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def alignPeptideIdentifications(self, list ids , list trafos ):
assert isinstance(ids, list) and all(isinstance(li, list) and all(isinstance(li_, PeptideIdentification) for li_ in li) for li in ids), 'arg ids wrong type'
assert isinstance(trafos, list) and all(isinstance(li, TransformationDescription) for li in trafos), 'arg trafos wrong type'
cdef libcpp_vector[libcpp_vector[_PeptideIdentification]] * v0 = new libcpp_vector[libcpp_vector[_PeptideIdentification]]()
cdef libcpp_vector[_PeptideIdentification] * v0_rec = new libcpp_vector[_PeptideIdentification]()
cdef PeptideIdentification item0_rec
cdef libcpp_vector[_PeptideIdentification].iterator it_ids_rec
for ids_rec in ids:
v0_rec.clear()
for item0_rec in ids_rec:
v0_rec.push_back(deref(item0_rec.inst.get()))
v0.push_back(deref(v0_rec))
cdef libcpp_vector[_TransformationDescription] * v1 = new libcpp_vector[_TransformationDescription]()
cdef TransformationDescription item1
for item1 in trafos:
v1.push_back(deref(item1.inst.get()))
self.inst.get().alignPeptideIdentifications(deref(v0), deref(v1))
cdef libcpp_vector[_TransformationDescription].iterator it_trafos = v1.begin()
replace_0 = []
while it_trafos != v1.end():
item1 = TransformationDescription.__new__(TransformationDescription)
item1.inst = shared_ptr[_TransformationDescription](new _TransformationDescription(deref(it_trafos)))
replace_0.append(item1)
inc(it_trafos)
trafos[:] = replace_0
del v1
cdef libcpp_vector[libcpp_vector[_PeptideIdentification]].iterator it_ids = v0.begin()
replace_0 = []
while it_ids != v0.end():
it_ids_rec = deref(it_ids).begin()
replace_1 = []
while it_ids_rec != deref(it_ids).end():
item0_rec = PeptideIdentification.__new__(PeptideIdentification)
item0_rec.inst = shared_ptr[_PeptideIdentification](new _PeptideIdentification(deref(it_ids_rec)))
replace_1.append(item0_rec)
inc(it_ids_rec)
replace_0.append(replace_1)
inc(it_ids)
ids[:] = replace_0
del v0
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