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Viewing changes to pyOpenMS/addons/IDRipper.pyx

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

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pyOpenMS/addons/IDRipper.pyx
 
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    def rip(self, dict ripped, list proteins, list peptides):
 
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        # Input types:
 
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        # ripped   :  libcpp_map[String, libcpp_pair[ libcpp_vector[ProteinIdentification], libcpp_vector[PeptideIdentification]]]
 
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        # proteins :  libcpp_vector[ProteinIdentification] 
 
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        # peptides :  libcpp_vector[PeptideIdentification] 
 
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        assert isinstance(proteins, list) and all(isinstance(li, ProteinIdentification) for li in proteins), 'arg proteins wrong type'
 
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        cdef libcpp_vector[_ProteinIdentification] * c_protein_vec = new libcpp_vector[_ProteinIdentification]()
 
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        cdef ProteinIdentification item1
 
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        for item1 in proteins:
 
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           c_protein_vec.push_back(deref(item1.inst.get()))
 
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        assert isinstance(peptides, list) and all(isinstance(li, PeptideIdentification) for li in peptides), 'arg peptides wrong type'
 
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        cdef libcpp_vector[_PeptideIdentification] * c_peptide_vec = new libcpp_vector[_PeptideIdentification]()
 
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        cdef PeptideIdentification item0
 
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        for item0 in peptides:
 
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           c_peptide_vec.push_back(deref(item0.inst.get()))
 
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        # dict -> pair ( list, list ) )
 
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        assert isinstance(ripped, dict) and all(isinstance(li, list) and len(li) == 2 and all( 
 
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                isinstance(pair_element[0], list) and isinstance(pair_element[1], list) and
 
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                all(isinstance(proteinid, ProteinIdentification) for proteinid in pair_element[0]) and 
 
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                all(isinstance(peptideid, PeptideIdentification) for peptideid in pair_element[1]) 
 
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            for pair_element in li) 
 
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        for li in ripped), 'arg proteins wrong type'
 
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        cdef libcpp_map[_String, libcpp_pair[ libcpp_vector[_ProteinIdentification], libcpp_vector[_PeptideIdentification]]] c_ripped
 
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        # declaration for the loop 
 
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        cdef libcpp_vector[_ProteinIdentification] * c_protein_vec_inner = new libcpp_vector[_ProteinIdentification]()
 
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        cdef ProteinIdentification i_item1
 
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        cdef libcpp_vector[_PeptideIdentification] * c_peptide_vec_inner = new libcpp_vector[_PeptideIdentification]()
 
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        cdef PeptideIdentification i_item0
 
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        cdef libcpp_pair[ libcpp_vector[_ProteinIdentification], libcpp_vector[_PeptideIdentification]] * aPair
 
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        for k,v in ripped.iteritems():
 
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            c_protein_vec_inner.clear()
 
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            c_peptide_vec_inner.clear()
 
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            prot_vec = v[0]
 
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            assert isinstance(prot_vec, list) and all(isinstance(li, ProteinIdentification) for li in prot_vec), 'arg proteins wrong type'
 
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            for i_item1 in prot_vec:
 
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               c_protein_vec_inner.push_back(deref(i_item1.inst.get()))
 
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            pep_vec = v[1]
 
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            assert isinstance(pep_vec, list) and all(isinstance(li, PeptideIdentification) for li in pep_vec), 'arg peptides wrong type'
 
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            for i_item0 in pep_vec:
 
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               c_peptide_vec_inner.push_back(deref(i_item0.inst.get()))
 
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            aPair = new libcpp_pair[ libcpp_vector[_ProteinIdentification], libcpp_vector[_PeptideIdentification]]( deref(c_protein_vec_inner), deref(c_peptide_vec_inner) )
 
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            assert isinstance(k, bytes), 'arg key in label_identifiers wrong type'
 
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            assert isinstance(v, float), 'arg value in label_identifiers wrong type'
 
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            c_ripped[ _String(<char *>k) ] = deref(aPair)
 
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            del aPair
 
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        #
 
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        ## Make the function call
 
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        # 
 
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        self.inst.get().rip(c_ripped, deref(c_protein_vec), deref(c_peptide_vec))
 
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        #
 
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        ## Get the data back from C++
 
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        #
 
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        replace = dict()
 
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        cdef libcpp_map[_String, libcpp_pair[ libcpp_vector[_ProteinIdentification], libcpp_vector[_PeptideIdentification]]].iterator it_ripped = c_ripped.begin()
 
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        cdef libcpp_pair[ libcpp_vector[_ProteinIdentification], libcpp_vector[_PeptideIdentification]] anotherPair
 
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        cdef libcpp_vector[_ProteinIdentification] another_c_protein_vec_inner 
 
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        cdef libcpp_vector[_PeptideIdentification] another_c_peptide_vec_inner 
 
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        cdef libcpp_vector[_ProteinIdentification].iterator it_prot
 
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        cdef libcpp_vector[_PeptideIdentification].iterator it_pep
 
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        cdef ProteinIdentification item_py_result_prot
 
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        cdef PeptideIdentification item_py_result_pep
 
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        while it_ripped != c_ripped.end():
 
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            # get the pair and the two vectors
 
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            anotherPair = deref(it_ripped).second
 
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            another_c_protein_vec_inner = anotherPair.first
 
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            another_c_peptide_vec_inner = anotherPair.second
 
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            replace_inner_protein = []
 
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            it_prot = another_c_protein_vec_inner.begin()
 
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            while it_prot != another_c_protein_vec_inner.end():
 
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                item_py_result_prot = ProteinIdentification.__new__(ProteinIdentification)   
 
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                item_py_result_prot.inst = shared_ptr[_ProteinIdentification](new _ProteinIdentification(deref(it_prot)))
 
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                replace_inner_protein.append(item_py_result_prot)
 
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                inc(it_prot)
 
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            replace_inner_peptide = []
 
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            it_pep = another_c_peptide_vec_inner.begin()
 
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            while it_pep != another_c_peptide_vec_inner.end():
 
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                item_py_result_pep = PeptideIdentification.__new__(PeptideIdentification)   
 
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                item_py_result_pep.inst = shared_ptr[_PeptideIdentification](new _PeptideIdentification(deref(it_pep)))
 
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                replace_inner_peptide.append(item_py_result_pep)
 
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                inc(it_pep)
 
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            replace[ <libcpp_string>deref(it_ripped).first ]  = [ replace_inner_protein, replace_inner_peptide] 
 
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            inc(it_ripped)
 
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        ripped.clear()
 
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        ripped.update(replace)
 
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        del c_peptide_vec
 
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        del c_protein_vec
 
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        del c_protein_vec_inner
 
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        del c_peptide_vec_inner
 
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