def finalize(cls, finalize_pure_virtuals=False):
""" Attempt to finalize a class by not exposing virtual methods.
Still exposes in the case of pure virtuals otherwise the class
could not be instantiated.
"""
if isinstance(cls, pd.mdecl_wrapper_t):
for x in cls:
finalize(x)
else:
matcher = pd.virtuality_type_matcher(pd.VIRTUALITY_TYPES.VIRTUAL)
if finalize_pure_virtuals:
matcher = matcher | pd.virtuality_type_matcher(
pd.VIRTUALITY_TYPES.PURE_VIRTUAL)
members = cls.decls(matcher,
decl_type=pd.member_calldef_t,
allow_empty=True)
members.set_virtuality(pd.VIRTUALITY_TYPES.NOT_VIRTUAL)
cls.decls(pd.access_type_matcher_t(pd.ACCESS_TYPES.PROTECTED),
allow_empty=True).exclude()
cls.decls(pd.access_type_matcher_t(pd.ACCESS_TYPES.PRIVATE),
allow_empty=True).exclude()
wrapper_needs = cls.is_wrapper_needed()
if len(wrapper_needs):
print "Finalize failed for: ", cls.name
for x in wrapper_needs:
print " ", x
def finalize(cls, finalize_pure_virtuals=False):
""" Attempt to finalize a class by not exposing virtual methods.
Still exposes in the case of pure virtuals otherwise the class
could not be instantiated.
"""
if isinstance(cls, pd.mdecl_wrapper_t):
for x in cls:
finalize(x)
else:
matcher = pd.virtuality_type_matcher( pd.VIRTUALITY_TYPES.VIRTUAL )
if finalize_pure_virtuals:
matcher = matcher | pd.virtuality_type_matcher( pd.VIRTUALITY_TYPES.PURE_VIRTUAL)
members = cls.decls( matcher,
decl_type=pd.member_calldef_t,
allow_empty=True)
members.set_virtuality( pd.VIRTUALITY_TYPES.NOT_VIRTUAL )
cls.decls(pd.access_type_matcher_t(pd.ACCESS_TYPES.PROTECTED),allow_empty=True).exclude()
cls.decls(pd.access_type_matcher_t(pd.ACCESS_TYPES.PRIVATE),allow_empty=True).exclude()
wrapper_needs = cls.is_wrapper_needed()
if len(wrapper_needs):
print "Finalize failed for: ", cls.name
for x in wrapper_needs:
print " ", x
def exportInterfaceClasses( mb ):
"""export virtual classes.
These classes can not instantiated directly from python.
"""
# do not add AlignlibBase. Adding it causes
# problems with get/set/cloneToolkit. The warning is
#
# WARNING: alignlib::Fragmentor [class]
# > warning W1023: Py++ will generate class wrapper - there are few functions that should be redefined in class wrapper. The functions are: getToolkit.
# Later, compilation will fail with:
# /usr/include/boost/python/object/value_holder.hpp: At global scope:
# /usr/include/boost/python/object/value_holder.hpp: In instantiation of boost::python::objects::value_holder<Fragmentor_wrapper>:
# /usr/include/boost/type_traits/alignment_of.hpp:52: instantiated from 'const size_t boost::detail::alignment_of_impl<boost::python::objects::value_holder<Fragmentor_wrapper> >::value'
# /usr/include/boost/type_traits/alignment_of.hpp:61: instantiated from 'boost::alignment_of<boost::python::objects::value_holder<Fragmentor_wrapper> >'
# /usr/include/boost/python/object/instance.hpp:30: instantiated from 'boost::python::objects::instance<boost::python::objects::value_holder<Fragmentor_wrapper> >'
# /usr/include/boost/python/object/instance.hpp:44: instantiated from 'const size_t boost::python::objects::additional_instance_size<boost::python::objects::value_holder<Fragmentor_wrapper> >::value'
# /usr/include/boost/python/class.hpp:499: instantiated from 'void boost::python::class_<T, X1, X2, X3>::initialize(const DefVisitor&) [with DefVisitor = boost::python::init<mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>, W = Fragmentor_wrapper, X1 = boost::python::bases<alignlib::AlignlibBase, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>, X2 = boost::noncopyable_::noncopyable, X3 = boost::python::detail::not_specified]'
# /usr/include/boost/python/class.hpp:629: instantiated from 'boost::python::class_<T, X1, X2, X3>::class_(const char*, const char*) [with W = Fragmentor_wrapper, X1 = boost::python::bases<alignlib::AlignlibBase, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_, mpl_::void_>, X2 = boost::noncopyable_::noncopyable, X3 = boost::python::detail::not_specified]'
# modules/Fragmentor.pypp.cpp:43: instantiated from here
# /usr/include/boost/python/object/value_holder.hpp:66: error: cannot declare field 'boost::python::objects::value_holder<Fragmentor_wrapper>::m_held' to be of abstract type 'Fragmentor_wrapper'
# modules/Fragmentor.pypp.cpp:11: note: because the following virtual functions are pure within 'Fragmentor_wrapper':
# ../alignlib/Fragmentor.h:63: note: virtual alignlib::HFragmentor alignlib::Fragmentor::getClone() const
# ../alignlib/Fragmentor.h:63: note: virtual alignlib::HFragmentor alignlib::Fragmentor::getNew() const
# ../alignlib/Fragmentor.h:72: note: virtual alignlib::HFragmentVector alignlib::Fragmentor::fragment(alignlib::HAlignment&, const alignlib::HAlignandum&, const alignlib::HAlignandum&)
# error: command 'gcc' failed with exit status 1
classes_to_export = set( [ 'AlignlibBase',
'Toolkit',
'Alignandum',
'Sequence',
'Profile',
'MultipleAlignment',
'MultAlignment',
'Alignator',
'MultipleAlignator',
'Iterator',
'Encoder',
'Fragmentor',
'Alignment',
'AlignmentIterator',
'Scorer',
'Weightor',
'LogOddor',
'Regularizor',
'Iterator2D',
'ResiduePair',
'Alignatum',
'EVDParameters',
'NormalDistributionParameters',
'Distor',
'Treetor',
'Tree',
'DistanceMatrix',
'Segment',
])
## TODO export substitution matrix
## include all classes
mb.classes( lambda x: x.name in classes_to_export ).include()
## do not include the increment/decrement and dereference operators, because there is no equivalent in python
## exlude functions while testing. Need to map return types later.
## default: exclude most operators
mb.member_operators( lambda x: x.name in ("operator++", "operator--",
"operator*", "operator->",
"operator()", "operator[]") ).exclude()
# mb.member_functions( lambda x: x.name == "getToolkit").exclude()
# mb.member_functions( lambda x: x.name == "setToolkit").exclude()
# mb.member_functions( lambda x: x.name == "cloneToolkit").exclude()
## do not export the internal iterator interfaces. This makes Alignment
## virtual and the wrapper will cause compilation to fail.
mb.classes( lambda x: x.name in ("Iterator", "ConstIterator")).exclude()
## see http://article.gmane.org/gmane.comp.python.c++/10177
## The following code is used to remove the wrapper classes for purely virtual classes.
for c in classes_to_export:
cls = mb.class_( c )
## remove virtual member functions. This will result in a class to be
## not virtual and hence no wrapper.
members = cls.decls( declarations.virtuality_type_matcher( declarations.VIRTUALITY_TYPES.PURE_VIRTUAL ),
decl_type=declarations.calldef.member_calldef_t,
allow_empty=True)
members.set_virtuality( declarations.VIRTUALITY_TYPES.NOT_VIRTUAL )
members = cls.decls( declarations.virtuality_type_matcher( declarations.VIRTUALITY_TYPES.ALL ),
decl_type=declarations.calldef.member_calldef_t,
allow_empty=True)
members.set_virtuality( declarations.VIRTUALITY_TYPES.NOT_VIRTUAL )
## do not wrap constructors, because compilation will fail for
## abstract classes.
try:
cls.constructors().exclude()
except RuntimeError:
print "no construtors for %s" % c
## export load/save functionality
classes_with_load_save = ("Alignandum", "Encoder")
exportSave( mb,
classes_with_load_save,
options,
generic = False )
exportLoad( mb,
classes_with_load_save,
options,
generic = False )
wrapperOrderFile = open(os.path.join(task.bldpath, '.wrapper_order.py'), 'a')
wrapperOrderFile.write(libraryName + '\n')
wrapperOrderFile.close()
# Set a standard name for every declaration
try:
for decl in mb.classes():
from pyplusplus.decl_wrappers.algorithm import create_valid_name
decl.alias = create_valid_name(decl.name)
except:
pass
# Disable virtuality unless specifically asked to do otherwise: this should avoid overrides
# and increase simulation speed
if( not task.virtuality ):
members = mb.global_ns.calldefs( declarations.virtuality_type_matcher( declarations.VIRTUALITY_TYPES.VIRTUAL ) , allow_empty=True)
if( members ):
members.set_virtuality( declarations.VIRTUALITY_TYPES.NOT_VIRTUAL )
# Execute includes user-specified code
for customCodeBlock in task.custom_code_include:
try:
exec customCodeBlock in locals()
except:
if Logs.verbose:
import traceback
traceback.print_exc()
print '\nWhile Processing FILEs: \n' + str(sources) + '\nLines: ' + str(customCodeBlock) + '\n'
# Execute user-specified code
