reqd'] == True or attribs[i]['type'] == 'lo_element':
outFile.write('\tm{0}.connectToParent(this);\n'.format(strFunctions.capp(attribs[i]['name'],attribs[i]['type'] == 'lo_element')))
else:
outFile.write('\tif (m{0} != NULL)\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('\t\tm{0}->connectToParent(this);\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('}\n\n\n')
def writeExt(fileOut, name):
capName = name.upper()
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('if (pkgName == "{0}")\n'.format(name))
fileOut.write('{\n')
fileOut.write(' return SWIGTYPE_p_{0}Extension;\n'.format(
strFunctions.cap(name)))
fileOut.write('}\n')
fileOut.write('#endif // USE_{0} \n\n'.format(capName))
def writeConnectToParent(outFile, element, sbmltypecode, attribs, isSedListOf, hasChildren=False, hasMath=False, baseClass='SedBase'):
#print 'isSedListOf={0} hasChildren={1} hasMath={2}'.format(isSedListOf, hasChildren, hasMath)
if isSedListOf or hasChildren == False:
return;
outFile.write('/*\n')
outFile.write(' * Read values from the given XMLAttributes set into their specific fields.\n')
outFile.write(' */\n')
outFile.write('void\n{0}::connectToChild ()\n'.format(element))
outFile.write('{\n')
outFile.write(' {0}::connectToChild();\n\n'.format(baseClass))
for i in range (0, len(attribs)):
if attribs[i]['type'] == 'lo_element' or ( attribs[i]['type'] == 'element' and attribs[i]['name'] != 'math'):
if attribs[i]['reqd'] == True or attribs[i]['type'] == 'lo_element':
outFile.write(' m{0}.connectToParent(this);\n'.format(strFunctions.capp(attribs[i]['name'],attribs[i]['type'] == 'lo_element')))
else:
outFile.write(' if (m{0} != NULL)\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write(' m{0}->connectToParent(this);\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('}\n\n\n')
def writeCode(name):
capName = name.upper()
codeName = name + '-register.cxx'
fileOut = open(codeName, 'w')
fileHeaders.addFilename(fileOut, codeName, name)
fileHeaders.addLicence(fileOut)
fileOut.write('\n')
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write(' {0}Extension::init();\n'.format(strFunctions.cap(name)))
fileOut.write('#endif\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 writeCode(name):
capName = name.upper()
codeName = name + '-register.cxx'
fileOut = open(codeName, 'w')
fileHeaders.addFilename(fileOut, codeName, name)
fileHeaders.addLicence(fileOut)
fileOut.write('\n')
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write(' {0}Extension::init();\n'.format(strFunctions.cap(name)))
fileOut.write('#endif\n')
def writeWriteElementsCPPCode(outFile,
element,
attributes,
hasChildren=False,
hasMath=False,
baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('/*\n')
outFile.write(' * write contained elements\n')
outFile.write(' */\n')
outFile.write(
'void\n{0}::writeElements (XMLOutputStream& stream) const\n'.format(
element))
outFile.write('{\n')
outFile.write('\t{0}::writeElements(stream);\n'.format(baseClass))
if hasChildren == True:
for i in range(0, len(attributes)):
if attributes[i]['type'] == 'element' and (
attributes[i]['name'] != 'Math'
and attributes[i]['name'] != 'math'):
outFile.write('\tif (isSet{0}() == true)\n'.format(
strFunctions.cap(attributes[i]['name'])))
outFile.write('\t{\n\t\t')
outFile.write('m{0}->write(stream);'.format(
strFunctions.cap(attributes[i]['name'])))
outFile.write('\n\t}\n')
if attributes[i]['type'] == 'lo_element':
outFile.write('\tif (getNum{0}s() > 0)\n'.format(
strFunctions.cap(attributes[i]['name'])))
outFile.write('\t{\n\t\t')
outFile.write('m{0}.write(stream);'.format(
strFunctions.cap(attributes[i]['name'])))
outFile.write('\n\t}\n')
if hasMath == True:
for i in range(0, len(attributes)):
if attributes[i]['type'] == 'element' and attributes[i][
'name'] == 'Math' or attributes[i]['name'] == 'math':
outFile.write('\tif (isSet{0}() == true)\n'.format('Math'))
outFile.write(
'\t{\n\t\twriteMathML(getMath(), stream, NULL);\n\t}\n')
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def createHeader(element, header):
type = element['name']
name = element['name']
if element.has_key('elementName'):
name = strFunctions.cap(element['elementName'])
if element.has_key('element'):
type = element['element']
writeClass(header, name, type, element['package'], element)
def writeCopyAttributes(attrs, output, tabs, name):
for i in range(0, len(attrs)):
attName = strFunctions.cap(attrs[i]['name'])
atttype = attrs[i]['type']
if atttype == 'element' and attName == 'Math':
output.write(
'{0}m{1} = {2}.m{1} != NULL ? {2}.m{1}->deepCopy() : NULL;\n'.
format(tabs, strFunctions.cap(attrs[i]['name']), name))
elif atttype == 'XMLNode*' or atttype == 'DimensionDescription*':
output.write(
'{0}m{1} = {2}.m{1} != NULL ? {2}.m{1}->clone() : NULL;\n'.
format(tabs, strFunctions.cap(attrs[i]['name']), name))
else:
output.write('{0}m{1} = {2}.m{1};\n'.format(
tabs,
strFunctions.capp(
attrs[i]['name'], atttype == 'lo_element'
or atttype == 'std::vector<double>'), name))
if atttype == 'double' or atttype == 'int' or atttype == 'uint' or atttype == 'bool':
output.write('{0}mIsSet{1} = {2}.mIsSet{1};\n'.format(
tabs, strFunctions.cap(attrs[i]['name']), name))
def writeSwigHeader(fileOut, name, plugins, classes):
capName = strFunctions.cap(name)
fileOut.write('#ifdef USE_{0}\n\n'.format(name.upper()))
fileOut.write('#include <sbml/packages/{0}/extension/{1}Extension.h>\n'.format(name, capName))
alreadyIncluded = []
for plugin in plugins:
package = name
if plugin.has_key('package') and plugin['package'] != None:
package = plugin['package']
capPackageName = strFunctions.cap(package)
if package != name and alreadyIncluded.count(package) == 0:
alreadyIncluded.append(package)
fileOut.write('#include <sbml/packages/{0}/extension/{1}Extension.h>\n'.format(package, capPackageName))
fileOut.write('#include <sbml/packages/{0}/common/{1}ExtensionTypes.h>\n'.format(package, capPackageName))
fileOut.write('#include <sbml/packages/{0}/extension/{1}{2}Plugin.h>\n'.format(name, capName, plugin['sbase']))
fileOut.write('#include <sbml/packages/{0}/common/{1}ExtensionTypes.h>\n'.format(name, capName))
for clazz in classes:
if clazz['typecode'] != 'HACK':
fileOut.write('#include <sbml/packages/{0}/sbml/{1}.h>\n'.format(name, clazz['name']))
fileOut.write('\n')
fileOut.write('#endif // USE_{0} \n\n'.format(name.upper()))
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 writeHeader(name):
capName = name.upper()
codeName = name + '-register.h'
fileOut = open(codeName, 'w')
fileHeaders.addFilename(fileOut, codeName, name)
fileHeaders.addLicence(fileOut)
fileOut.write('\n')
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write(
' #include <sbml/packages/{0}/extension/{1}Extension.h>\n'.format(
name, strFunctions.cap(name)))
fileOut.write('#endif\n\n')
def writeAddFunction(code, type, listOf, name):
code.write('/**\n')
code.write(' * Adds a copy the given \"{0}\" to this {1}.\n'.format(
type, listOf))
code.write(' *\n')
code.write(' * @param {0}; the {1} object to add\n'.format(
strFunctions.objAbbrev(type), type))
code.write(' *\n')
code.write(' * @return integer value indicating success/failure of the\n')
code.write(' * function. @if clike The value is drawn from the\n')
code.write(
' * enumeration #OperationReturnValues_t. @endif The possible values\n'
)
code.write(' * returned by this function are:\n')
code.write(' * @li LIBSBML_OPERATION_SUCCESS\n')
code.write(' * @li LIBSBML_INVALID_ATTRIBUTE_VALUE\n')
code.write(' */\n')
code.write('int\n')
code.write('{0}::add{1}(const {2}* {3})\n'.format(
listOf, strFunctions.cap(name), type, strFunctions.objAbbrev(type)))
code.write('{\n')
code.write(' if ({0} == NULL)\n'.format(strFunctions.objAbbrev(type)))
code.write(' {\n')
code.write(' return LIBSBML_OPERATION_FAILED;\n')
code.write(' }\n')
code.write(' else if ({0}->hasRequiredAttributes() == false)\n'.format(
strFunctions.objAbbrev(type)))
code.write(' {\n')
code.write(' return LIBSBML_INVALID_OBJECT;\n')
code.write(' }\n')
code.write(' else if (getLevel() != {0}->getLevel())\n'.format(
strFunctions.objAbbrev(type)))
code.write(' {\n')
code.write(' return LIBSBML_LEVEL_MISMATCH;\n')
code.write(' }\n')
code.write(' else if (getVersion() != {0}->getVersion())\n'.format(
strFunctions.objAbbrev(type)))
code.write(' {\n')
code.write(' return LIBSBML_VERSION_MISMATCH;\n')
code.write(' }\n')
code.write(
' else if (matchesRequiredSBMLNamespacesForAddition(static_cast<const SBase *>({0})) == false)\n'
.format(strFunctions.objAbbrev(type)))
code.write(' {\n')
code.write(' return LIBSBML_NAMESPACES_MISMATCH;\n')
code.write(' }\n')
code.write(' else\n')
code.write(' {\n')
code.write('\tappend({0});\n'.format(strFunctions.objAbbrev(type)))
code.write(' return LIBSBML_OPERATION_SUCCESS;\n')
code.write(' }\n')
code.write('}\n\n\n')
def writeWriteElementsCPPCode(outFile, element, attributes, hasChildren=False, hasMath=False, baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('/*\n')
outFile.write(' * write contained elements\n')
outFile.write(' */\n')
outFile.write('void\n{0}::writeElements (XMLOutputStream& stream) const\n'.format(element))
outFile.write('{\n')
outFile.write('\t{0}::writeElements(stream);\n'.format(baseClass))
if hasChildren == True:
for i in range(0, len(attributes)):
if attributes[i]['type'] == 'element' and (attributes[i]['name'] != 'Math' and attributes[i]['name'] != 'math'):
outFile.write('\tif (isSet{0}() == true)\n'.format(strFunctions.cap(attributes[i]['name'])))
outFile.write('\t{\n\t\t')
outFile.write('m{0}->write(stream);'.format(strFunctions.cap(attributes[i]['name'])))
outFile.write('\n\t}\n')
if attributes[i]['type'] == 'lo_element':
outFile.write('\tif (getNum{0}() > 0)\n'.format(strFunctions.capp(attributes[i]['name'])))
outFile.write('\t{\n\t\t')
outFile.write('m{0}.write(stream);'.format(strFunctions.capp(attributes[i]['name'])))
outFile.write('\n\t}\n')
if containsType(attributes, 'std::vector<double>'):
vector = getByType(attributes, 'std::vector<double>')
outFile.write('\tif(has{0}())\n'.format(strFunctions.capp(vector['name'])))
outFile.write('\t{\n')
outFile.write('\t\tfor (std::vector<double>::const_iterator it = m{0}.begin(); it != m{0}.end(); ++it)\n'.format(strFunctions.capp(vector['name'])))
outFile.write('\t\t{\n')
outFile.write('\t\t\tstream.startElement("{0}");\n'.format(vector['name']))
outFile.write('\t\t\tstream.setAutoIndent(false);\n')
outFile.write('\t\t\tstream << " " << *it << " ";\n')
outFile.write('\t\t\tstream.endElement("{0}");\n'.format(vector['name']))
outFile.write('\t\t\tstream.setAutoIndent(true);\n')
outFile.write('\t\t}\n')
outFile.write('\t}\n')
if hasMath == True:
for i in range(0, len(attributes)):
if attributes[i]['type'] == 'element' and attributes[i]['name'] == 'Math' or attributes[i]['name'] == 'math':
outFile.write('\tif (isSet{0}() == true)\n'.format('Math'))
outFile.write('\t{\n\t\twriteMathML(getMath(), stream, NULL);\n\t}\n')
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def writeJavaExt(fileOut, name):
capName = name.upper()
fileOut.write('/**\n')
fileOut.write(' * casting to most specific SBMLExtension object\n */\n\n')
fileOut.write('#ifdef USE_{0}\n'.format(capName))
fileOut.write('%pragma(java) modulecode =\n')
fileOut.write('%{\n')
fileOut.write(' if (pkgName.equals("{0}"))\n'.format(name))
fileOut.write(' {\n')
fileOut.write(' return new {0}Extension(cPtr, owner);\n'.format(strFunctions.cap(name)))
fileOut.write(' }\n')
fileOut.write('%}\n')
fileOut.write('#endif // USE_{0}\n\n'.format(capName))
def writeCreateLOObject(fileOut, mem, ifCount):
name = strFunctions.cap(mem['name'])
if ifCount == 1:
fileOut.write(' if (name == "listOf{0}s" ) \n'.format(name))
else:
fileOut.write(' else if (name == "listOf{0}s" ) \n'.format(name))
fileOut.write(' { \n')
fileOut.write(' object = &m{0}s;\n\n'.format(name))
fileOut.write(' if (targetPrefix.empty() == true) \n')
fileOut.write(' { \n')
fileOut.write(' m{0}s.getSBMLDocument()->enableDefaultNS(mURI, true); \n'.format(name))
fileOut.write(' } \n')
fileOut.write(' } \n')
def writeClass(header, nameOfElement, typeOfElement, nameOfPackage, elementDict):
header.write('class LIBSEDML_EXTERN {0} :'.format(generalFunctions.writeListOf(nameOfElement)))
header.write(' public SedListOf\n{0}\n\n'.format('{'))
header.write('public:\n\n')
writeConstructors(nameOfElement, typeOfElement, nameOfPackage, header)
writeGetFunctions(header, nameOfElement, typeOfElement)
header.write('\t/**\n')
header.write('\t * Adds a copy the given \"{0}\" to this {1}.\n'.format(nameOfElement, generalFunctions.writeListOf(nameOfElement)))
header.write('\t *\n')
header.write('\t * @param {0}; the {1} object to add\n'.format(strFunctions.objAbbrev(nameOfElement), nameOfElement))
header.write('\t *\n')
header.write('\t * @return integer value indicating success/failure of the\n')
header.write('\t * function. @if clike The value is drawn from the\n')
header.write('\t * enumeration #OperationReturnValues_t. @endif The possible values\n')
header.write('\t * returned by this function are:\n')
header.write('\t * @li LIBSEDML_OPERATION_SUCCESS\n')
header.write('\t * @li LIBSEDML_INVALID_ATTRIBUTE_VALUE\n')
header.write('\t */\n')
header.write('\tint add{0}(const {1}* {2});\n\n\n'.format(nameOfElement, typeOfElement, strFunctions.objAbbrev(nameOfElement)))
header.write('\t/**\n')
header.write('\t * Get the number of {0} objects in this {1}.\n'.format(nameOfElement, generalFunctions.writeListOf(nameOfElement)))
header.write('\t *\n')
header.write('\t * @return the number of {0} objects in this {1}\n'.format(nameOfElement, generalFunctions.writeListOf(nameOfElement)))
header.write('\t */\n')
header.write('\tunsigned int getNum{0}s() const;\n\n\n'.format(nameOfElement))
if elementDict.has_key('abstract') == False or (elementDict.has_key('abstract') and elementDict['abstract'] == False):
header.write('\t/**\n')
header.write('\t * Creates a new {0} object, adds it to the\n'.format(nameOfElement))
header.write('\t * {0} and returns the {1} object created. \n'.format(generalFunctions.writeListOf(nameOfElement), nameOfElement))
header.write('\t *\n')
header.write('\t * @return a new {0} object instance\n'.format(nameOfElement))
header.write('\t *\n')
header.write('\t * @see add{0}(const {1}* {2})\n'.format(nameOfElement, typeOfElement, strFunctions.objAbbrev(nameOfElement)))
header.write('\t */\n')
header.write('\t{0}* create{1}();\n\n\n'.format(typeOfElement, nameOfElement))
elif elementDict.has_key('concrete'):
for elem in elementDict['concrete']:
header.write('\t/**\n')
header.write('\t * Creates a new {0} object, adds it to the\n'.format(nameOfElement))
header.write('\t * {0} and returns the {1} object created. \n'.format(generalFunctions.writeListOf(nameOfElement), nameOfElement))
header.write('\t *\n')
header.write('\t * @return a new {0} object instance\n'.format(nameOfElement))
header.write('\t *\n')
header.write('\t * @see add{0}(const {1}* {2})\n'.format(nameOfElement, typeOfElement, strFunctions.objAbbrev(nameOfElement)))
header.write('\t */\n')
header.write('\t{0}* create{1}();\n\n\n'.format(elem['element'], strFunctions.cap(elem['name'])))
writeRemoveFunctions(header, nameOfElement, typeOfElement)
generalFunctions.writeCommonHeaders(header, nameOfElement, None, True)
header.write('protected:\n\n')
writeProtectedFunctions(header, nameOfElement, nameOfPackage)
header.write('\n};\n\n')
def writeClass(header, nameOfElement, typeOfElement, nameOfPackage, elementDict):
header.write('class LIBSEDML_EXTERN {0} :'.format(generalFunctions.writeListOf(nameOfElement)))
header.write(' public SedListOf\n{0}\n\n'.format('{'))
header.write('public:\n\n')
writeConstructors(nameOfElement, typeOfElement, nameOfPackage, header)
writeGetFunctions(header, nameOfElement, typeOfElement)
header.write(' /**\n')
header.write(' * Adds a copy the given \"{0}\" to this {1}.\n'.format(nameOfElement, generalFunctions.writeListOf(nameOfElement)))
header.write(' *\n')
header.write(' * @param {0}; the {1} object to add\n'.format(strFunctions.objAbbrev(nameOfElement), nameOfElement))
header.write(' *\n')
header.write(' * @return integer value indicating success/failure of the\n')
header.write(' * function. @if clike The value is drawn from the\n')
header.write(' * enumeration #OperationReturnValues_t. @endif The possible values\n')
header.write(' * returned by this function are:\n')
header.write(' * @li LIBSEDML_OPERATION_SUCCESS\n')
header.write(' * @li LIBSEDML_INVALID_ATTRIBUTE_VALUE\n')
header.write(' */\n')
header.write(' int add{0}(const {1}* {2});\n\n\n'.format(nameOfElement, typeOfElement, strFunctions.objAbbrev(nameOfElement)))
header.write(' /**\n')
header.write(' * Get the number of {0} objects in this {1}.\n'.format(nameOfElement, generalFunctions.writeListOf(nameOfElement)))
header.write(' *\n')
header.write(' * @return the number of {0} objects in this {1}\n'.format(nameOfElement, generalFunctions.writeListOf(nameOfElement)))
header.write(' */\n')
header.write(' unsigned int getNum{0}s() const;\n\n\n'.format(nameOfElement))
if elementDict.has_key('abstract') == False or (elementDict.has_key('abstract') and elementDict['abstract'] == False):
header.write(' /**\n')
header.write(' * Creates a new {0} object, adds it to the\n'.format(nameOfElement))
header.write(' * {0} and returns the {1} object created.\n'.format(generalFunctions.writeListOf(nameOfElement), nameOfElement))
header.write(' *\n')
header.write(' * @return a new {0} object instance\n'.format(nameOfElement))
header.write(' *\n')
header.write(' * @see add{0}(const {1}* {2})\n'.format(nameOfElement, typeOfElement, strFunctions.objAbbrev(nameOfElement)))
header.write(' */\n')
header.write(' {0}* create{1}();\n\n\n'.format(typeOfElement, nameOfElement))
elif elementDict.has_key('concrete'):
for elem in elementDict['concrete']:
header.write(' /**\n')
header.write(' * Creates a new {0} object, adds it to the\n'.format(nameOfElement))
header.write(' * {0} and returns the {1} object created.\n'.format(generalFunctions.writeListOf(nameOfElement), nameOfElement))
header.write(' *\n')
header.write(' * @return a new {0} object instance\n'.format(nameOfElement))
header.write(' *\n')
header.write(' * @see add{0}(const {1}* {2})\n'.format(nameOfElement, typeOfElement, strFunctions.objAbbrev(nameOfElement)))
header.write(' */\n')
header.write(' {0}* create{1}();\n\n\n'.format(elem['element'], strFunctions.cap(elem['name'])))
writeRemoveFunctions(header, nameOfElement, typeOfElement)
generalFunctions.writeCommonHeaders(header, nameOfElement, None, True)
header.write('protected:\n\n')
writeProtectedFunctions(header, nameOfElement, nameOfPackage)
header.write('\n};\n\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 writeWriteAttributesCPPCode(outFile, element, attribs, baseClass='SedBase'):
writeInternalStart(outFile)
outFile.write('/*\n')
outFile.write(' * Write values of XMLAttributes to the output stream.\n')
outFile.write(' */\n')
outFile.write('\tvoid\n{0}::writeAttributes (XMLOutputStream& stream) const\n'.format(element))
outFile.write('{\n')
outFile.write('\t{0}::writeAttributes(stream);\n\n'.format(baseClass))
for i in range (0, len(attribs)):
if attribs[i]['type'] != 'element' and attribs[i]['type'] != 'lo_element':
outFile.write('\tif (isSet{0}() == true)\n'.format(strFunctions.cap(attribs[i]['name'])))
outFile.write('\t\tstream.writeAttribute("{0}", getPrefix(), m{1});\n\n'.format(attribs[i]['name'], strFunctions.cap(attribs[i]['name'])))
outFile.write('}\n\n\n')
writeInternalEnd(outFile)
def writeGetFunction(attrib, output, element):
att = generalFunctions.parseAttributeForC(attrib)
attName = att[0]
capAttName = att[1]
attType = att[2]
if att[3] == 'const char *':
attTypeCode = 'char *'
else:
attTypeCode = att[3]
num = att[4]
if attrib['type'] == 'std::vector<double>':
return
elif attrib['type'] != 'element' and attrib['type'] != 'lo_element' and attrib['type'] != 'XMLNode*':
output.write('LIBSEDML_EXTERN\n')
output.write('{0}\n'.format(attTypeCode))
output.write('{0}_get{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
elif attrib['type'] == 'XMLNode*':
output.write('LIBSEDML_EXTERN\n')
output.write('XMLNode_t*\n')
output.write('{0}_get{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
elif attrib['type'] == 'element':
if attrib['name'] == 'Math' or attrib['name'] == 'math':
output.write('LIBSEDML_EXTERN\n')
output.write('ASTNode_t*\n')
output.write('{0}_getMath'.format(element))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
else:
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t*\n'.format(strFunctions.cap(attrib['element'])))
output.write('{0}_get{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t*\n'.format(strFunctions.cap(attrib['element'])))
output.write('{0}_create{1}'.format(element, capAttName))
output.write('({0}_t * {1});\n\n\n'.format(element, strFunctions.objAbbrev(element)))
def writeListOfSubElements(attrib, output, element):
loname = generalFunctions.writeListOf(strFunctions.cap(attrib['name']))
output.write('LIBSEDML_EXTERN\n')
output.write('int\n')
output.write('{0}_add{1}({0}_t * {2}, '.format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write('{0}_t * {1});\n\n\n'.format(attrib['element'], strFunctions.objAbbrev(attrib['element'])))
if attrib.has_key('abstract') == False or (attrib.has_key('abstract') and attrib['abstract'] == False):
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_create{1}({0}_t * {2}' .format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write(');\n\n\n')
elif attrib.has_key('concrete'):
for elem in attrib['concrete']:
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(elem['element']))
output.write('{0}_create{1}({0}_t * {2}' .format(element, strFunctions.cap(elem['name']), strFunctions.objAbbrev(element)))
output.write(');\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('SedListOf_t *\n')
output.write('{0}_get{1}({0}_t * {2})'.format(element, loname, strFunctions.objAbbrev(element)))
output.write(';\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_get{1}({0}_t * {2}, '.format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write('unsigned int n);\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_get{1}ById({0}_t * {2}, '.format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write('const char * sid);\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('unsigned int\n')
output.write('{0}_getNum{1}s({0}_t * {2}' .format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write(');\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_remove{1}({0}_t * {2}, '.format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write('unsigned int n);\n\n\n')
output.write('LIBSEDML_EXTERN\n')
output.write('{0}_t *\n'.format(attrib['element']))
output.write('{0}_remove{1}ById({0}_t * {2}, '.format(element, strFunctions.cap(attrib['name']), strFunctions.objAbbrev(element)))
output.write('const char * sid);\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 createHeader(element, header):
type = element["name"]
name = element["name"]
if element.has_key("elementName"):
name = strFunctions.cap(element["elementName"])
if element.has_key("element"):
type = element["element"]
writeConstructors(element["name"], element["package"], header)
writeAttributeFunctions(element["attribs"], header, element["name"], element)
writeHasReqdAttrFunction(header, element["name"])
if element["hasChildren"] == True or element["hasMath"] == True:
writeHasReqdElementsFunction(header, element["name"])
if element["hasListOf"] == True:
writeListOfHeaders(header, name, type, element)
